WorldWideScience

Sample records for global sequence information

  1. 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.

  2. Inter-laboratory evaluation of the EUROFORGEN Global ancestry-informative SNP panel by massively parallel sequencing using the Ion PGM™.

    Science.gov (United States)

    Eduardoff, M; Gross, T E; Santos, C; de la Puente, M; Ballard, D; Strobl, C; Børsting, C; Morling, N; Fusco, L; Hussing, C; Egyed, B; Souto, L; Uacyisrael, J; Syndercombe Court, D; Carracedo, Á; Lareu, M V; Schneider, P M; Parson, W; Phillips, C; Parson, W; Phillips, C

    2016-07-01

    The EUROFORGEN Global ancestry-informative SNP (AIM-SNPs) panel is a forensic multiplex of 128 markers designed to differentiate an individual's ancestry from amongst the five continental population groups of Africa, Europe, East Asia, Native America, and Oceania. A custom multiplex of AmpliSeq™ PCR primers was designed for the Global AIM-SNPs to perform massively parallel sequencing using the Ion PGM™ system. This study assessed individual SNP genotyping precision using the Ion PGM™, the forensic sensitivity of the multiplex using dilution series, degraded DNA plus simple mixtures, and the ancestry differentiation power of the final panel design, which required substitution of three original ancestry-informative SNPs with alternatives. Fourteen populations that had not been previously analyzed were genotyped using the custom multiplex and these studies allowed assessment of genotyping performance by comparison of data across five laboratories. Results indicate a low level of genotyping error can still occur from sequence misalignment caused by homopolymeric tracts close to the target SNP, despite careful scrutiny of candidate SNPs at the design stage. Such sequence misalignment required the exclusion of component SNP rs2080161 from the Global AIM-SNPs panel. However, the overall genotyping precision and sensitivity of this custom multiplex indicates the Ion PGM™ assay for the Global AIM-SNPs is highly suitable for forensic ancestry analysis with massively parallel sequencing. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  3. Fast global sequence alignment technique

    KAUST Repository

    Bonny, Mohamed Talal; Salama, Khaled N.

    2011-01-01

    fast alignment algorithm, called 'Alignment By Scanning' (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the wellknown sequence alignment algorithms, the 'GAP' (which is heuristic) and the 'Needleman

  4. Fast global sequence alignment technique

    KAUST Repository

    Bonny, Mohamed Talal

    2011-11-01

    Bioinformatics database is growing exponentially in size. Processing these large amount of data may take hours of time even if super computers are used. One of the most important processing tool in Bioinformatics is sequence alignment. We introduce fast alignment algorithm, called \\'Alignment By Scanning\\' (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the wellknown sequence alignment algorithms, the \\'GAP\\' (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 51% enhancement in alignment score when it is compared with the GAP Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  5. Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information

    DEFF Research Database (Denmark)

    Hebsgaard, Stefan M.; Korning, Peter G.; Tolstrup, Niels

    1996-01-01

    Artificial neural networks have been combined with a rule based system to predict intron splice sites in the dicot plant Arabidopsis thaliana. A two step prediction scheme, where a global prediction of the coding potential regulates a cutoff level for a local predicition of splice sites, is refin...

  6. Inter-laboratory evaluation of the EUROFORGEN Global ancestry-informative SNP panel by massively parallel sequencing using the Ion PGM™

    DEFF Research Database (Denmark)

    Eduardoff, M; Gross, T E; Santos, C

    2016-01-01

    Seq™ PCR primers was designed for the Global AIM-SNPs to perform massively parallel sequencing using the Ion PGM™ system. This study assessed individual SNP genotyping precision using the Ion PGM™, the forensic sensitivity of the multiplex using dilution series, degraded DNA plus simple mixtures...

  7. Global information infrastructure.

    Science.gov (United States)

    Lindberg, D A

    1994-01-01

    The High Performance Computing and Communications Program (HPCC) is a multiagency federal initiative under the leadership of the White House Office of Science and Technology Policy, established by the High Performance Computing Act of 1991. It has been assigned a critical role in supporting the international collaboration essential to science and to health care. Goals of the HPCC are to extend USA leadership in high performance computing and networking technologies; to improve technology transfer for economic competitiveness, education, and national security; and to provide a key part of the foundation for the National Information Infrastructure. The first component of the National Institutes of Health to participate in the HPCC, the National Library of Medicine (NLM), recently issued a solicitation for proposals to address a range of issues, from privacy to 'testbed' networks, 'virtual reality,' and more. These efforts will build upon the NLM's extensive outreach program and other initiatives, including the Unified Medical Language System (UMLS), MEDLARS, and Grateful Med. New Internet search tools are emerging, such as Gopher and 'Knowbots'. Medicine will succeed in developing future intelligent agents to assist in utilizing computer networks. Our ability to serve patients is so often restricted by lack of information and knowledge at the time and place of medical decision-making. The new technologies, properly employed, will also greatly enhance our ability to serve the patient.

  8. Information decomposition method to analyze symbolical sequences

    International Nuclear Information System (INIS)

    Korotkov, E.V.; Korotkova, M.A.; Kudryashov, N.A.

    2003-01-01

    The information decomposition (ID) method to analyze symbolical sequences is presented. This method allows us to reveal a latent periodicity of any symbolical sequence. The ID method is shown to have advantages in comparison with application of the Fourier transformation, the wavelet transform and the dynamic programming method to look for latent periodicity. Examples of the latent periods for poetic texts, DNA sequences and amino acids are presented. Possible origin of a latent periodicity for different symbolical sequences is discussed

  9. Sequencing Information Management System (SIMS). Final report

    Energy Technology Data Exchange (ETDEWEB)

    Fields, C.

    1996-02-15

    A feasibility study to develop a requirements analysis and functional specification for a data management system for large-scale DNA sequencing laboratories resulted in a functional specification for a Sequencing Information Management System (SIMS). This document reports the results of this feasibility study, and includes a functional specification for a SIMS relational schema. The SIMS is an integrated information management system that supports data acquisition, management, analysis, and distribution for DNA sequencing laboratories. The SIMS provides ad hoc query access to information on the sequencing process and its results, and partially automates the transfer of data between laboratory instruments, analysis programs, technical personnel, and managers. The SIMS user interfaces are designed for use by laboratory technicians, laboratory managers, and scientists. The SIMS is designed to run in a heterogeneous, multiplatform environment in a client/server mode. The SIMS communicates with external computational and data resources via the internet.

  10. Information Security Management in Context of Globalization

    OpenAIRE

    Wawak, Slawomir

    2012-01-01

    Modern information technologies are the engine of globalization. At the same time, the global market influences the way of looking at information security. Information security thus becomes an increasingly important field. The article discuses the results of research on information security management systems in public administration in Poland.

  11. Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments.

    Science.gov (United States)

    Daily, Jeff

    2016-02-10

    Sequence alignment algorithms are a key component of many bioinformatics applications. Though various fast Smith-Waterman local sequence alignment implementations have been developed for x86 CPUs, most are embedded into larger database search tools. In addition, fast implementations of Needleman-Wunsch global sequence alignment and its semi-global variants are not as widespread. This article presents the first software library for local, global, and semi-global pairwise intra-sequence alignments and improves the performance of previous intra-sequence implementations. A faster intra-sequence local pairwise alignment implementation is described and benchmarked, including new global and semi-global variants. Using a 375 residue query sequence a speed of 136 billion cell updates per second (GCUPS) was achieved on a dual Intel Xeon E5-2670 24-core processor system, the highest reported for an implementation based on Farrar's 'striped' approach. Rognes's SWIPE optimal database search application is still generally the fastest available at 1.2 to at best 2.4 times faster than Parasail for sequences shorter than 500 amino acids. However, Parasail was faster for longer sequences. For global alignments, Parasail's prefix scan implementation is generally the fastest, faster even than Farrar's 'striped' approach, however the opal library is faster for single-threaded applications. The software library is designed for 64 bit Linux, OS X, or Windows on processors with SSE2, SSE41, or AVX2. Source code is available from https://github.com/jeffdaily/parasail under the Battelle BSD-style license. Applications that require optimal alignment scores could benefit from the improved performance. For the first time, SIMD global, semi-global, and local alignments are available in a stand-alone C library.

  12. INFORMATION AND KNOWLEDGE IN A GLOBAL CONTEXT

    Directory of Open Access Journals (Sweden)

    Florina BRAN

    2015-12-01

    Full Text Available Information and knowledge are two important entities, which make up present stage of globalization, based mostly on their dynamics. This paper is providing an overview of information and knowledge in global context, highlighting the importance of information society that turned into knowledge society in the beginning of the 21 century, being driven by Internet – the latter, as part of globalization process. Modern economic theories recognise the importance of information in economic process because its impact on globalization process in economy was essential, and change the way how markets and companies work and represent the key factor of new era of economic development. This paper presents main results from available literature about the relationship between information, knowledge and economic theory in a global conterxt and finally explained the benefits of the knowledge economy to all countries.

  13. Concepts for a global resources information system

    Science.gov (United States)

    Billingsley, F. C.; Urena, J. L.

    1984-01-01

    The objective of the Global Resources Information System (GRIS) is to establish an effective and efficient information management system to meet the data access requirements of NASA and NASA-related scientists conducting large-scale, multi-disciplinary, multi-mission scientific investigations. Using standard interfaces and operating guidelines, diverse data systems can be integrated to provide the capabilities to access and process multiple geographically dispersed data sets and to develop the necessary procedures and algorithms to derive global resource information.

  14. 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.

  15. A metadata initiative for global information discovery

    Science.gov (United States)

    Christian, E.

    2001-01-01

    The Global Information Locator Service (GILS) encompasses a global vision framed by the fundamental values of open societies. Societal values such as a free flow of information impose certain requirements on the society's information infrastructure. These requirements in turn shape the various laws, policies, standards, and technologies that determine the infrastructure design. A particular focus of GILS is the requirement to provide the means for people to discover sources of data and information. Information discovery in the GILS vision is designed to be decentralized yet coherent, and globally comprehensive yet useful for detailed data. This article introduces basic concepts and design issues, with emphasis on the techniques by which GILS supports interoperability. It explains the practical implications of GILS for the common roles of organizations involved in handling information, from content provider through system engineer and intermediary to searcher. The article provides examples of GILS initiatives in various types of communities: bibliographic, geographic, environmental, and government. ?? 2001 Elsevier Science Inc.

  16. Knowledge Management and Global Information Dissemination

    Science.gov (United States)

    Umunadi, Ejiwoke Kennedy

    2014-01-01

    The paper looked at knowledge management and global information dissemination. Knowledge is a very powerful tool for survival, growth and development. It can be seen as the information, understanding and skills that you gain through education or experience. The paper was addressed under the following sub-headings: Knowledge management knowledge…

  17. Development of Global Soil Information Facilities

    Directory of Open Access Journals (Sweden)

    N H Batjes

    2013-02-01

    Full Text Available ISRIC - World Soil Information has a mandate to serve the international community as custodian of global soil information and to increase awareness and understanding of the role of soils in major global issues. To adapt to the current demand for soil information, ISRIC is updating its enterprise data management system, including procedures for registering acquired data, such as lineage, versioning, quality assessment, and control. Data can be submitted, queried, and analysed using a growing range of web-based services - ultimately aiming at full and open exchange of data, metadata, and products - through the ICSU-accredited World Data Centre for Soils.

  18. Information technology and global change science

    Energy Technology Data Exchange (ETDEWEB)

    Baxter, F.P.

    1990-01-01

    The goal of this paper is to identify and briefly describe major existing and near term information technologies that cold have a positive impact on the topics being discussed at this conference by helping to manage the data of global change science and helping global change scientists conduct their research. Desktop computer systems have changed dramatically during the past seven years. Faster data processing can be expected in the future through full development of traditional serial computer architectures. Some other proven information technologies may be currently underutilized by global change scientists. Relational database management systems and good organization of data through the use of thoughtful database design would enable the scientific community to better share and maintain quality research data. Custodians of the data should use rigorous data administration to ensure integrity and long term value of the data resource. Still other emerging information technologies that involve the use of artificial intelligence, parallel computer architectures, and new sensors for data collection will be in relatively common use in the near term and should become part of the global science community's technical toolkit. Consideration should also be given to the establishment of Information Analysis Centers to facilitate effective organization and management of interdisciplinary data and the prototype testing and use of advanced information technology to facilitate rapid and cost-effective integration of these tools into global change science. 8 refs.

  19. Global games with noisy sharing of information

    KAUST Repository

    Touri, Behrouz

    2014-12-15

    We provide a framework for the study of global games with noisy sharing of information. In contrast to the previous works where it is shown that an intuitive threshold policy is an equilibrium for such games, we show that noisy sharing of information leads to non-existence of such an equilibrium. We also investigate the group best-response dynamics of two groups of agents sharing the same information to threshold policies based on each group\\'s observation and show the convergence of such dynamics.

  20. Global games with noisy sharing of information

    KAUST Repository

    Touri, Behrouz; Shamma, Jeff S.

    2014-01-01

    We provide a framework for the study of global games with noisy sharing of information. In contrast to the previous works where it is shown that an intuitive threshold policy is an equilibrium for such games, we show that noisy sharing of information leads to non-existence of such an equilibrium. We also investigate the group best-response dynamics of two groups of agents sharing the same information to threshold policies based on each group's observation and show the convergence of such dynamics.

  1. Global information sampling in the honey bee

    Science.gov (United States)

    Johnson, Brian R.

    2008-06-01

    Central to the question of task allocation in social insects is how workers acquire information. Patrolling is a curious behavior in which bees meander over the face of the comb inspecting cells. Several authors have suggested it allows bees to collect global information, but this has never been formally evaluated. This study explores this hypothesis by answering three questions. First, do bees gather information in a consistent manner as they patrol? Second, do they move far enough to get a sense of task demand in distant areas of the nest? And third, is patrolling a commonly performed task? Focal animal observations were used to address the first two predictions, while a scan sampling study was used to address the third. The results were affirmative for each question. While patrolling, workers collected information by performing periodic clusters of cell inspections. Patrolling bees not only traveled far enough to frequently change work zone; they often visited every part of the nest. Finally, the majority of the bees in the middle-age caste were shown to move throughout the nest over the course of a few hours in a manner suggestive of patrolling. Global information collection is contrary to much current theory, which assumes that workers respond to local information only. This study thus highlights the nonmutually exclusive nature of various information collection regimes in social insects.

  2. Analyticity and the Global Information Field

    Directory of Open Access Journals (Sweden)

    Evgeni A. Solov'ev

    2015-03-01

    Full Text Available The relation between analyticity in mathematics and the concept of a global information field in physics is reviewed. Mathematics is complete in the complex plane only. In the complex plane, a very powerful tool appears—analyticity. According to this property, if an analytic function is known on the countable set of points having an accumulation point, then it is known everywhere. This mysterious property has profound consequences in quantum physics. Analyticity allows one to obtain asymptotic (approximate results in terms of some singular points in the complex plane which accumulate all necessary data on a given process. As an example, slow atomic collisions are presented, where the cross-sections of inelastic transitions are determined by branch-points of the adiabatic energy surface at a complex internuclear distance. Common aspects of the non-local nature of analyticity and a recently introduced interpretation of classical electrodynamics and quantum physics as theories of a global information field are discussed.

  3. Workshop Proceedings: Utilizing global information systems

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1998-03-01

    This one day workshop was attended by 50 delegates representing 20 countries. Fourteen papers dealing with cleaner production/cleaner technology global information systems were presented. The objective of the workshop was to increase cooperation and interaction on international clean production/clean technology information transfer activities and to identify ways to ensure continued cooperation and system improvements. Topics discussed included information format to meet user needs; coordination of effort to avoid duplication and to encourage consistency in information delivery; and marketing, to expand the dissemination of information on cleaner production/cleaner technology. In terms of information format, content, systems and reliability were identified as target issues. The group discussing coordination of effort suggested that a wholesale/retail approach to information dissemination be adopted. The group also called for regular meetings to supplement communication via the Internet. The marketing group suggested that there is a need to show the benefits of technologies and to establish links to industrial associations as being critical to success.

  4. Image encryption using random sequence generated from generalized information domain

    International Nuclear Information System (INIS)

    Zhang Xia-Yan; Wu Jie-Hua; Zhang Guo-Ji; Li Xuan; Ren Ya-Zhou

    2016-01-01

    A novel image encryption method based on the random sequence generated from the generalized information domain and permutation–diffusion architecture is proposed. The random sequence is generated by reconstruction from the generalized information file and discrete trajectory extraction from the data stream. The trajectory address sequence is used to generate a P-box to shuffle the plain image while random sequences are treated as keystreams. A new factor called drift factor is employed to accelerate and enhance the performance of the random sequence generator. An initial value is introduced to make the encryption method an approximately one-time pad. Experimental results show that the random sequences pass the NIST statistical test with a high ratio and extensive analysis demonstrates that the new encryption scheme has superior security. (paper)

  5. The"minimum information about an environmental sequence" (MIENS) specification

    Energy Technology Data Exchange (ETDEWEB)

    Yilmaz, P.; Kottmann, R.; Field, D.; Knight, R.; Cole, J.R.; Amaral-Zettler, L.; Gilbert, J.A.; Karsch-Mizrachi, I.; Johnston, A.; Cochrane, G.; Vaughan, R.; Hunter, C.; Park, J.; Morrison, N.; Rocca-Serra, P.; Sterk, P.; Arumugam, M.; Baumgartner, L.; Birren, B.W.; Blaser, M.J.; Bonazzi, V.; Bork, P.; Buttigieg, P. L.; Chain, P.; Costello, E.K.; Huot-Creasy, H.; Dawyndt, P.; DeSantis, T.; Fierer, N.; Fuhrman, J.; Gallery, R.E.; Gibbs, R.A.; Giglio, M.G.; Gil, I. San; Gonzalez, A.; Gordon, J.I.; Guralnick, R.; Hankeln, W.; Highlander, S.; Hugenholtz, P.; Jansson, J.; Kennedy, J.; Knights, D.; Koren, O.; Kuczynski, J.; Kyrpides, N.; Larsen, R.; Lauber, C.L.; Legg, T.; Ley, R.E.; Lozupone, C.A.; Ludwig, W.; Lyons, D.; Maguire, E.; Methe, B.A.; Meyer, F.; Nakieny, S.; Nelson, K.E.; Nemergut, D.; Neufeld, J.D.; Pace, N.R.; Palanisamy, G.; Peplies, J.; Peterson, J.; Petrosino, J.; Proctor, L.; Raes, J.; Ratnasingham, S.; Ravel, J.; Relman, D.A.; Assunta-Sansone, S.; Schriml, L.; Sodergren, E.; Spor, A.; Stombaugh, J.; Tiedje, J.M.; Ward, D.V.; Weinstock, G.M.; Wendel, D.; White, O.; Wikle, A.; Wortman, J.R.; Glockner, F.O.; Bushman, F.D.; Charlson, E.; Gevers, D.; Kelley, S.T.; Neubold, L.K.; Oliver, A.E.; Pruesse, E.; Quast, C.; Schloss, P.D.; Sinha, R.; Whitely, A.

    2010-10-15

    We present the Genomic Standards Consortium's (GSC) 'Minimum Information about an ENvironmental Sequence' (MIENS) standard for describing marker genes. Adoption of MIENS will enhance our ability to analyze natural genetic diversity across the Tree of Life as it is currently being documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.

  6. Limitations in global information on species occurrences

    Directory of Open Access Journals (Sweden)

    Carsten Meyer

    2016-07-01

    Full Text Available Detailed information on species distributions is crucial for answering central questions in biogeography, ecology, evolutionary biology and conservation. Millions of species occurrence records have been mobilized via international data-sharing networks, but inherent biases, gaps and uncertainties hamper broader application. In my PhD thesis, I presented the first comprehensive analyses of global patterns and drivers of these limitations across different taxonomic groups and spatial scales. Integrating 300 million occurrence records for terrestrial vertebrates and plants with comprehensive taxonomic databases, expert range maps and regional checklists, I demonstrated extensive taxonomic, geographical and temporal biases, gaps and uncertainties. I identified key socio-economic drivers of data bias across different taxonomic groups and spatial scales. The results of my dissertation provide an empirical baseline for effectively accounting for data limitations in distribution models, as well as for prioritizing and monitoring efforts to collate additional occurrence information.

  7. Environmental safety of the global information space

    Directory of Open Access Journals (Sweden)

    В’ячеслав Степанович Волошин

    2015-03-01

    Databases of full-text publications – journals, articles, monographs- are surely a means of salvation for science. There already exist a large number of such portals. Besides, advantages and disadvantages of electronic subscriptions to periodicals should certainly be considered. The former include the following most evident ones: aggregation of large data arrays, saving money on a subscription, an opportunity to work with relevant publications, thematic collections of materials, availability of records, simultaneous access of an unlimited number of users and others. Nevertheless, there are many disadvantages that make it difficult to work with full-text publications. They are the following: selective representativeness of publication numbers, complexity of keyword search, occasional presence of obsolete text formats, printed versions, possible psychological barrier, physiological incompatibility with computer equipment, fatigue caused by prolonged work on the computer. The Internet was followed by the appearance of global control networks, their aims ranging from control of a human life support to a unified control of humanity. So, the formed global information space promises the man to get access to almost any information source. Meanwhile, environmental safety of the man, his/her objective biological psyche and abilities in harmonious development are at serious risk

  8. Globalization and Trust: Non-financial Information

    Directory of Open Access Journals (Sweden)

    Oscar Banda Lefaure

    2015-09-01

    Full Text Available Changes in the way of doing business that have resulted from globalization of markets have enabled countless benefits, but also a significant number of risks, that have been evident as since 2001 revelations about financial scandals around the world have occurred one after another. These unfortunate events showed the vulnerability to which investors (and other stakeholders are exposed for not having timely, clear and accurate information of the business progress in which they invest, and therefore not being able to take precautions. In addition, these business disasters have shown how the most unscrupulous executives do not hesitate to act illegally to hide their shady financial and accounting manoeuvres, in order to promote their personal benefit. Then the executive compensations policy lies behind. At this juncture, the importance of migrating to a new model of disclosure where the global financial community can take shelter of these malpractices and trust the board controls and the management stablishes has been increasing. This new model of disclosure has one of its pillars in non-financial information reports. This is not an alchemist solution, but is one of many efforts to be undertaken by companies to recover damaged trust. The international financial crisis affecting the world economy at the moment is another example of the need to give greater trust to the stakeholders –through transparency in the information they provide–. Only then, their participation in the capital market will be maintained and increased, and the costs that brings widespread lack of trust in which we live will be reduced.

  9. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

    DEFF Research Database (Denmark)

    Yilmaz, Pelin; Kottmann, Renzo; Field, Dawn

    2011-01-01

    Here we present a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences--the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for describing the environment from which a biological sample originates. The 'environment...

  10. PIMS sequencing extension: a laboratory information management system for DNA sequencing facilities

    Directory of Open Access Journals (Sweden)

    Baldwin Stephen A

    2011-03-01

    Full Text Available Abstract Background Facilities that provide a service for DNA sequencing typically support large numbers of users and experiment types. The cost of services is often reduced by the use of liquid handling robots but the efficiency of such facilities is hampered because the software for such robots does not usually integrate well with the systems that run the sequencing machines. Accordingly, there is a need for software systems capable of integrating different robotic systems and managing sample information for DNA sequencing services. In this paper, we describe an extension to the Protein Information Management System (PIMS that is designed for DNA sequencing facilities. The new version of PIMS has a user-friendly web interface and integrates all aspects of the sequencing process, including sample submission, handling and tracking, together with capture and management of the data. Results The PIMS sequencing extension has been in production since July 2009 at the University of Leeds DNA Sequencing Facility. It has completely replaced manual data handling and simplified the tasks of data management and user communication. Samples from 45 groups have been processed with an average throughput of 10000 samples per month. The current version of the PIMS sequencing extension works with Applied Biosystems 3130XL 96-well plate sequencer and MWG 4204 or Aviso Theonyx liquid handling robots, but is readily adaptable for use with other combinations of robots. Conclusions PIMS has been extended to provide a user-friendly and integrated data management solution for DNA sequencing facilities that is accessed through a normal web browser and allows simultaneous access by multiple users as well as facility managers. The system integrates sequencing and liquid handling robots, manages the data flow, and provides remote access to the sequencing results. The software is freely available, for academic users, from http://www.pims-lims.org/.

  11. PIMS sequencing extension: a laboratory information management system for DNA sequencing facilities.

    Science.gov (United States)

    Troshin, Peter V; Postis, Vincent Lg; Ashworth, Denise; Baldwin, Stephen A; McPherson, Michael J; Barton, Geoffrey J

    2011-03-07

    Facilities that provide a service for DNA sequencing typically support large numbers of users and experiment types. The cost of services is often reduced by the use of liquid handling robots but the efficiency of such facilities is hampered because the software for such robots does not usually integrate well with the systems that run the sequencing machines. Accordingly, there is a need for software systems capable of integrating different robotic systems and managing sample information for DNA sequencing services. In this paper, we describe an extension to the Protein Information Management System (PIMS) that is designed for DNA sequencing facilities. The new version of PIMS has a user-friendly web interface and integrates all aspects of the sequencing process, including sample submission, handling and tracking, together with capture and management of the data. The PIMS sequencing extension has been in production since July 2009 at the University of Leeds DNA Sequencing Facility. It has completely replaced manual data handling and simplified the tasks of data management and user communication. Samples from 45 groups have been processed with an average throughput of 10000 samples per month. The current version of the PIMS sequencing extension works with Applied Biosystems 3130XL 96-well plate sequencer and MWG 4204 or Aviso Theonyx liquid handling robots, but is readily adaptable for use with other combinations of robots. PIMS has been extended to provide a user-friendly and integrated data management solution for DNA sequencing facilities that is accessed through a normal web browser and allows simultaneous access by multiple users as well as facility managers. The system integrates sequencing and liquid handling robots, manages the data flow, and provides remote access to the sequencing results. The software is freely available, for academic users, from http://www.pims-lims.org/.

  12. U.S. Global Change Research Program National Climate Assessment Global Change Information System

    Science.gov (United States)

    Tilmes, Curt

    2012-01-01

    The program: a) Coordinates Federal research to better understand and prepare the nation for global change. b) Priori4zes and supports cutting edge scientific work in global change. c) Assesses the state of scientific knowledge and the Nation s readiness to respond to global change. d) Communicates research findings to inform, educate, and engage the global community.

  13. Human genome and genetic sequencing research and informed consent

    International Nuclear Information System (INIS)

    Iwakawa, Mayumi

    2003-01-01

    On March 29, 2001, the Ethical Guidelines for Human Genome and Genetic Sequencing Research were established. They have intended to serve as ethical guidelines for all human genome and genetic sequencing research practice, for the purpose of upholding respect for human dignity and rights and enforcing use of proper methods in the pursuit of human genome and genetic sequencing research, with the understanding and cooperation of the public. The RadGenomics Project has prepared a research protocol and informed consent document that follow these ethical guidelines. We have endeavored to protect the privacy of individual information, and have established a procedure for examination of research practices by an ethics committee. Here we report our procedure in order to offer this concept to the patients. (authors)

  14. MACSIMS : multiple alignment of complete sequences information management system

    Directory of Open Access Journals (Sweden)

    Plewniak Frédéric

    2006-06-01

    Full Text Available Abstract Background In the post-genomic era, systems-level studies are being performed that seek to explain complex biological systems by integrating diverse resources from fields such as genomics, proteomics or transcriptomics. New information management systems are now needed for the collection, validation and analysis of the vast amount of heterogeneous data available. Multiple alignments of complete sequences provide an ideal environment for the integration of this information in the context of the protein family. Results MACSIMS is a multiple alignment-based information management program that combines the advantages of both knowledge-based and ab initio sequence analysis methods. Structural and functional information is retrieved automatically from the public databases. In the multiple alignment, homologous regions are identified and the retrieved data is evaluated and propagated from known to unknown sequences with these reliable regions. In a large-scale evaluation, the specificity of the propagated sequence features is estimated to be >99%, i.e. very few false positive predictions are made. MACSIMS is then used to characterise mutations in a test set of 100 proteins that are known to be involved in human genetic diseases. The number of sequence features associated with these proteins was increased by 60%, compared to the features available in the public databases. An XML format output file allows automatic parsing of the MACSIM results, while a graphical display using the JalView program allows manual analysis. Conclusion MACSIMS is a new information management system that incorporates detailed analyses of protein families at the structural, functional and evolutionary levels. MACSIMS thus provides a unique environment that facilitates knowledge extraction and the presentation of the most pertinent information to the biologist. A web server and the source code are available at http://bips.u-strasbg.fr/MACSIMS/.

  15. 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...

  16. A bibliometric analysis of global research on genome sequencing ...

    African Journals Online (AJOL)

    The results show that disease and protein related researches were the leading research focuses, and comparative genomics and evolution related research had strong potential in the near future. Key words: Genome sequencing, research trend, scientometrics, science citation index expanded (SCI-Expanded), word cluster ...

  17. Global Information Enterprise (GIE) Modeling and Simulation (GIESIM)

    National Research Council Canada - National Science Library

    Bell, Paul

    2005-01-01

    ... AND S) toolkits into the Global Information Enterprise (GIE) Modeling and Simulation (GIESim) framework to create effective user analysis of candidate communications architectures and technologies...

  18. The US Global Change Data and Information Management Program Plan

    International Nuclear Information System (INIS)

    1992-01-01

    The US Global Change Research Program (USGCRP) requires massive quantities of highly diverse data and information to improve our understanding of global change processes. The Committee on Earth and Environmental Sciences (CEES) comprises Federal agencies that need to provide reliable data and information for this purpose from existing programs and archives and from new activities designed to improve upon the data and information. This US Global Change Data and Information Management Program Plan commits the participating Federal agencies to work with each other, with academia, and with the international community to make it as easy as possible for researchers and others to access and use global change data and information. Toward this end, the agencies are organizing a Global Change Data and Information System (GCDIS), which takes advantage of the mission resources and responsibilities of each agency. Sources for global change data and information are national and international agency programs, including those focused on the USGCRP, such as NASA's Earth Observing System [EOS] and other agency global change initiatives and those contributing to the USGCRP from other agency programs not focused on global change. Data and information include raw data from observation systems, value-added data from data assembly activities, and derived data and information from models and other investigations. Additional data and information are identified from appropriate sources including academia and the international community

  19. Information empowerment: predeparture resource training for students in global health.

    Science.gov (United States)

    Rana, Gurpreet K

    2014-04-01

    The Taubman Health Sciences Library (THL) collaborates with health sciences schools to provide information skills instruction for students preparing for international experiences. THL enhances students' global health learning through predeparture instruction for students who are involved in global health research, clinical internships, and international collaborations. This includes teaching international literature searching skills, providing country-specific data sources, building awareness of relevant mobile resources, and encouraging investigation of international news. Information skills empower creation of stronger global partnerships. Use of information resources has enhanced international research and training experiences, built lifelong learning foundations, and contributed to the university's global engagement. THL continues to assess predeparture instruction.

  20. Information security protecting the global enterprise

    CERN Document Server

    Pipkin, Donald L

    2000-01-01

    In this book, IT security expert Donald Pipkin addresses every aspect of information security: the business issues, the technical process issues, and the legal issues. Pipkin starts by reviewing the key business issues: estimating the value of information assets, evaluating the cost to the organization if they are lost or disclosed, and determining the appropriate levels of protection and response to security incidents. Next, he walks through the technical processes required to build a consistent, reasonable information security system, with appropriate intrusion detection and reporting features. Finally, Pipkin reviews the legal issues associated with information security, including corporate officers' personal liability for taking care that information is protected. The book's coverage is applicable to businesses of any size, from 50 employees to 50,000 or more, and ideal for everyone who needs at least a basic understanding of information security: network/system administrators, managers, planners, archite...

  1. Global Reference Tables for Management Information Systems

    Data.gov (United States)

    Social Security Administration — This database is a collection of reference tables that store common information used throughout SSA. These tables standardize code structures and code usage of SSA...

  2. Statistical distributions of optimal global alignment scores of random protein sequences

    Directory of Open Access Journals (Sweden)

    Tang Jiaowei

    2005-10-01

    Full Text Available Abstract Background The inference of homology from statistically significant sequence similarity is a central issue in sequence alignments. So far the statistical distribution function underlying the optimal global alignments has not been completely determined. Results In this study, random and real but unrelated sequences prepared in six different ways were selected as reference datasets to obtain their respective statistical distributions of global alignment scores. All alignments were carried out with the Needleman-Wunsch algorithm and optimal scores were fitted to the Gumbel, normal and gamma distributions respectively. The three-parameter gamma distribution performs the best as the theoretical distribution function of global alignment scores, as it agrees perfectly well with the distribution of alignment scores. The normal distribution also agrees well with the score distribution frequencies when the shape parameter of the gamma distribution is sufficiently large, for this is the scenario when the normal distribution can be viewed as an approximation of the gamma distribution. Conclusion We have shown that the optimal global alignment scores of random protein sequences fit the three-parameter gamma distribution function. This would be useful for the inference of homology between sequences whose relationship is unknown, through the evaluation of gamma distribution significance between sequences.

  3. Always look on both sides: phylogenetic information conveyed by simple sequence repeat allele sequences.

    Directory of Open Access Journals (Sweden)

    Stéphanie Barthe

    Full Text Available Simple sequence repeat (SSR markers are widely used tools for inferences about genetic diversity, phylogeography and spatial genetic structure. Their applications assume that variation among alleles is essentially caused by an expansion or contraction of the number of repeats and that, accessorily, mutations in the target sequences follow the stepwise mutation model (SMM. Generally speaking, PCR amplicon sizes are used as direct indicators of the number of SSR repeats composing an allele with the data analysis either ignoring the extent of allele size differences or assuming that there is a direct correlation between differences in amplicon size and evolutionary distance. However, without precisely knowing the kind and distribution of polymorphism within an allele (SSR and the associated flanking region (FR sequences, it is hard to say what kind of evolutionary message is conveyed by such a synthetic descriptor of polymorphism as DNA amplicon size. In this study, we sequenced several SSR alleles in multiple populations of three divergent tree genera and disentangled the types of polymorphisms contained in each portion of the DNA amplicon containing an SSR. The patterns of diversity provided by amplicon size variation, SSR variation itself, insertions/deletions (indels, and single nucleotide polymorphisms (SNPs observed in the FRs were compared. Amplicon size variation largely reflected SSR repeat number. The amount of variation was as large in FRs as in the SSR itself. The former contributed significantly to the phylogenetic information and sometimes was the main source of differentiation among individuals and populations contained by FR and SSR regions of SSR markers. The presence of mutations occurring at different rates within a marker's sequence offers the opportunity to analyse evolutionary events occurring on various timescales, but at the same time calls for caution in the interpretation of SSR marker data when the distribution of within

  4. 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.

  5. Building Global Competitiveness through Information Security ...

    African Journals Online (AJOL)

    If you would like more information about how to print, save, and work with PDFs, Highwire Press provides a helpful Frequently Asked Questions about PDFs. Alternatively, you can download the PDF file directly to your computer, from where it can be opened using a PDF reader. To download the PDF, click the Download link ...

  6. Globalization on Trial: The Human Condition and the Information ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    He also focuses on our education system and how it will have to adapt to meet the new challenges of our global, information age. Globalization on Trial will interest ... Farhang Rajaee is a Visiting Associate Professor at the College of the Humanities, Carleton University, Ottawa, Canada. Professor Rajaee received his PhD ...

  7. Integrating genome-based informatics to modernize global disease monitoring, information sharing, and response

    DEFF Research Database (Denmark)

    Aarestrup, Frank Møller; Brown, Eric W; Detter, Chris

    2012-01-01

    The rapid advancement of genome technologies holds great promise for improving the quality and speed of clinical and public health laboratory investigations and for decreasing their cost. The latest generation of genome DNA sequencers can provide highly detailed and robust information on disease...... typing methods to provide point-of-care clinical diagnosis and other essential information for quicker and better treatment of patients. Provided there is free-sharing of information by all clinical and public health laboratories, these genomic tools could spawn a global system of linked databases......-causing microbes, and in the near future these technologies will be suitable for routine use in national, regional, and global public health laboratories. With additional improvements in instrumentation, these next- or third-generation sequencers are likely to replace conventional culture-based and molecular...

  8. Architectural Design for the Global Legal Information Network

    Science.gov (United States)

    Kalpakis, Konstantinos

    1999-01-01

    In this report, we provide a summary of our activities regarding the goals, requirements analysis, design, and prototype implementation for the Global Legal Information Network, a joint effort between the Law Library of Congress and NASA.

  9. The minimum information about a genome sequence (MIGS) specification

    Science.gov (United States)

    Field, Dawn; Garrity, George; Gray, Tanya; Morrison, Norman; Selengut, Jeremy; Sterk, Peter; Tatusova, Tatiana; Thomson, Nicholas; Allen, Michael J; Angiuoli, Samuel V; Ashburner, Michael; Axelrod, Nelson; Baldauf, Sandra; Ballard, Stuart; Boore, Jeffrey; Cochrane, Guy; Cole, James; Dawyndt, Peter; De Vos, Paul; dePamphilis, Claude; Edwards, Robert; Faruque, Nadeem; Feldman, Robert; Gilbert, Jack; Gilna, Paul; Glöckner, Frank Oliver; Goldstein, Philip; Guralnick, Robert; Haft, Dan; Hancock, David; Hermjakob, Henning; Hertz-Fowler, Christiane; Hugenholtz, Phil; Joint, Ian; Kagan, Leonid; Kane, Matthew; Kennedy, Jessie; Kowalchuk, George; Kottmann, Renzo; Kolker, Eugene; Kravitz, Saul; Kyrpides, Nikos; Leebens-Mack, Jim; Lewis, Suzanna E; Li, Kelvin; Lister, Allyson L; Lord, Phillip; Maltsev, Natalia; Markowitz, Victor; Martiny, Jennifer; Methe, Barbara; Mizrachi, Ilene; Moxon, Richard; Nelson, Karen; Parkhill, Julian; Proctor, Lita; White, Owen; Sansone, Susanna-Assunta; Spiers, Andrew; Stevens, Robert; Swift, Paul; Taylor, Chris; Tateno, Yoshio; Tett, Adrian; Turner, Sarah; Ussery, David; Vaughan, Bob; Ward, Naomi; Whetzel, Trish; Gil, Ingio San; Wilson, Gareth; Wipat, Anil

    2008-01-01

    With the quantity of genomic data increasing at an exponential rate, it is imperative that these data be captured electronically, in a standard format. Standardization activities must proceed within the auspices of open-access and international working bodies. To tackle the issues surrounding the development of better descriptions of genomic investigations, we have formed the Genomic Standards Consortium (GSC). Here, we introduce the minimum information about a genome sequence (MIGS) specification with the intent of promoting participation in its development and discussing the resources that will be required to develop improved mechanisms of metadata capture and exchange. As part of its wider goals, the GSC also supports improving the ‘transparency’ of the information contained in existing genomic databases. PMID:18464787

  10. The minimum information about a genome sequence (MIGS) specification

    DEFF Research Database (Denmark)

    Field, D; Garrity, G; Gray, T

    2008-01-01

    With the quantity of genomic data increasing at an exponential rate, it is imperative that these data be captured electronically, in a standard format. Standardization activities must proceed within the auspices of open-access and international working bodies. To tackle the issues surrounding the...... that will be required to develop improved mechanisms of metadata capture and exchange. As part of its wider goals, the GSC also supports improving the 'transparency' of the information contained in existing genomic databases....... the development of better descriptions of genomic investigations, we have formed the Genomic Standards Consortium (GSC). Here, we introduce the minimum information about a genome sequence (MIGS) specification with the intent of promoting participation in its development and discussing the resources...

  11. Information-Theoretical Analysis of EEG Microstate Sequences in Python

    Directory of Open Access Journals (Sweden)

    Frederic von Wegner

    2018-06-01

    Full Text Available We present an open-source Python package to compute information-theoretical quantities for electroencephalographic data. Electroencephalography (EEG measures the electrical potential generated by the cerebral cortex and the set of spatial patterns projected by the brain's electrical potential on the scalp surface can be clustered into a set of representative maps called EEG microstates. Microstate time series are obtained by competitively fitting the microstate maps back into the EEG data set, i.e., by substituting the EEG data at a given time with the label of the microstate that has the highest similarity with the actual EEG topography. As microstate sequences consist of non-metric random variables, e.g., the letters A–D, we recently introduced information-theoretical measures to quantify these time series. In wakeful resting state EEG recordings, we found new characteristics of microstate sequences such as periodicities related to EEG frequency bands. The algorithms used are here provided as an open-source package and their use is explained in a tutorial style. The package is self-contained and the programming style is procedural, focusing on code intelligibility and easy portability. Using a sample EEG file, we demonstrate how to perform EEG microstate segmentation using the modified K-means approach, and how to compute and visualize the recently introduced information-theoretical tests and quantities. The time-lagged mutual information function is derived as a discrete symbolic alternative to the autocorrelation function for metric time series and confidence intervals are computed from Markov chain surrogate data. The software package provides an open-source extension to the existing implementations of the microstate transform and is specifically designed to analyze resting state EEG recordings.

  12. Towards a Global Sustainable Information Society (GSIS?

    Directory of Open Access Journals (Sweden)

    Christian Fuchs

    2008-07-01

    sustainability and vice versa. The discourse on the information society has been accompanied by discussion on how to measure the transition towards this new social formation. Institutions such as the EU, the OECD, and the UN, US Census Bureau, the ASEAN, or WSIS are using and discussing various indicators for measurement. These indicators are classified according to various typologies. There are on the one hand indicators of sustainability that focus on ecological aspects and on the other hand indicators that besides the ecological dimension also take into account broader societal issues. The EU and the UN use a classification scheme that groups indicators according to environmental, economic, social, and institutional aspects. The discourse on sustainability has shifted from an early ecological focus towards the inclusion of economic, political, cultural, and social issues. The approach suggested in this paper argues that sustainability is a multimodal issue having an ecological, a technological, an economic, a political, and a cultural dimension. Existing sustainability indicators lack aspects of information and ICT, existing information society indicators lack aspects of sustainability. What is needed are indicators that measure the degree to which a sustainable information society has been achieved in the various societal dimensions.

  13. The Global Drought Information System - A Decision Support Tool with Global Applications

    Science.gov (United States)

    Arndt, D. S.; Brewer, M.; Heim, R. R., Jr.

    2014-12-01

    Drought is a natural hazard which can cause famine in developing countries and severe economic hardship in developed countries. Given current concerns with the increasing frequency and magnitude of droughts in many regions of the world, especially in the light of expected climate change, drought monitoring and dissemination of early warning information in a timely fashion on a global scale is a critical concern as an important adaptation and mitigation strategy. While a number of nations, and a few continental-scale activities have developed drought information system activities, a global drought early warning system (GDEWS) remains elusive, despite the benefits highlighted by ministers to the Global Earth Observation System of System in 2008. In an effort to begin a process of drought monitoring with international collaboration, the National Integrated Drought Information System's (NIDIS) U.S. Drought Portal, a web-based information system created to address drought services and early warning in the United States, including drought monitoring, forecasting, impacts, mitigation, research, and education, volunteered to develop a prototype Global Drought Monitoring Portal (GDMP). Through integration of data and information at the global level, and with four continental-level partners, the GDMP has proven successful as a tool to monitor drought around the globe. At a past meeting between NIDIS, the World Meteorological Organization, and the Global Earth Observation System of Systems, it was recommended that the GDMP form the basis for a Global Drought Information System (GDIS). Currently, GDIS activities are focused around providing operational global drought monitoring products and assessments, incorporating additional drought monitoring information, especially from those areas without regional or continental-scale input, and incorporating drought-specific climate forecast information from the World Climate Research Programme. Additional GDIS pilot activities are

  14. Global repeat discovery and estimation of genomic copy number in a large, complex genome using a high-throughput 454 sequence survey

    Directory of Open Access Journals (Sweden)

    Varala Kranthi

    2007-05-01

    Full Text Available Abstract Background Extensive computational and database tools are available to mine genomic and genetic databases for model organisms, but little genomic data is available for many species of ecological or agricultural significance, especially those with large genomes. Genome surveys using conventional sequencing techniques are powerful, particularly for detecting sequences present in many copies per genome. However these methods are time-consuming and have potential drawbacks. High throughput 454 sequencing provides an alternative method by which much information can be gained quickly and cheaply from high-coverage surveys of genomic DNA. Results We sequenced 78 million base-pairs of randomly sheared soybean DNA which passed our quality criteria. Computational analysis of the survey sequences provided global information on the abundant repetitive sequences in soybean. The sequence was used to determine the copy number across regions of large genomic clones or contigs and discover higher-order structures within satellite repeats. We have created an annotated, online database of sequences present in multiple copies in the soybean genome. The low bias of pyrosequencing against repeat sequences is demonstrated by the overall composition of the survey data, which matches well with past estimates of repetitive DNA content obtained by DNA re-association kinetics (Cot analysis. Conclusion This approach provides a potential aid to conventional or shotgun genome assembly, by allowing rapid assessment of copy number in any clone or clone-end sequence. In addition, we show that partial sequencing can provide access to partial protein-coding sequences.

  15. Exploiting sequence and stability information for directing nanobody stability engineering.

    Science.gov (United States)

    Kunz, Patrick; Flock, Tilman; Soler, Nicolas; Zaiss, Moritz; Vincke, Cécile; Sterckx, Yann; Kastelic, Damjana; Muyldermans, Serge; Hoheisel, Jörg D

    2017-09-01

    Variable domains of camelid heavy-chain antibodies, commonly named nanobodies, have high biotechnological potential. In view of their broad range of applications in research, diagnostics and therapy, engineering their stability is of particular interest. One important aspect is the improvement of thermostability, because it can have immediate effects on conformational stability, protease resistance and aggregation propensity of the protein. We analyzed the sequences and thermostabilities of 78 purified nanobody binders. From this data, potentially stabilizing amino acid variations were identified and studied experimentally. Some mutations improved the stability of nanobodies by up to 6.1°C, with an average of 2.3°C across eight modified nanobodies. The stabilizing mechanism involves an improvement of both conformational stability and aggregation behavior, explaining the variable degree of stabilization in individual molecules. In some instances, variations predicted to be stabilizing actually led to thermal destabilization of the proteins. The reasons for this contradiction between prediction and experiment were investigated. The results reveal a mutational strategy to improve the biophysical behavior of nanobody binders and indicate a species-specificity of nanobody architecture. This study illustrates the potential and limitations of engineering nanobody thermostability by merging sequence information with stability data, an aspect that is becoming increasingly important with the recent development of high-throughput biophysical methods. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  16. Effects of Information Capitalism and Globalization on Teaching and Learning

    Science.gov (United States)

    Adeoye, Blessing F., Ed.; Tomei, Lawrence, Ed.

    2014-01-01

    As computers and Internet connections become widely available in schools and classrooms, it is critical to examine cross-cultural issues in the utilization of information and communication technologies. "Effects of Information Capitalism and Globalization on Teaching and Learning" examines issues concerning emerging multimedia…

  17. Marketing library and information services II a global outlook

    CERN Document Server

    Gupta, Dinesh K; Massisimo, Angels

    2013-01-01

    With contributions from library and information professionals (practitioners, researchers, faculty members, consultants, and others), Marketing Library and Information Services: A Global Outlook highlights a variety of exemplary LIS marketing practices and efforts from around the globe. The following broad topics are explored: changing marketing concepts; marketing library

  18. Comprehensive Information Retrieval and Model Input Sequence (CIRMIS)

    International Nuclear Information System (INIS)

    Friedrichs, D.R.

    1977-04-01

    The Comprehensive Information Retrieval and Model Input Sequence (CIRMIS) was developed to provide the research scientist with man--machine interactive capabilities in a real-time environment, and thereby produce results more quickly and efficiently. The CIRMIS system was originally developed to increase data storage and retrieval capabilities and ground-water model control for the Hanford site. The overall configuration, however, can be used in other areas. The CIRMIS system provides the user with three major functions: retrieval of well-based data, special application for manipulating surface data or background maps, and the manipulation and control of ground-water models. These programs comprise only a portion of the entire CIRMIS system. A complete description of the CIRMIS system is given in this report. 25 figures, 7 tables

  19. Agile Data Management with the Global Change Information System

    Science.gov (United States)

    Duggan, B.; Aulenbach, S.; Tilmes, C.; Goldstein, J.

    2013-12-01

    We describe experiences applying agile software development techniques to the realm of data management during the development of the Global Change Information System (GCIS), a web service and API for authoritative global change information under development by the US Global Change Research Program. Some of the challenges during system design and implementation have been : (1) balancing the need for a rigorous mechanism for ensuring information quality with the realities of large data sets whose contents are often in flux, (2) utilizing existing data to inform decisions about the scope and nature of new data, and (3) continuously incorporating new knowledge and concepts into a relational data model. The workflow for managing the content of the system has much in common with the development of the system itself. We examine various aspects of agile software development and discuss whether or how we have been able to use them for data curation as well as software development.

  20. Living is information processing: from molecules to global systems

    OpenAIRE

    Farnsworth, Keith D.; Nelson, John; Gershenson, Carlos

    2012-01-01

    We extend the concept that life is an informational phenomenon, at every level of organisation, from molecules to the global ecological system. According to this thesis: (a) living is information processing, in which memory is maintained by both molecular states and ecological states as well as the more obvious nucleic acid coding; (b) this information processing has one overall function - to perpetuate itself; and (c) the processing method is filtration (cognition) of, and synthesis of, info...

  1. GRIN-Global: An International Project to Develop a Global Plant Genebank Information Management System

    Science.gov (United States)

    The mission of the GRIN-Global Project is to create a new, scalable version of the Germplasm Resource Information System (GRIN) to provide the world’s crop genebanks with a powerful, flexible, easy-to-use plant genetic resource (PGR) information management system. The system will help safeguard PGR ...

  2. Sequential Optimization of Global Sequence Alignments Relative to Different Cost Functions

    KAUST Repository

    Odat, Enas M.

    2011-05-01

    The purpose of this dissertation is to present a methodology to model global sequence alignment problem as directed acyclic graph which helps to extract all possible optimal alignments. Moreover, a mechanism to sequentially optimize sequence alignment problem relative to different cost functions is suggested. Sequence alignment is mostly important in computational biology. It is used to find evolutionary relationships between biological sequences. There are many algo- rithms that have been developed to solve this problem. The most famous algorithms are Needleman-Wunsch and Smith-Waterman that are based on dynamic program- ming. In dynamic programming, problem is divided into a set of overlapping sub- problems and then the solution of each subproblem is found. Finally, the solutions to these subproblems are combined into a final solution. In this thesis it has been proved that for two sequences of length m and n over a fixed alphabet, the suggested optimization procedure requires O(mn) arithmetic operations per cost function on a single processor machine. The algorithm has been simulated using C#.Net programming language and a number of experiments have been done to verify the proved statements. The results of these experiments show that the number of optimal alignments is reduced after each step of optimization. Furthermore, it has been verified that as the sequence length increased linearly then the number of optimal alignments increased exponentially which also depends on the cost function that is used. Finally, the number of executed operations increases polynomially as the sequence length increase linearly.

  3. Mixed multiscale finite element methods using approximate global information based on partial upscaling

    KAUST Repository

    Jiang, Lijian; Efendiev, Yalchin; Mishev, IIya

    2009-01-01

    The use of limited global information in multiscale simulations is needed when there is no scale separation. Previous approaches entail fine-scale simulations in the computation of the global information. The computation of the global information

  4. Delayed processing of global shape information in developmental prosopagnosia

    DEFF Research Database (Denmark)

    Gerlach, Christian; Klargaard, Solja K.; Petersen, Anders

    2017-01-01

    individuals with DP in Navon’s paradigm we find evidence of a reduced global precedence effect: The DPs are slower than controls to process global but not local shape information. Importantly, and in contrast to previous studies, we demonstrate that the DPs perform normally in a comprehensive test of visual......There is accumulating evidence suggesting that a central deficit in developmental prosopagnosia (DP), a disorder characterized by profound and lifelong difficulties with face recognition, concerns impaired holistic processing. Some of this evidence comes from studies using Navon’s paradigm where...... individuals with DP show a greater local or reduced global bias compared with controls. However, it has not been established what gives rise to this altered processing bias. Is it a reduced global precedence effect, changes in susceptibility to interference effects or both? By analyzing the performance of 10...

  5. Distress vocalization sequences broadcasted by bats carry redundant information.

    Science.gov (United States)

    Hechavarría, Julio C; Beetz, M Jerome; Macias, Silvio; Kössl, Manfred

    2016-07-01

    Distress vocalizations (also known as alarm or screams) are an important component of the vocal repertoire of a number of animal species, including bats, humans, monkeys and birds, among others. Although the behavioral relevance of distress vocalizations is undeniable, at present, little is known about the rules that govern vocalization production when in alarmful situations. In this article, we show that when distressed, bats of the species Carollia perspicillata produce repetitive vocalization sequences in which consecutive syllables are likely to be similar to one another regarding their physical attributes. The uttered distress syllables are broadband (12-73 kHz) with most of their energy focussing at 23 kHz. Distress syllables are short (~4 ms), their average sound pressure level is close to 70 dB SPL, and they are produced at high repetition rates (every 14 ms). We discuss that, because of their physical attributes, bat distress vocalizations could serve a dual purpose: (1) advertising threatful situations to conspecifics, and (2) informing the threatener that the bats are ready to defend themselves. We also discuss possible advantages of advertising danger/discomfort using repetitive utterances, a calling strategy that appears to be ubiquitous across the animal kingdom.

  6. Mitochondrial DNA sequencing of cat hair: an informative forensic tool.

    Science.gov (United States)

    Tarditi, Christy R; Grahn, Robert A; Evans, Jeffrey J; Kurushima, Jennifer D; Lyons, Leslie A

    2011-01-01

    Approximately 81.7 million cats are in 37.5 million U.S. households. Shed fur can be criminal evidence because of transfer to victims, suspects, and/or their belongings. To improve cat hairs as forensic evidence, the mtDNA control region from single hairs, with and without root tags, was sequenced. A dataset of a 402-bp control region segment from 174 random-bred cats representing four U.S. geographic areas was generated to determine the informativeness of the mtDNA region. Thirty-two mtDNA mitotypes were observed ranging in frequencies from 0.6-27%. Four common types occurred in all populations. Low heteroplasmy, 1.7%, was determined. Unique mitotypes were found in 18 individuals, 10.3% of the population studied. The calculated discrimination power implied that 8.3 of 10 randomly selected individuals can be excluded by this region. The genetic characteristics of the region and the generated dataset support the use of this cat mtDNA region in forensic applications. 2010 American Academy of Forensic Sciences. Published 2010. This article is a U.S. Government work and is in the public domain in the U.S.A.

  7. Earth science information: Planning for the integration and use of global change information

    Science.gov (United States)

    Lousma, Jack R.

    1992-01-01

    Activities and accomplishments of the first six months of the Consortium for International Earth Science Information Network (CIESIN's) 1992 technical program have focused on four main missions: (1) the development and implementation of plans for initiation of the Socioeconomic Data and Applications Center (SEDAC) as part of the EOSDIS Program; (2) the pursuit and development of a broad-based global change information cooperative by providing systems analysis and integration between natural science and social science data bases held by numerous federal agencies and other sources; (3) the fostering of scientific research into the human dimensions of global change and providing integration between natural science and social science data and information; and (4) the serving of CIESIN as a gateway for global change data and information distribution through development of the Global Change Research Information Office and other comprehensive knowledge sharing systems.

  8. Information content in reflected global navigation satellite system signals

    DEFF Research Database (Denmark)

    Høeg, Per; Carlstrom, Anders

    2011-01-01

    The direct signals from satellites in global satellite navigation satellites systems (GNSS) as, GPS, GLONASS and GALILEO, constitute the primary source for positioning, navigation and timing from space. But also the reflected GNSS signals contain an important information content of signal travel...

  9. Global Information Justice: Rights, Responsibilities, and Caring Connections.

    Science.gov (United States)

    Smith, Martha

    2001-01-01

    Explains the concept of global information justice and describes it as an ethical ideal, as an organizing principle for a model for analysis, and as a direction for policy making. Discusses the use of new technologies; access to technology; ownership; privacy; security; community; and the Universal Declaration of Human Rights. (Author/LRW)

  10. Provenance Representation in the Global Change Information System (GCIS)

    Science.gov (United States)

    Tilmes, Curt

    2012-01-01

    Global climate change is a topic that has become very controversial despite strong support within the scientific community. It is common for agencies releasing information about climate change to be served with Freedom of Information Act (FOIA) requests for everything that led to that conclusion. Capturing and presenting the provenance, linking to the research papers, data sets, models, analyses, observation instruments and satellites, etc. supporting key findings has the potential to mitigate skepticism in this domain. The U.S. Global Change Research Program (USGCRP) is now coordinating the production of a National Climate Assessment (NCA) that presents our best understanding of global change. We are now developing a Global Change Information System (GCIS) that will present the content of that report and its provenance, including the scientific support for the findings of the assessment. We are using an approach that will present this information both through a human accessible web site as well as a machine readable interface for automated mining of the provenance graph. We plan to use the developing W3C PROV Data Model and Ontology for this system.

  11. An accurate and rapid continuous wavelet dynamic time warping algorithm for unbalanced global mapping in nanopore sequencing

    KAUST Repository

    Han, Renmin; Li, Yu; Wang, Sheng; Gao, Xin

    2017-01-01

    Long-reads, point-of-care, and PCR-free are the promises brought by nanopore sequencing. Among various steps in nanopore data analysis, the global mapping between the raw electrical current signal sequence and the expected signal sequence from

  12. Application of Quaternion in improving the quality of global sequence alignment scores for an ambiguous sequence target in Streptococcus pneumoniae DNA

    Science.gov (United States)

    Lestari, D.; Bustamam, A.; Novianti, T.; Ardaneswari, G.

    2017-07-01

    DNA sequence can be defined as a succession of letters, representing the order of nucleotides within DNA, using a permutation of four DNA base codes including adenine (A), guanine (G), cytosine (C), and thymine (T). The precise code of the sequences is determined using DNA sequencing methods and technologies, which have been developed since the 1970s and currently become highly developed, advanced and highly throughput sequencing technologies. So far, DNA sequencing has greatly accelerated biological and medical research and discovery. However, in some cases DNA sequencing could produce any ambiguous and not clear enough sequencing results that make them quite difficult to be determined whether these codes are A, T, G, or C. To solve these problems, in this study we can introduce other representation of DNA codes namely Quaternion Q = (PA, PT, PG, PC), where PA, PT, PG, PC are the probability of A, T, G, C bases that could appear in Q and PA + PT + PG + PC = 1. Furthermore, using Quaternion representations we are able to construct the improved scoring matrix for global sequence alignment processes, by applying a dot product method. Moreover, this scoring matrix produces better and higher quality of the match and mismatch score between two DNA base codes. In implementation, we applied the Needleman-Wunsch global sequence alignment algorithm using Octave, to analyze our target sequence which contains some ambiguous sequence data. The subject sequences are the DNA sequences of Streptococcus pneumoniae families obtained from the Genebank, meanwhile the target DNA sequence are received from our collaborator database. As the results we found the Quaternion representations improve the quality of the sequence alignment score and we can conclude that DNA sequence target has maximum similarity with Streptococcus pneumoniae.

  13. Linked Open Data in the Global Change Information System (GCIS)

    Science.gov (United States)

    Tilmes, Curt A.

    2012-01-01

    The U.S. Global Change Research Program (http://globalchange.gov) coordinates and integrates federal research on changes in the global environment and their implications for society. The USGCRP is developing a Global Change Information System (GCIS) that will centralize access to data and information related to global change across the U.S. federal government. The first implementation will focus on the 2013 National Climate Assessment (NCA) . (http://assessment.globalchange.gov) The NCA integrates, evaluates, and interprets the findings of the USGCRP; analyzes the effects of global change on the natural environment, agriculture, energy production and use, land and water resources, transportation, human health and welfare, human social systems, and biological diversity; and analyzes current trends in global change, both human-induced and natural, and projects major trends for the subsequent 25 to 100 years. The NCA has received over 500 distinct technical inputs to the process, many of which are reports distilling and synthesizing even more information, coming from thousands of individuals around the federal, state and local governments, academic institutions and non-governmental organizations. The GCIS will present a web-based version of the NCA including annotations linking the findings and content of the NCA with the scientific research, datasets, models, observations, etc. that led to its conclusions. It will use semantic tagging and a linked data approach, assigning globally unique, persistent, resolvable identifiers to all of the related entities and capturing and presenting the relationships between them, both internally and referencing out to other linked data sources and back to agency data centers. The developing W3C PROV Data Model and ontology will be used to capture the provenance trail and present it in both human readable web pages and machine readable formats such as RDF and SPARQL. This will improve visibility into the assessment process, increase

  14. Threshold policy for global games with noisy information sharing

    KAUST Repository

    Mahdavifar, Hessam

    2015-12-15

    It is known that global games with noisy sharing of information do not admit a certain type of threshold policies [1]. Motivated by this result, we investigate the existence of threshold-type policies on global games with noisy sharing of information and show that such equilibrium strategies exist and are unique if the sharing of information happens over a sufficiently noisy environment. To show this result, we establish that if a threshold function is an equilibrium strategy, then it will be a solution to a fixed point equation. Then, we show that for a sufficiently noisy environment, the functional fixed point equation leads to a contraction mapping, and hence, its iterations converge to a unique continuous threshold policy.

  15. Sharing Data to Build a Medical Information Commons: From Bermuda to the Global Alliance.

    Science.gov (United States)

    Cook-Deegan, Robert; Ankeny, Rachel A; Maxson Jones, Kathryn

    2017-08-31

    The Human Genome Project modeled its open science ethos on nematode biology, most famously through daily release of DNA sequence data based on the 1996 Bermuda Principles. That open science philosophy persists, but daily, unfettered release of data has had to adapt to constraints occasioned by the use of data from individual people, broader use of data not only by scientists but also by clinicians and individuals, the global reach of genomic applications and diverse national privacy and research ethics laws, and the rising prominence of a diverse commercial genomics sector. The Global Alliance for Genomics and Health was established to enable the data sharing that is essential for making meaning of genomic variation. Data-sharing policies and practices will continue to evolve as researchers, health professionals, and individuals strive to construct a global medical and scientific information commons.

  16. 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

  17. International earth science information network for global change decision making

    Energy Technology Data Exchange (ETDEWEB)

    Autrey-Hunley, C.; Kuhn, W.R.; Kasischke, E.; Trichel, M.T.; Coppola, R.

    1991-01-01

    Effective environmental decision making depends upon the ability to predict physical changes in the environment, societal responses to these changes, and how both the physical changes and societal responses will be affected by changes in government regulations, public perceptions and the environment. Technological advances in remote sensing have provided a wealth of earth science data necessary to study global change problems; the Earth Observatory System will provide an unprecedented data source in the late 1990's. The Consortium for an International Earth Science Information Network (CIESIN) will combine earth science data (both satellite and ground-based) with data on the social sciences (e.g., economics, demographics, public health) to support informed policy decisions and to transfer knowledge on global change and its causes to the public.

  18. Event Sequence Analysis of the Air Intelligence Agency Information Operations Center Flight Operations

    National Research Council Canada - National Science Library

    Larsen, Glen

    1998-01-01

    This report applies Event Sequence Analysis, methodology adapted from aircraft mishap investigation, to an investigation of the performance of the Air Intelligence Agency's Information Operations Center (IOC...

  19. The earth knowledge base and the global information society

    Directory of Open Access Journals (Sweden)

    A Martynenko

    2006-01-01

    Full Text Available Today many countries have applied the strategy of developing an information-oriented society and data infrastructure. Although varying it their details and means of realization, all these policies have the same aim - to build a global information society. Here in Russia this crucial role belongs to the Electronic (Digital Earth initiative, which integrates geoinformation technologies in the Earth Knowledge Base (EKB. It i designed to promote the economic, social and scientific progress. An analysis of the problem has been done in the article.

  20. Functional region prediction with a set of appropriate homologous sequences-an index for sequence selection by integrating structure and sequence information with spatial statistics

    Science.gov (United States)

    2012-01-01

    Background The detection of conserved residue clusters on a protein structure is one of the effective strategies for the prediction of functional protein regions. Various methods, such as Evolutionary Trace, have been developed based on this strategy. In such approaches, the conserved residues are identified through comparisons of homologous amino acid sequences. Therefore, the selection of homologous sequences is a critical step. It is empirically known that a certain degree of sequence divergence in the set of homologous sequences is required for the identification of conserved residues. However, the development of a method to select homologous sequences appropriate for the identification of conserved residues has not been sufficiently addressed. An objective and general method to select appropriate homologous sequences is desired for the efficient prediction of functional regions. Results We have developed a novel index to select the sequences appropriate for the identification of conserved residues, and implemented the index within our method to predict the functional regions of a protein. The implementation of the index improved the performance of the functional region prediction. The index represents the degree of conserved residue clustering on the tertiary structure of the protein. For this purpose, the structure and sequence information were integrated within the index by the application of spatial statistics. Spatial statistics is a field of statistics in which not only the attributes but also the geometrical coordinates of the data are considered simultaneously. Higher degrees of clustering generate larger index scores. We adopted the set of homologous sequences with the highest index score, under the assumption that the best prediction accuracy is obtained when the degree of clustering is the maximum. The set of sequences selected by the index led to higher functional region prediction performance than the sets of sequences selected by other sequence

  1. Global sequence diversity of the lactate dehydrogenase gene in Plasmodium falciparum.

    Science.gov (United States)

    Simpalipan, Phumin; Pattaradilokrat, Sittiporn; Harnyuttanakorn, Pongchai

    2018-01-09

    Antigen-detecting rapid diagnostic tests (RDTs) have been recommended by the World Health Organization for use in remote areas to improve malaria case management. Lactate dehydrogenase (LDH) of Plasmodium falciparum is one of the main parasite antigens employed by various commercial RDTs. It has been hypothesized that the poor detection of LDH-based RDTs is attributed in part to the sequence diversity of the gene. To test this, the present study aimed to investigate the genetic diversity of the P. falciparum ldh gene in Thailand and to construct the map of LDH sequence diversity in P. falciparum populations worldwide. The ldh gene was sequenced for 50 P. falciparum isolates in Thailand and compared with hundreds of sequences from P. falciparum populations worldwide. Several indices of molecular variation were calculated, including the proportion of polymorphic sites, the average nucleotide diversity index (π), and the haplotype diversity index (H). Tests of positive selection and neutrality tests were performed to determine signatures of natural selection on the gene. Mean genetic distance within and between species of Plasmodium ldh was analysed to infer evolutionary relationships. Nucleotide sequences of P. falciparum ldh could be classified into 9 alleles, encoding 5 isoforms of LDH. L1a was the most common allelic type and was distributed in P. falciparum populations worldwide. Plasmodium falciparum ldh sequences were highly conserved, with haplotype and nucleotide diversity values of 0.203 and 0.0004, respectively. The extremely low genetic diversity was maintained by purifying selection, likely due to functional constraints. Phylogenetic analysis inferred the close genetic relationship of P. falciparum to malaria parasites of great apes, rather than to other human malaria parasites. This study revealed the global genetic variation of the ldh gene in P. falciparum, providing knowledge for improving detection of LDH-based RDTs and supporting the candidacy of

  2. Unique features of a global human ectoparasite identified through sequencing of the bed bug genome.

    Science.gov (United States)

    Benoit, Joshua B; Adelman, Zach N; Reinhardt, Klaus; Dolan, Amanda; Poelchau, Monica; Jennings, Emily C; Szuter, Elise M; Hagan, Richard W; Gujar, Hemant; Shukla, Jayendra Nath; Zhu, Fang; Mohan, M; Nelson, David R; Rosendale, Andrew J; Derst, Christian; Resnik, Valentina; Wernig, Sebastian; Menegazzi, Pamela; Wegener, Christian; Peschel, Nicolai; Hendershot, Jacob M; Blenau, Wolfgang; Predel, Reinhard; Johnston, Paul R; Ioannidis, Panagiotis; Waterhouse, Robert M; Nauen, Ralf; Schorn, Corinna; Ott, Mark-Christoph; Maiwald, Frank; Johnston, J Spencer; Gondhalekar, Ameya D; Scharf, Michael E; Peterson, Brittany F; Raje, Kapil R; Hottel, Benjamin A; Armisén, David; Crumière, Antonin Jean Johan; Refki, Peter Nagui; Santos, Maria Emilia; Sghaier, Essia; Viala, Sèverine; Khila, Abderrahman; Ahn, Seung-Joon; Childers, Christopher; Lee, Chien-Yueh; Lin, Han; Hughes, Daniel S T; Duncan, Elizabeth J; Murali, Shwetha C; Qu, Jiaxin; Dugan, Shannon; Lee, Sandra L; Chao, Hsu; Dinh, Huyen; Han, Yi; Doddapaneni, Harshavardhan; Worley, Kim C; Muzny, Donna M; Wheeler, David; Panfilio, Kristen A; Vargas Jentzsch, Iris M; Vargo, Edward L; Booth, Warren; Friedrich, Markus; Weirauch, Matthew T; Anderson, Michelle A E; Jones, Jeffery W; Mittapalli, Omprakash; Zhao, Chaoyang; Zhou, Jing-Jiang; Evans, Jay D; Attardo, Geoffrey M; Robertson, Hugh M; Zdobnov, Evgeny M; Ribeiro, Jose M C; Gibbs, Richard A; Werren, John H; Palli, Subba R; Schal, Coby; Richards, Stephen

    2016-02-02

    The bed bug, Cimex lectularius, has re-established itself as a ubiquitous human ectoparasite throughout much of the world during the past two decades. This global resurgence is likely linked to increased international travel and commerce in addition to widespread insecticide resistance. Analyses of the C. lectularius sequenced genome (650 Mb) and 14,220 predicted protein-coding genes provide a comprehensive representation of genes that are linked to traumatic insemination, a reduced chemosensory repertoire of genes related to obligate hematophagy, host-symbiont interactions, and several mechanisms of insecticide resistance. In addition, we document the presence of multiple putative lateral gene transfer events. Genome sequencing and annotation establish a solid foundation for future research on mechanisms of insecticide resistance, human-bed bug and symbiont-bed bug associations, and unique features of bed bug biology that contribute to the unprecedented success of C. lectularius as a human ectoparasite.

  3. Unique features of a global human ectoparasite identified through sequencing of the bed bug genome

    Science.gov (United States)

    Benoit, Joshua B.; Adelman, Zach N.; Reinhardt, Klaus; Dolan, Amanda; Poelchau, Monica; Jennings, Emily C.; Szuter, Elise M.; Hagan, Richard W.; Gujar, Hemant; Shukla, Jayendra Nath; Zhu, Fang; Mohan, M.; Nelson, David R.; Rosendale, Andrew J.; Derst, Christian; Resnik, Valentina; Wernig, Sebastian; Menegazzi, Pamela; Wegener, Christian; Peschel, Nicolai; Hendershot, Jacob M.; Blenau, Wolfgang; Predel, Reinhard; Johnston, Paul R.; Ioannidis, Panagiotis; Waterhouse, Robert M.; Nauen, Ralf; Schorn, Corinna; Ott, Mark-Christoph; Maiwald, Frank; Johnston, J. Spencer; Gondhalekar, Ameya D.; Scharf, Michael E.; Peterson, Brittany F.; Raje, Kapil R.; Hottel, Benjamin A.; Armisén, David; Crumière, Antonin Jean Johan; Refki, Peter Nagui; Santos, Maria Emilia; Sghaier, Essia; Viala, Sèverine; Khila, Abderrahman; Ahn, Seung-Joon; Childers, Christopher; Lee, Chien-Yueh; Lin, Han; Hughes, Daniel S. T.; Duncan, Elizabeth J.; Murali, Shwetha C.; Qu, Jiaxin; Dugan, Shannon; Lee, Sandra L.; Chao, Hsu; Dinh, Huyen; Han, Yi; Doddapaneni, Harshavardhan; Worley, Kim C.; Muzny, Donna M.; Wheeler, David; Panfilio, Kristen A.; Vargas Jentzsch, Iris M.; Vargo, Edward L.; Booth, Warren; Friedrich, Markus; Weirauch, Matthew T.; Anderson, Michelle A. E.; Jones, Jeffery W.; Mittapalli, Omprakash; Zhao, Chaoyang; Zhou, Jing-Jiang; Evans, Jay D.; Attardo, Geoffrey M.; Robertson, Hugh M.; Zdobnov, Evgeny M.; Ribeiro, Jose M. C.; Gibbs, Richard A.; Werren, John H.; Palli, Subba R.; Schal, Coby; Richards, Stephen

    2016-01-01

    The bed bug, Cimex lectularius, has re-established itself as a ubiquitous human ectoparasite throughout much of the world during the past two decades. This global resurgence is likely linked to increased international travel and commerce in addition to widespread insecticide resistance. Analyses of the C. lectularius sequenced genome (650 Mb) and 14,220 predicted protein-coding genes provide a comprehensive representation of genes that are linked to traumatic insemination, a reduced chemosensory repertoire of genes related to obligate hematophagy, host–symbiont interactions, and several mechanisms of insecticide resistance. In addition, we document the presence of multiple putative lateral gene transfer events. Genome sequencing and annotation establish a solid foundation for future research on mechanisms of insecticide resistance, human–bed bug and symbiont–bed bug associations, and unique features of bed bug biology that contribute to the unprecedented success of C. lectularius as a human ectoparasite. PMID:26836814

  4. Highly accurate fluorogenic DNA sequencing with information theory-based error correction.

    Science.gov (United States)

    Chen, Zitian; Zhou, Wenxiong; Qiao, Shuo; Kang, Li; Duan, Haifeng; Xie, X Sunney; Huang, Yanyi

    2017-12-01

    Eliminating errors in next-generation DNA sequencing has proved challenging. Here we present error-correction code (ECC) sequencing, a method to greatly improve sequencing accuracy by combining fluorogenic sequencing-by-synthesis (SBS) with an information theory-based error-correction algorithm. ECC embeds redundancy in sequencing reads by creating three orthogonal degenerate sequences, generated by alternate dual-base reactions. This is similar to encoding and decoding strategies that have proved effective in detecting and correcting errors in information communication and storage. We show that, when combined with a fluorogenic SBS chemistry with raw accuracy of 98.1%, ECC sequencing provides single-end, error-free sequences up to 200 bp. ECC approaches should enable accurate identification of extremely rare genomic variations in various applications in biology and medicine.

  5. Inferences about the global scenario of human T-cell lymphotropic virus type 1 infection using data mining of viral sequences

    Directory of Open Access Journals (Sweden)

    Thessika Hialla Almeida Araujo

    2014-07-01

    Full Text Available Human T-cell lymphotropic virus type 1 (HTLV-1 is mainly associated with two diseases: tropical spastic paraparesis/HTLV-1-associated myelopathy (TSP/HAM and adult T-cell leukaemia/lymphoma. This retrovirus infects five-10 million individuals throughout the world. Previously, we developed a database that annotates sequence data from GenBank and the present study aimed to describe the clinical, molecular and epidemiological scenarios of HTLV-1 infection through the stored sequences in this database. A total of 2,545 registered complete and partial sequences of HTLV-1 were collected and 1,967 (77.3% of those sequences represented unique isolates. Among these isolates, 93% contained geographic origin information and only 39% were related to any clinical status. A total of 1,091 sequences contained information about the geographic origin and viral subtype and 93% of these sequences were identified as subtype “a”. Ethnicity data are very scarce. Regarding clinical status data, 29% of the sequences were generated from TSP/HAM and 67.8% from healthy carrier individuals. Although the data mining enabled some inferences about specific aspects of HTLV-1 infection to be made, due to the relative scarcity of data of available sequences, it was not possible to delineate a global scenario of HTLV-1 infection.

  6. Global Perspectives on Activated Sludge Community Composition analyzed using 16S rRNA amplicon sequencing

    DEFF Research Database (Denmark)

    Nierychlo, Marta; Saunders, Aaron Marc; Albertsen, Mads

    communities, and in this study activated sludge sampled from 32 Wastewater Treatment Plants (WWTPs) around the world was described and compared. The top abundant bacteria in the global activated sludge ecosystem were found and the core population shared by multiple samples was investigated. The results......Activated sludge is the most commonly applied bioprocess throughout the world for wastewater treatment. Microorganisms are key to the process, yet our knowledge of their identity and function is still limited. High-througput16S rRNA amplicon sequencing can reliably characterize microbial...

  7. The existence and global attractivity of almost periodic sequence solution of discrete-time neural networks

    International Nuclear Information System (INIS)

    Huang Zhenkun; Wang Xinghua; Gao Feng

    2006-01-01

    In this Letter, we discuss discrete-time analogue of a continuous-time cellular neural network. Sufficient conditions are obtained for the existence of a unique almost periodic sequence solution which is globally attractive. Our results demonstrate dynamics of the formulated discrete-time analogue as mathematical models for the continuous-time cellular neural network in almost periodic case. Finally, a computer simulation illustrates the suitability of our discrete-time analogue as numerical algorithms in simulating the continuous-time cellular neural network conveniently

  8. The limit space of a Cauchy sequence of globally hyperbolic spacetimes

    Energy Technology Data Exchange (ETDEWEB)

    Noldus, Johan [Universiteit Gent, Vakgroep Wiskundige analyse, Galglaan 2, 9000 Gent (Belgium)

    2004-02-21

    In this second paper, I construct a limit space of a Cauchy sequence of globally hyperbolic spacetimes. In section 2, I work gradually towards a construction of the limit space. I prove that the limit space is unique up to isometry. I also show that, in general, the limit space has quite complicated causal behaviour. This work prepares the final paper in which I shall study in more detail properties of the limit space and the moduli space of (compact) globally hyperbolic spacetimes (cobordisms). As a fait divers, I give in this paper a suitable definition of dimension of a Lorentz space in agreement with the one given by Gromov in the Riemannian case. The difference in philosophy between Lorentzian and Riemannian geometry is one of relativism versus absolutism. In the latter every point distinguishes itself while in the former in general two elements get distinguished by a third, different, one.

  9. The limit space of a Cauchy sequence of globally hyperbolic spacetimes

    International Nuclear Information System (INIS)

    Noldus, Johan

    2004-01-01

    In this second paper, I construct a limit space of a Cauchy sequence of globally hyperbolic spacetimes. In section 2, I work gradually towards a construction of the limit space. I prove that the limit space is unique up to isometry. I also show that, in general, the limit space has quite complicated causal behaviour. This work prepares the final paper in which I shall study in more detail properties of the limit space and the moduli space of (compact) globally hyperbolic spacetimes (cobordisms). As a fait divers, I give in this paper a suitable definition of dimension of a Lorentz space in agreement with the one given by Gromov in the Riemannian case. The difference in philosophy between Lorentzian and Riemannian geometry is one of relativism versus absolutism. In the latter every point distinguishes itself while in the former in general two elements get distinguished by a third, different, one

  10. Thai Youths and Global Warming: Media Information, Awareness, and Lifestyle Activities

    Science.gov (United States)

    Chokriensukchai, Kanchana; Tamang, Ritendra

    2010-01-01

    This study examines the exposure of Thai youths to media information on global warming, the relationship between exposure to global warming information and awareness of global warming, and the relationship between that awareness and lifestyle activities that contribute to global warming. A focus group of eight Thai youths provided information that…

  11. Gathering and using information on a global scale

    Science.gov (United States)

    Mathews, C. W.

    1977-01-01

    The importance of information gathered, integrated and analyzed over broad regions of the world is discussed. Means of acquiring information on critical areas are outlined, and the particular role that remote sensing can play is described in each case. The possible implementation of a global information system and some of the current difficulties in initiation of such a system on an operational basis are explored. In this way, issues will be surfaced for consideration. Topics include: the importance of innovative leadership, and some actions that the government might take, both in Congress and in the Executive Branch; the relationship of U.S. government activities to international interests and to industry; and the need to stimulate more private sector initiative and to transfer responsibilities from government to commercial interests.

  12. Effects of informed consent for individual genome sequencing on relevant knowledge.

    Science.gov (United States)

    Kaphingst, K A; Facio, F M; Cheng, M-R; Brooks, S; Eidem, H; Linn, A; Biesecker, B B; Biesecker, L G

    2012-11-01

    Increasing availability of individual genomic information suggests that patients will need knowledge about genome sequencing to make informed decisions, but prior research is limited. In this study, we examined genome sequencing knowledge before and after informed consent among 311 participants enrolled in the ClinSeq™ sequencing study. An exploratory factor analysis of knowledge items yielded two factors (sequencing limitations knowledge; sequencing benefits knowledge). In multivariable analysis, high pre-consent sequencing limitations knowledge scores were significantly related to education [odds ratio (OR): 8.7, 95% confidence interval (CI): 2.45-31.10 for post-graduate education, and OR: 3.9; 95% CI: 1.05, 14.61 for college degree compared with less than college degree] and race/ethnicity (OR: 2.4, 95% CI: 1.09, 5.38 for non-Hispanic Whites compared with other racial/ethnic groups). Mean values increased significantly between pre- and post-consent for the sequencing limitations knowledge subscale (6.9-7.7, p benefits knowledge subscale (7.0-7.5, p < 0.0001); increase in knowledge did not differ by sociodemographic characteristics. This study highlights gaps in genome sequencing knowledge and underscores the need to target educational efforts toward participants with less education or from minority racial/ethnic groups. The informed consent process improved genome sequencing knowledge. Future studies could examine how genome sequencing knowledge influences informed decision making. © 2012 John Wiley & Sons A/S.

  13. Global Information Resources on Rice for Research and Development

    Directory of Open Access Journals (Sweden)

    Shri RAM

    2012-12-01

    Full Text Available Various issues concerning the progress of rice research are related to ambiguous germplasm identification, difficulty in tracing pedigree information, and lack of integration between genetic resources, characterization, breeding, evaluation and utilization data. These issues are the constraints in developing knowledge-intensive crop improvement programs. The rapid growth, development and the global spread of modern information and communication technology allow quick adoption in fundamental research. Thus, there is a need to provide an opportunity for the establishment of services which describe the rice information for better accessibility to information resources used by researchers to enhance the competitiveness. This work reviews some of available resources on rice bioinformatics and their roles in elucidating and propagating biological and genomic information in rice research. These reviews will also enable stakeholders to understand and adopt the change in research and development and share knowledge with the global community of agricultural scientists. The establishment like International Rice Information System, Rice Genome Research Project and Integrated Rice Genome Explorer are major initiatives for the improvement of rice. Creation of databases for comparative studies of rice and other cereals are major steps in further improvement of genetic compositions. This paper will also highlight some of the initiatives and organizations working in the field of rice improvement and explore the availability of the various web resources for the purpose of research and development of rice. We are developing a meta web server for integration of online resources such as databases, web servers and journals in the area of bioinformatics. This integrated platform, with acronym iBIRA, is available online at ibiranet.in. The resources reviewed here are the excerpts from the resources integrated in iBIRA.

  14. Vision for an Open, Global Greenhouse Gas Information System (GHGIS)

    Science.gov (United States)

    Duren, R. M.; Butler, J. H.; Rotman, D.; Ciais, P.; Greenhouse Gas Information System Team

    2010-12-01

    Over the next few years, an increasing number of entities ranging from international, national, and regional governments, to businesses and private land-owners, are likely to become more involved in efforts to limit atmospheric concentrations of greenhouse gases. In such a world, geospatially resolved information about the location, amount, and rate of greenhouse gas (GHG) emissions will be needed, as well as the stocks and flows of all forms of carbon through the earth system. The ability to implement policies that limit GHG concentrations would be enhanced by a global, open, and transparent greenhouse gas information system (GHGIS). An operational and scientifically robust GHGIS would combine ground-based and space-based observations, carbon-cycle modeling, GHG inventories, synthesis analysis, and an extensive data integration and distribution system, to provide information about anthropogenic and natural sources, sinks, and fluxes of greenhouse gases at temporal and spatial scales relevant to decision making. The GHGIS effort was initiated in 2008 as a grassroots inter-agency collaboration intended to identify the needs for such a system, assess the capabilities of current assets, and suggest priorities for future research and development. We will present a vision for an open, global GHGIS including latest analysis of system requirements, critical gaps, and relationship to related efforts at various agencies, the Group on Earth Observations, and the Intergovernmental Panel on Climate Change.

  15. Global information network on chemicals (GINC) and its Asian component

    International Nuclear Information System (INIS)

    Kaminuma, Tsuguchika; Nakata, Kotoko

    2003-01-01

    The Global Information Network on Chemicals (GINC) is an effort to build a global information network that links international, national, and other organizations working for the safe management of chemicals in order to exchange information and improve communications. The project was originally proposed in 1993 by one of the authors then at the National Institute of Health Sciences (NIHS) of Japan to the International Program on Chemical Safety (IPCS), which is a joint project of World Health Organization (WHO), International Labor Organization (ILO), and United Nations Environment Program (UNEP). The base support system was first implemented at NIHS using the Internet/World Wide Web (WWW) technology in 1995. The project was then endorsed by the Intergovernmental Forum on Chemical Safety (IFCS) and was adopted by the Inter-Organization Program for the Sound Management of Chemicals (IOMC). However, the base system (http://www.nihs.go.jp/GINC/index.html) has been developed and maintained solely by the NIHS group under the support of the Ministry of Health and Welfare (MHW), Japan. Asia, particularly East Asia and the Pacific region, was chosen as the feasibility study region for this project. During the period from December 1994 to July 2002, NIHS hosted eight meetings on this project held in Tokyo

  16. Towards a Global Greenhouse Gas Information System (GHGIS)

    Science.gov (United States)

    Duren, Riley; Butler, James; Rotman, Doug; Miller, Charles; Decola, Phil; Sheffner, Edwin; Tucker, Compton; Mitchiner, John; Jonietz, Karl; Dimotakis, Paul

    2010-05-01

    Over the next few years, an increasing number of entities ranging from international, national, and regional governments, to businesses and private land-owners, are likely to become more involved in efforts to limit atmospheric concentrations of greenhouse gases. In such a world, geospatially resolved information about the location, amount, and rate of greenhouse gas (GHG) emissions will be needed, as well as the stocks and flows of all forms of carbon through terrestrial ecosystems and in the oceans. The ability to implement policies that limit GHG concentrations would be enhanced by a global, open, and transparent greenhouse gas information system (GHGIS). An operational and scientifically robust GHGIS would combine ground-based and space-based observations, carbon-cycle modeling, GHG inventories, meta-analysis, and an extensive data integration and distribution system, to provide information about sources, sinks, and fluxes of greenhouse gases at policy-relevant temporal and spatial scales. The GHGIS effort was initiated in 2008 as a grassroots inter-agency collaboration intended to rigorously identify the needs for such a system, assess the capabilities of current assets, and suggest priorities for future research and development. We will present a status of the GHGIS effort including our latest analysis and ideas for potential near-term pilot projects with potential relevance to European initiatives including the Global Monitoring for Environment and Security (GMES) and the Integrated Carbon Observing System (ICOS).

  17. Requirements for a Global Greenhouse Gas Information System

    Science.gov (United States)

    Duren, R.; Boland, S.; Lempert, R.; Miller, C.

    2008-12-01

    A global greenhouse gas information system will prove a critical component of any successful effort to mitigate climate change which relies on limiting the atmospheric concentration of greenhouse gases. The system will provide the situational awareness necessary to actively reduce emissions, influence land use change, and sequester carbon. The information from such a system will be subject to intense scrutiny. Therefore, an effective system must openly and transparently produce data of unassailable quality. A global greenhouse gas information system will likely require a combination of space-and air-based remote- sensing assets, ground-based measurements, carbon cycle modeling and self-reporting. The specific requirements on such a system will be shaped by the degree of international cooperation it enjoys and the needs of the policy regime it aims to support, which might range from verifying treaty obligations, to certifying the tradable permits and offsets underlying a market in greenhouse gas emission reductions, to providing a comprehensive inventory of high and low emitters that could be used by non-governmental organizations and other international actors. While some technical studies have examined particular system components in single scenarios, there remains a need for a comprehensive survey of the range of potential requirements, options, and strategies for the overall system. We have initiated such a survey and recently hosted a workshop which engaged a diverse community of stakeholders to begin synthesizing requirements for such a system, with an initial focus on carbon dioxide. In this paper we describe our plan for completing the definition of the requirements, options, and strategies for a global greenhouse gas monitoring system. We discuss our overall approach and provide a status on the initial requirements synthesis activity.

  18. Is central dogma a global property of cellular information flow?

    Science.gov (United States)

    Piras, Vincent; Tomita, Masaru; Selvarajoo, Kumar

    2012-01-01

    The central dogma of molecular biology has come under scrutiny in recent years. Here, we reviewed high-throughput mRNA and protein expression data of Escherichia coli, Saccharomyces cerevisiae, and several mammalian cells. At both single cell and population scales, the statistical comparisons between the entire transcriptomes and proteomes show clear correlation structures. In contrast, the pair-wise correlations of single transcripts to proteins show nullity. These data suggest that the organizing structure guiding cellular processes is observed at omics-wide scale, and not at single molecule level. The central dogma, thus, globally emerges as an average integrated flow of cellular information.

  19. Is central dogma a global property of cellular information flow?

    Directory of Open Access Journals (Sweden)

    Vincent ePiras

    2012-11-01

    Full Text Available The central dogma of molecular biology has come under scrutiny in recent years. Here, we reviewed high-throughput mRNA and protein expression data of Escherichia coli, Saccharomyces cerevisiae, and several mammalian cells. At both single cell and population scales, the statistical comparisons between the entire transcriptomes and proteomes show clear correlation structures. In contrast, the pair-wise correlations of single transcript to protein show nullity. These data suggest that the organizing structure guiding cellular processes is observed at omics-wide scale and not at single molecule level. The central dogma, thus, globally emerges as an average integrated flow of cellular information.

  20. Medan City: Informality and the Historical Global City

    Science.gov (United States)

    Sudarmadji, N.; Tyaghita, B.; Astuti, P. T.; Etleen, D.

    2018-05-01

    As projected by UN that two-thirds of Indonesia’s population will live in urban areas by 2050, rapid urbanization is happening in Indonesian cities. Initial research on eight Indonesian Cities (which includes Medan, Jatinegara, Bandung, Surakarta, Yogyakarta, Surabaya, Balikpapan, and Manado) by Tunas Nusa Foundation since 2012 shows that urbanization of each city has happened throughout history creating cultural, economic, and environmental networks that are distinct from one city to another. While the networks remain until today and continuously shapes the urban agglomeration pattern, not all parts of the city could undergo subsequent development that confirms the existing pattern, leading to the creation informality. Nor could it make future planning that comprehends the nature of its integrated urban dynamic beyond its current administrative authority. In this paper, we would like to share our study for Medan, North Sumatra as it shows a portrait of a city with a long relationship to a global network since the Maritime trade era. Medan has become home to many ethnic groups which have sailed and migrated as part of a global economic agenda creating a strong economic network between port cities along the Malacca Strait. The city has kept its role in the global economic network until today, to name a few, becoming the frontier for the Indonesia-Malaysia-Thailand Growth Triangle. While we celebrate Medan’s potential to become a global city with major infrastructure development as well as cultural assets as its advantage in the future, we argue that microscale cohesion supported by government policy in agreed planning documents are fundamental for the city to thrive amidst the challenges it is facing. Yet, these cultural assets, as well as micro scale cohesion in Medan City today, are still undermined. Thus, informality in Medan exists as result of ignorance and marginalization of certain socio-cultural groups, abandoning places and identity, as well as the

  1. Information management for global environmental change, including the Carbon Dioxide Information Analysis Center

    Energy Technology Data Exchange (ETDEWEB)

    Stoss, F.W. [Oak Ridge National Lab., TN (United States). Carbon Dioxide Information Analysis Center

    1994-06-01

    The issue of global change is international in scope. A body of international organizations oversees the worldwide coordination of research and policy initiatives. In the US the National Science and Technology Council (NSTC) was established in November of 1993 to provide coordination of science, space, and technology policies throughout the federal government. NSTC is organized into nine proposed committees. The Committee on Environmental and Natural Resources (CERN) oversees the US Department of Energy`s Global Change Research Program (USGCRP). As part of the USGCRP, the US Department of Energy`s Global Change Research Program aims to improve the understanding of Earth systems and to strengthen the scientific basis for the evaluation of policy and government action in response to potential global environmental changes. This paper examines the information and data management roles of several international and national programs, including Oak Ridge National Laboratory`s (ORNL`s) global change information programs. An emphasis will be placed on the Carbon Dioxide Information Analysis Center (CDIAC), which also serves as the World Data Center-A for Atmospheric Trace Gases.

  2. DEVELOPMENT OF INFORMATION SERVICES AND PRODUCTS IN UZBEKISTAN DURING GLOBALIZATION

    Directory of Open Access Journals (Sweden)

    Feruza Khayrullaevna Sidikova

    2014-10-01

    Full Text Available The main purpose of the article is investigation of the issues of development of information services and products in Uzbekistan during globalization role of information and communicative technologies in development international business and trade. As the results of the research there revealed a connection of introducing electronic commerce and business in practice of firms, corporation and banks there conducted changes in the character of carrying out commercial and financial transactions, interrelations with partners and clients, elaborations and introduction business strategies and competition itself. In the conclusion there offered the suggestions of joining and adjusting to each other varying legislation of different countries and developing international system of taxation of Internet commerce satisfying all participants of electronic trading transactions.

  3. Global transformation of erythrocyte properties via engagement of an SH2-like sequence in band 3.

    Science.gov (United States)

    Puchulu-Campanella, Estela; Turrini, Francesco M; Li, Yen-Hsing; Low, Philip S

    2016-11-29

    Src homology 2 (SH2) domains are composed of weakly conserved sequences of ∼100 aa that bind phosphotyrosines in signaling proteins and thereby mediate intra- and intermolecular protein-protein interactions. In exploring the mechanism whereby tyrosine phosphorylation of the erythrocyte anion transporter, band 3, triggers membrane destabilization, vesiculation, and fragmentation, we discovered a SH2 signature motif positioned between membrane-spanning helices 4 and 5. Evidence that this exposed cytoplasmic sequence contributes to a functional SH2-like domain is provided by observations that: (i) it contains the most conserved sequence of SH2 domains, GSFLVR; (ii) it binds the tyrosine phosphorylated cytoplasmic domain of band 3 (cdb3-PO 4 ) with K d = 14 nM; (iii) binding of cdb3-PO 4 to erythrocyte membranes is inhibited both by antibodies against the SH2 signature sequence and dephosphorylation of cdb3-PO 4 ; (iv) label transfer experiments demonstrate the covalent transfer of photoactivatable biotin from isolated cdb3-PO 4 (but not cdb3) to band 3 in erythrocyte membranes; and (v) phosphorylation-induced binding of cdb3-PO 4 to the membrane-spanning domain of band 3 in intact cells causes global changes in membrane properties, including (i) displacement of a glycolytic enzyme complex from the membrane, (ii) inhibition of anion transport, and (iii) rupture of the band 3-ankyrin bridge connecting the spectrin-based cytoskeleton to the membrane. Because SH2-like motifs are not retrieved by normal homology searches for SH2 domains, but can be found in many tyrosine kinase-regulated transport proteins using modified search programs, we suggest that related cases of membrane transport proteins containing similar motifs are widespread in nature where they participate in regulation of cell properties.

  4. Complete Genome Sequences of Isolates of Enterococcus faecium Sequence Type 117, a Globally Disseminated Multidrug-Resistant Clone

    Science.gov (United States)

    Tedim, Ana P.; Lanza, Val F.; Manrique, Marina; Pareja, Eduardo; Ruiz-Garbajosa, Patricia; Cantón, Rafael; Baquero, Fernando; Tobes, Raquel

    2017-01-01

    ABSTRACT The emergence of nosocomial infections by multidrug-resistant sequence type 117 (ST117) Enterococcus faecium has been reported in several European countries. ST117 has been detected in Spanish hospitals as one of the main causes of bloodstream infections. We analyzed genome variations of ST117 strains isolated in Madrid and describe the first ST117 closed genome sequences. PMID:28360174

  5. GLOBIL: WWF's Global Observation and Biodiversity Information Portal

    Science.gov (United States)

    Shapiro, A. C.; Nijsten, L.; Schmitt, S.; Tibaldeschi, P.

    2015-04-01

    Despite ever increasing availability of satellite imagery and spatial data, conservation managers, decision makers and planners are often unable to analyze data without special knowledge or software. WWF is bridging this gap by putting extensive spatial data into an easy to use online mapping environment, to allow visualization, manipulation and analysis of large data sets by any user. Consistent, reliable and repeatable ecosystem monitoring information for priority eco-regions is needed to increase transparency in WWF's global conservation work, to measure conservation impact, and to provide communications with the general public and organization members. Currently, much of this monitoring and evaluation data is isolated, incompatible, or inaccessible and not readily usable or available for those without specialized software or knowledge. Launched in 2013 by WWF Netherlands and WWF Germany, the Global Observation and Biodiversity Information Portal (GLOBIL) is WWF's new platform to unite, centralize, standardize and visualize geo-spatial data and information from more than 150 active GIS users worldwide via cloud-based ArcGIS Online. GLOBIL is increasing transparency, providing baseline data for monitoring and evaluation while communicating impacts and conservation successes to the public. GLOBIL is currently being used in the worldwide marine campaign as an advocacy tool for establishing more marine protected areas, and a monitoring interface to track the progress towards ocean protection goals. In the Kavango-Zambezi (KAZA) Transfrontier Conservation area, local partners are using the platform to monitor land cover changes, barriers to species migrations, potential human-wildlife conflict and local conservation impacts in vast wildlife corridor. In East Africa, an early warning system is providing conservation practitioners with real-time alerts of threats particularly to protected areas and World Heritage Sites by industrial extractive activities. And for

  6. Children inhibit global information when the forest is dense and local information when the forest is sparse.

    Science.gov (United States)

    Krakowski, Claire-Sara; Borst, Grégoire; Vidal, Julie; Houdé, Olivier; Poirel, Nicolas

    2018-09-01

    Visual environments are composed of global shapes and local details that compete for attentional resources. In adults, the global level is processed more rapidly than the local level, and global information must be inhibited in order to process local information when the local information and global information are in conflict. Compared with adults, children present less of a bias toward global visual information and appear to be more sensitive to the density of local elements that constitute the global level. The current study aimed, for the first time, to investigate the key role of inhibition during global/local processing in children. By including two different conditions of global saliency during a negative priming procedure, the results showed that when the global level was salient (dense hierarchical figures), 7-year-old children and adults needed to inhibit the global level to process the local information. However, when the global level was less salient (sparse hierarchical figures), only children needed to inhibit the local level to process the global information. These results confirm a weaker global bias and the greater impact of saliency in children than in adults. Moreover, the results indicate that, regardless of age, inhibition of the most salient hierarchical level is systematically required to select the less salient but more relevant level. These findings have important implications for future research in this area. Copyright © 2018 Elsevier Inc. All rights reserved.

  7. Global search demand for varicose vein information on the internet.

    Science.gov (United States)

    El-Sheikha, Joseph

    2015-09-01

    Changes in internet search trends can provide healthcare professionals detailed information on prevalence of disease and symptoms. Chronic venous disease, more commonly known as varicose veins, is a common symptomatic disease among the adult population. This study aims to measure the change in global search demand for varicose vein information using Google over the past 8 years. The Google Trends instrument was used to measure the change in demand for the use of the local name for varicose veins in several countries across the world between January 2006 and December 2012. The measurements were normalised onto a scale relative to the largest volume of search requests received during a designated time and geographical location. Comparison of national levels of private healthcare and healthcare spending per capita to search demand was also undertaken using Organisation for Economic Co-operation and development economic measurements. Global interest has increased significantly, with linear regression demonstrating a 3.72% year-on-year increase in demand over the 8-year time period (r(2 )= 0.385, p demand significantly increased in the northern hemisphere (p demand compared to cooler winter months (demand (r(2 )= 0.120 p = 0.306). Healthcare spending per capita did not relate to search demand (r(2 )= 0.450 p = 0.077). There is increasing demand for information about varicose veins on the internet, especially during the warmer months of the year. Online search demand does not appear to be related to healthcare spending. © The Author(s) 2014.

  8. 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.

  9. Global seismic inversion as the next standard step in the processing sequence

    Energy Technology Data Exchange (ETDEWEB)

    Maver, Kim G.; Hansen, Lars S.; Jepsen, Anne-Marie; Rasmussen, Klaus B.

    1998-12-31

    Seismic inversion of post stack seismic data has until recently been regarded as a reservoir oriented method since the standard inversion techniques rely on extensive well control and a detailed user derived input model. Most seismic inversion techniques further requires a stable wavelet. As a consequence seismic inversion is mainly utilised in mature areas focusing of specific zones only after the seismic data has been interpreted and is well understood. By using an advanced 3-D global technique, seismic inversion is presented as the next standard step in the processing sequence. The technique is robust towards noise within the seismic data, utilizes a time variant wavelet, and derives a low frequency model utilizing the stacking velocities and only limited well control. 4 figs.

  10. Global transcriptional profiling of the toxic dinoflagellate Alexandrium fundyense using Massively Parallel Signature Sequencing

    Directory of Open Access Journals (Sweden)

    Anderson Donald M

    2006-04-01

    Full Text Available Abstract Background Dinoflagellates are one of the most important classes of marine and freshwater algae, notable both for their functional diversity and ecological significance. They occur naturally as free-living cells, as endosymbionts of marine invertebrates and are well known for their involvement in "red tides". Dinoflagellates are also notable for their unusual genome content and structure, which suggests that the organization and regulation of dinoflagellate genes may be very different from that of most eukaryotes. To investigate the content and regulation of the dinoflagellate genome, we performed a global analysis of the transcriptome of the toxic dinoflagellate Alexandrium fundyense under nitrate- and phosphate-limited conditions using Massively Parallel Signature Sequencing (MPSS. Results Data from the two MPSS libraries showed that the number of unique signatures found in A. fundyense cells is similar to that of humans and Arabidopsis thaliana, two eukaryotes that have been extensively analyzed using this method. The general distribution, abundance and expression patterns of the A. fundyense signatures were also quite similar to other eukaryotes, and at least 10% of the A. fundyense signatures were differentially expressed between the two conditions. RACE amplification and sequencing of a subset of signatures showed that multiple signatures arose from sequence variants of a single gene. Single signatures also mapped to different sequence variants of the same gene. Conclusion The MPSS data presented here provide a quantitative view of the transcriptome and its regulation in these unusual single-celled eukaryotes. The observed signature abundance and distribution in Alexandrium is similar to that of other eukaryotes that have been analyzed using MPSS. Results of signature mapping via RACE indicate that many signatures result from sequence variants of individual genes. These data add to the growing body of evidence for widespread gene

  11. Identifying Statistical Dependence in Genomic Sequences via Mutual Information Estimates

    Directory of Open Access Journals (Sweden)

    Wojciech Szpankowski

    2007-12-01

    Full Text Available Questions of understanding and quantifying the representation and amount of information in organisms have become a central part of biological research, as they potentially hold the key to fundamental advances. In this paper, we demonstrate the use of information-theoretic tools for the task of identifying segments of biomolecules (DNA or RNA that are statistically correlated. We develop a precise and reliable methodology, based on the notion of mutual information, for finding and extracting statistical as well as structural dependencies. A simple threshold function is defined, and its use in quantifying the level of significance of dependencies between biological segments is explored. These tools are used in two specific applications. First, they are used for the identification of correlations between different parts of the maize zmSRp32 gene. There, we find significant dependencies between the 5′ untranslated region in zmSRp32 and its alternatively spliced exons. This observation may indicate the presence of as-yet unknown alternative splicing mechanisms or structural scaffolds. Second, using data from the FBI's combined DNA index system (CODIS, we demonstrate that our approach is particularly well suited for the problem of discovering short tandem repeats—an application of importance in genetic profiling.

  12. Introducing difference recurrence relations for faster semi-global alignment of long sequences.

    Science.gov (United States)

    Suzuki, Hajime; Kasahara, Masahiro

    2018-02-19

    The read length of single-molecule DNA sequencers is reaching 1 Mb. Popular alignment software tools widely used for analyzing such long reads often take advantage of single-instruction multiple-data (SIMD) operations to accelerate calculation of dynamic programming (DP) matrices in the Smith-Waterman-Gotoh (SWG) algorithm with a fixed alignment start position at the origin. Nonetheless, 16-bit or 32-bit integers are necessary for storing the values in a DP matrix when sequences to be aligned are long; this situation hampers the use of the full SIMD width of modern processors. We proposed a faster semi-global alignment algorithm, "difference recurrence relations," that runs more rapidly than the state-of-the-art algorithm by a factor of 2.1. Instead of calculating and storing all the values in a DP matrix directly, our algorithm computes and stores mainly the differences between the values of adjacent cells in the matrix. Although the SWG algorithm and our algorithm can output exactly the same result, our algorithm mainly involves 8-bit integer operations, enabling us to exploit the full width of SIMD operations (e.g., 32) on modern processors. We also developed a library, libgaba, so that developers can easily integrate our algorithm into alignment programs. Our novel algorithm and optimized library implementation will facilitate accelerating nucleotide long-read analysis algorithms that use pairwise alignment stages. The library is implemented in the C programming language and available at https://github.com/ocxtal/libgaba .

  13. Global Carrier Rates of Rare Inherited Disorders Using Population Exome Sequences.

    Directory of Open Access Journals (Sweden)

    Kohei Fujikura

    Full Text Available Exome sequencing has revealed the causative mutations behind numerous rare, inherited disorders, but it is challenging to find reliable epidemiological values for rare disorders. Here, I provide a genetic epidemiology method to identify the causative mutations behind rare, inherited disorders using two population exome sequences (1000 Genomes and NHLBI. I created global maps of carrier rate distribution for 18 recessive disorders in 16 diverse ethnic populations. Out of a total of 161 mutations associated with 18 recessive disorders, I detected 24 mutations in either or both exome studies. The genetic mapping revealed strong international spatial heterogeneities in the carrier patterns of the inherited disorders. I next validated this methodology by statistically evaluating the carrier rate of one well-understood disorder, sickle cell anemia (SCA. The population exome-based epidemiology of SCA [African (allele frequency (AF = 0.0454, N = 2447, Asian (AF = 0, N = 286, European (AF = 0.000214, N = 4677, and Hispanic (AF = 0.0111, N = 362] was not significantly different from that obtained from a clinical prevalence survey. A pair-wise proportion test revealed no significant differences between the two exome projects in terms of AF (46/48 cases; P > 0.05. I conclude that population exome-based carrier rates can form the foundation for a prospectively maintained database of use to clinical geneticists. Similar modeling methods can be applied to many inherited disorders.

  14. (DeCentralization of the Global Informational Ecosystem

    Directory of Open Access Journals (Sweden)

    Johanna Möller

    2017-09-01

    Full Text Available Centralization and decentralization are key concepts in debates that focus on the (antidemocratic character of digital societies. Centralization is understood as the control over communication and data flows, and decentralization as giving it (back to users. Communication and media research focuses on centralization put forward by dominant digital media platforms, such as Facebook and Google, and governments. Decentralization is investigated regarding its potential in civil society, i.e., hacktivism, (encryption technologies, and grass-root technology movements. As content-based media companies increasingly engage with technology, they move into the focus of critical media studies. Moreover, as formerly nationally oriented companies now compete with global media platforms, they share several interests with civil society decentralization agents. Based on 26 qualitative interviews with leading media managers, we investigate (decentralization strategies applied by content-oriented media companies. Theoretically, this perspective on media companies as agents of (decentralization expands (decentralization research beyond traditional democratic stakeholders by considering economic actors within the “global informational ecosystem” (Birkinbine, Gómez, & Wasko, 2017. We provide a three-dimensional framework to empirically investigate (decentralization. From critical media studies, we borrow the (decentralization of data and infrastructures, from media business research, the (decentralization of content distribution.

  15. Intergenic DNA sequences from the human X chromosome reveal high rates of global gene flow

    Directory of Open Access Journals (Sweden)

    Wall Jeffrey D

    2008-11-01

    Full Text Available Abstract Background Despite intensive efforts devoted to collecting human polymorphism data, little is known about the role of gene flow in the ancestry of human populations. This is partly because most analyses have applied one of two simple models of population structure, the island model or the splitting model, which make unrealistic biological assumptions. Results Here, we analyze 98-kb of DNA sequence from 20 independently evolving intergenic regions on the X chromosome in a sample of 90 humans from six globally diverse populations. We employ an isolation-with-migration (IM model, which assumes that populations split and subsequently exchange migrants, to independently estimate effective population sizes and migration rates. While the maximum effective size of modern humans is estimated at ~10,000, individual populations vary substantially in size, with African populations tending to be larger (2,300–9,000 than non-African populations (300–3,300. We estimate mean rates of bidirectional gene flow at 4.8 × 10-4/generation. Bidirectional migration rates are ~5-fold higher among non-African populations (1.5 × 10-3 than among African populations (2.7 × 10-4. Interestingly, because effective sizes and migration rates are inversely related in African and non-African populations, population migration rates are similar within Africa and Eurasia (e.g., global mean Nm = 2.4. Conclusion We conclude that gene flow has played an important role in structuring global human populations and that migration rates should be incorporated as critical parameters in models of human demography.

  16. Chronology of Eocene-Miocene sequences on the New Jersey shallow shelf: implications for regional, interregional, and global correlations

    Science.gov (United States)

    Browning, James V.; Miller, Kenneth G.; Sugarman, Peter J.; Barron, John; McCarthy, Francine M.G.; Kulhanek, Denise K.; Katz, Miriam E.; Feigenson, Mark D.

    2013-01-01

    Integrated Ocean Drilling Program Expedition 313 continuously cored and logged latest Eocene to early-middle Miocene sequences at three sites (M27, M28, and M29) on the inner-middle continental shelf offshore New Jersey, providing an opportunity to evaluate the ages, global correlations, and significance of sequence boundaries. We provide a chronology for these sequences using integrated strontium isotopic stratigraphy and biostratigraphy (primarily calcareous nannoplankton, diatoms, and dinocysts [dinoflagellate cysts]). Despite challenges posed by shallow-water sediments, age resolution is typically ±0.5 m.y. and in many sequences is as good as ±0.25 m.y. Three Oligocene sequences were sampled at Site M27 on sequence bottomsets. Fifteen early to early-middle Miocene sequences were dated at Sites M27, M28, and M29 across clinothems in topsets, foresets (where the sequences are thickest), and bottomsets. A few sequences have coarse (∼1 m.y.) or little age constraint due to barren zones; we constrain the age estimates of these less well dated sequences by applying the principle of superposition, i.e., sediments above sequence boundaries in any site are younger than the sediments below the sequence boundaries at other sites. Our age control provides constraints on the timing of deposition in the clinothem; sequences on the topsets are generally the youngest in the clinothem, whereas the bottomsets generally are the oldest. The greatest amount of time is represented on foresets, although we have no evidence for a correlative conformity. Our chronology provides a baseline for regional and interregional correlations and sea-level reconstructions: (1) we correlate a major increase in sedimentation rate precisely with the timing of the middle Miocene climate changes associated with the development of a permanent East Antarctic Ice Sheet; and (2) the timing of sequence boundaries matches the deep-sea oxygen isotopic record, implicating glacioeustasy as a major driver

  17. DeepProbe: Information Directed Sequence Understanding and Chatbot Design via Recurrent Neural Networks

    OpenAIRE

    Yin, Zi; Chang, Keng-hao; Zhang, Ruofei

    2017-01-01

    Information extraction and user intention identification are central topics in modern query understanding and recommendation systems. In this paper, we propose DeepProbe, a generic information-directed interaction framework which is built around an attention-based sequence to sequence (seq2seq) recurrent neural network. DeepProbe can rephrase, evaluate, and even actively ask questions, leveraging the generative ability and likelihood estimation made possible by seq2seq models. DeepProbe makes...

  18. Subfamily logos: visualization of sequence deviations at alignment positions with high information content

    Directory of Open Access Journals (Sweden)

    Beitz Eric

    2006-06-01

    Full Text Available Abstract Background Recognition of relevant sequence deviations can be valuable for elucidating functional differences between protein subfamilies. Interesting residues at highly conserved positions can then be mutated and experimentally analyzed. However, identification of such sites is tedious because automated approaches are scarce. Results Subfamily logos visualize subfamily-specific sequence deviations. The display is similar to classical sequence logos but extends into the negative range. Positive, upright characters correspond to residues which are characteristic for the subfamily, negative, upside-down characters to residues typical for the remaining sequences. The symbol height is adjusted to the information content of the alignment position. Residues which are conserved throughout do not appear. Conclusion Subfamily logos provide an intuitive display of relevant sequence deviations. The method has proven to be valid using a set of 135 aligned aquaporin sequences in which established subfamily-specific positions were readily identified by the algorithm.

  19. 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

  20. Globalization and information access tools: the way forward for ...

    African Journals Online (AJOL)

    PROMOTING ACCESS TO AFRICAN RESEARCH ... Globalization is a process of interaction and integration among people, ... face the new challenges so as to render more effective services to library clientele in the globalized environment.

  1. 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.

  2. SoilInfo App: global soil information on your palm

    Science.gov (United States)

    Hengl, Tomislav; Mendes de Jesus, Jorge

    2015-04-01

    ISRIC ' World Soil Information has released in 2014 and app for mobile de- vices called 'SoilInfo' (http://soilinfo-app.org) and which aims at providing free access to the global soil data. SoilInfo App (available for Android v.4.0 Ice Cream Sandwhich or higher, and Apple v.6.x and v.7.x iOS) currently serves the Soil- Grids1km data ' a stack of soil property and class maps at six standard depths at a resolution of 1 km (30 arc second) predicted using automated geostatistical mapping and global soil data models. The list of served soil data includes: soil organic carbon (), soil pH, sand, silt and clay fractions (%), bulk density (kg/m3), cation exchange capacity of the fine earth fraction (cmol+/kg), coarse fragments (%), World Reference Base soil groups, and USDA Soil Taxonomy suborders (DOI: 10.1371/journal.pone.0105992). New soil properties and classes will be continuously added to the system. SoilGrids1km are available for download under a Creative Commons non-commercial license via http://soilgrids.org. They are also accessible via a Representational State Transfer API (http://rest.soilgrids.org) service. SoilInfo App mimics common weather apps, but is also largely inspired by the crowdsourcing systems such as the OpenStreetMap, Geo-wiki and similar. Two development aspects of the SoilInfo App and SoilGrids are constantly being worked on: Data quality in terms of accuracy of spatial predictions and derived information, and Data usability in terms of ease of access and ease of use (i.e. flexibility of the cyberinfrastructure / functionalities such as the REST SoilGrids API, SoilInfo App etc). The development focus in 2015 is on improving the thematic and spatial accuracy of SoilGrids predictions, primarily by using finer resolution covariates (250 m) and machine learning algorithms (such as random forests) to improve spatial predictions.

  3. Constraint Satisfaction Inference : Non-probabilistic Global Inference for Sequence Labelling

    NARCIS (Netherlands)

    Canisius, S.V.M.; van den Bosch, A.; Daelemans, W.; Basili, R.; Moschitti, A.

    2006-01-01

    We present a new method for performing sequence labelling based on the idea of using a machine-learning classifier to generate several possible output sequences, and then applying an inference procedure to select the best sequence among those. Most sequence labelling methods following a similar

  4. Magnetic resonance for T-staging of nasopharyngeal carcinoma. The most informative pair of sequences

    International Nuclear Information System (INIS)

    Lau, Kam Y.; Kan, Wai K.; Sze, Wai M.

    2004-01-01

    The objective of this study was to evaluate the most informative pair of sequences in magnetic resonance (MR) for T-staging of nasopharyngeal carcinoma (NPC). The MR images of 134 patients with newly diagnosed NRC, from 1996 to 2002, were retrospectively reviewed. All the patients were scanned using 1.5 Tesla MR systems. The images of the nasopharynx were reviewed by two qualified radiologists to determine the positive findings and the T-stage by Union Internationale Contre le Cancer (UICC) (6th edition) System, using each sequence separately. The T-stage derived from a single MR sequence was then compared with the T-stage based on the five selected sequences to assess the number and percentage of patients who were being understaged. Therefore, the overall percentage accuracy of each single sequence could be determined. A pair of sequences providing information to achieve almost 100% diagnostic accuracy was then derived. The overall percentage accuracy of five individual sequences of the nasopharynx is as follows: contrast-enhanced (CE) fat suppression (FS) axial T1 (94.8%), CE FS coronal T1 (88.1%), FS axial T2 (85.8%), non-contrast enhanced (NE) axial T1 (78.4%) and NE coronal T1 (77.6%). CE FS axial T1 has the best accuracy. All the structures that are missed in CE FS axial T1 which lead to apparent understaging, are appreciated in NE axial T1-weighted images. Individual sequences supplement each other in the NPC staging. CE FS axial T1 is the most informative individual sequence. Combination of CE FS axial T1 and NE axial T1 of the nasopharynx provides sufficient information to achieve almost 100% diagnostic accuracy in T-staging; therefore, both should be included in the MR-staging protocol. (author)

  5. Collecting Information for Rating Global Assessment of Functioning (GAF): Sources of Information and Methods for Information Collection.

    Science.gov (United States)

    I H, Monrad Aas

    2014-11-01

    Global Assessment of Functioning (GAF) is an assessment instrument that is known worldwide. It is widely used for rating the severity of illness. Results from evaluations in psychiatry should characterize the patients. Rating of GAF is based on collected information. The aim of the study is to identify the factors involved in collecting information that is relevant for rating GAF, and gaps in knowledge where it is likely that further development would play a role for improved scoring. A literature search was conducted with a combination of thorough hand search and search in the bibliographic databases PubMed, PsycINFO, Google Scholar, and Campbell Collaboration Library of Systematic Reviews. Collection of information for rating GAF depends on two fundamental factors: the sources of information and the methods for information collection. Sources of information are patients, informants, health personnel, medical records, letters of referral and police records about violence and substance abuse. Methods for information collection include the many different types of interview - unstructured, semi-structured, structured, interviews for Axis I and II disorders, semistructured interviews for rating GAF, and interviews of informants - as well as instruments for rating symptoms and functioning, and observation. The different sources of information, and methods for collection, frequently result in inconsistencies in the information collected. The variation in collected information, and lack of a generally accepted algorithm for combining collected information, is likely to be important for rated GAF values, but there is a fundamental lack of knowledge about the degree of importance. Research to improve GAF has not reached a high level. Rated GAF values are likely to be influenced by both the sources of information used and the methods employed for information collection, but the lack of research-based information about these influences is fundamental. Further development of

  6. Inferring influenza global transmission networks without complete phylogenetic information.

    Science.gov (United States)

    Aris-Brosou, Stéphane

    2014-03-01

    Influenza is one of the most severe respiratory infections affecting humans throughout the world, yet the dynamics of its global transmission network are still contentious. Here, I describe a novel combination of phylogenetics, time series, and graph theory to analyze 14.25 years of data stratified in space and in time, focusing on the main target of the human immune response, the hemagglutinin gene. While bypassing the complete phylogenetic inference of huge data sets, the method still extracts information suggesting that waves of genetic or of nucleotide diversity circulate continuously around the globe for subtypes that undergo sustained transmission over several seasons, such as H3N2 and pandemic H1N1/09, while diversity of prepandemic H1N1 viruses had until 2009 a noncontinuous transmission pattern consistent with a source/sink model. Irrespective of the shift in the structure of H1N1 diversity circulation with the emergence of the pandemic H1N1/09 strain, US prevalence peaks during the winter months when genetic diversity is at its lowest. This suggests that a dominant strain is generally responsible for epidemics and that monitoring genetic and/or nucleotide diversity in real time could provide public health agencies with an indirect estimate of prevalence.

  7. Global Food Security Index Studies and Satellite Information

    Science.gov (United States)

    Medina, T. A.; Ganti-Agrawal, S.; Joshi, D.; Lakhankar, T.

    2017-12-01

    Food yield is equal to the total crop harvest per unit cultivated area. During the elapsed time of germination and frequent harvesting, both human and climate related effects determine a country's' contribution towards global food security. Each country across the globe's annual income per capita was collected to then determine nine countries for further studies. For a location to be chosen, its income per capita needed to be considered poor, uprising or wealthy. Both physical land cover and regional climate helped categorize potential parameters thought to be studied. Once selected, Normalized Difference Vegetation Index (NDVI) data was collected for Ethiopia, Liberia, Indonesia, United States, Norway, Russia, Kuwait and Saudi Arabia over the recent 16 years for approximately every 16 days starting from early in the year 2000. Software languages such as Geographic Information System (GIS), MatLab and Excel were used to determine how population size, income and deforestation directly determines agricultural yields. Because of high maintenance requirements for large harvests when forest areas are cleared, they often have a reduction in soil quality, requiring fertilizer use to produce sufficient crop yields. Total area and vegetation index of each country is to be studied, to determine crop and deforestation percentages. To determine how deforestation impacts future income and crop yield predictions of each country studied. By using NDVI results a parameter is to be potentially found that will help define an index, to create an equation that will determine a country's annual income and ability to provide for their families and themselves.

  8. Relationships between emm and multilocus sequence types within a global collection of Streptococcus pyogenes

    Directory of Open Access Journals (Sweden)

    McGregor Karen F

    2008-04-01

    Full Text Available Abstract Background The M type-specific surface protein antigens encoded by the 5' end of emm genes are targets of protective host immunity and attractive vaccine candidates against infection by Streptococcus pyogenes, a global human pathogen. A history of genetic change in emm was evaluated for a worldwide collection of > 500 S. pyogenes isolates that were defined for genetic background by multilocus sequence typing of housekeeping genes. Results Organisms were categorized by genotypes that roughly correspond to throat specialists, skin specialists, and generalists often recovered from infections at either tissue site. Recovery of distant clones sharing the same emm type was ~4-fold higher for skin specialists and generalists, as compared to throat specialists. Importantly, emm type was often a poor marker for clone. Recovery of clones that underwent recombinational replacement with a new emm type was most evident for the throat and skin specialists. The average ratio of nonsynonymous substitutions per nonsynonymous site (Ka and synonymous substitutions per synonymous site (Ks was 4.9, 1.5 and 1.3 for emm types of the throat specialist, skin specialist and generalist groups, respectively. Conclusion Data indicate that the relationships between emm type and genetic background differ among the three host tissue-related groups, and that the selection pressures acting on emm appear to be strongest for the throat specialists. Since positive selection is likely due in part to a protective host immune response, the findings may have important implications for vaccine design and vaccination strategies.

  9. Global Transcriptome Sequencing Identifies Chlamydospore Specific Markers in Candida albicans and Candida dubliniensis

    LENUS (Irish Health Repository)

    Palige, Katja

    2013-04-15

    Candida albicans and Candida dubliniensis are pathogenic fungi that are highly related but differ in virulence and in some phenotypic traits. During in vitro growth on certain nutrient-poor media, C. albicans and C. dubliniensis are the only yeast species which are able to produce chlamydospores, large thick-walled cells of unknown function. Interestingly, only C. dubliniensis forms pseudohyphae with abundant chlamydospores when grown on Staib medium, while C. albicans grows exclusively as a budding yeast. In order to further our understanding of chlamydospore development and assembly, we compared the global transcriptional profile of both species during growth in liquid Staib medium by RNA sequencing. We also included a C. albicans mutant in our study which lacks the morphogenetic transcriptional repressor Nrg1. This strain, which is characterized by its constitutive pseudohyphal growth, specifically produces masses of chlamydospores in Staib medium, similar to C. dubliniensis. This comparative approach identified a set of putatively chlamydospore-related genes. Two of the homologous C. albicans and C. dubliniensis genes (CSP1 and CSP2) which were most strongly upregulated during chlamydospore development were analysed in more detail. By use of the green fluorescent protein as a reporter, the encoded putative cell wall related proteins were found to exclusively localize to C. albicans and C. dubliniensis chlamydospores. Our findings uncover the first chlamydospore specific markers in Candida species and provide novel insights in the complex morphogenetic development of these important fungal pathogens.

  10. Power spectral density and scaling exponent of high frequency global solar radiation sequences

    Science.gov (United States)

    Calif, Rudy; Schmitt, François G.; Huang, Yongxiang

    2013-04-01

    The part of the solar power production from photovlotaïcs systems is constantly increasing in the electric grids. Solar energy converter devices such as photovoltaic cells are very sensitive to instantaneous solar radiation fluctuations. Thus rapid variation of solar radiation due to changes in the local meteorological condition can induce large amplitude fluctuations of the produced electrical power and reduce the overall efficiency of the system. When large amount of photovoltaic electricity is send into a weak or small electricity network such as island network, the electric grid security can be in jeopardy due to these power fluctuations. The integration of this energy in the electrical network remains a major challenge, due to the high variability of solar radiation in time and space. To palliate these difficulties, it is essential to identify the characteristic of these fluctuations in order to anticipate the eventuality of power shortage or power surge. The objective of this study is to present an approach based on Empirical Mode Decomposition (EMD) and Hilbert-Huang Transform (HHT) to highlight the scaling properties of global solar irradiance data G(t). The scale of invariance is detected on this dataset using the Empirical Mode Decomposition in association with arbitrary-order Hilbert spectral analysis, a generalization of (HHT) or Hilbert Spectral Analysis (HSA). The first step is the EMD, consists in decomposing the normalized global solar radiation data G'(t) into several Intrinsic Mode Functions (IMF) Ci(t) without giving an a priori basis. Consequently, the normalized original solar radiation sequence G'(t) can be written as a sum of Ci(t) with a residual rn. From all IMF modes, a joint PDF P(f,A) of locally and instantaneous frequency f and amplitude A, is estimated. To characterize the scaling behavior in amplitude-frequency space, an arbitrary-order Hilbert marginal spectrum is defined to: Iq(f) = 0 P (f,A)A dA (1) with q × 0 In case of scale

  11. Space Applications and Global Information Infrastructure: a Global Approach against Epidemics

    Science.gov (United States)

    Bastos, C. R.

    2002-01-01

    Brazilian space expenditures correspond to a low-middle rank among the space-faring nations. In this regard, international partnerships have opened doors for the country to take part in a wider range of projects than it would be possible if carried out on its own. Within the above framework, this paper will address a concept in which countries join efforts in pursuit of common objectives and needs in the field of health, countries whose similarities tend to make them face the same types of health problems. Exactly for this reason, such countries can get together and share the costs, risks and ultimately the benefits of their joint efforts. Infectious diseases are mankind's leading causes of death. And their agents travel around the world by the action of their vectors: insects, birds, winds, infected individuals, and others. The ways how Global Information Infrastructure and Space applications can be very helpful in the detection, identification, tracking and fighting migratory diseases will then be discussed. A concept for an international cooperative initiative is presented, addressing its composition, its implementation, the international coordination requirements, the financial and funding issues related to its implementation and sustainability, and the roles to be played by such an organization. The funding issue deserves a closer attention, since many good ideas are killed by financial problems in their early implementation stages. Finally, a conclusion drives the audience's attention towards the potential advantages of space-based assets in covering large portions of the Earth, and consequently being suitable for global initiatives for the benefit of mankind.

  12. Global Education: What the Research Shows. Information Capsule. Volume 0604

    Science.gov (United States)

    Blazer, Christie

    2006-01-01

    Teaching from a global perspective is important because the lives of people around the world are increasingly interconnected through politics, economics, technology, and the environment. Global education teaches students to understand and appreciate people from different cultural backgrounds; view events from a variety of perspectives; recognize…

  13. Evolution of biological sequences implies an extreme value distribution of type I for both global and local pairwise alignment scores.

    Science.gov (United States)

    Bastien, Olivier; Maréchal, Eric

    2008-08-07

    Confidence in pairwise alignments of biological sequences, obtained by various methods such as Blast or Smith-Waterman, is critical for automatic analyses of genomic data. Two statistical models have been proposed. In the asymptotic limit of long sequences, the Karlin-Altschul model is based on the computation of a P-value, assuming that the number of high scoring matching regions above a threshold is Poisson distributed. Alternatively, the Lipman-Pearson model is based on the computation of a Z-value from a random score distribution obtained by a Monte-Carlo simulation. Z-values allow the deduction of an upper bound of the P-value (1/Z-value2) following the TULIP theorem. Simulations of Z-value distribution is known to fit with a Gumbel law. This remarkable property was not demonstrated and had no obvious biological support. We built a model of evolution of sequences based on aging, as meant in Reliability Theory, using the fact that the amount of information shared between an initial sequence and the sequences in its lineage (i.e., mutual information in Information Theory) is a decreasing function of time. This quantity is simply measured by a sequence alignment score. In systems aging, the failure rate is related to the systems longevity. The system can be a machine with structured components, or a living entity or population. "Reliability" refers to the ability to operate properly according to a standard. Here, the "reliability" of a sequence refers to the ability to conserve a sufficient functional level at the folded and maturated protein level (positive selection pressure). Homologous sequences were considered as systems 1) having a high redundancy of information reflected by the magnitude of their alignment scores, 2) which components are the amino acids that can independently be damaged by random DNA mutations. From these assumptions, we deduced that information shared at each amino acid position evolved with a constant rate, corresponding to the

  14. Evolution of biological sequences implies an extreme value distribution of type I for both global and local pairwise alignment scores

    Directory of Open Access Journals (Sweden)

    Maréchal Eric

    2008-08-01

    Full Text Available Abstract Background Confidence in pairwise alignments of biological sequences, obtained by various methods such as Blast or Smith-Waterman, is critical for automatic analyses of genomic data. Two statistical models have been proposed. In the asymptotic limit of long sequences, the Karlin-Altschul model is based on the computation of a P-value, assuming that the number of high scoring matching regions above a threshold is Poisson distributed. Alternatively, the Lipman-Pearson model is based on the computation of a Z-value from a random score distribution obtained by a Monte-Carlo simulation. Z-values allow the deduction of an upper bound of the P-value (1/Z-value2 following the TULIP theorem. Simulations of Z-value distribution is known to fit with a Gumbel law. This remarkable property was not demonstrated and had no obvious biological support. Results We built a model of evolution of sequences based on aging, as meant in Reliability Theory, using the fact that the amount of information shared between an initial sequence and the sequences in its lineage (i.e., mutual information in Information Theory is a decreasing function of time. This quantity is simply measured by a sequence alignment score. In systems aging, the failure rate is related to the systems longevity. The system can be a machine with structured components, or a living entity or population. "Reliability" refers to the ability to operate properly according to a standard. Here, the "reliability" of a sequence refers to the ability to conserve a sufficient functional level at the folded and maturated protein level (positive selection pressure. Homologous sequences were considered as systems 1 having a high redundancy of information reflected by the magnitude of their alignment scores, 2 which components are the amino acids that can independently be damaged by random DNA mutations. From these assumptions, we deduced that information shared at each amino acid position evolved with a

  15. Cenozoic global sea level, sequences, and the New Jersey transect: Results from coastal plain and continental slope drilling

    Science.gov (United States)

    Miller, K.G.; Mountain, Gregory S.; Browning, J.V.; Kominz, M.; Sugarman, P.J.; Christie-Blick, N.; Katz, M.E.; Wright, J.D.

    1998-01-01

    The New Jersey Sea Level Transect was designed to evaluate the relationships among global sea level (eustatic) change, unconformity-bounded sequences, and variations in subsidence, sediment supply, and climate on a passive continental margin. By sampling and dating Cenozoic strata from coastal plain and continental slope locations, we show that sequence boundaries correlate (within ??0.5 myr) regionally (onshore-offshore) and interregionally (New Jersey-Alabama-Bahamas), implicating a global cause. Sequence boundaries correlate with ??18O increases for at least the past 42 myr, consistent with an ice volume (glacioeustatic) control, although a causal relationship is not required because of uncertainties in ages and correlations. Evidence for a causal connection is provided by preliminary Miocene data from slope Site 904 that directly link ??18O increases with sequence boundaries. We conclude that variation in the size of ice sheets has been a primary control on the formation of sequence boundaries since ~42 Ma. We speculate that prior to this, the growth and decay of small ice sheets caused small-amplitude sea level changes (changes on mid-ocean ridges. Although our results are consistent with the general number and timing of Paleocene to middle Miocene sequences published by workers at Exxon Production Research Company, our estimates of sea level amplitudes are substantially lower than theirs. Lithofacies patterns within sequences follow repetitive, predictable patterns: (1) coastal plain sequences consist of basal transgressive sands overlain by regressive highstand silts and quartz sands; and (2) although slope lithofacies variations are subdued, reworked sediments constitute lowstand deposits, causing the strongest, most extensive seismic reflections. Despite a primary eustatic control on sequence boundaries, New Jersey sequences were also influenced by changes in tectonics, sediment supply, and climate. During the early to middle Eocene, low siliciclastic and

  16. Applications of statistical physics and information theory to the analysis of DNA sequences

    Science.gov (United States)

    Grosse, Ivo

    2000-10-01

    DNA carries the genetic information of most living organisms, and the of genome projects is to uncover that genetic information. One basic task in the analysis of DNA sequences is the recognition of protein coding genes. Powerful computer programs for gene recognition have been developed, but most of them are based on statistical patterns that vary from species to species. In this thesis I address the question if there exist universal statistical patterns that are different in coding and noncoding DNA of all living species, regardless of their phylogenetic origin. In search for such species-independent patterns I study the mutual information function of genomic DNA sequences, and find that it shows persistent period-three oscillations. To understand the biological origin of the observed period-three oscillations, I compare the mutual information function of genomic DNA sequences to the mutual information function of stochastic model sequences. I find that the pseudo-exon model is able to reproduce the mutual information function of genomic DNA sequences. Moreover, I find that a generalization of the pseudo-exon model can connect the existence and the functional form of long-range correlations to the presence and the length distributions of coding and noncoding regions. Based on these theoretical studies I am able to find an information-theoretical quantity, the average mutual information (AMI), whose probability distributions are significantly different in coding and noncoding DNA, while they are almost identical in all studied species. These findings show that there exist universal statistical patterns that are different in coding and noncoding DNA of all studied species, and they suggest that the AMI may be used to identify genes in different living species, irrespective of their taxonomic origin.

  17. An accurate and rapid continuous wavelet dynamic time warping algorithm for unbalanced global mapping in nanopore sequencing

    KAUST Repository

    Han, Renmin

    2017-12-24

    Long-reads, point-of-care, and PCR-free are the promises brought by nanopore sequencing. Among various steps in nanopore data analysis, the global mapping between the raw electrical current signal sequence and the expected signal sequence from the pore model serves as the key building block to base calling, reads mapping, variant identification, and methylation detection. However, the ultra-long reads of nanopore sequencing and an order of magnitude difference in the sampling speeds of the two sequences make the classical dynamic time warping (DTW) and its variants infeasible to solve the problem. Here, we propose a novel multi-level DTW algorithm, cwDTW, based on continuous wavelet transforms with different scales of the two signal sequences. Our algorithm starts from low-resolution wavelet transforms of the two sequences, such that the transformed sequences are short and have similar sampling rates. Then the peaks and nadirs of the transformed sequences are extracted to form feature sequences with similar lengths, which can be easily mapped by the original DTW. Our algorithm then recursively projects the warping path from a lower-resolution level to a higher-resolution one by building a context-dependent boundary and enabling a constrained search for the warping path in the latter. Comprehensive experiments on two real nanopore datasets on human and on Pandoraea pnomenusa, as well as two benchmark datasets from previous studies, demonstrate the efficiency and effectiveness of the proposed algorithm. In particular, cwDTW can almost always generate warping paths that are very close to the original DTW, which are remarkably more accurate than the state-of-the-art methods including FastDTW and PrunedDTW. Meanwhile, on the real nanopore datasets, cwDTW is about 440 times faster than FastDTW and 3000 times faster than the original DTW. Our program is available at https://github.com/realbigws/cwDTW.

  18. Globalization on Trial: The Human Condition and the Information ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    What is the human condition at the dawning of the global age? ... scholars,and students in the social sciences and, particularly, the humanities; donors, ... affecting the nature of human civilization, and with the interaction between Islamic and ...

  19. E-business Environment in the Global Information Society

    OpenAIRE

    Vymětal, Dominik; Suchánek, Petr

    2009-01-01

    In today´s digital 21st century, almost all businesses face intense competition from competitors all around the globe. There are no borders and business area for the all companies is almost unlimited. As the main supports of mentioned fact are globalization and ICT´s development. Influences such as globalization, increased popularity of outsourcing and offshoring have recently combined to produce an environment where ICT graduates need to have up-to-date and industry-relevant knowledge and sk...

  20. Globalization: Ecological consequences of global-scale connectivity in people, resources and information

    Science.gov (United States)

    Globalization is a phenomenon affecting all facets of the Earth System. Within the context of ecological systems, it is becoming increasingly apparent that global connectivity among terrestrial systems, the atmosphere, and oceans is driving many ecological dynamics at finer scales and pushing thresh...

  1. Reference evapotranspiration forecasting based on local meteorological and global climate information screened by partial mutual information

    Science.gov (United States)

    Fang, Wei; Huang, Shengzhi; Huang, Qiang; Huang, Guohe; Meng, Erhao; Luan, Jinkai

    2018-06-01

    In this study, reference evapotranspiration (ET0) forecasting models are developed for the least economically developed regions subject to meteorological data scarcity. Firstly, the partial mutual information (PMI) capable of capturing the linear and nonlinear dependence is investigated regarding its utility to identify relevant predictors and exclude those that are redundant through the comparison with partial linear correlation. An efficient input selection technique is crucial for decreasing model data requirements. Then, the interconnection between global climate indices and regional ET0 is identified. Relevant climatic indices are introduced as additional predictors to comprise information regarding ET0, which ought to be provided by meteorological data unavailable. The case study in the Jing River and Beiluo River basins, China, reveals that PMI outperforms the partial linear correlation in excluding the redundant information, favouring the yield of smaller predictor sets. The teleconnection analysis identifies the correlation between Nino 1 + 2 and regional ET0, indicating influences of ENSO events on the evapotranspiration process in the study area. Furthermore, introducing Nino 1 + 2 as predictors helps to yield more accurate ET0 forecasts. A model performance comparison also shows that non-linear stochastic models (SVR or RF with input selection through PMI) do not always outperform linear models (MLR with inputs screen by linear correlation). However, the former can offer quite comparable performance depending on smaller predictor sets. Therefore, efforts such as screening model inputs through PMI and incorporating global climatic indices interconnected with ET0 can benefit the development of ET0 forecasting models suitable for data-scarce regions.

  2. Digitizing the Non-Digital: Creating a Global Context for Events, Artifacts, Ideas, and Information

    Directory of Open Access Journals (Sweden)

    Deborah L. MacPherson

    2006-06-01

    Full Text Available This paper discusses some of the problems associated with search and digital-rights management in the emerging age of interconnectivity. An open-source system called Context Driven Topologies (CDT is proposed to create one global context of geography, knowledge domains, and Internet addresses, using centralized spatial databases, geometry, and maps. The same concept can be described by different words, the same image can be interpreted a thousand ways by every viewer, but mathematics is a set of rules to ensure that certain relationships or sequences will be precisely regenerated. Therefore, unlike most of today’s digital records, CDTs are based on mathematics first, images second, words last. The aim is to permanently link the highest quality events, artifacts, ideas, and information into one record documenting the quickest paths to the most relevant information for specific data, users, and tasks. A model demonstration project using CDT to organize, search, and place information in new contexts while protecting the authors’ intent is also introduced.

  3. 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.

  4. Alpha-gamma phase amplitude coupling subserves information transfer during perceptual sequence learning.

    Science.gov (United States)

    Tzvi, Elinor; Bauhaus, Leon J; Kessler, Till U; Liebrand, Matthias; Wöstmann, Malte; Krämer, Ulrike M

    2018-03-01

    Cross-frequency coupling is suggested to serve transfer of information between wide-spread neuronal assemblies and has been shown to underlie many cognitive functions including learning and memory. In previous work, we found that alpha (8-13 Hz) - gamma (30-48 Hz) phase amplitude coupling (αγPAC) is decreased during sequence learning in bilateral frontal cortex and right parietal cortex. We interpreted this to reflect decreased demands for visuo-motor mapping once the sequence has been encoded. In the present study, we put this hypothesis to the test by adding a "simple" condition to the standard serial reaction time task (SRTT) with minimal needs for visuo-motor mapping. The standard SRTT in our paradigm entailed a perceptual sequence allowing for implicit learning of a sequence of colors with randomly assigned motor responses. Sequence learning in this case was thus not associated with reduced demands for visuo-motor mapping. Analysis of oscillatory power revealed a learning-related alpha decrease pointing to a stronger recruitment of occipito-parietal areas when encoding the perceptual sequence. Replicating our previous findings but in contrast to our hypothesis, αγPAC was decreased in sequence compared to random trials over right frontal and parietal cortex. It also tended to be smaller compared to trials requiring a simple motor sequence. We additionally analyzed αγPAC in resting-state data of a separate cohort. PAC in electrodes over right parietal cortex was significantly stronger compared to sequence trials and tended to be higher compared to simple and random trials of the SRTT data. We suggest that αγPAC in right parietal cortex reflects a "default-mode" brain state, which gets perturbed to allow for encoding of visual regularities into memory. Copyright © 2018 Elsevier Inc. All rights reserved.

  5. 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...

  6. Sequencing Genetics Information: Integrating Data into Information Literacy for Undergraduate Biology Students

    Science.gov (United States)

    MacMillan, Don

    2010-01-01

    This case study describes an information literacy lab for an undergraduate biology course that leads students through a range of resources to discover aspects of genetic information. The lab provides over 560 students per semester with the opportunity for hands-on exploration of resources in steps that simulate the pathways of higher-level…

  7. A Teaching-Learning Sequence of Colour Informed by History and Philosophy of Science

    Science.gov (United States)

    Maurício, Paulo; Valente, Bianor; Chagas, Isabel

    2017-01-01

    In this work, we present a teaching-learning sequence on colour intended to a pre-service elementary teacher programme informed by History and Philosophy of Science. Working in a socio-constructivist framework, we made an excursion on the history of colour. Our excursion through history of colour, as well as the reported misconception on colour…

  8. Information-Theoretic Properties of Auditory Sequences Dynamically Influence Expectation and Memory.

    Science.gov (United States)

    Agres, Kat; Abdallah, Samer; Pearce, Marcus

    2018-01-01

    A basic function of cognition is to detect regularities in sensory input to facilitate the prediction and recognition of future events. It has been proposed that these implicit expectations arise from an internal predictive coding model, based on knowledge acquired through processes such as statistical learning, but it is unclear how different types of statistical information affect listeners' memory for auditory stimuli. We used a combination of behavioral and computational methods to investigate memory for non-linguistic auditory sequences. Participants repeatedly heard tone sequences varying systematically in their information-theoretic properties. Expectedness ratings of tones were collected during three listening sessions, and a recognition memory test was given after each session. Information-theoretic measures of sequential predictability significantly influenced listeners' expectedness ratings, and variations in these properties had a significant impact on memory performance. Predictable sequences yielded increasingly better memory performance with increasing exposure. Computational simulations using a probabilistic model of auditory expectation suggest that listeners dynamically formed a new, and increasingly accurate, implicit cognitive model of the information-theoretic structure of the sequences throughout the experimental session. Copyright © 2017 Cognitive Science Society, Inc.

  9. Core Genome Multilocus Sequence Typing for Identification of Globally Distributed Clonal Groups and Differentiation of Outbreak Strains of Listeria monocytogenes

    OpenAIRE

    Chen, Yi; Gonzalez-Escalona, Narjol; Hammack, Thomas S.; Allard, Marc W.; Strain, Errol A.; Brown, Eric W.

    2016-01-01

    ABSTRACT Many listeriosis outbreaks are caused by a few globally distributed clonal groups, designated clonal complexes or epidemic clones, of Listeria monocytogenes, several of which have been defined by classic multilocus sequence typing (MLST) schemes targeting 6 to 8 housekeeping or virulence genes. We have developed and evaluated core genome MLST (cgMLST) schemes and applied them to isolates from multiple clonal groups, including those associated with 39 listeriosis outbreaks. The cgMLST...

  10. Postmodern Educational Capitalism, Global Information Systems and New Media Networks

    Science.gov (United States)

    Peters, Michael A.

    2012-01-01

    This article reinterprets Lyotard's argument in "The Postmodern Condition" as a basis for a radical political economy approach to knowledge capitalism focusing on post-industrialism in order to put the case that education and knowledge are increasingly becoming part of a globally integrated world capitalism (IWC) that is structured through…

  11. Transparency Under Scrutiny: Information Disclosure in Global Environmental Governance.

    NARCIS (Netherlands)

    Gupta, A.

    2008-01-01

    Although transparency is a key concept of our times, it remains a relatively understudied phenomenon in global environmental politics. The link between transparency and accountable, legitimate and effective governance is assumed, yet the nature and workings of this link require further scrutiny.

  12. Global Warming: Implications for Library and Information Professionals

    African Journals Online (AJOL)

    The major finding is that global warming is an issue that cannot be resolved overnight or with any one policy. It is an intergenerational problem which needs to be addressed by ensuring that how people live on this planet takes climate change seriously into account. The major recommendation is that library buildings should ...

  13. MendeLIMS: a web-based laboratory information management system for clinical genome sequencing.

    Science.gov (United States)

    Grimes, Susan M; Ji, Hanlee P

    2014-08-27

    Large clinical genomics studies using next generation DNA sequencing require the ability to select and track samples from a large population of patients through many experimental steps. With the number of clinical genome sequencing studies increasing, it is critical to maintain adequate laboratory information management systems to manage the thousands of patient samples that are subject to this type of genetic analysis. To meet the needs of clinical population studies using genome sequencing, we developed a web-based laboratory information management system (LIMS) with a flexible configuration that is adaptable to continuously evolving experimental protocols of next generation DNA sequencing technologies. Our system is referred to as MendeLIMS, is easily implemented with open source tools and is also highly configurable and extensible. MendeLIMS has been invaluable in the management of our clinical genome sequencing studies. We maintain a publicly available demonstration version of the application for evaluation purposes at http://mendelims.stanford.edu. MendeLIMS is programmed in Ruby on Rails (RoR) and accesses data stored in SQL-compliant relational databases. Software is freely available for non-commercial use at http://dna-discovery.stanford.edu/software/mendelims/.

  14. Improving probe set selection for microbial community analysis by leveraging taxonomic information of training sequences

    Directory of Open Access Journals (Sweden)

    Jiang Tao

    2011-10-01

    Full Text Available Abstract Background Population levels of microbial phylotypes can be examined using a hybridization-based method that utilizes a small set of computationally-designed DNA probes targeted to a gene common to all. Our previous algorithm attempts to select a set of probes such that each training sequence manifests a unique theoretical hybridization pattern (a binary fingerprint to a probe set. It does so without taking into account similarity between training gene sequences or their putative taxonomic classifications, however. We present an improved algorithm for probe set selection that utilizes the available taxonomic information of training gene sequences and attempts to choose probes such that the resultant binary fingerprints cluster into real taxonomic groups. Results Gene sequences manifesting identical fingerprints with probes chosen by the new algorithm are more likely to be from the same taxonomic group than probes chosen by the previous algorithm. In cases where they are from different taxonomic groups, underlying DNA sequences of identical fingerprints are more similar to each other in probe sets made with the new versus the previous algorithm. Complete removal of large taxonomic groups from training data does not greatly decrease the ability of probe sets to distinguish those groups. Conclusions Probe sets made from the new algorithm create fingerprints that more reliably cluster into biologically meaningful groups. The method can readily distinguish microbial phylotypes that were excluded from the training sequences, suggesting novel microbes can also be detected.

  15. Improving probe set selection for microbial community analysis by leveraging taxonomic information of training sequences.

    Science.gov (United States)

    Ruegger, Paul M; Della Vedova, Gianluca; Jiang, Tao; Borneman, James

    2011-10-10

    Population levels of microbial phylotypes can be examined using a hybridization-based method that utilizes a small set of computationally-designed DNA probes targeted to a gene common to all. Our previous algorithm attempts to select a set of probes such that each training sequence manifests a unique theoretical hybridization pattern (a binary fingerprint) to a probe set. It does so without taking into account similarity between training gene sequences or their putative taxonomic classifications, however. We present an improved algorithm for probe set selection that utilizes the available taxonomic information of training gene sequences and attempts to choose probes such that the resultant binary fingerprints cluster into real taxonomic groups. Gene sequences manifesting identical fingerprints with probes chosen by the new algorithm are more likely to be from the same taxonomic group than probes chosen by the previous algorithm. In cases where they are from different taxonomic groups, underlying DNA sequences of identical fingerprints are more similar to each other in probe sets made with the new versus the previous algorithm. Complete removal of large taxonomic groups from training data does not greatly decrease the ability of probe sets to distinguish those groups. Probe sets made from the new algorithm create fingerprints that more reliably cluster into biologically meaningful groups. The method can readily distinguish microbial phylotypes that were excluded from the training sequences, suggesting novel microbes can also be detected.

  16. SoilGrids1km— global soil information based on automated mapping

    NARCIS (Netherlands)

    Hengl, T.; Mendes de Jesus, J.S.; Macmillan, R.A.; Batjes, N.H.; Heuvelink, G.B.M.; Carvalho Ribeiro, E.D.; Samuel Rosa, A.; Kempen, B.; Leenaars, J.G.B.; Walsh, M.G.; Ruiperez Gonzalez, M.

    2014-01-01

    Background Soils are widely recognized as a non-renewable natural resource and as biophysical carbon sinks. As such, there is a growing requirement for global soil information. Although several global soil information systems already exist, these tend to suffer from inconsistencies and limited

  17. 75 FR 70714 - Global Free Flow of Information on the Internet

    Science.gov (United States)

    2010-11-18

    .... 100921457-0561-02] RIN 0660-XA20 Global Free Flow of Information on the Internet AGENCY: National... of comment period. SUMMARY: The Department of Commerce's Internet Policy Task Force announces that... on the global free flow of information on the Internet has been reopened and will extend until 5 p.m...

  18. Exploring global consumer attitudes toward nutrition information on food labels.

    Science.gov (United States)

    Wills, Josephine M; Schmidt, David B; Pillo-Blocka, Francy; Cairns, Georgina

    2009-05-01

    In many parts of the world, food companies, consumers, and governments are re-examining the provision of nutrition information on food labels. It is important that the nutrition information provided be appropriate and understandable to the consumer and that it impact food-choice behaviors. Potentially, food labeling represents a valuable tool to help consumers make informed decisions about their diet and lifestyle. Food information organizations worldwide have been following consumer trends in the use of this information as well as consumer attitudes about food, nutrition, and health. This paper summarizes a workshop that examined consumer attitudes gathered regionally with the aim of establishing commonalities and differences.

  19. Information performances and illative sequences: Sequential organization of explanations of chemical phase equilibrium

    Science.gov (United States)

    Brown, Nathaniel James Swanton

    While there is consensus that conceptual change is surprisingly difficult, many competing theories of conceptual change co-exist in the literature. This dissertation argues that this discord is partly the result of an inadequate account of the unwritten rules of human social interaction that underlie the field's preferred methodology---semi-structured interviewing. To better understand the contributions of interaction during explanations, I analyze eight undergraduate general chemistry students as they attempt to explain to various people, for various reasons, why phenomena involving chemical phase equilibrium occur. Using the methods of interaction analysis, I characterize the unwritten, but systematic, rules that these participants follow as they explain. The result is a description of the contributions of interaction to explaining. Each step in each explanation is a jointly performed expression of a subject-predicate relation, an interactive accomplishment I call an information performance (in-form, for short). Unlike clauses, in-forms need not have a coherent grammatical structure. Unlike speaker turns, in-forms have the clear function of expressing information. Unlike both clauses and speaker turns, in-forms are a co-construction, jointly performed by both the primary speaker and the other interlocutor. The other interlocutor strongly affects the form and content of each explanation by giving or withholding feedback at the end of each in-form, moments I call feedback-relevant places. While in-forms are the bricks out of which the explanation is constructed, they are secured by a series of inferential links I call an illative sequence. Illative sequences are forward-searching, starting with a remembered fact or observation and following a chain of inferences in the hope it leads to the target phenomenon. The participants treat an explanation as a success if the illative sequence generates an in-form that describes the phenomenon. If the illative sequence does

  20. Globalization Competencies in Information Systems and E-Learning

    OpenAIRE

    Pawlowski, Jan; Holtkamp, Philipp; Kalb, Hendrik

    2010-01-01

    Abstract. Internationalization and globalization competences play a major role for graduates and employees in IS related enterprises. In contrast to other disciplines such as Business or Economics, the IS discipline rarely addresses this competence area. In the paper, we identify generic competence areas: coordination, communication, and cooperation. We derive domain specific competences for the field of E-Learning in Higher Education. The paper concludes with an outlook of promising research...

  1. Multi-scale coding of genomic information: From DNA sequence to genome structure and function

    International Nuclear Information System (INIS)

    Arneodo, Alain; Vaillant, Cedric; Audit, Benjamin; Argoul, Francoise; D'Aubenton-Carafa, Yves; Thermes, Claude

    2011-01-01

    Understanding how chromatin is spatially and dynamically organized in the nucleus of eukaryotic cells and how this affects genome functions is one of the main challenges of cell biology. Since the different orders of packaging in the hierarchical organization of DNA condition the accessibility of DNA sequence elements to trans-acting factors that control the transcription and replication processes, there is actually a wealth of structural and dynamical information to learn in the primary DNA sequence. In this review, we show that when using concepts, methodologies, numerical and experimental techniques coming from statistical mechanics and nonlinear physics combined with wavelet-based multi-scale signal processing, we are able to decipher the multi-scale sequence encoding of chromatin condensation-decondensation mechanisms that play a fundamental role in regulating many molecular processes involved in nuclear functions.

  2. Development and the Information Age: Four Global Scenarios for the ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    Around the world, new information and communication technologies are increasingly affecting societies and their governments, industries, communities, and individuals. The Information Revolution is producing astonishing transformation in virtually all spheres of human activity. But how can these technologies help to ...

  3. Threshold policy for global games with noisy information sharing

    KAUST Repository

    Mahdavifar, Hessam; Beirami, Ahmad; Touri, Behrouz; Shamma, Jeff S.

    2015-01-01

    of information and show that such equilibrium strategies exist and are unique if the sharing of information happens over a sufficiently noisy environment. To show this result, we establish that if a threshold function is an equilibrium strategy, then it will be a

  4. Noninvasive estimation of global activation sequence using the extended Kalman filter.

    Science.gov (United States)

    Liu, Chenguang; He, Bin

    2011-03-01

    A new algorithm for 3-D imaging of the activation sequence from noninvasive body surface potentials is proposed. After formulating the nonlinear relationship between the 3-D activation sequence and the body surface recordings during activation, the extended Kalman filter (EKF) is utilized to estimate the activation sequence in a recursive way. The state vector containing the activation sequence is optimized during iteration by updating the error variance/covariance matrix. A new regularization scheme is incorporated into the "predict" procedure of EKF to tackle the ill-posedness of the inverse problem. The EKF-based algorithm shows good performance in simulation under single-site pacing. Between the estimated activation sequences and true values, the average correlation coefficient (CC) is 0.95, and the relative error (RE) is 0.13. The average localization error (LE) when localizing the pacing site is 3.0 mm. Good results are also obtained under dual-site pacing (CC = 0.93, RE = 0.16, and LE = 4.3 mm). Furthermore, the algorithm shows robustness to noise. The present promising results demonstrate that the proposed EKF-based inverse approach can noninvasively estimate the 3-D activation sequence with good accuracy and the new algorithm shows good features due to the application of EKF.

  5. Refined repetitive sequence searches utilizing a fast hash function and cross species information retrievals

    Directory of Open Access Journals (Sweden)

    Reneker Jeff

    2005-05-01

    Full Text Available Abstract Background Searching for small tandem/disperse repetitive DNA sequences streamlines many biomedical research processes. For instance, whole genomic array analysis in yeast has revealed 22 PHO-regulated genes. The promoter regions of all but one of them contain at least one of the two core Pho4p binding sites, CACGTG and CACGTT. In humans, microsatellites play a role in a number of rare neurodegenerative diseases such as spinocerebellar ataxia type 1 (SCA1. SCA1 is a hereditary neurodegenerative disease caused by an expanded CAG repeat in the coding sequence of the gene. In bacterial pathogens, microsatellites are proposed to regulate expression of some virulence factors. For example, bacteria commonly generate intra-strain diversity through phase variation which is strongly associated with virulence determinants. A recent analysis of the complete sequences of the Helicobacter pylori strains 26695 and J99 has identified 46 putative phase-variable genes among the two genomes through their association with homopolymeric tracts and dinucleotide repeats. Life scientists are increasingly interested in studying the function of small sequences of DNA. However, current search algorithms often generate thousands of matches – most of which are irrelevant to the researcher. Results We present our hash function as well as our search algorithm to locate small sequences of DNA within multiple genomes. Our system applies information retrieval algorithms to discover knowledge of cross-species conservation of repeat sequences. We discuss our incorporation of the Gene Ontology (GO database into these algorithms. We conduct an exhaustive time analysis of our system for various repetitive sequence lengths. For instance, a search for eight bases of sequence within 3.224 GBases on 49 different chromosomes takes 1.147 seconds on average. To illustrate the relevance of the search results, we conduct a search with and without added annotation terms for the

  6. Phylum-Level Conservation of Regulatory Information in Nematodes despite Extensive Non-coding Sequence Divergence

    Science.gov (United States)

    Gordon, Kacy L.; Arthur, Robert K.; Ruvinsky, Ilya

    2015-01-01

    Gene regulatory information guides development and shapes the course of evolution. To test conservation of gene regulation within the phylum Nematoda, we compared the functions of putative cis-regulatory sequences of four sets of orthologs (unc-47, unc-25, mec-3 and elt-2) from distantly-related nematode species. These species, Caenorhabditis elegans, its congeneric C. briggsae, and three parasitic species Meloidogyne hapla, Brugia malayi, and Trichinella spiralis, represent four of the five major clades in the phylum Nematoda. Despite the great phylogenetic distances sampled and the extensive sequence divergence of nematode genomes, all but one of the regulatory elements we tested are able to drive at least a subset of the expected gene expression patterns. We show that functionally conserved cis-regulatory elements have no more extended sequence similarity to their C. elegans orthologs than would be expected by chance, but they do harbor motifs that are important for proper expression of the C. elegans genes. These motifs are too short to be distinguished from the background level of sequence similarity, and while identical in sequence they are not conserved in orientation or position. Functional tests reveal that some of these motifs contribute to proper expression. Our results suggest that conserved regulatory circuitry can persist despite considerable turnover within cis elements. PMID:26020930

  7. Phylum-Level Conservation of Regulatory Information in Nematodes despite Extensive Non-coding Sequence Divergence.

    Directory of Open Access Journals (Sweden)

    Kacy L Gordon

    2015-05-01

    Full Text Available Gene regulatory information guides development and shapes the course of evolution. To test conservation of gene regulation within the phylum Nematoda, we compared the functions of putative cis-regulatory sequences of four sets of orthologs (unc-47, unc-25, mec-3 and elt-2 from distantly-related nematode species. These species, Caenorhabditis elegans, its congeneric C. briggsae, and three parasitic species Meloidogyne hapla, Brugia malayi, and Trichinella spiralis, represent four of the five major clades in the phylum Nematoda. Despite the great phylogenetic distances sampled and the extensive sequence divergence of nematode genomes, all but one of the regulatory elements we tested are able to drive at least a subset of the expected gene expression patterns. We show that functionally conserved cis-regulatory elements have no more extended sequence similarity to their C. elegans orthologs than would be expected by chance, but they do harbor motifs that are important for proper expression of the C. elegans genes. These motifs are too short to be distinguished from the background level of sequence similarity, and while identical in sequence they are not conserved in orientation or position. Functional tests reveal that some of these motifs contribute to proper expression. Our results suggest that conserved regulatory circuitry can persist despite considerable turnover within cis elements.

  8. [Study on quality evaluation of sequence and SSR information in transcriptome of Astragalus membranacus].

    Science.gov (United States)

    Chang, Yue; Yang, Song; Liu, Zhen-Peng; Ren, Wei-Chao; Liu, Jie; Ma, Wei

    2016-04-01

    In this study, 454/Roche GS FLX sequencing technology was used to obtain the data of the Astragalus membranaceus. Four hundred and fifty-four Sequencing System Software was applied to carry out the transcription of the group from scratch. Using MISA tools, 9 893 unigenes were selected for the sequence of the genome of A. membranaceus, and the information of SSR locus was analyzed. According to the result, the average length of reads was 413 bp, about 86% of the reads was involved in the splicing, the length of the N50 was 1 205 bp, the number of unigenes was measured by the whole transcript. 1 729 SSR loci in the A. membranaceus transcriptome were searched, the occurrence frequency of SSR was 9.24%, the frequency of SSR in the whole transcriptome was 13.42%, the average length of SSR was 7.97 kb. One hundred and twenty-seven kinds of core repeat sequences were found, the dominant type was TG/AC type of dinucleotide, it appeared to account for 4.25% of the total SSR locus. The results of the sequence of the transcription of the A. membranaceus transcriptome revealed the overall expression, and a large number of unigenessequence was obtained, and the SSR locus in the genome of the A. membranaceus is high, and the type is diverse, and the polymorphism of the gene is high. Copyright© by the Chinese Pharmaceutical Association.

  9. Delayed processing of global shape information in developmental prosopagnosia

    DEFF Research Database (Denmark)

    Gerlach, Christian; Klargaard, Solja K.; Petersen, Anders

    2017-01-01

    There is accumulating evidence suggesting that a central deficit in developmental prosopagnosia (DP), a disorder characterized by profound and lifelong difficulties with face recognition, concerns impaired holistic processing. Some of this evidence comes from studies using Navon’s paradigm where...... that this reduced global precedence effect correlates both with the DPs’ face recognition abilities, as well as their ability to recognize degraded (non-face) objects. We suggest that the DPs’ impaired performance in all three domains (Navon, face and object recognition) may be related to the same dysfunction...

  10. The Role of Information Professionals in Reducing the Effects of Global Warming through Knowledge Management

    Directory of Open Access Journals (Sweden)

    Lect. Ph. D. Priti Jain

    2009-05-01

    Full Text Available As a result of global environmental change, global warming is the greatest environmental challenge in the 21st century. It could lead to the ultimate end of existence of earth and man. Potential catastrophic effects on the environment and for human life are one of the biggest concerns and most widely discussed issues in the world. This paper will explore how Information Professionals can build knowledge management related to global warming and thus make their contribution towards a sustainable environment. With a brief discussion of causes, effects, solutions and challenges related to global warming, the conclusion suggests a way forward for librarians and information professionals.

  11. Towards rationally redesigning bacterial signaling systems using information encoded in abundant sequence data

    Science.gov (United States)

    Cheng, Ryan; Morcos, Faruck; Levine, Herbert; Onuchic, Jose

    2014-03-01

    An important challenge in biology is to distinguish the subset of residues that allow bacterial two-component signaling (TCS) proteins to preferentially interact with their correct TCS partner such that they can bind and transfer signal. Detailed knowledge of this information would allow one to search sequence-space for mutations that can systematically tune the signal transmission between TCS partners as well as re-encode a TCS protein to preferentially transfer signals to a non-partner. Motivated by the notion that this detailed information is found in sequence data, we explore the mutual sequence co-evolution between signaling partners to infer how mutations can positively or negatively alter their interaction. Using Direct Coupling Analysis (DCA) for determining evolutionarily conserved interprotein interactions, we apply a DCA-based metric to quantify mutational changes in the interaction between TCS proteins and demonstrate that it accurately correlates with experimental mutagenesis studies probing the mutational change in the in vitro phosphotransfer. Our methodology serves as a potential framework for the rational design of TCS systems as well as a framework for the system-level study of protein-protein interactions in sequence-rich systems. This research has been supported by the NSF INSPIRE award MCB-1241332 and by the CTBP sponsored by the NSF (Grant PHY-1308264).

  12. Sequence exploration reveals information bias among molecular markers used in phylogenetic reconstruction for Colletotrichum species.

    Science.gov (United States)

    Rampersad, Sephra N; Hosein, Fazeeda N; Carrington, Christine Vf

    2014-01-01

    The Colletotrichum gloeosporioides species complex is among the most destructive fungal plant pathogens in the world, however, identification of isolates of quarantine importance to the intra-specific level is confounded by a number of factors that affect phylogenetic reconstruction. Information bias and quality parameters were investigated to determine whether nucleotide sequence alignments and phylogenetic trees accurately reflect the genetic diversity and phylogenetic relatedness of individuals. Sequence exploration of GAPDH, ACT, TUB2 and ITS markers indicated that the query sequences had different patterns of nucleotide substitution but were without evidence of base substitution saturation. Regions of high entropy were much more dispersed in the ACT and GAPDH marker alignments than for the ITS and TUB2 markers. A discernible bimodal gap in the genetic distance frequency histograms was produced for the ACT and GAPDH markers which indicated successful separation of intra- and inter-specific sequences in the data set. Overall, analyses indicated clear differences in the ability of these markers to phylogenetically separate individuals to the intra-specific level which coincided with information bias.

  13. Development and the Information Age: Four Global Scenarios for the ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    Around the world, new information and communication technologies are increasingly ... is producing astonishing transformation in virtually all spheres of human activity. ... IDRC has signed a Memorandum of Understanding (MoU) with the ...

  14. DoD Global Information Grid Mission Assurance

    National Research Council Canada - National Science Library

    Bargar, Anthony

    2008-01-01

    ... for espionage and the criminal theft of data. GIG mission assurance works to ensure the DoD is able to accomplish its critical missions when networks, services, or information are unavailable, degraded, or distrusted...

  15. Mexico and Latin America: Their Progress in Globalizing Information Services

    OpenAIRE

    Lau, Jesús

    1998-01-01

    Information development in Latin America has evolved, despite the costly economic, social and political adjustments carried out in most countries in the last two decades. New open market policies and technological developments has helped the region to increase their links with the rest of the world. Libraries can now use faster and more reliable telephone services and can acquire computer and network technology with less import barriers. Information demand is assumed to be greater in quali...

  16. Global data breaches responsible for the disclosure of personal information

    CSIR Research Space (South Africa)

    Botha, Johannes G

    2017-06-01

    Full Text Available , which occurred in 2012 already, revealed more than 68m user’s credentials (IdentityForce 2016). The Municipal Transportation Agency of San Francisco was infected with malware in November 2016. This attack caused the systems to lock down, allowing... potentially lead to identity theft and other related crimes. PII can include an individual’s government issued identification; contact information; birth date and place; online account information; medical, employment or financial records; biometric...

  17. Application of the accident management information needs methodology to a severe accident sequence

    International Nuclear Information System (INIS)

    Ward, L.W.; Hanson, D.J.; Nelson, W.R.; Solberg, D.E.

    1989-01-01

    The U.S. Nuclear Regulatory Commission (NRC) is conducting an Accident Management Research Program that emphasizes the application of severe accident research results to enhance the capability of plant operating personnel to effectively manage severe accidents. A methodology to identify and assess the information needs of the operating staff of a nuclear power plant during a severe accident has been developed as part of the research program designed to resolve this issue. The methodology identifies the information needs of the plant personnel during a wide range of accident conditions, the existing plant measurements capable of supplying these information needs and what, if any minor additions to instrument and display systems would enhance the capability to manage accidents, known limitations on the capability of these measurements to function properly under the conditions that will be present during a wide range of severe accidents, and areas in which the information systems could mislead plant personnel. This paper presents an application of this methodology to a severe accident sequence to demonstrate its use in identifying the information which is available for management of the event. The methodology has been applied to a severe accident sequence in a Pressurized Water Reactor with a large dry containment. An examination of the capability of the existing measurements was then performed to determine whether the information needs can be supplied

  18. Sequential Optimization of Global Sequence Alignments Relative to Different Cost Functions

    KAUST Repository

    Odat, Enas M.

    2011-01-01

    The algorithm has been simulated using C#.Net programming language and a number of experiments have been done to verify the proved statements. The results of these experiments show that the number of optimal alignments is reduced after each step of optimization. Furthermore, it has been verified that as the sequence length increased linearly then the number of optimal alignments increased exponentially which also depends on the cost function that is used. Finally, the number of executed operations increases polynomially as the sequence length increase linearly.

  19. Google and global market search: information signals and knowledge indices

    NARCIS (Netherlands)

    Millar-Schijf, Carla C.J.M.; Choi, Chong-Ju; Millar, Hartley

    2008-01-01

    With perfect information an economically rational market is expected. In the ICT age the introduction of a shopping/price comparison facility (Froogle) by a company with a search reputation as pre-eminent as Google leads to the expectation that it will allow comparison of products in terms not only

  20. INFORMATION TECHNOLOGIES AND THEIR ROLE IN THE GLOBAL INNOVATION ECONOMY

    Directory of Open Access Journals (Sweden)

    S. S. Burkow

    2013-01-01

    Full Text Available This paper deals with analysis of role of the informative communicational technologies sector in modern economic. The mechanism of its infl uence on increasing economic in developed and developing countries is shown and increasing of services providing effectiveness in social sphere of developing countries is demonstrated.

  1. Using small RNA (sRNA) deep sequencing to understand global virus distribution in plants

    Science.gov (United States)

    Small RNAs (sRNAs), a class of regulatory RNAs, have been used to serve as the specificity determinants of suppressing gene expression in plants and animals. Next generation sequencing (NGS) uncovered the sRNA landscape in most organisms including their associated microbes. In the current study, w...

  2. Microbial Culturomics Application for Global Health: Noncontiguous Finished Genome Sequence and Description of Pseudomonas massiliensis Strain CB-1T sp. nov. in Brazil.

    Science.gov (United States)

    Bardet, Lucie; Cimmino, Teresa; Buffet, Clémence; Michelle, Caroline; Rathored, Jaishriram; Tandina, Fatalmoudou; Lagier, Jean-Christophe; Khelaifia, Saber; Abrahão, Jônatas; Raoult, Didier; Rolain, Jean-Marc

    2018-02-01

    Culturomics is a new postgenomics field that explores the microbial diversity of the human gut coupled with taxono-genomic strategy. Culturomics, and the microbiome science more generally, are anticipated to transform global health diagnostics and inform the ways in which gut microbial diversity contributes to human health and disease, and by extension, to personalized medicine. Using culturomics, we report in this study the description of strain CB1 T ( = CSUR P1334 = DSM 29075), a new species isolated from a stool specimen from a 37-year-old Brazilian woman. This description includes phenotypic characteristics and complete genome sequence and annotation. Strain CB1 T is a gram-negative aerobic and motile bacillus, exhibits neither catalase nor oxidase activities, and presents a 98.3% 16S rRNA sequence similarity with Pseudomonas putida. The 4,723,534 bp long genome contains 4239 protein-coding genes and 74 RNA genes, including 15 rRNA genes (5 16S rRNA, 4 23S rRNA, and 6 5S rRNA) and 59 tRNA genes. Strain CB1 T was named Pseudomonas massiliensis sp. nov. and classified into the family Pseudomonadaceae. This study demonstrates the usefulness of microbial culturomics in exploration of human microbiota in diverse geographies and offers new promise for incorporating new omics technologies for innovation in diagnostic medicine and global health.

  3. Clinical decision support for whole genome sequence information leveraging a service-oriented architecture: a prototype.

    Science.gov (United States)

    Welch, Brandon M; Rodriguez-Loya, Salvador; Eilbeck, Karen; Kawamoto, Kensaku

    2014-01-01

    Whole genome sequence (WGS) information could soon be routinely available to clinicians to support the personalized care of their patients. At such time, clinical decision support (CDS) integrated into the clinical workflow will likely be necessary to support genome-guided clinical care. Nevertheless, developing CDS capabilities for WGS information presents many unique challenges that need to be overcome for such approaches to be effective. In this manuscript, we describe the development of a prototype CDS system that is capable of providing genome-guided CDS at the point of care and within the clinical workflow. To demonstrate the functionality of this prototype, we implemented a clinical scenario of a hypothetical patient at high risk for Lynch Syndrome based on his genomic information. We demonstrate that this system can effectively use service-oriented architecture principles and standards-based components to deliver point of care CDS for WGS information in real-time.

  4. On the Concept of Cis-regulatory Information: From Sequence Motifs to Logic Functions

    Science.gov (United States)

    Tarpine, Ryan; Istrail, Sorin

    The regulatory genome is about the “system level organization of the core genomic regulatory apparatus, and how this is the locus of causality underlying the twin phenomena of animal development and animal evolution” (E.H. Davidson. The Regulatory Genome: Gene Regulatory Networks in Development and Evolution, Academic Press, 2006). Information processing in the regulatory genome is done through regulatory states, defined as sets of transcription factors (sequence-specific DNA binding proteins which determine gene expression) that are expressed and active at the same time. The core information processing machinery consists of modular DNA sequence elements, called cis-modules, that interact with transcription factors. The cis-modules “read” the information contained in the regulatory state of the cell through transcription factor binding, “process” it, and directly or indirectly communicate with the basal transcription apparatus to determine gene expression. This endowment of each gene with the information-receiving capacity through their cis-regulatory modules is essential for the response to every possible regulatory state to which it might be exposed during all phases of the life cycle and in all cell types. We present here a set of challenges addressed by our CYRENE research project aimed at studying the cis-regulatory code of the regulatory genome. The CYRENE Project is devoted to (1) the construction of a database, the cis-Lexicon, containing comprehensive information across species about experimentally validated cis-regulatory modules; and (2) the software development of a next-generation genome browser, the cis-Browser, specialized for the regulatory genome. The presentation is anchored on three main computational challenges: the Gene Naming Problem, the Consensus Sequence Bottleneck Problem, and the Logic Function Inference Problem.

  5. 77 FR 37430 - BSEE Information Collection Activity: Global Positioning System for MODUs, Extension of a...

    Science.gov (United States)

    2012-06-21

    ... major weather event, like a hurricane, lessees and operators need to report new GPS information to BSEE...-0012; OMB Control Number 1014-0013] BSEE Information Collection Activity: Global Positioning System for... Paperwork Reduction Act of 1995 (PRA), BSEE is inviting comments on a collection of information pertaining...

  6. Incorporating Global Information Security and Assurance in I.S. Education

    Science.gov (United States)

    White, Garry L.; Hewitt, Barbara; Kruck, S. E.

    2013-01-01

    Over the years, the news media has reported numerous information security incidents. Because of identity theft, terrorism, and other criminal activities, President Obama has made information security a national priority. Not only is information security and assurance an American priority, it is also a global issue. This paper discusses the…

  7. Global and Local Processing of Incidental Information and Memory Retrieval at 6 Months.

    Science.gov (United States)

    Bhatt, Ramesh S.; And Others

    1994-01-01

    Five experiments examined the role of global and local cues in memory retrieval in infancy. Results showed that infants encode and remember for substantial periods of time not only the shape of figures displayed in their periphery but also the global organization of these figures. They also adapt this information when responding to new events.…

  8. Action-embedded transformational leadership in self-managing global information systems development teams

    NARCIS (Netherlands)

    Eseryel, U. Yeliz; Eseryel, Deniz

    While software development teams are becoming more and more distributed around the globe, most software development methodologies used by global teams prescribe self-managing teams. Transformational leadership is the key to successful information systems development and use for competitive

  9. Patent challenges for standard-setting in the global economy : lessons from information and communication industry

    NARCIS (Netherlands)

    Maskus, K.; Merrill, S.A.; Bekkers, R.N.A.; Sandy Block, Marc; Contreras, Jorge; Gilbert, Richard; Goodman, David; Marasco, Amy; Simcoe, Tim; Smoot, Oliver; Suttmeier, Richard; Updegrove, Andrew

    2014-01-01

    Patent Challenges for Standard-Setting in the Global Economy: Lessons from Information and Communication Technology examines how leading national and multinational standard-setting organizations (SSOs) address patent disclosures, licensing terms, transfers of patent ownership, and other issues that

  10. 77 FR 58412 - Meeting of the Global Justice Information Sharing Initiative Federal Advisory Committee

    Science.gov (United States)

    2012-09-20

    ... support of the Administration's justice priorities. The GAC will guide and monitor the development of the Global information sharing concept. It will advise the Assistant Attorney General, OJP; the Attorney...

  11. 76 FR 13226 - Meeting of the Department of Justice Global Justice Information Sharing Initiative Federal...

    Science.gov (United States)

    2011-03-10

    ... coordination of national policy, practices, and technical solutions in support of the Administration's justice priorities. The GAC will guide and monitor the development of the Global information sharing concept. It will...

  12. A Secure and Efficient Communications Architecture for Global Information Grid Users Via Cooperating Space Assets

    National Research Council Canada - National Science Library

    Hubenko, Jr, Victor P

    2008-01-01

    With the Information Age in full and rapid development, users expect to have global, seamless, ubiquitous, secure, and efficient communications capable of providing access to real-time applications and collaboration...

  13. Extracting information from an ensemble of GCMs to reliably assess future global runoff change

    NARCIS (Netherlands)

    Sperna Weiland, F.C.; Beek, L.P.H. van; Weerts, A.H.; Bierkens, M.F.P.

    2011-01-01

    Future runoff projections derived from different global climate models (GCMs) show large differences. Therefore, within this study the, information from multiple GCMs has been combined to better assess hydrological changes. For projections of precipitation and temperature the Reliability ensemble

  14. Genome sequencing - the ultimate answer to global real time genotyping and surveillance?

    DEFF Research Database (Denmark)

    Hendriksen, Rene S.

    2013-01-01

    organised to discuss the possibility of using WGS as diagnostic tool on a global scale. These meetings were attended by scientists and policy makers from around the world. The general conclusion of these meetings was that the technology exists and that the spread in the application should be linked...

  15. Moving target detection based on temporal-spatial information fusion for infrared image sequences

    Science.gov (United States)

    Toing, Wu-qin; Xiong, Jin-yu; Zeng, An-jun; Wu, Xiao-ping; Xu, Hao-peng

    2009-07-01

    Moving target detection and localization is one of the most fundamental tasks in visual surveillance. In this paper, through analyzing the advantages and disadvantages of the traditional approaches about moving target detection, a novel approach based on temporal-spatial information fusion is proposed for moving target detection. The proposed method combines the spatial feature in single frame and the temporal properties within multiple frames of an image sequence of moving target. First, the method uses the spatial image segmentation for target separation from background and uses the local temporal variance for extracting targets and wiping off the trail artifact. Second, the logical "and" operator is used to fuse the temporal and spatial information. In the end, to the fusion image sequence, the morphological filtering and blob analysis are used to acquire exact moving target. The algorithm not only requires minimal computation and memory but also quickly adapts to the change of background and environment. Comparing with other methods, such as the KDE, the Mixture of K Gaussians, etc., the simulation results show the proposed method has better validity and higher adaptive for moving target detection, especially in infrared image sequences with complex illumination change, noise change, and so on.

  16. Automatic exchange of information: towards a new global standard of tax transparency

    OpenAIRE

    Miguel Eduardo Pecho Trigueros

    2014-01-01

    Tax authorities are increasingly relying on mutual cooperation with their foreign peers to enforce more effectively their internal tax laws. After the banking scandals of 2008 and the subsequent global financial crisis, the Global Forum on Transparency and Exchange of Information for TaxPurposes has proposed the exchange of information upon request as the fiscal transparency standard. However, some measures adopted by the European Union, previous initiatives from the Organization for Economic...

  17. How could disclosing incidental information from whole-genome sequencing affect patient behavior?

    Science.gov (United States)

    Christensen, Kurt D; Green, Robert C

    2013-06-01

    In this article, we argue that disclosure of incidental findings from whole-genome sequencing has the potential to motivate individuals to change health behaviors through psychological mechanisms that differ from typical risk assessment interventions. Their ability to do so, however, is likely to be highly contingent upon the nature of the incidental findings and how they are disclosed, the context of the disclosure and the characteristics of the patient. Moreover, clinicians need to be aware that behavioral responses may occur in unanticipated ways. This article argues for commentators and policy makers to take a cautious but optimistic perspective while empirical evidence is collected through ongoing research involving whole-genome sequencing and the disclosure of incidental information.

  18. The Role of Global and Local Visual Information during Gaze-Cued Orienting of Attention.

    Science.gov (United States)

    Munsters, Nicolette M; van den Boomen, Carlijn; Hooge, Ignace T C; Kemner, Chantal

    2016-01-01

    Gaze direction is an important social communication tool. Global and local visual information are known to play specific roles in processing socially relevant information from a face. The current study investigated whether global visual information has a primary role during gaze-cued orienting of attention and, as such, may influence quality of interaction. Adults performed a gaze-cueing task in which a centrally presented face cued (valid or invalid) the location of a peripheral target through a gaze shift. We measured brain activity (electroencephalography) towards the cue and target and behavioral responses (manual and saccadic reaction times) towards the target. The faces contained global (i.e. lower spatial frequencies), local (i.e. higher spatial frequencies), or a selection of both global and local (i.e. mid-band spatial frequencies) visual information. We found a gaze cue-validity effect (i.e. valid versus invalid), but no interaction effects with spatial frequency content. Furthermore, behavioral responses towards the target were in all cue conditions slower when lower spatial frequencies were not present in the gaze cue. These results suggest that whereas gaze-cued orienting of attention can be driven by both global and local visual information, global visual information determines the speed of behavioral responses towards other entities appearing in the surrounding of gaze cue stimuli.

  19. A Proposed Clinical Decision Support Architecture Capable of Supporting Whole Genome Sequence Information

    Directory of Open Access Journals (Sweden)

    Brandon M. Welch

    2014-04-01

    Full Text Available Whole genome sequence (WGS information may soon be widely available to help clinicians personalize the care and treatment of patients. However, considerable barriers exist, which may hinder the effective utilization of WGS information in a routine clinical care setting. Clinical decision support (CDS offers a potential solution to overcome such barriers and to facilitate the effective use of WGS information in the clinic. However, genomic information is complex and will require significant considerations when developing CDS capabilities. As such, this manuscript lays out a conceptual framework for a CDS architecture designed to deliver WGS-guided CDS within the clinical workflow. To handle the complexity and breadth of WGS information, the proposed CDS framework leverages service-oriented capabilities and orchestrates the interaction of several independently-managed components. These independently-managed components include the genome variant knowledge base, the genome database, the CDS knowledge base, a CDS controller and the electronic health record (EHR. A key design feature is that genome data can be stored separately from the EHR. This paper describes in detail: (1 each component of the architecture; (2 the interaction of the components; and (3 how the architecture attempts to overcome the challenges associated with WGS information. We believe that service-oriented CDS capabilities will be essential to using WGS information for personalized medicine.

  20. A proposed clinical decision support architecture capable of supporting whole genome sequence information.

    Science.gov (United States)

    Welch, Brandon M; Loya, Salvador Rodriguez; Eilbeck, Karen; Kawamoto, Kensaku

    2014-04-04

    Whole genome sequence (WGS) information may soon be widely available to help clinicians personalize the care and treatment of patients. However, considerable barriers exist, which may hinder the effective utilization of WGS information in a routine clinical care setting. Clinical decision support (CDS) offers a potential solution to overcome such barriers and to facilitate the effective use of WGS information in the clinic. However, genomic information is complex and will require significant considerations when developing CDS capabilities. As such, this manuscript lays out a conceptual framework for a CDS architecture designed to deliver WGS-guided CDS within the clinical workflow. To handle the complexity and breadth of WGS information, the proposed CDS framework leverages service-oriented capabilities and orchestrates the interaction of several independently-managed components. These independently-managed components include the genome variant knowledge base, the genome database, the CDS knowledge base, a CDS controller and the electronic health record (EHR). A key design feature is that genome data can be stored separately from the EHR. This paper describes in detail: (1) each component of the architecture; (2) the interaction of the components; and (3) how the architecture attempts to overcome the challenges associated with WGS information. We believe that service-oriented CDS capabilities will be essential to using WGS information for personalized medicine.

  1. GRIN-Global: An International Project to Develop a Global Plant Genebank and Information Management System

    Science.gov (United States)

    Many of the world's national genebanks, responsible for the safeguarding and availability of their country's Plant Genetic Resource (PGR) collections, have lacked access to high quality IT needed to document and manage their collections electronically. The Germplasm Resource Information System (GRI...

  2. Exploiting global information in complex network repair processes

    Institute of Scientific and Technical Information of China (English)

    Tianyu WANG; Jun ZHANG; Sebastian WANDELT

    2017-01-01

    Robustness of complex networks has been studied for decades,with a particular focus on network attack.Research on network repair,on the other hand,has been conducted only very lately,given the even higher complexity and absence of an effective evaluation metric.A recently proposed network repair strategy is self-healing,which aims to repair networks for larger compo nents at a low cost only with local information.In this paper,we discuss the effectiveness and effi ciency of self-healing,which limits network repair to be a multi-objective optimization problem and makes it difficult to measure its optimality.This leads us to a new network repair evaluation metric.Since the time complexity of the computation is very high,we devise a greedy ranking strategy.Evaluations on both real-world and random networks show the effectiveness of our new metric and repair strategy.Our study contributes to optimal network repair algorithms and provides a gold standard for future studies on network repair.

  3. Providing Global Change Information for Decision-Making: Capturing and Presenting Provenance

    Science.gov (United States)

    Ma, Xiaogang; Fox, Peter; Tilmes, Curt; Jacobs, Katherine; Waple, Anne

    2014-01-01

    Global change information demands access to data sources and well-documented provenance to provide evidence needed to build confidence in scientific conclusions and, in specific applications, to ensure the information's suitability for use in decision-making. A new generation of Web technology, the Semantic Web, provides tools for that purpose. The topic of global change covers changes in the global environment (including alterations in climate, land productivity, oceans or other water resources, atmospheric composition and or chemistry, and ecological systems) that may alter the capacity of the Earth to sustain life and support human systems. Data and findings associated with global change research are of great public, government, and academic concern and are used in policy and decision-making, which makes the provenance of global change information especially important. In addition, since different types of decisions benefit from different types of information, understanding how to capture and present the provenance of global change information is becoming more of an imperative in adaptive planning.

  4. Information data systems for a global change technology initiative architecture trade study

    Science.gov (United States)

    Murray, Nicholas D.

    1991-01-01

    The Global Change Technology Initiative (GCTI) was established to develop technology which will enable use of satellite systems of Earth observations on a global scale, enable use of the observations to predictively model Earth's changes, and provide scientists, government, business, and industry with quick access to the resulting information. At LaRC, a GCTI Architecture Trade Study was undertaken to develop and evaluate the architectural implications to meet the requirements of the global change studies and the eventual implementation of a global change system. The output of the trade study are recommended technologies for the GCTI. That portion of the study concerned with the information data system is documented. The information data system for an earth global change modeling system can be very extensive and beyond affordability in terms of today's costs. Therefore, an incremental approach to gaining a system is most likely. An options approach to levels of capability versus needed technologies was developed. The primary drivers of the requirements for the information data system evaluation were the needed science products, the science measurements, the spacecraft orbits, the instruments configurations, and the spacecraft configurations and their attendant architectures. The science products requirements were not studied here; however, some consideration of the product needs were included in the evaluation results. The information data system technology items were identified from the viewpoint of the desirable overall information system characteristics.

  5. Global monitoring of dynamic information systems a case study in the international supply chain

    NARCIS (Netherlands)

    Pruksasri, P.; Berg, J. van den; Hofman, W.J.

    2014-01-01

    Global information systems are becoming more complex and dynamic everyday: huge amounts of data and messages through those systems show dynamically changing traffic patterns. Because of this, diagnosing when sub-systems are not working properly is difficult. System failures or errors in information

  6. Influence of globalization on creation of the information society in Russia

    Directory of Open Access Journals (Sweden)

    Т А Полякова

    2008-03-01

    Full Text Available Legal problems of influence of globalization on creation of the information society in Russia, and also the basic directions of development of the international cooperation in the given area to use information and telecommunicational technologies for development of some new forms and methods of training and for improving quality of education.

  7. The GRIN-Global Information Management System – Public Interface Demonstration and Input Opportunity

    Science.gov (United States)

    The GRIN-Global (GG) Information Management System, under development for the past three years, provides the world's crop genebanks and plant genetic resource (PGR) users with a powerful, flexible, easy-to-use PGR information management system. Developed jointly by the USDA Agricultural Research Ser...

  8. The GRIN-Global Information Management System – A Preview and Opportunity for Public User Input

    Science.gov (United States)

    The GRIN-Global Information Management System, under development for the past two years, will provide the world's crop genebanks and plant genetic resource (PGR) users with a powerful, flexible, easy-to-use PGR information management system. Developed jointly by the USDA Agricultural Research Servi...

  9. Information Processing and Firm-Internal Environment Contingencies: Performance Impact on Global New Product Development

    DEFF Research Database (Denmark)

    Kleinschmidt, Elko; de Brentani, Ulrike; Salomo, Søren

    2010-01-01

    , functionally, geographically and culturally. To this end, an IT-communication strength is essential, one that is nested in an internal organizational environment that ensures its effective functioning. Using organizational information processing (OIP) theory as a framework, superior global NPD program......Innovation in its essence is an information processing activity. Thus, a major factor impacting the success of new product development (NPD) programs, especially those responding to global markets, is the firm's ability to access, share and apply NPD information, which is often widely dispersed...

  10. Running a network on a shoestring: the Global Invasive Species Information Network

    Science.gov (United States)

    Jarnevich, Catherine S.; Simpson, Annie; Graham, James J; Newman, Gregory J.; Bargeron, Chuck T.

    2015-01-01

    The Global Invasive Species Information Network (GISIN) was conceptualized in 2004 to aggregate and disseminate invasive species data in a standardized way. A decade later the GISIN community has implemented a data portal and three of six GISIN data aggregation models in the GISIN data exchange Protocol, including invasive species status information, resource URLs, and occurrence data. The portal is based on a protocol developed by representatives from 15 countries and 27 organizations of the global invasive species information management community. The GISIN has 19 data providers sharing 34,343 species status records, 1,693,073 occurrences, and 15,601 resource URLs. While the GISIN's goal is to be global, much of its data and funding are provided by the United States. Several initiatives use the GISIN as their information backbone, such as the Great Lakes Early Detection Network (GLEDN) and the North American Invasive Species Network (NAISN). Here we share several success stories and organizational challenges that remain.

  11. Coding Local and Global Binary Visual Features Extracted From Video Sequences

    Science.gov (United States)

    Baroffio, Luca; Canclini, Antonio; Cesana, Matteo; Redondi, Alessandro; Tagliasacchi, Marco; Tubaro, Stefano

    2015-11-01

    Binary local features represent an effective alternative to real-valued descriptors, leading to comparable results for many visual analysis tasks, while being characterized by significantly lower computational complexity and memory requirements. When dealing with large collections, a more compact representation based on global features is often preferred, which can be obtained from local features by means of, e.g., the Bag-of-Visual-Word (BoVW) model. Several applications, including for example visual sensor networks and mobile augmented reality, require visual features to be transmitted over a bandwidth-limited network, thus calling for coding techniques that aim at reducing the required bit budget, while attaining a target level of efficiency. In this paper we investigate a coding scheme tailored to both local and global binary features, which aims at exploiting both spatial and temporal redundancy by means of intra- and inter-frame coding. In this respect, the proposed coding scheme can be conveniently adopted to support the Analyze-Then-Compress (ATC) paradigm. That is, visual features are extracted from the acquired content, encoded at remote nodes, and finally transmitted to a central controller that performs visual analysis. This is in contrast with the traditional approach, in which visual content is acquired at a node, compressed and then sent to a central unit for further processing, according to the Compress-Then-Analyze (CTA) paradigm. In this paper we experimentally compare ATC and CTA by means of rate-efficiency curves in the context of two different visual analysis tasks: homography estimation and content-based retrieval. Our results show that the novel ATC paradigm based on the proposed coding primitives can be competitive with CTA, especially in bandwidth limited scenarios.

  12. Coding Local and Global Binary Visual Features Extracted From Video Sequences.

    Science.gov (United States)

    Baroffio, Luca; Canclini, Antonio; Cesana, Matteo; Redondi, Alessandro; Tagliasacchi, Marco; Tubaro, Stefano

    2015-11-01

    Binary local features represent an effective alternative to real-valued descriptors, leading to comparable results for many visual analysis tasks while being characterized by significantly lower computational complexity and memory requirements. When dealing with large collections, a more compact representation based on global features is often preferred, which can be obtained from local features by means of, e.g., the bag-of-visual word model. Several applications, including, for example, visual sensor networks and mobile augmented reality, require visual features to be transmitted over a bandwidth-limited network, thus calling for coding techniques that aim at reducing the required bit budget while attaining a target level of efficiency. In this paper, we investigate a coding scheme tailored to both local and global binary features, which aims at exploiting both spatial and temporal redundancy by means of intra- and inter-frame coding. In this respect, the proposed coding scheme can conveniently be adopted to support the analyze-then-compress (ATC) paradigm. That is, visual features are extracted from the acquired content, encoded at remote nodes, and finally transmitted to a central controller that performs the visual analysis. This is in contrast with the traditional approach, in which visual content is acquired at a node, compressed and then sent to a central unit for further processing, according to the compress-then-analyze (CTA) paradigm. In this paper, we experimentally compare the ATC and the CTA by means of rate-efficiency curves in the context of two different visual analysis tasks: 1) homography estimation and 2) content-based retrieval. Our results show that the novel ATC paradigm based on the proposed coding primitives can be competitive with the CTA, especially in bandwidth limited scenarios.

  13. Importance of Viral Sequence Length and Number of Variable and Informative Sites in Analysis of HIV Clustering.

    Science.gov (United States)

    Novitsky, Vlad; Moyo, Sikhulile; Lei, Quanhong; DeGruttola, Victor; Essex, M

    2015-05-01

    To improve the methodology of HIV cluster analysis, we addressed how analysis of HIV clustering is associated with parameters that can affect the outcome of viral clustering. The extent of HIV clustering and tree certainty was compared between 401 HIV-1C near full-length genome sequences and subgenomic regions retrieved from the LANL HIV Database. Sliding window analysis was based on 99 windows of 1,000 bp and 45 windows of 2,000 bp. Potential associations between the extent of HIV clustering and sequence length and the number of variable and informative sites were evaluated. The near full-length genome HIV sequences showed the highest extent of HIV clustering and the highest tree certainty. At the bootstrap threshold of 0.80 in maximum likelihood (ML) analysis, 58.9% of near full-length HIV-1C sequences but only 15.5% of partial pol sequences (ViroSeq) were found in clusters. Among HIV-1 structural genes, pol showed the highest extent of clustering (38.9% at a bootstrap threshold of 0.80), although it was significantly lower than in the near full-length genome sequences. The extent of HIV clustering was significantly higher for sliding windows of 2,000 bp than 1,000 bp. We found a strong association between the sequence length and proportion of HIV sequences in clusters, and a moderate association between the number of variable and informative sites and the proportion of HIV sequences in clusters. In HIV cluster analysis, the extent of detectable HIV clustering is directly associated with the length of viral sequences used, as well as the number of variable and informative sites. Near full-length genome sequences could provide the most informative HIV cluster analysis. Selected subgenomic regions with a high extent of HIV clustering and high tree certainty could also be considered as a second choice.

  14. Mixed multiscale finite element methods using approximate global information based on partial upscaling

    KAUST Repository

    Jiang, Lijian

    2009-10-02

    The use of limited global information in multiscale simulations is needed when there is no scale separation. Previous approaches entail fine-scale simulations in the computation of the global information. The computation of the global information is expensive. In this paper, we propose the use of approximate global information based on partial upscaling. A requirement for partial homogenization is to capture long-range (non-local) effects present in the fine-scale solution, while homogenizing some of the smallest scales. The local information at these smallest scales is captured in the computation of basis functions. Thus, the proposed approach allows us to avoid the computations at the scales that can be homogenized. This results in coarser problems for the computation of global fields. We analyze the convergence of the proposed method. Mathematical formalism is introduced, which allows estimating the errors due to small scales that are homogenized. The proposed method is applied to simulate two-phase flows in heterogeneous porous media. Numerical results are presented for various permeability fields, including those generated using two-point correlation functions and channelized permeability fields from the SPE Comparative Project (Christie and Blunt, SPE Reserv Evalu Eng 4:308-317, 2001). We consider simple cases where one can identify the scales that can be homogenized. For more general cases, we suggest the use of upscaling on the coarse grid with the size smaller than the target coarse grid where multiscale basis functions are constructed. This intermediate coarse grid renders a partially upscaled solution that contains essential non-local information. Numerical examples demonstrate that the use of approximate global information provides better accuracy than purely local multiscale methods. © 2009 Springer Science+Business Media B.V.

  15. A Scaffold Analysis Tool Using Mate-Pair Information in Genome Sequencing

    Directory of Open Access Journals (Sweden)

    Pan-Gyu Kim

    2008-01-01

    Full Text Available We have developed a Windows-based program, ConPath, as a scaffold analyzer. ConPath constructs scaffolds by ordering and orienting separate sequence contigs by exploiting the mate-pair information between contig-pairs. Our algorithm builds directed graphs from link information and traverses them to find the longest acyclic graphs. Using end read pairs of fixed-sized mate-pair libraries, ConPath determines relative orientations of all contigs, estimates the gap size of each adjacent contig pair, and reports wrong assembly information by validating orientations and gap sizes. We have utilized ConPath in more than 10 microbial genome projects, including Mannheimia succiniciproducens and Vibro vulnificus, where we verified contig assembly and identified several erroneous contigs using the four types of error defined in ConPath. Also, ConPath supports some convenient features and viewers that permit investigation of each contig in detail; these include contig viewer, scaffold viewer, edge information list, mate-pair list, and the printing of complex scaffold structures.

  16. Globalization

    Directory of Open Access Journals (Sweden)

    Tulio Rosembuj

    2006-12-01

    Full Text Available There is no singular globalization, nor is the result of an individual agent. We could start by saying that global action has different angles and subjects who perform it are different, as well as its objectives. The global is an invisible invasion of materials and immediate effects.

  17. Globalization

    OpenAIRE

    Tulio Rosembuj

    2006-01-01

    There is no singular globalization, nor is the result of an individual agent. We could start by saying that global action has different angles and subjects who perform it are different, as well as its objectives. The global is an invisible invasion of materials and immediate effects.

  18. Informational and linguistic analysis of large genomic sequence collections via efficient Hadoop cluster algorithms.

    Science.gov (United States)

    Ferraro Petrillo, Umberto; Roscigno, Gianluca; Cattaneo, Giuseppe; Giancarlo, Raffaele

    2018-06-01

    Information theoretic and compositional/linguistic analysis of genomes have a central role in bioinformatics, even more so since the associated methodologies are becoming very valuable also for epigenomic and meta-genomic studies. The kernel of those methods is based on the collection of k-mer statistics, i.e. how many times each k-mer in {A,C,G,T}k occurs in a DNA sequence. Although this problem is computationally very simple and efficiently solvable on a conventional computer, the sheer amount of data available now in applications demands to resort to parallel and distributed computing. Indeed, those type of algorithms have been developed to collect k-mer statistics in the realm of genome assembly. However, they are so specialized to this domain that they do not extend easily to the computation of informational and linguistic indices, concurrently on sets of genomes. Following the well-established approach in many disciplines, and with a growing success also in bioinformatics, to resort to MapReduce and Hadoop to deal with 'Big Data' problems, we present KCH, the first set of MapReduce algorithms able to perform concurrently informational and linguistic analysis of large collections of genomic sequences on a Hadoop cluster. The benchmarking of KCH that we provide indicates that it is quite effective and versatile. It is also competitive with respect to the parallel and distributed algorithms highly specialized to k-mer statistics collection for genome assembly problems. In conclusion, KCH is a much needed addition to the growing number of algorithms and tools that use MapReduce for bioinformatics core applications. The software, including instructions for running it over Amazon AWS, as well as the datasets are available at http://www.di-srv.unisa.it/KCH. umberto.ferraro@uniroma1.it. Supplementary data are available at Bioinformatics online.

  19. A fingerprint classification algorithm based on combination of local and global information

    Science.gov (United States)

    Liu, Chongjin; Fu, Xiang; Bian, Junjie; Feng, Jufu

    2011-12-01

    Fingerprint recognition is one of the most important technologies in biometric identification and has been wildly applied in commercial and forensic areas. Fingerprint classification, as the fundamental procedure in fingerprint recognition, can sharply decrease the quantity for fingerprint matching and improve the efficiency of fingerprint recognition. Most fingerprint classification algorithms are based on the number and position of singular points. Because the singular points detecting method only considers the local information commonly, the classification algorithms are sensitive to noise. In this paper, we propose a novel fingerprint classification algorithm combining the local and global information of fingerprint. Firstly we use local information to detect singular points and measure their quality considering orientation structure and image texture in adjacent areas. Furthermore the global orientation model is adopted to measure the reliability of singular points group. Finally the local quality and global reliability is weighted to classify fingerprint. Experiments demonstrate the accuracy and effectivity of our algorithm especially for the poor quality fingerprint images.

  20. China's Mission in Surveying, Mapping and Geographic Information during Global Governance

    Science.gov (United States)

    Jia, D.; Xue, C.; Chen, X.

    2018-04-01

    In the new era, it is proposed that China should be transformed from a participant and a cooperator into a designer, an impeller and a leader, continue taking an effect of responsible great power, increase public product supply, perfect a global governance system and contribute to China's wisdom and China's schemes during global governance, thus surveying and mapping geographic information takes on great mission. On the one hand, we have to timely grasp global geographic information data resources to provide an important scientific data support for China's wisdom and China's schemes. On the other hand, we have to provide surveying and mapping geographic information infrastructure construction and public products for developing countries, support location services within a global territorial scope, and realize the smoothness of talent flow, material flow and information flow between China and countries in the world. Meanwhile, external assistance and international communication and cooperation of surveying and mapping geographic information are also enhanced, and popularization and application of a geographic information technology in underdeveloped countries and regions are promoted.

  1. Systems Factorial Technology provides new insights on global-local information processing in autism spectrum disorders.

    Science.gov (United States)

    Johnson, Shannon A; Blaha, Leslie M; Houpt, Joseph W; Townsend, James T

    2010-02-01

    Previous studies of global-local processing in autism spectrum disorders (ASDs) have indicated mixed findings, with some evidence of a local processing bias, or preference for detail-level information, and other results suggesting typical global advantage, or preference for the whole or gestalt. Findings resulting from this paradigm have been used to argue for or against a detail focused processing bias in ASDs, and thus have important theoretical implications. We applied Systems Factorial Technology, and the associated Double Factorial Paradigm (both defined in the text), to examine information processing characteristics during a divided attention global-local task in high-functioning individuals with an ASD and typically developing controls. Group data revealed global advantage for both groups, contrary to some current theories of ASDs. Information processing models applied to each participant revealed that task performance, although showing no differences at the group level, was supported by different cognitive mechanisms in ASD participants compared to controls. All control participants demonstrated inhibitory parallel processing and the majority demonstrated a minimum-time stopping rule. In contrast, ASD participants showed exhaustive parallel processing with mild facilitatory interactions between global and local information. Thus our results indicate fundamental differences in the stopping rules and channel dependencies in individuals with an ASD.

  2. A Novel Computational Method for Detecting DNA Methylation Sites with DNA Sequence Information and Physicochemical Properties.

    Science.gov (United States)

    Pan, Gaofeng; Jiang, Limin; Tang, Jijun; Guo, Fei

    2018-02-08

    DNA methylation is an important biochemical process, and it has a close connection with many types of cancer. Research about DNA methylation can help us to understand the regulation mechanism and epigenetic reprogramming. Therefore, it becomes very important to recognize the methylation sites in the DNA sequence. In the past several decades, many computational methods-especially machine learning methods-have been developed since the high-throughout sequencing technology became widely used in research and industry. In order to accurately identify whether or not a nucleotide residue is methylated under the specific DNA sequence context, we propose a novel method that overcomes the shortcomings of previous methods for predicting methylation sites. We use k -gram, multivariate mutual information, discrete wavelet transform, and pseudo amino acid composition to extract features, and train a sparse Bayesian learning model to do DNA methylation prediction. Five criteria-area under the receiver operating characteristic curve (AUC), Matthew's correlation coefficient (MCC), accuracy (ACC), sensitivity (SN), and specificity-are used to evaluate the prediction results of our method. On the benchmark dataset, we could reach 0.8632 on AUC, 0.8017 on ACC, 0.5558 on MCC, and 0.7268 on SN. Additionally, the best results on two scBS-seq profiled mouse embryonic stem cells datasets were 0.8896 and 0.9511 by AUC, respectively. When compared with other outstanding methods, our method surpassed them on the accuracy of prediction. The improvement of AUC by our method compared to other methods was at least 0.0399 . For the convenience of other researchers, our code has been uploaded to a file hosting service, and can be downloaded from: https://figshare.com/s/0697b692d802861282d3.

  3. A Novel Computational Method for Detecting DNA Methylation Sites with DNA Sequence Information and Physicochemical Properties

    Directory of Open Access Journals (Sweden)

    Gaofeng Pan

    2018-02-01

    Full Text Available DNA methylation is an important biochemical process, and it has a close connection with many types of cancer. Research about DNA methylation can help us to understand the regulation mechanism and epigenetic reprogramming. Therefore, it becomes very important to recognize the methylation sites in the DNA sequence. In the past several decades, many computational methods—especially machine learning methods—have been developed since the high-throughout sequencing technology became widely used in research and industry. In order to accurately identify whether or not a nucleotide residue is methylated under the specific DNA sequence context, we propose a novel method that overcomes the shortcomings of previous methods for predicting methylation sites. We use k-gram, multivariate mutual information, discrete wavelet transform, and pseudo amino acid composition to extract features, and train a sparse Bayesian learning model to do DNA methylation prediction. Five criteria—area under the receiver operating characteristic curve (AUC, Matthew’s correlation coefficient (MCC, accuracy (ACC, sensitivity (SN, and specificity—are used to evaluate the prediction results of our method. On the benchmark dataset, we could reach 0.8632 on AUC, 0.8017 on ACC, 0.5558 on MCC, and 0.7268 on SN. Additionally, the best results on two scBS-seq profiled mouse embryonic stem cells datasets were 0.8896 and 0.9511 by AUC, respectively. When compared with other outstanding methods, our method surpassed them on the accuracy of prediction. The improvement of AUC by our method compared to other methods was at least 0.0399 . For the convenience of other researchers, our code has been uploaded to a file hosting service, and can be downloaded from: https://figshare.com/s/0697b692d802861282d3.

  4. Linked Data for Fighting Global Hunger:Experiences in setting standards for Agricultural Information Management

    Science.gov (United States)

    Baker, Thomas; Keizer, Johannes

    FAO, the Food and Agriculture Organization of the UN, has the global goal to defeat hunger and eliminate poverty. One of its core functions is the generation, dissemination and application of information and knowledge. Since 2000, the Agricultural InformationManagement Standards (AIMS) activity in FAO's Knowledge Exchange and Capacity Building Division has promoted the use of Semantic Web standards to improve information sharing within a global network of research institutes and related partner organizations. The strategy emphasizes the use of simple descriptive metadata, thesauri, and ontologies for integrating access to information from a wide range of sources for both scientific and non-expert audiences. An early adopter of Semantic Web technology, the AIMS strategy is evolving to help information providers in nineteen language areas use modern Linked Data methods to improve the quality of life in developing rural areas, home to seventy percent of the world's poor and hungry people.

  5. Location of core diagnostic information across various sequences in brain MRI and implications for efficiency of MRI scanner utilization.

    Science.gov (United States)

    Sharma, Aseem; Chatterjee, Arindam; Goyal, Manu; Parsons, Matthew S; Bartel, Seth

    2015-04-01

    Targeting redundancy within MRI can improve its cost-effective utilization. We sought to quantify potential redundancy in our brain MRI protocols. In this retrospective review, we aggregated 207 consecutive adults who underwent brain MRI and reviewed their medical records to document clinical indication, core diagnostic information provided by MRI, and its clinical impact. Contributory imaging abnormalities constituted positive core diagnostic information whereas absence of imaging abnormalities constituted negative core diagnostic information. The senior author selected core sequences deemed sufficient for extraction of core diagnostic information. For validating core sequences selection, four readers assessed the relative ease of extracting core diagnostic information from the core sequences. Potential redundancy was calculated by comparing the average number of core sequences to the average number of sequences obtained. Scanning had been performed using 9.4±2.8 sequences over 37.3±12.3 minutes. Core diagnostic information was deemed extractable from 2.1±1.1 core sequences, with an assumed scanning time of 8.6±4.8 minutes, reflecting a potential redundancy of 74.5%±19.1%. Potential redundancy was least in scans obtained for treatment planning (14.9%±25.7%) and highest in scans obtained for follow-up of benign diseases (81.4%±12.6%). In 97.4% of cases, all four readers considered core diagnostic information to be either easily extractable from core sequences or the ease to be equivalent to that from the entire study. With only one MRI lacking clinical impact (0.48%), overutilization did not seem to contribute to potential redundancy. High potential redundancy that can be targeted for more efficient scanner utilization exists in brain MRI protocols.

  6. The role of INGVterremoti blog in information management during the earthquake sequence in central Italy

    Directory of Open Access Journals (Sweden)

    Maurizio Pignone

    2017-01-01

    Full Text Available In this paper, we describe the role the INGVterremoti blog in information management during the first part of the earthquake sequence in central Italy (August 24 to September 30. In the last four years, we have been working on the INGVterremoti blog in order to provide quick updates on the ongoing seismic activity in Italy and in-depth scientific information. These include articles on specific historical earthquakes, seismic hazard, geological interpretations, source models from different type of data, effects at the surface, and so on. We have delivered information in quasi-real-time also about all the recent magnitude M≥4.0 earthquakes in Italy, the strongest events in the Mediterranean and in the world. During the 2016 central Italy, the INGVterremoti blog has continuously released information about seismic sequences with three types of posts: i updates on the ongoing seismic activity; ii reports on the activities carried out by the INGV teams in the field and any other working groups; iii in-depth scientific articles describing some specific analysis and results. All the blog posts have been shared automatically and in real time on the other social media of the INGVterremoti platform, also to counter the bad information and to fight rumors. These include Facebook, Twitter and INGVterremoti App on IOS and Android. As well, both the main INGV home page (http://www.ingv.it and the INGV earthquake portal (http://terremoti.ingv.it have published the contents of the blog on dedicated pages that were fed automatically. The work done day by day on the INGVterremoti blog has been coordinated with the INGV Press Office that has written several press releases based on the contents of the blog. Since August 24, 53 articles were published on the blog they have had more than 1.9 million views and 1 million visitors. The peak in the number of views, which was more than 800,000 in a single day, was registered on August 24, 2016, following the M 6

  7. LigandRFs: random forest ensemble to identify ligand-binding residues from sequence information alone

    KAUST Repository

    Chen, Peng

    2014-12-03

    Background Protein-ligand binding is important for some proteins to perform their functions. Protein-ligand binding sites are the residues of proteins that physically bind to ligands. Despite of the recent advances in computational prediction for protein-ligand binding sites, the state-of-the-art methods search for similar, known structures of the query and predict the binding sites based on the solved structures. However, such structural information is not commonly available. Results In this paper, we propose a sequence-based approach to identify protein-ligand binding residues. We propose a combination technique to reduce the effects of different sliding residue windows in the process of encoding input feature vectors. Moreover, due to the highly imbalanced samples between the ligand-binding sites and non ligand-binding sites, we construct several balanced data sets, for each of which a random forest (RF)-based classifier is trained. The ensemble of these RF classifiers forms a sequence-based protein-ligand binding site predictor. Conclusions Experimental results on CASP9 and CASP8 data sets demonstrate that our method compares favorably with the state-of-the-art protein-ligand binding site prediction methods.

  8. Position-specific prediction of methylation sites from sequence conservation based on information theory.

    Science.gov (United States)

    Shi, Yinan; Guo, Yanzhi; Hu, Yayun; Li, Menglong

    2015-07-23

    Protein methylation plays vital roles in many biological processes and has been implicated in various human diseases. To fully understand the mechanisms underlying methylation for use in drug design and work in methylation-related diseases, an initial but crucial step is to identify methylation sites. The use of high-throughput bioinformatics methods has become imperative to predict methylation sites. In this study, we developed a novel method that is based only on sequence conservation to predict protein methylation sites. Conservation difference profiles between methylated and non-methylated peptides were constructed by the information entropy (IE) in a wider neighbor interval around the methylation sites that fully incorporated all of the environmental information. Then, the distinctive neighbor residues were identified by the importance scores of information gain (IG). The most representative model was constructed by support vector machine (SVM) for Arginine and Lysine methylation, respectively. This model yielded a promising result on both the benchmark dataset and independent test set. The model was used to screen the entire human proteome, and many unknown substrates were identified. These results indicate that our method can serve as a useful supplement to elucidate the mechanism of protein methylation and facilitate hypothesis-driven experimental design and validation.

  9. Automatic exchange of information: towards a new global standard of tax transparency

    Directory of Open Access Journals (Sweden)

    Miguel Eduardo Pecho Trigueros

    2014-07-01

    Full Text Available Tax authorities are increasingly relying on mutual cooperation with their foreign peers to enforce more effectively their internal tax laws. After the banking scandals of 2008 and the subsequent global financial crisis, the Global Forum on Transparency and Exchange of Information for TaxPurposes has proposed the exchange of information upon request as the fiscal transparency standard. However, some measures adopted by the European Union, previous initiatives from the Organization for Economic Cooperation and Development (OECD and, above all, the introduction of the Foreign Account Tax Compliance Act (Fatca by the United States in 2010 have promoted the need to adopt the automatic exchange of information as the new fiscal transparency standard. Automatic exchange of information allows home countries to verify whether their taxpayers have correctly included foreign income, allowing tax authorities to have early warning of possible noncompliance cases. In February 2014, the OECD published its proposal for a new global model of automatic exchange of financial account information. The new global model contains the necessary legal instruments and due diligence and reporting procedures, mainly for financial institutions.

  10. 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

  11. O papel das sequências narrativas na estrutura global de reportagens = The role of narrative sequences in the global structure of reports

    Directory of Open Access Journals (Sweden)

    Gustavo Ximenes Cunha

    2013-04-01

    Full Text Available Este artigo estuda a função macroestrutural que as sequências narrativas exercem no gênero reportagem. Com base no Modelo de Análise Modular do Discurso (ROULET et al., 2001, analisamos seis reportagens. Após as análises, constatamos que as sequências desses textos não exercem papel meramente informativo. Ao contrário, a maior parte delas tem o estatuto de subordinadas e funcionam como argumentos com que o jornalista defende uma opinião. Nesse sentido, este trabalho mostra que, em reportagens, a narração é um recurso que auxilia o jornalista a produzir os efeitos de objetividade e de imparcialidade, porque baseia suas afirmações nos acontecimentos narrados. As sequências não são meramente informativas.This paper studies the macroestrutural function of narrative sequences of reports. We analyze six reports and we use the principles of Modular Approach to Discourse Analysis (ROULET et al., 2001. We observe that the narrative sequences are not merely informative. They have subordinate status and they act as arguments to defend an opinion. So, this work shows that in reports the narration is a resource to produce the effects of objectivity and impartiality.

  12. Globalization

    OpenAIRE

    Andru?cã Maria Carmen

    2013-01-01

    The field of globalization has highlighted an interdependence implied by a more harmonious understanding determined by the daily interaction between nations through the inducement of peace and the management of streamlining and the effectiveness of the global economy. For the functioning of the globalization, the developing countries that can be helped by the developed ones must be involved. The international community can contribute to the institution of the development environment of the gl...

  13. Global climate change and human health: Information needs, research priorities, and strategic considerations

    Energy Technology Data Exchange (ETDEWEB)

    Farrell, M.P.; Kanciruk, P. (Oak Ridge National Lab., TN (USA)); O' Hara, F.M. Jr. (O' Hara (Fred M., Jr.), Oak Ridge, TN (USA))

    1989-01-01

    The US Global Research Plan and the International Geosphere-Biosphere Programme were created to assess the effects of global climate change but have not been able to devote much attention to the consequences climate change will have on human health and welfare. Although researchers and policy makers recognize that climate change will have complex effects on resources, in general, the social and medical sciences have not received appropriate international attention under the banner of global change. To address this imbalance, the public health research community needs to launch a international coordinated effort so that the social and medical sciences are as fully represented as other scientific disciplines. This document discusses the information needs, research priorities and strategic considerations of the global change and its impact on human health.

  14. Information communications technologies that surpass the global communications network. Sekai tsushinmo o koeru joho tsushin gijutsu

    Energy Technology Data Exchange (ETDEWEB)

    1990-05-01

    Development of information communications technologies that surpass the global communications network is being pushed forward in order to establish the global village that McLuhan foretold in 1964. Effects of hybrid intensification with the intensification of communications technologies and computer technologies have become evident as facsimiles, automated teller machines of banks, home videos, automatic response telephones with synthetic voices, compact disks, portable telephones, video games and high-definition televisions were developed and put to use in a wide range. Intensification and integration of computer technologies and communications technologies has every possibility, but it also has a peculiar aspect of lacking guiding principles. Uncertain factors of the values of informations in the market are ever increasing, and their true values are yet to be found. Anyhow, it is a long way to the goal of the global village.

  15. Correction of projective distortion in long-image-sequence mosaics without prior information

    Science.gov (United States)

    Yang, Chenhui; Mao, Hongwei; Abousleman, Glen; Si, Jennie

    2010-04-01

    Image mosaicking is the process of piecing together multiple video frames or still images from a moving camera to form a wide-area or panoramic view of the scene being imaged. Mosaics have widespread applications in many areas such as security surveillance, remote sensing, geographical exploration, agricultural field surveillance, virtual reality, digital video, and medical image analysis, among others. When mosaicking a large number of still images or video frames, the quality of the resulting mosaic is compromised by projective distortion. That is, during the mosaicking process, the image frames that are transformed and pasted to the mosaic become significantly scaled down and appear out of proportion with respect to the mosaic. As more frames continue to be transformed, important target information in the frames can be lost since the transformed frames become too small, which eventually leads to the inability to continue further. Some projective distortion correction techniques make use of prior information such as GPS information embedded within the image, or camera internal and external parameters. Alternatively, this paper proposes a new algorithm to reduce the projective distortion without using any prior information whatsoever. Based on the analysis of the projective distortion, we approximate the projective matrix that describes the transformation between image frames using an affine model. Using singular value decomposition, we can deduce the affine model scaling factor that is usually very close to 1. By resetting the image scale of the affine model to 1, the transformed image size remains unchanged. Even though the proposed correction introduces some error in the image matching, this error is typically acceptable and more importantly, the final mosaic preserves the original image size after transformation. We demonstrate the effectiveness of this new correction algorithm on two real-world unmanned air vehicle (UAV) sequences. The proposed method is

  16. The States of Sub Saharan Africa on the way to the Global Information Society

    Directory of Open Access Journals (Sweden)

    Konstantin A. Pantserev

    2010-12-01

    Full Text Available The paper devotes to the problem of overcoming of the digital divide in the Sub Saharan African States. On the example of Kenya the author speaks about the comparative success of the development of the information technologies in Africa and in turn underlines the most significant obstacles on the way of African states to the global information society and suggests the means how to overcome them.

  17. THE FACTOR OF ENERGY-INFORMATION SECURITY IN THE FRAMEWORK OF GLOBAL CIVILIZATION-RELATED CHANGES

    OpenAIRE

    Alexey Viktorovich SUHORUKHIH

    2015-01-01

    The paper examined the grounds having involved global social and cultural changes, and emphasized the precedence taken by an energy-information component to the geopolitical dynamics of the civilization continuum. The study emphasized the relevance of new facets in social and cultural insight urged to respond to challenges of direct mental hazards emerging over the world, and requirement of energy-information security the civilization has sought for, assumed to be the framework for considerin...

  18. Globalization, Information Technology and Higher Education in Nigeria: The Roles of Library Professionals

    Science.gov (United States)

    Uwhekadom, Ejimaji Emmanuel; Olawolu, Oladunni Elizabeth

    2013-01-01

    The influence of globalization and information technology on higher education in Nigeria was investigated through a descriptive survey design. Forty-five professional librarians from University of Port Harcourt, Port Harcourt, Ignatius Ajuru University of Education, Rumuolumeni Port Harcourt, Federal College of Education (Technical) Omoku Rivers…

  19. Quantitative assessment of drivers of recent global temperature variability: an information theoretic approach

    Science.gov (United States)

    Bhaskar, Ankush; Ramesh, Durbha Sai; Vichare, Geeta; Koganti, Triven; Gurubaran, S.

    2017-12-01

    Identification and quantification of possible drivers of recent global temperature variability remains a challenging task. This important issue is addressed adopting a non-parametric information theory technique, the Transfer Entropy and its normalized variant. It distinctly quantifies actual information exchanged along with the directional flow of information between any two variables with no bearing on their common history or inputs, unlike correlation, mutual information etc. Measurements of greenhouse gases: CO2, CH4 and N2O; volcanic aerosols; solar activity: UV radiation, total solar irradiance ( TSI) and cosmic ray flux ( CR); El Niño Southern Oscillation ( ENSO) and Global Mean Temperature Anomaly ( GMTA) made during 1984-2005 are utilized to distinguish driving and responding signals of global temperature variability. Estimates of their relative contributions reveal that CO2 ({˜ } 24 %), CH4 ({˜ } 19 %) and volcanic aerosols ({˜ }23 %) are the primary contributors to the observed variations in GMTA. While, UV ({˜ } 9 %) and ENSO ({˜ } 12 %) act as secondary drivers of variations in the GMTA, the remaining play a marginal role in the observed recent global temperature variability. Interestingly, ENSO and GMTA mutually drive each other at varied time lags. This study assists future modelling efforts in climate science.

  20. Imaging 2015 Mw 7.8 Gorkha Earthquake and Its Aftershock Sequence Combining Multiple Calibrated Global Seismic Arrays

    Science.gov (United States)

    LI, B.; Ghosh, A.

    2016-12-01

    The 2015 Mw 7.8 Gorkha earthquake provides a good opportunity to study the tectonics and earthquake hazards in the Himalayas, one of the most seismically active plate boundaries. Details of the seismicity patterns and associated structures in the Himalayas are poorly understood mainly due to limited instrumentation. Here, we apply a back-projection method to study the mainshock rupture and the following aftershock sequence using four large aperture global seismic arrays. All the arrays show eastward rupture propagation of about 130 km and reveal similar evolution of seismic energy radiation, with strong high-frequency energy burst about 50 km north of Kathmandu. Each single array, however, is typically limited by large azimuthal gap, low resolution, and artifacts due to unmodeled velocity structures. Therefore, we use a self-consistent empirical calibration method to combine four different arrays to image the Gorkha event. It greatly improves the resolution, can better track rupture and reveal details that cannot be resolved by any individual array. In addition, we also use the same arrays at teleseismic distances and apply a back-projection technique to detect and locate the aftershocks immediately following the Gorkha earthquake. We detect about 2.5 times the aftershocks recorded by the Advance National Seismic System comprehensive earthquake catalog during the 19 days following the mainshock. The aftershocks detected by the arrays show an east-west trend in general, with majority of the aftershocks located at the eastern part of the rupture patch and surrounding the rupture zone of the largest Mw 7.3 aftershock. Overall spatiotemporal aftershock pattern agrees well with global catalog, with our catalog showing more details relative to the standard global catalog. The improved aftershock catalog enables us to better study the aftershock dynamics, stress evolution in this region. Moreover, rapid and better imaging of aftershock distribution may aid rapid response

  1. Through Increasing "Information Literacy" Capital and Habitus (Agency): The Complementary Impact on Composition Skills When Appropriately Sequenced

    Science.gov (United States)

    Karas, Timothy

    2017-01-01

    Through a case study approach of a cohort of community college students at a single community college, the impact on success rates in composition courses was analyzed based on the sequence of completing an information literacy course. Two student cohorts were sampled based on completing an information literacy course prior to, or concurrently with…

  2. Act local, think global: how the Malawi experience of scaling up antiretroviral treatment has informed global policy

    Directory of Open Access Journals (Sweden)

    Anthony D. Harries

    2016-09-01

    Full Text Available Abstract The scale-up of antiretroviral therapy (ART in Malawi was based on a public health approach adapted to its resource-poor setting, with principles and practices borrowed from the successful tuberculosis control framework. From 2004 to 2015, the number of new patients started on ART increased from about 3000 to over 820,000. Despite being a small country, Malawi has made a significant contribution to the 15 million people globally on ART and has also contributed policy and service delivery innovations that have supported international guidelines and scale up in other countries. The first set of global guidelines for scaling up ART released by the World Health Organization (WHO in 2002 focused on providing clinical guidance. In Malawi, the ART guidelines adopted from the outset a more operational and programmatic approach with recommendations on health systems and services that were needed to deliver HIV treatment to affected populations. Seven years after the start of national scale-up, Malawi launched a new strategy offering all HIV-infected pregnant women lifelong ART regardless of the CD4-cell count, named Option B+. This strategy was subsequently incorporated into a WHO programmatic guide in 2012 and WHO ART guidelines in 2013, and has since then been adopted by the majority of countries worldwide. In conclusion, the Malawi experience of ART scale-up has become a blueprint for a public health response to HIV and has informed international efforts to end the AIDS epidemic by 2030.

  3. Act local, think global: how the Malawi experience of scaling up antiretroviral treatment has informed global policy.

    Science.gov (United States)

    Harries, Anthony D; Ford, Nathan; Jahn, Andreas; Schouten, Erik J; Libamba, Edwin; Chimbwandira, Frank; Maher, Dermot

    2016-09-06

    The scale-up of antiretroviral therapy (ART) in Malawi was based on a public health approach adapted to its resource-poor setting, with principles and practices borrowed from the successful tuberculosis control framework. From 2004 to 2015, the number of new patients started on ART increased from about 3000 to over 820,000. Despite being a small country, Malawi has made a significant contribution to the 15 million people globally on ART and has also contributed policy and service delivery innovations that have supported international guidelines and scale up in other countries. The first set of global guidelines for scaling up ART released by the World Health Organization (WHO) in 2002 focused on providing clinical guidance. In Malawi, the ART guidelines adopted from the outset a more operational and programmatic approach with recommendations on health systems and services that were needed to deliver HIV treatment to affected populations. Seven years after the start of national scale-up, Malawi launched a new strategy offering all HIV-infected pregnant women lifelong ART regardless of the CD4-cell count, named Option B+. This strategy was subsequently incorporated into a WHO programmatic guide in 2012 and WHO ART guidelines in 2013, and has since then been adopted by the majority of countries worldwide. In conclusion, the Malawi experience of ART scale-up has become a blueprint for a public health response to HIV and has informed international efforts to end the AIDS epidemic by 2030.

  4. Core Genome Multilocus Sequence Typing for Identification of Globally Distributed Clonal Groups and Differentiation of Outbreak Strains of Listeria monocytogenes.

    Science.gov (United States)

    Chen, Yi; Gonzalez-Escalona, Narjol; Hammack, Thomas S; Allard, Marc W; Strain, Errol A; Brown, Eric W

    2016-10-15

    Many listeriosis outbreaks are caused by a few globally distributed clonal groups, designated clonal complexes or epidemic clones, of Listeria monocytogenes, several of which have been defined by classic multilocus sequence typing (MLST) schemes targeting 6 to 8 housekeeping or virulence genes. We have developed and evaluated core genome MLST (cgMLST) schemes and applied them to isolates from multiple clonal groups, including those associated with 39 listeriosis outbreaks. The cgMLST clusters were congruent with MLST-defined clonal groups, which had various degrees of diversity at the whole-genome level. Notably, cgMLST could distinguish among outbreak strains and epidemiologically unrelated strains of the same clonal group, which could not be achieved using classic MLST schemes. The precise selection of cgMLST gene targets may not be critical for the general identification of clonal groups and outbreak strains. cgMLST analyses further identified outbreak strains, including those associated with recent outbreaks linked to contaminated French-style cheese, Hispanic-style cheese, stone fruit, caramel apple, ice cream, and packaged leafy green salad, as belonging to major clonal groups. We further developed lineage-specific cgMLST schemes, which can include accessory genes when core genomes do not possess sufficient diversity, and this provided additional resolution over species-specific cgMLST. Analyses of isolates from different common-source listeriosis outbreaks revealed various degrees of diversity, indicating that the numbers of allelic differences should always be combined with cgMLST clustering and epidemiological evidence to define a listeriosis outbreak. Classic multilocus sequence typing (MLST) schemes targeting internal fragments of 6 to 8 genes that define clonal complexes or epidemic clones have been widely employed to study L. monocytogenes biodiversity and its relation to pathogenicity potential and epidemiology. We demonstrated that core genome MLST

  5. Globalization and advances in information and communication technologies: the impact on nursing and health.

    Science.gov (United States)

    Abbott, Patricia A; Coenen, Amy

    2008-01-01

    Globalization and information and communication technology (ICT) continue to change us and the world we live in. Nursing stands at an opportunity intersection where challenging global health issues, an international workforce shortage, and massive growth of ICT combine to create a very unique space for nursing leadership and nursing intervention. Learning from prior successes in the field can assist nurse leaders in planning and advancing strategies for global health using ICT. Attention to lessons learned will assist in combating the technological apartheid that is already present in many areas of the globe and will highlight opportunities for innovative applications in health. ICT has opened new channels of communication, creating the beginnings of a global information society that will facilitate access to isolated areas where health needs are extreme and where nursing can contribute significantly to the achievement of "Health for All." The purpose of this article is to discuss the relationships between globalization, health, and ICT, and to illuminate opportunities for nursing in this flattening and increasingly interconnected world.

  6. Telecommunication Sector of the Russian Economy: Transformation Into a Global Information and Telecommunication Infrastructure

    Directory of Open Access Journals (Sweden)

    Fokina Elena Anatolyevna

    2014-12-01

    Full Text Available The author concerns the current state and possible ways of telecommunication sector of the Russian economy development in the conditions of world economy globalization and suggests that the process of globalization reflects the current stage of telecommunication companies’ capital internationalization. The analysis of telecommunication sector shows that it is not only a perspective, highmargin and dynamically developing sector but is still one of the most integrated into the system of world economic relations. The stages of Russian telecommunication companies’ capital internationalization are determined, the internal connections between internationalization process and globalization are revealed. It is revealed that the new information and communication technologies development and expansion results in substantial increase in cooperation between economical entities and provides a sustainable long-term economical growth of telecommunication enterprises. The financial and operational data determining the effectiveness of telecommunication companies’ activity are presented. The analysis of tendencies promoting the extension of the market activity of Russian telecommunication companies at global information and telecommunication infrastructure shows that the main tendencies are the following ones: foreign capital inflow increase, capital integration and expansion of new services based on technologies convergence. The author reasonably concludes in recent times, the telecommunication sector of the Russian economy formation and development is determined by the existing global trends.

  7. Entropy-based analysis and bioinformatics-inspired integration of global economic information transfer.

    Directory of Open Access Journals (Sweden)

    Jinkyu Kim

    Full Text Available The assessment of information transfer in the global economic network helps to understand the current environment and the outlook of an economy. Most approaches on global networks extract information transfer based mainly on a single variable. This paper establishes an entirely new bioinformatics-inspired approach to integrating information transfer derived from multiple variables and develops an international economic network accordingly. In the proposed methodology, we first construct the transfer entropies (TEs between various intra- and inter-country pairs of economic time series variables, test their significances, and then use a weighted sum approach to aggregate information captured in each TE. Through a simulation study, the new method is shown to deliver better information integration compared to existing integration methods in that it can be applied even when intra-country variables are correlated. Empirical investigation with the real world data reveals that Western countries are more influential in the global economic network and that Japan has become less influential following the Asian currency crisis.

  8. Entropy-based analysis and bioinformatics-inspired integration of global economic information transfer.

    Science.gov (United States)

    Kim, Jinkyu; Kim, Gunn; An, Sungbae; Kwon, Young-Kyun; Yoon, Sungroh

    2013-01-01

    The assessment of information transfer in the global economic network helps to understand the current environment and the outlook of an economy. Most approaches on global networks extract information transfer based mainly on a single variable. This paper establishes an entirely new bioinformatics-inspired approach to integrating information transfer derived from multiple variables and develops an international economic network accordingly. In the proposed methodology, we first construct the transfer entropies (TEs) between various intra- and inter-country pairs of economic time series variables, test their significances, and then use a weighted sum approach to aggregate information captured in each TE. Through a simulation study, the new method is shown to deliver better information integration compared to existing integration methods in that it can be applied even when intra-country variables are correlated. Empirical investigation with the real world data reveals that Western countries are more influential in the global economic network and that Japan has become less influential following the Asian currency crisis.

  9. Democracy or Informational Autocracy? The Internet's Role in the Global Society of the 21st Century

    Directory of Open Access Journals (Sweden)

    Tarcisio Teixeira

    2016-10-01

    Full Text Available Employing the deductive method, it analyzes the effects of the Internet, combined with the globalization context, in different sectors, from the economic aspect of the global ecommerce to the political consequences, which is inferred when ideological movements emerge on social networks. This incurs the current crisis scenario of state sovereignty, given the failure of states to regulate the virtual space, now marked by neoliberal practices and poorly distributed information. Finally, it contrasts with the Internet as an instrument of domination and social emancipation, in a scenario of excessive consumption of electronic devices and their use to achieve effective democracy.

  10. 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

  11. Communications satellites in the national and global health care information infrastructure: their role, impact, and issues

    Science.gov (United States)

    Zuzek, J. E.; Bhasin, K. B.

    1996-01-01

    Health care services delivered from a distance, known collectively as telemedicine, are being increasingly demonstrated on various transmission media. Telemedicine activities have included diagnosis by a doctor at a remote location, emergency and disaster medical assistance, medical education, and medical informatics. The ability of communications satellites to offer communication channels and bandwidth on demand, connectivity to mobile, remote and under served regions, and global access will afford them a critical role for telemedicine applications within the National and Global Information Infrastructure (NII/GII). The importance that communications satellites will have in telemedicine applications within the NII/GII the differences in requirements for NII vs. GII, the major issues such as interoperability, confidentiality, quality, availability, and costs, and preliminary conclusions for future usability based on the review of several recent trails at national and global levels are presented.

  12. Progress toward an Integrated Global Greenhouse Gas Information System (IG3IS)

    Science.gov (United States)

    DeCola, P.; Butler, J. H.; Stanitski, D.; Tarasova, O. A.; Terblanche, D. E.; Duren, R. M.; Gurney, K. R.; Manning, A.; Reimann, S.; Ciais, P.; Arnold, T.; Burston, J.; Rayner, P. J.; Wofsy, S. C.; Hamburg, S.; Zavala-Araiza, D.; Miller, J. B.; Gerbig, C.; Vogel, F. R.; Canadell, J.

    2016-12-01

    Accurate and precise atmospheric long-term measurements of greenhouse gas (GHG) concentrations have revealed the rapid and unceasing rise of global GHG concentrations due to human socioeconomic activity. Long-term observations also show a resulting rise in global temperatures and evidence of negative impacts on society. In response to this mounting evidence, nations, sub-national governments, private enterprises and individuals are establishing and accelerating efforts to reduce GHG emissions while meeting the needs for global development and increasing energy access. With this motivation, WMO and its partners have called for an Integrated Global Greenhouse Information System (IG3IS). The IG3IS will serve as an international coordinating mechanism to establish and propagate consistent methods and standards to help assess emission-reduction actions. For the IG3IS initiative to succeed the end users must understand, trust, and recognize the value of the information they receive, and act more effectively in response. Over time, the IG3IS framework will be capable of promoting and accepting advancing technical capabilities (e.g., new satellite observations), continually improving the quality of and confidence in such information. By combining accurate atmospheric measurements with enhanced socioeconomic activity data and model analyses we can meet the overarching goals of IG3IS to: Reduce uncertainty of emission inventory reporting, Locate, quantify and prioritize previously unknown emission reduction opportunities, and Provide national and sub-national governments with timely and quantified information to support their assessment of progress towards their mitigation goals. An effective IG3IS will provide on-going, observation-based information on the relative success of GHG management efforts on policy-relevant scales and the response of the global carbon cycle to a warming world. The presentation will cover the principles and objectives of IG3IS, as well as progress

  13. Forecasting an invasive species’ distribution with global distribution data, local data, and physiological information

    Science.gov (United States)

    Jarnevich, Catherine S.; Young, Nicholas E.; Talbert, Marian; Talbert, Colin

    2018-01-01

    Understanding invasive species distributions and potential invasions often requires broad‐scale information on the environmental tolerances of the species. Further, resource managers are often faced with knowing these broad‐scale relationships as well as nuanced environmental factors related to their landscape that influence where an invasive species occurs and potentially could occur. Using invasive buffelgrass (Cenchrus ciliaris), we developed global models and local models for Saguaro National Park, Arizona, USA, based on location records and literature on physiological tolerances to environmental factors to investigate whether environmental relationships of a species at a global scale are also important at local scales. In addition to correlative models with five commonly used algorithms, we also developed a model using a priori user‐defined relationships between occurrence and environmental characteristics based on a literature review. All correlative models at both scales performed well based on statistical evaluations. The user‐defined curves closely matched those produced by the correlative models, indicating that the correlative models may be capturing mechanisms driving the distribution of buffelgrass. Given climate projections for the region, both global and local models indicate that conditions at Saguaro National Park may become more suitable for buffelgrass. Combining global and local data with correlative models and physiological information provided a holistic approach to forecasting invasive species distributions.

  14. Globalization

    DEFF Research Database (Denmark)

    Plum, Maja

    Globalization is often referred to as external to education - a state of affair facing the modern curriculum with numerous challenges. In this paper it is examined as internal to curriculum; analysed as a problematization in a Foucaultian sense. That is, as a complex of attentions, worries, ways...... of reasoning, producing curricular variables. The analysis is made through an example of early childhood curriculum in Danish Pre-school, and the way the curricular variable of the pre-school child comes into being through globalization as a problematization, carried forth by the comparative practices of PISA...

  15. Globalization

    OpenAIRE

    F. Gerard Adams

    2008-01-01

    The rapid globalization of the world economy is causing fundamental changes in patterns of trade and finance. Some economists have argued that globalization has arrived and that the world is “flat†. While the geographic scope of markets has increased, the author argues that new patterns of trade and finance are a result of the discrepancies between “old†countries and “new†. As the differences are gradually wiped out, particularly if knowledge and technology spread worldwide, the t...

  16. Plastid, nuclear and reverse transcriptase sequences in the mitochondrial genome of Oenothera: is genetic information transferred between organelles via RNA?

    Science.gov (United States)

    Schuster, W; Brennicke, A

    1987-01-01

    We describe an open reading frame (ORF) with high homology to reverse transcriptase in the mitochondrial genome of Oenothera. This ORF displays all the characteristics of an active plant mitochondrial gene with a possible ribosome binding site and 39% T in the third codon position. It is located between a sequence fragment from the plastid genome and one of nuclear origin downstream from the gene encoding subunit 5 of the NADH dehydrogenase. The nuclear derived sequence consists of 528 nucleotides from the small ribosomal RNA and contains an expansion segment unique to nuclear rRNAs. The plastid sequence contains part of the ribosomal protein S4 and the complete tRNA(Ser). The observation that only transcribed sequences have been found i more than one subcellular compartment in higher plants suggests that interorganellar transfer of genetic information may occur via RNA and subsequent local reverse transcription and genomic integration. PMID:14650433

  17. Not All Order Memory Is Equal: Test Demands Reveal Dissociations in Memory for Sequence Information

    Science.gov (United States)

    Jonker, Tanya R.; MacLeod, Colin M.

    2017-01-01

    Remembering the order of a sequence of events is a fundamental feature of episodic memory. Indeed, a number of formal models represent temporal context as part of the memory system, and memory for order has been researched extensively. Yet, the nature of the code(s) underlying sequence memory is still relatively unknown. Across 4 experiments that…

  18. Coordinating the Global Information Grid Initiative with the NG9-1-1 Initiative

    Energy Technology Data Exchange (ETDEWEB)

    Michael Schmitt

    2008-05-01

    As the Department of Defense develops the Global Information Grid, the Department of Transportation develops the Next Generation 9-1-1 system. Close examinations of these initiatives show that the two are similar in architectures, applications, and communications interoperability. These similarities are extracted from the lowest user level to the highest commander rank that will be involved in each network. Once the similarities are brought into perspective, efforts should be made to collaborate between the two departments.

  19. Automatic Exchange of Information as the new global standard: the end of (offshore tax evasion) history?

    OpenAIRE

    Meinzer, Markus

    2017-01-01

    Automatic exchange of information (AEoI) for tax purposes has become the global standard for international tax cooperation in 2013. As a tool for containing offshore tax evasion, it has encountered opposition in the past and continues to be fraught with challenges. This paper recapitulates the rationale for AEoI, including estimates on the magnitudes of assets held offshore, with a specific focus on Turkish assets held in Germany (chapter 1). Subsequently, chapter 2 summarises the recent hist...

  20. The NIAID Division of AIDS enterprise information system: integrated decision support for global clinical research programs

    Science.gov (United States)

    Gupta, Nitin; Varghese, Suresh; Virkar, Hemant

    2011-01-01

    The National Institute of Allergy and Infectious Diseases (NIAID) Division of AIDS (DAIDS) Enterprise Information System (DAIDS-ES) is a web-based system that supports NIAID in the scientific, strategic, and tactical management of its global clinical research programs for HIV/AIDS vaccines, prevention, and therapeutics. Different from most commercial clinical trials information systems, which are typically protocol-driven, the DAIDS-ES was built to exchange information with those types of systems and integrate it in ways that help scientific program directors lead the research effort and keep pace with the complex and ever-changing global HIV/AIDS pandemic. Whereas commercially available clinical trials support systems are not usually disease-focused, DAIDS-ES was specifically designed to capture and incorporate unique scientific, demographic, and logistical aspects of HIV/AIDS treatment, prevention, and vaccine research in order to provide a rich source of information to guide informed decision-making. Sharing data across its internal components and with external systems, using defined vocabularies, open standards and flexible interfaces, the DAIDS-ES enables NIAID, its global collaborators and stakeholders, access to timely, quality information about NIAID-supported clinical trials which is utilized to: (1) analyze the research portfolio, assess capacity, identify opportunities, and avoid redundancies; (2) help support study safety, quality, ethics, and regulatory compliance; (3) conduct evidence-based policy analysis and business process re-engineering for improved efficiency. This report summarizes how the DAIDS-ES was conceptualized, how it differs from typical clinical trial support systems, the rationale for key design choices, and examples of how it is being used to advance the efficiency and effectiveness of NIAID's HIV/AIDS clinical research programs. PMID:21816958

  1. Situation models and memory: the effects of temporal and causal information on recall sequence.

    Science.gov (United States)

    Brownstein, Aaron L; Read, Stephen J

    2007-10-01

    Participants watched an episode of the television show Cheers on video and then reported free recall. Recall sequence followed the sequence of events in the story; if one concept was observed immediately after another, it was recalled immediately after it. We also made a causal network of the show's story and found that recall sequence followed causal links; effects were recalled immediately after their causes. Recall sequence was more likely to follow causal links than temporal sequence, and most likely to follow causal links that were temporally sequential. Results were similar at 10-minute and 1-week delayed recall. This is the most direct and detailed evidence reported on sequential effects in recall. The causal network also predicted probability of recall; concepts with more links and concepts on the main causal chain were most likely to be recalled. This extends the causal network model to more complex materials than previous research.

  2. Generation of global hourly radiation sequences using a Transition Markov matrix for Madrid. Generacion de secuencias horarias de radiacion global utilizando matrices de transicion de Markov, para la localidad de Madrid

    Energy Technology Data Exchange (ETDEWEB)

    Mora, Ll

    1989-11-01

    The aim of this work is the generation of sequences of hourly global radiation which have similar statistically characteristics of real sequences for the city of Madrid (Spain). For this generation, a first order Markov model has been proposed. The input parameters of simulation method are the following: The maximum value of hourly radiation and the average monthly value of the transparency normalized index. The maximum value of hourly radiation has been calculated as a function of the solar height by an empirical expression. The transparency normalized index has been defined as the ratio among the measured hourly global radiation to the maximum value for the corresponding solar height. The method is based on the following observations: -The transparency normalized index shows a significant correlation only for two consecutive hours. -The months with the same average transparency normalized indies have similar probability density function. Global solar radiation, time series, simulation, Markov transition matrix, solar energy.

  3. SoilGrids1km — Global Soil Information Based on Automated Mapping

    Science.gov (United States)

    Hengl, Tomislav; de Jesus, Jorge Mendes; MacMillan, Robert A.; Batjes, Niels H.; Heuvelink, Gerard B. M.; Ribeiro, Eloi; Samuel-Rosa, Alessandro; Kempen, Bas; Leenaars, Johan G. B.; Walsh, Markus G.; Gonzalez, Maria Ruiperez

    2014-01-01

    Background Soils are widely recognized as a non-renewable natural resource and as biophysical carbon sinks. As such, there is a growing requirement for global soil information. Although several global soil information systems already exist, these tend to suffer from inconsistencies and limited spatial detail. Methodology/Principal Findings We present SoilGrids1km — a global 3D soil information system at 1 km resolution — containing spatial predictions for a selection of soil properties (at six standard depths): soil organic carbon (g kg−1), soil pH, sand, silt and clay fractions (%), bulk density (kg m−3), cation-exchange capacity (cmol+/kg), coarse fragments (%), soil organic carbon stock (t ha−1), depth to bedrock (cm), World Reference Base soil groups, and USDA Soil Taxonomy suborders. Our predictions are based on global spatial prediction models which we fitted, per soil variable, using a compilation of major international soil profile databases (ca. 110,000 soil profiles), and a selection of ca. 75 global environmental covariates representing soil forming factors. Results of regression modeling indicate that the most useful covariates for modeling soils at the global scale are climatic and biomass indices (based on MODIS images), lithology, and taxonomic mapping units derived from conventional soil survey (Harmonized World Soil Database). Prediction accuracies assessed using 5–fold cross-validation were between 23–51%. Conclusions/Significance SoilGrids1km provide an initial set of examples of soil spatial data for input into global models at a resolution and consistency not previously available. Some of the main limitations of the current version of SoilGrids1km are: (1) weak relationships between soil properties/classes and explanatory variables due to scale mismatches, (2) difficulty to obtain covariates that capture soil forming factors, (3) low sampling density and spatial clustering of soil profile locations. However, as the Soil

  4. SoilGrids1km--global soil information based on automated mapping.

    Directory of Open Access Journals (Sweden)

    Tomislav Hengl

    Full Text Available BACKGROUND: Soils are widely recognized as a non-renewable natural resource and as biophysical carbon sinks. As such, there is a growing requirement for global soil information. Although several global soil information systems already exist, these tend to suffer from inconsistencies and limited spatial detail. METHODOLOGY/PRINCIPAL FINDINGS: We present SoilGrids1km--a global 3D soil information system at 1 km resolution--containing spatial predictions for a selection of soil properties (at six standard depths: soil organic carbon (g kg-1, soil pH, sand, silt and clay fractions (%, bulk density (kg m-3, cation-exchange capacity (cmol+/kg, coarse fragments (%, soil organic carbon stock (t ha-1, depth to bedrock (cm, World Reference Base soil groups, and USDA Soil Taxonomy suborders. Our predictions are based on global spatial prediction models which we fitted, per soil variable, using a compilation of major international soil profile databases (ca. 110,000 soil profiles, and a selection of ca. 75 global environmental covariates representing soil forming factors. Results of regression modeling indicate that the most useful covariates for modeling soils at the global scale are climatic and biomass indices (based on MODIS images, lithology, and taxonomic mapping units derived from conventional soil survey (Harmonized World Soil Database. Prediction accuracies assessed using 5-fold cross-validation were between 23-51%. CONCLUSIONS/SIGNIFICANCE: SoilGrids1km provide an initial set of examples of soil spatial data for input into global models at a resolution and consistency not previously available. Some of the main limitations of the current version of SoilGrids1km are: (1 weak relationships between soil properties/classes and explanatory variables due to scale mismatches, (2 difficulty to obtain covariates that capture soil forming factors, (3 low sampling density and spatial clustering of soil profile locations. However, as the SoilGrids system is

  5. Progress toward an Integrated Global GHG Information System (IG3IS)

    Science.gov (United States)

    DeCola, Philip

    2016-04-01

    Accurate and precise atmospheric measurements of greenhouse gas (GHG) concentrations have shown the inexorable rise of global GHG concentrations due to human socioeconomic activity. Scientific observations also show a resulting rise in global temperatures and evidence of negative impacts on society. In response to this amassing evidence, nations, states, cities and private enterprises are accelerating efforts to reduce emissions of GHGs, and the UNFCCC process recently forged the Paris Agreement. Emission reduction strategies will vary by nation, region, and economic sector (e.g., INDCs), but regardless of the strategies and mechanisms applied, the ability to implement policies and manage them effectively over time will require consistent, reliable and timely information. A number of studies [e.g., Verifying Greenhouse Gas Emissions: Methods to Support International Climate Agreements (2010); GEO Carbon Strategy (2010); IPCC Task Force on National GHG Inventories: Expert Meeting Report on Uncertainty and Validation of Emission Inventories (2010)] have reported on the state of carbon cycle research, observations and models and the ability of these atmospheric observations and models to independently validate and improve the accuracy of self-reported emission inventories based on fossil fuel usage and land use activities. These studies concluded that by enhancing our in situ and remote-sensing observations and atmospheric data assimilation modeling capabilities, a GHG information system could be achieved in the coming decade to serve the needs of policies and actions to reduce GHG emissions. Atmospheric measurements and models are already being used to provide emissions information on a global and continental scale through existing networks, but these efforts currently provide insufficient information at the human-dimensions where nations, states, cities, and private enterprises can take valuable, and additional action that can reduce emissions for a specific GHG

  6. The Global Heat Health Information Network (GHHIN): Putting the Pieces Together

    Science.gov (United States)

    Jones, H.; Shumake, J.; Trtanj, J.

    2017-12-01

    Human exposure to extreme heat is one of the principal and most manageable impacts of climate on human health. Yet, every year worldwide, tens of thousands of people die as a result of avoidable heat-induced health consequences and countless others experience reduced labor productivity, physiological stress and ill health. The IPCC predicts with high confidence, that the observed trend of longer lasting, more frequent, more intense, and earlier onset heat waves will continue into the future. This situation requires the global health community to aggressively confront this recognized risk. Many countries and cities worldwide have developed heat action plans or heat health early warning systems, but these efforts are only connected in an ad-hoc fashion, use a broad range of non-standardized tools, methods, and approaches, and lack a clear mechanism to learn from each other in order to more rapidly advance health protection. To address this gap and accelerate heat health protection, the Global Heat Health Information Network (GHHIN) was launched in June 2016, by the WMO/WHO joint office for Climate and Health and the NOAA Climate Program Office. GHHIN is envisioned to be an independent, voluntary, member driven forum of scientists, professionals, and policymakers focused on enhancing and multiplying the global and local learning and resilience-building for heat health that is already occurring. GHHIN seeks to serve as a catalyst, knowledge broker, disseminator of good practices, and a forum for facilitating exchange and identifying needs. GHHIN will promote evidence-driven interventions, shared-learning, co-production of information, synthesis of priorities and capacity building to empower actors to take more effective and informed life-saving preparedness and planning measures. GHHIN is working toward several activities in 2018. The first Global Heat Health Synthesis report will be published to synthesize the state of science and practice to monitor, predict, and

  7. Assessing the Primary Data Hosted by the Spanish Node of the Global Biodiversity Information Facility (GBIF)

    Science.gov (United States)

    Otegui, Javier; Ariño, Arturo H.; Encinas, María A.; Pando, Francisco

    2013-01-01

    In order to effectively understand and cope with the current ‘biodiversity crisis’, having large-enough sets of qualified data is necessary. Information facilitators such as the Global Biodiversity Information Facility (GBIF) are ensuring increasing availability of primary biodiversity records by linking data collections spread over several institutions that have agreed to publish their data in a common access schema. We have assessed the primary records that one such publisher, the Spanish node of GBIF (GBIF.ES), hosts on behalf of a number of institutions, considered to be a highly representative sample of the total mass of available data for a country in order to know the quantity and quality of the information made available. Our results may provide an indication of the overall fitness-for-use in these data. We have found a number of patterns in the availability and accrual of data that seem to arise naturally from the digitization processes. Knowing these patterns and features may help deciding when and how these data can be used. Broadly, the error level seems low. The available data may be of capital importance for the development of biodiversity research, both locally and globally. However, wide swaths of records lack data elements such as georeferencing or taxonomical levels. Although the remaining information is ample and fit for many uses, improving the completeness of the records would likely increase the usability span for these data. PMID:23372828

  8. TRX-LOGOS - a graphical tool to demonstrate DNA information content dependent upon backbone dynamics in addition to base sequence.

    Science.gov (United States)

    Fortin, Connor H; Schulze, Katharina V; Babbitt, Gregory A

    2015-01-01

    It is now widely-accepted that DNA sequences defining DNA-protein interactions functionally depend upon local biophysical features of DNA backbone that are important in defining sites of binding interaction in the genome (e.g. DNA shape, charge and intrinsic dynamics). However, these physical features of DNA polymer are not directly apparent when analyzing and viewing Shannon information content calculated at single nucleobases in a traditional sequence logo plot. Thus, sequence logos plots are severely limited in that they convey no explicit information regarding the structural dynamics of DNA backbone, a feature often critical to binding specificity. We present TRX-LOGOS, an R software package and Perl wrapper code that interfaces the JASPAR database for computational regulatory genomics. TRX-LOGOS extends the traditional sequence logo plot to include Shannon information content calculated with regard to the dinucleotide-based BI-BII conformation shifts in phosphate linkages on the DNA backbone, thereby adding a visual measure of intrinsic DNA flexibility that can be critical for many DNA-protein interactions. TRX-LOGOS is available as an R graphics module offered at both SourceForge and as a download supplement at this journal. To demonstrate the general utility of TRX logo plots, we first calculated the information content for 416 Saccharomyces cerevisiae transcription factor binding sites functionally confirmed in the Yeastract database and matched to previously published yeast genomic alignments. We discovered that flanking regions contain significantly elevated information content at phosphate linkages than can be observed at nucleobases. We also examined broader transcription factor classifications defined by the JASPAR database, and discovered that many general signatures of transcription factor binding are locally more information rich at the level of DNA backbone dynamics than nucleobase sequence. We used TRX-logos in combination with MEGA 6.0 software

  9. High-density rhesus macaque oligonucleotide microarray design using early-stage rhesus genome sequence information and human genome annotations

    Directory of Open Access Journals (Sweden)

    Magness Charles L

    2007-01-01

    Full Text Available Abstract Background Until recently, few genomic reagents specific for non-human primate research have been available. To address this need, we have constructed a macaque-specific high-density oligonucleotide microarray by using highly fragmented low-pass sequence contigs from the rhesus genome project together with the detailed sequence and exon structure of the human genome. Using this method, we designed oligonucleotide probes to over 17,000 distinct rhesus/human gene orthologs and increased by four-fold the number of available genes relative to our first-generation expressed sequence tag (EST-derived array. Results We constructed a database containing 248,000 exon sequences from 23,000 human RefSeq genes and compared each human exon with its best matching sequence in the January 2005 version of the rhesus genome project list of 486,000 DNA contigs. Best matching rhesus exon sequences for each of the 23,000 human genes were then concatenated in the proper order and orientation to produce a rhesus "virtual transcriptome." Microarray probes were designed, one per gene, to the region closest to the 3' untranslated region (UTR of each rhesus virtual transcript. Each probe was compared to a composite rhesus/human transcript database to test for cross-hybridization potential yielding a final probe set representing 18,296 rhesus/human gene orthologs, including transcript variants, and over 17,000 distinct genes. We hybridized mRNA from rhesus brain and spleen to both the EST- and genome-derived microarrays. Besides four-fold greater gene coverage, the genome-derived array also showed greater mean signal intensities for genes present on both arrays. Genome-derived probes showed 99.4% identity when compared to 4,767 rhesus GenBank sequence tag site (STS sequences indicating that early stage low-pass versions of complex genomes are of sufficient quality to yield valuable functional genomic information when combined with finished genome information from

  10. INFORMATION THREATS IN A GLOBALIZED WORLD: ECONOMICS, POLITICS, SOCIETY (EXPERIENCE OF UKRAINE

    Directory of Open Access Journals (Sweden)

    Anatoliy Holovka

    2016-11-01

    Full Text Available The scientific article deals with both integral vision of the contemporary informative risks in the globalized world and their classification. The essence of the informative security is exposed, which is one of main factors of steady development of the modern informative society. In consideration of the foreign practice, the experience of Ukraine is also analyzed in counteraction to the contemporary informative threats. The effective policy of safety and counteraction to the informative threats is one of the basic constituents of the state national safety system and at the same time testifies to the correct character of connections between the public organs and the society. Under the conditions of unrestrained progress of information technologies and general informatization in all sectors of people’s life (politics, economy, defense, energy etc., providing of control and defense of informative space of the country becomes much more difficult task. Modern Ukrainian realities certify convincingly, that Ukraine is in an extremely difficult political situation that influences all spheres of Ukrainians’ life. The key reason of such situation is a military-informative aggression against Ukraine from Russia, which is the fact of waging a «hybrid war». As it is known, this type of war combines the application of both classic soldiery instruments (military technique, firearms, regular troops and methods of informative influence (cyber-attack, informative diversions, aggressive propaganda, impact on public opinion. This factor encourages such research. The object of the study is the phenomenon of information risks in the modern world. Subject of research – is the impact of modern information threats to the state and society, namely the economic, political and social spheres. For a holistic analysis of the subject of research was used appropriate methodology – systematic approach, method of comparative analysis, general scientific methods

  11. Global Drought Services: Collaborations Toward an Information System for Early Warning

    Science.gov (United States)

    Hayes, M. J.; Pulwarty, R. S.; Svoboda, M.

    2014-12-01

    Drought is a hazard that lends itself well to diligent, sustained monitoring and early warning. However, unlike most hazards, the fact that droughts typically evolve slowly, can last for months or years and cover vast areas spanning multiple political boundaries/jurisdictions and economic sectors can make it a daunting task to monitor, develop plans for, and identify appropriate, proactive mitigation strategies. The National Drought Mitigation Center (NDMC) and National Integrated Drought Information System (NIDIS) have been working together to reduce societal vulnerability to drought by helping decision makers at all levels to: 1) implement drought early warning/forecasting and decision support systems; 2) support and advocate for better collection of, and understanding of drought impacts; and 3) increase long-term resilience to drought through proactive planning. The NDMC and NIDIS risk management approach has been the basis from which many partners around the world are developing a collaboration and coordination nexus with an ultimate goal of building comprehensive global drought early warning information systems (GDEWIS). The core emphasis of this model is on developing and applying useful and usable information that can be integrated and transferred freely to other regions around the globe. The High-Level Ministerial Declaration on Drought, the Integrated Drought Management Programme (IDMP) co-led by the WMO and the Global Water Partnership (GWP), and the Global Framework for Climate Services are drawing extensively from the integrated NDMC-NIDIS risk management framework. This presentation will describe, in detail, the various drought resources, tools, services, and collaborations already being provided and undertaken at the national and regional scales by the NDMC, NIDIS, and their partners. The presentation will be forward-looking, identifying improvements in existing and proposed mechanisms to help strengthen national and international drought early

  12. The EUSTACE project: delivering global, daily information on surface air temperature

    Science.gov (United States)

    Ghent, D.; Rayner, N. A.

    2017-12-01

    Day-to-day variations in surface air temperature affect society in many ways; however, daily surface air temperature measurements are not available everywhere. A global daily analysis cannot be achieved with measurements made in situ alone, so incorporation of satellite retrievals is needed. To achieve this, in the EUSTACE project (2015-2018, https://www.eustaceproject.eu) we have developed an understanding of the relationships between traditional (land and marine) surface air temperature measurements and retrievals of surface skin temperature from satellite measurements, i.e. Land Surface Temperature, Ice Surface Temperature, Sea Surface Temperature and Lake Surface Water Temperature. Here we discuss the science needed to produce a fully-global daily analysis (or ensemble of analyses) of surface air temperature on the centennial scale, integrating different ground-based and satellite-borne data types. Information contained in the satellite retrievals is used to create globally-complete fields in the past, using statistical models of how surface air temperature varies in a connected way from place to place. This includes developing new "Big Data" analysis methods as the data volumes involved are considerable. We will present recent progress along this road in the EUSTACE project, i.e.: • identifying inhomogeneities in daily surface air temperature measurement series from weather stations and correcting for these over Europe; • estimating surface air temperature over all surfaces of Earth from surface skin temperature retrievals; • using new statistical techniques to provide information on higher spatial and temporal scales than currently available, making optimum use of information in data-rich eras. Information will also be given on how interested users can become involved.

  13. Global polar geospatial information service retrieval based on search engine and ontology reasoning

    Science.gov (United States)

    Chen, Nengcheng; E, Dongcheng; Di, Liping; Gong, Jianya; Chen, Zeqiang

    2007-01-01

    In order to improve the access precision of polar geospatial information service on web, a new methodology for retrieving global spatial information services based on geospatial service search and ontology reasoning is proposed, the geospatial service search is implemented to find the coarse service from web, the ontology reasoning is designed to find the refined service from the coarse service. The proposed framework includes standardized distributed geospatial web services, a geospatial service search engine, an extended UDDI registry, and a multi-protocol geospatial information service client. Some key technologies addressed include service discovery based on search engine and service ontology modeling and reasoning in the Antarctic geospatial context. Finally, an Antarctica multi protocol OWS portal prototype based on the proposed methodology is introduced.

  14. The Global Invasive Species Information Network: contributing to GEO Task BI-07-01b

    Science.gov (United States)

    Graham, J.; Morisette, J. T.; Simpson, A.

    2009-12-01

    Invasive alien species (IAS) threaten biodiversity and exert a tremendous cost on society for IAS prevention and eradication. They endanger natural ecosystem functioning and seriously impact biodiversity and agricultural production. The task definition for the GEO task BI-07-01b: Invasive Species Monitoring System is to characterize, monitor, and predict changes in the distribution of invasive species. This includes characterizing the current requirements and capacity for invasive species monitoring and developing strategies for implementing cross-search functionality among existing online invasive species information systems from around the globe. The Task is being coordinated by members of the Global Invasive Species Information Network (GISIN) and their partners. Information on GISIN and a prototype of the network is available at www.gisin.org. This talk will report on the current status of GISIN and review how researchers can either contribute to or utilize data from this network.

  15. Why Replacing Legacy Systems Is So Hard in Global Software Development: An Information Infrastructure Perspective

    DEFF Research Database (Denmark)

    Matthiesen, Stina; Bjørn, Pernille

    2015-01-01

    We report on an ethnographic study of an outsourcing global software development (GSD) setup between a Danish IT company and an Indian IT vendor developing a system to replace a legacy system for social services administration in Denmark. Physical distance and GSD collaboration issues tend...... to be obvious explanations for why GSD tasks fail to reach completion; however, we account for the difficulties within the technical nature of software system task. We use the framework of information infrastructure to show how replacing a legacy system in governmental information infrastructures includes...... the work of tracing back to knowledge concerning law, technical specifications, as well as how information infrastructures have dynamically evolved over time. Not easily carried out in a GSD setup is the work around technical tasks that requires careful examination of mundane technical aspects, standards...

  16. Globally COnstrained Local Function Approximation via Hierarchical Modelling, a Framework for System Modelling under Partial Information

    DEFF Research Database (Denmark)

    Øjelund, Henrik; Sadegh, Payman

    2000-01-01

    be obtained. This paper presents a new approach for system modelling under partial (global) information (or the so called Gray-box modelling) that seeks to perserve the benefits of the global as well as local methodologies sithin a unified framework. While the proposed technique relies on local approximations......Local function approximations concern fitting low order models to weighted data in neighbourhoods of the points where the approximations are desired. Despite their generality and convenience of use, local models typically suffer, among others, from difficulties arising in physical interpretation...... simultaneously with the (local estimates of) function values. The approach is applied to modelling of a linear time variant dynamic system under prior linear time invariant structure where local regression fails as a result of high dimensionality....

  17. Sequence- vs. chip-assisted genomic selection: accurate biological information is advised.

    Science.gov (United States)

    Pérez-Enciso, Miguel; Rincón, Juan C; Legarra, Andrés

    2015-05-09

    The development of next-generation sequencing technologies (NGS) has made the use of whole-genome sequence data for routine genetic evaluations possible, which has triggered a considerable interest in animal and plant breeding fields. Here, we investigated whether complete or partial sequence data can improve upon existing SNP (single nucleotide polymorphism) array-based selection strategies by simulation using a mixed coalescence - gene-dropping approach. We simulated 20 or 100 causal mutations (quantitative trait nucleotides, QTN) within 65 predefined 'gene' regions, each 10 kb long, within a genome composed of ten 3-Mb chromosomes. We compared prediction accuracy by cross-validation using a medium-density chip (7.5 k SNPs), a high-density (HD, 17 k) and sequence data (335 k). Genetic evaluation was based on a GBLUP method. The simulations showed: (1) a law of diminishing returns with increasing number of SNPs; (2) a modest effect of SNP ascertainment bias in arrays; (3) a small advantage of using whole-genome sequence data vs. HD arrays i.e. ~4%; (4) a minor effect of NGS errors except when imputation error rates are high (≥20%); and (5) if QTN were known, prediction accuracy approached 1. Since this is obviously unrealistic, we explored milder assumptions. We showed that, if all SNPs within causal genes were included in the prediction model, accuracy could also dramatically increase by ~40%. However, this criterion was highly sensitive to either misspecification (including wrong genes) or to the use of an incomplete gene list; in these cases, accuracy fell rapidly towards that reached when all SNPs from sequence data were blindly included in the model. Our study shows that, unless an accurate prior estimate on the functionality of SNPs can be included in the predictor, there is a law of diminishing returns with increasing SNP density. As a result, use of whole-genome sequence data may not result in a highly increased selection response over high

  18. Importance of the temporal structure of movement sequences on the ability of monkeys to use serial order information.

    Science.gov (United States)

    Deffains, Marc; Legallet, Eric; Apicella, Paul

    2011-10-01

    also used in the repeated sequence. This performance advantage was most prominently detectable when temporal prediction of forthcoming target stimuli was optimized. Taken together, the present findings demonstrate that the monkey's capacity to make use of serial order information to speed task performance was dependent on the temporal structure of the motor sequence.

  19. An HMM posterior decoder for sequence feature prediction that includes homology information

    DEFF Research Database (Denmark)

    Käll, Lukas; Krogh, Anders Stærmose; Sonnhammer, Erik L. L.

    2005-01-01

    Motivation: When predicting sequence features like transmembrane topology, signal peptides, coil-coil structures, protein secondary structure or genes, extra support can be gained from homologs. Results: We present here a general hidden Markov model (HMM) decoding algorithm that combines probabil......Motivation: When predicting sequence features like transmembrane topology, signal peptides, coil-coil structures, protein secondary structure or genes, extra support can be gained from homologs. Results: We present here a general hidden Markov model (HMM) decoding algorithm that combines......://phobius.cgb.ki.se/poly.html . An implementation of the algorithm is available on request from the authors....

  20. On the long-lasting sequences of coral reef terraces from SE Sulawesi (Indonesia): Distribution, formation, and global significance

    Science.gov (United States)

    Pedoja, Kevin; Husson, Laurent; Bezos, Antoine; Pastier, Anne-Morwenn; Imran, Andy Muhammad; Arias-Ruiz, Camilo; Sarr, Anta-Clarisse; Elliot, Mary; Pons-Branchu, Edwige; Nexer, Maëlle; Regard, Vincent; Hafidz, Abdul; Robert, Xavier; Benoit, Laurent; Delcaillau, Bernard; Authemayou, Christine; Dumoulin, Caroline; Choblet, Gaël

    2018-05-01

    Many islands of the eastern Indonesian Archipelago exhibit Late Cenozoic sequences of coral reef terraces. In SE Sulawesi, on the Tukang Besi and Buton archipelagos, we identified 23 islands bearing such sequences. Remote sensing imagery and field mapping combined to U/Th and 14C dating enable to establish a chronologic framework of the reef terrace sequences from Wangi-Wangi, Buton as well as on the neighbouring, smaller islands of Ular, Siumpu and Kadatua. We identified the terraces from the last interglacial maximum (MIS 5e) at elevations lower than 20 m except on W Kadatua where it is raised at 34 ± 5 m. Such elevations yield low to moderate Upper Pleistocene uplift rates (<0.3 mm yr-1). On SE Buton Island, a sequence culminates at 650 m and includes at least 40 undated strandlines. Next to this exceptional sequence, on the Sampolawa Peninsula, 18 strandlines culminate at 430 m. Dated samples at the base of this sequence (<40 m) yield mean Middle Pleistocene uplift rates of 0.14 ± 0.09 mm yr-1. Extrapolation of these uplift rates compared to the geological setting suggests that the sequences of the Sampolawa Peninsula provide a record of sea-level high-stands for the last 3.8 ± 0.6 Ma. The sequences on SE Buton Island therefore constitute the best preserved long-lasting geomorphic record of Plio-Quaternary sea-level stands worldwide.

  1. Degree product rule tempers explosive percolation in the absence of global information

    Science.gov (United States)

    Trevelyan, Alexander J.; Tsekenis, Georgios; Corwin, Eric I.

    2018-02-01

    We introduce a guided network growth model, which we call the degree product rule process, that uses solely local information when adding new edges. For small numbers of candidate edges our process gives rise to a second-order phase transition, but becomes first order in the limit of global choice. We provide the set of critical exponents required to characterize the nature of this percolation transition. Such a process permits interventions which can delay the onset of percolation while tempering the explosiveness caused by cluster product rule processes.

  2. Toward allotetraploid cotton genome assembly: integration of a high-density molecular genetic linkage map with DNA sequence information

    Science.gov (United States)

    2012-01-01

    Background Cotton is the world’s most important natural textile fiber and a significant oilseed crop. Decoding cotton genomes will provide the ultimate reference and resource for research and utilization of the species. Integration of high-density genetic maps with genomic sequence information will largely accelerate the process of whole-genome assembly in cotton. Results In this paper, we update a high-density interspecific genetic linkage map of allotetraploid cultivated cotton. An additional 1,167 marker loci have been added to our previously published map of 2,247 loci. Three new marker types, InDel (insertion-deletion) and SNP (single nucleotide polymorphism) developed from gene information, and REMAP (retrotransposon-microsatellite amplified polymorphism), were used to increase map density. The updated map consists of 3,414 loci in 26 linkage groups covering 3,667.62 cM with an average inter-locus distance of 1.08 cM. Furthermore, genome-wide sequence analysis was finished using 3,324 informative sequence-based markers and publicly-available Gossypium DNA sequence information. A total of 413,113 EST and 195 BAC sequences were physically anchored and clustered by 3,324 sequence-based markers. Of these, 14,243 ESTs and 188 BACs from different species of Gossypium were clustered and specifically anchored to the high-density genetic map. A total of 2,748 candidate unigenes from 2,111 ESTs clusters and 63 BACs were mined for functional annotation and classification. The 337 ESTs/genes related to fiber quality traits were integrated with 132 previously reported cotton fiber quality quantitative trait loci, which demonstrated the important roles in fiber quality of these genes. Higher-level sequence conservation between different cotton species and between the A- and D-subgenomes in tetraploid cotton was found, indicating a common evolutionary origin for orthologous and paralogous loci in Gossypium. Conclusion This study will serve as a valuable genomic resource

  3. Stock return predictability and market integration: The role of global and local information

    Directory of Open Access Journals (Sweden)

    David G. McMillan

    2016-12-01

    Full Text Available This paper examines the predictability of a range of international stock markets where we allow the presence of both local and global predictive factors. Recent research has argued that US returns have predictive power for international stock returns. We expand this line of research, following work on market integration, to include a more general definition of the global factor, based on principal components analysis. Results identify three global expected returns factors, one related to the major stock markets of the US, UK and Asia and one related to the other markets analysed. The third component is related to dividend growth. A single dominant realised returns factor is also noted. A forecasting exercise comparing the principal components based factors to a US return factor and local market only factors, as well as the historical mean benchmark finds supportive evidence for the former approach. It is hoped that the results from this paper will be informative on three counts. First, to academics interested in understanding the dynamics asset price movement. Second, to market participants who aim to time the market and engage in portfolio and risk management. Third, to those (policy makers and others who are interested in linkages across international markets and the nature and degree of integration.

  4. The vulnerability of being ill informed: the Trans-Pacific Partnership Agreement and Global Public Health.

    Science.gov (United States)

    Greenberg, Henry; Shiau, Stephanie

    2014-09-01

    The Trans Pacific Partnership Agreement (TPPA) is a regional trade agreement currently being negotiated by 11 Pacific Rim countries, excluding China. While the negotiations are being conducted under a veil of secrecy, substantive leaks over the past 4 years have revealed a broad view of the proposed contents. As it stands the TPPA poses serious risks to global public health, particularly chronic, non-communicable diseases. At greatest risk are national tobacco regulations, regulations governing the emergence of generic drugs and controls over food imports by transnational corporations. Aside from a small group of public health professionals from Australia, the academic public health community has missed these threats to the global community, although many other health-related entities, international lawyers and health-conscious politicians have voiced serious concerns. As of mid-2014 there has been no comment in the leading public health journals. This large lacuna in interest or recognition reflects the larger problem that the public health education community has all but ignored global non-communicable diseases. Without such a focus, the risks are unseen and the threats not perceived. This cautionary tale of the TPPA reflects the vulnerability of being ill informed of contemporary realities. © The Author 2014. Published by Oxford University Press on behalf of Faculty of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  5. Sustainable Mobility: Using a Global Energy Model to Inform Vehicle Technology Choices in a Decarbonized Economy

    Directory of Open Access Journals (Sweden)

    Timothy Wallington

    2013-04-01

    Full Text Available The reduction of CO2 emissions associated with vehicle use is an important element of a global transition to sustainable mobility and is a major long-term challenge for society. Vehicle and fuel technologies are part of a global energy system, and assessing the impact of the availability of clean energy technologies and advanced vehicle technologies on sustainable mobility is a complex task. The global energy transition (GET model accounts for interactions between the different energy sectors, and we illustrate its use to inform vehicle technology choices in a decarbonizing economy. The aim of this study is to assess how uncertainties in future vehicle technology cost, as well as how developments in other energy sectors, affect cost-effective fuel and vehicle technology choices. Given the uncertainties in future costs and efficiencies for light-duty vehicle and fuel technologies, there is no clear fuel/vehicle technology winner that can be discerned at the present time. We conclude that a portfolio approach with research and development of multiple fuel and vehicle technology pathways is the best way forward to achieve the desired result of affordable and sustainable personal mobility. The practical ramifications of this analysis are illustrated in the portfolio approach to providing sustainable mobility adopted by the Ford Motor Company.

  6. Integrating remote sensing, geographic information systems and global positioning system techniques with hydrological modeling

    Science.gov (United States)

    Thakur, Jay Krishna; Singh, Sudhir Kumar; Ekanthalu, Vicky Shettigondahalli

    2017-07-01

    Integration of remote sensing (RS), geographic information systems (GIS) and global positioning system (GPS) are emerging research areas in the field of groundwater hydrology, resource management, environmental monitoring and during emergency response. Recent advancements in the fields of RS, GIS, GPS and higher level of computation will help in providing and handling a range of data simultaneously in a time- and cost-efficient manner. This review paper deals with hydrological modeling, uses of remote sensing and GIS in hydrological modeling, models of integrations and their need and in last the conclusion. After dealing with these issues conceptually and technically, we can develop better methods and novel approaches to handle large data sets and in a better way to communicate information related with rapidly decreasing societal resources, i.e. groundwater.

  7. Evaluation of haplotype diversity of Achatina fulica (Lissachatina) [Bowdich] from Indian sub-continent by means of 16S rDNA sequence and its phylogenetic relationships with other global populations.

    Science.gov (United States)

    Ayyagari, Vijaya Sai; Sreerama, Krupanidhi

    2017-08-01

    Achatina fulica (Lissachatina fulica) is one of the most invasive species found across the globe causing a significant damage to crops, vegetables, and horticultural plants. This terrestrial snail is native to east Africa and spread to different parts of the world by introductions. India, a hot spot for biodiversity of several endemic gastropods, has witnessed an outburst of this snail population in several parts of the country posing a serious threat to crop loss and also to human health. With an objective to evaluate the genetic diversity of this snail, we have sampled this snail from different parts of India and analyzed its haplotype diversity by means of 16S rDNA sequence information. Apart from this, we have studied the phylogenetic relationships of the isolates sequenced in the present study in relation with other global populations by Bayesian and Maximum-likelihood approaches. Of the isolates sequenced, haplotype 'C' is the predominant one. A new haplotype 'S' from the state of Odisha was observed. The isolates sequenced in the present study clustered with its conspecifics from the Indian sub-continent. Haplotype network analyses were also carried out for studying the evolution of different haplotypes. It was observed that haplotype 'S' was associated with a Mauritius haplotype 'H', indicating the possibility of multiple introductions of A. fulica to India.

  8. HemeBIND: a novel method for heme binding residue prediction by combining structural and sequence information

    Directory of Open Access Journals (Sweden)

    Hu Jianjun

    2011-05-01

    Full Text Available Abstract Background Accurate prediction of binding residues involved in the interactions between proteins and small ligands is one of the major challenges in structural bioinformatics. Heme is an essential and commonly used ligand that plays critical roles in electron transfer, catalysis, signal transduction and gene expression. Although much effort has been devoted to the development of various generic algorithms for ligand binding site prediction over the last decade, no algorithm has been specifically designed to complement experimental techniques for identification of heme binding residues. Consequently, an urgent need is to develop a computational method for recognizing these important residues. Results Here we introduced an efficient algorithm HemeBIND for predicting heme binding residues by integrating structural and sequence information. We systematically investigated the characteristics of binding interfaces based on a non-redundant dataset of heme-protein complexes. It was found that several sequence and structural attributes such as evolutionary conservation, solvent accessibility, depth and protrusion clearly illustrate the differences between heme binding and non-binding residues. These features can then be separately used or combined to build the structure-based classifiers using support vector machine (SVM. The results showed that the information contained in these features is largely complementary and their combination achieved the best performance. To further improve the performance, an attempt has been made to develop a post-processing procedure to reduce the number of false positives. In addition, we built a sequence-based classifier based on SVM and sequence profile as an alternative when only sequence information can be used. Finally, we employed a voting method to combine the outputs of structure-based and sequence-based classifiers, which demonstrated remarkably better performance than the individual classifier alone

  9. Automatic Time Sequence Alignment in Contrast Enhanced MRI by Maximization of Mutual Information

    National Research Council Canada - National Science Library

    Positano, Vicenzo

    2001-01-01

    The use of contrast medium allows joining the high-resolution anatomical information provided by standard magnetic resonance with functional information obtained by means of the diffusion of contrast...

  10. [Sex differences in relationship between creativity and hemispheric information processing in global and local levels].

    Science.gov (United States)

    Razumnikova, O M; Vol'f, N V

    2012-01-01

    Sex differences in creativity related global-local hemispheric selective processing were examined by hierarchical letter presenting in conditions of their perception and comparison. Fifty-six right-handed males and 68 females (aged 17-22 years) participated in the experiments. Originality-imagery was assessed by a computer-based Torrance 'Incomplete Figures' test software. Verbal creativity was valued by original sentence using of three nouns from remote semantic categories. The results show that irrespectively of the sex factor and the type of creative thinking, its originality is provided by high speed of right-hemispheric processes of information selection on the global level and delay in the interhemispheric communication. Relationships between originality of ideas and hemispheric attentional characteristics are presented mostly in men while verbal creative problem solving, and in women while figurative original thinking. Originality of verbal activity in men is more associated with success of selective processes in the left hemisphere, but in women--with selective functions of both hemispheres. Figurative thinking in men is less related to hemispheric characteristics of attention compared with women. Increase of figurative originality in women is accompanied acceleration of processes of selection of the information in the right hemisphere, and also higher efficiency of local attention as well as speeds ofglobal processing in the left hemisphere.

  11. Climate Services Information System Activities in Support of The Global Framework for Climate Services Implementation

    Science.gov (United States)

    Timofeyeva-Livezey, M. M.; Horsfall, F. M. C.; Pulwarty, R. S.; Klein-Tank, A.; Kolli, R. K.; Hechler, P.; Dilley, M.; Ceron, J. P.; Goodess, C.

    2017-12-01

    The WMO Commission on Climatology (CCl) supports the implementation of the Global Framework for Climate Services (GFCS) with a particular focus on the Climate Services Information System (CSIS), which is the core operational component of GFCS at the global, regional, and national level. CSIS is designed for producing, packaging and operationally delivering authoritative climate information data and products through appropriate operational systems, practices, data exchange, technical standards, authentication, communication, and product delivery. Its functions include climate analysis and monitoring, assessment and attribution, prediction (monthly, seasonal, decadal), and projection (centennial scale) as well as tailoring the associated products tUEAo suit user requirements. A central, enabling piece of implementation of CSIS is a Climate Services Toolkit (CST). In its development phase, CST exists as a prototype (www.wmo.int/cst) as a compilation of tools for generating tailored data and products for decision-making, with a special focus on national requirements in developing countries. WMO provides a server to house the CST prototype as well as support operations and maintenance. WMO members provide technical expertise and other in-kind support, including leadership of the CSIS development team. Several recent WMO events have helped with the deployment of CST within the eight countries that have been recognized by GFCS as illustrative for developing their climate services at national levels. Currently these countries are developing climate services projects focusing service development and delivery for selected economic sectors, such as for health, agriculture, energy, water resources, and hydrometeorological disaster risk reduction. These countries are working together with their respective WMO Regional Climate Centers (RCCs), which provide technical assistance with implementation of climate services projects at the country level and facilitate development of

  12. Timing and sequencing of events marking the transition to adulthood in two informal settlements in Nairobi, Kenya.

    Science.gov (United States)

    Beguy, Donatien; Kabiru, Caroline W; Zulu, Eliya M; Ezeh, Alex C

    2011-06-01

    Young people living in poor urban informal settlements face unique challenges as they transition to adulthood. This exploratory paper uses retrospective information from the baseline survey of a 3-year prospective study to examine the timing and sequencing of four key markers (first sex, marriage, birth, and independent housing) of the transition to adulthood among 3,944 adolescents in two informal settlements in Nairobi city, Kenya. Event history analysis techniques are employed to examine the timing of the events. Results indicate that there is no significant gender difference with regard to first sexual debut among adolescents. For many boys and girls, the first sexual experience occurs outside of marriage or other union. For males, the sequencing of entry begins with entry into first sex, followed by independent housing. Conversely, for females, the sequencing begins with first sex and then parenthood. Apart from sexual debut, the patterns of entry into union and parenthood do not differ much from what was observed for Nairobi as a whole. The space constraints that typify the two slums may have influenced the pattern of leaving home observed. We discuss these and other findings in light of their implications for young people's health and well-being in resource-poor settings in urban areas.

  13. Ion torrent personal genome machine sequencing for genomic typing of Neisseria meningitidis for rapid determination of multiple layers of typing information.

    Science.gov (United States)

    Vogel, Ulrich; Szczepanowski, Rafael; Claus, Heike; Jünemann, Sebastian; Prior, Karola; Harmsen, Dag

    2012-06-01

    Neisseria meningitidis causes invasive meningococcal disease in infants, toddlers, and adolescents worldwide. DNA sequence-based typing, including multilocus sequence typing, analysis of genetic determinants of antibiotic resistance, and sequence typing of vaccine antigens, has become the standard for molecular epidemiology of the organism. However, PCR of multiple targets and consecutive Sanger sequencing provide logistic constraints to reference laboratories. Taking advantage of the recent development of benchtop next-generation sequencers (NGSs) and of BIGSdb, a database accommodating and analyzing genome sequence data, we therefore explored the feasibility and accuracy of Ion Torrent Personal Genome Machine (PGM) sequencing for genomic typing of meningococci. Three strains from a previous meningococcus serogroup B community outbreak were selected to compare conventional typing results with data generated by semiconductor chip-based sequencing. In addition, sequencing of the meningococcal type strain MC58 provided information about the general performance of the technology. The PGM technology generated sequence information for all target genes addressed. The results were 100% concordant with conventional typing results, with no further editing being necessary. In addition, the amount of typing information, i.e., nucleotides and target genes analyzed, could be substantially increased by the combined use of genome sequencing and BIGSdb compared to conventional methods. In the near future, affordable and fast benchtop NGS machines like the PGM might enable reference laboratories to switch to genomic typing on a routine basis. This will reduce workloads and rapidly provide information for laboratory surveillance, outbreak investigation, assessment of vaccine preventability, and antibiotic resistance gene monitoring.

  14. An Observational Study of Children's Involvement in Informed Consent for Exome Sequencing Research.

    Science.gov (United States)

    Miller, Victoria A; Werner-Lin, Allison; Walser, Sarah A; Biswas, Sawona; Bernhardt, Barbara A

    2017-02-01

    The goal of this study was to examine children's involvement in consent sessions for exome sequencing research and associations of involvement with provider and parent communication. Participants included 44 children (8-17 years) from five cohorts who were offered participation in an exome sequencing study. The consent sessions were audiotaped, transcribed, and coded. Providers attempted to facilitate the child's involvement in the majority (73%) of sessions, and most (75%) children also verbally participated. Provider facilitation was strongly associated with likelihood of child participation. These findings underscore that strategies such as asking for children's opinions and soliciting their questions show respect for children and may increase the likelihood that they are engaged and involved in decisions about research participation.

  15. Combining information from linkage and association mapping for next-generation sequencing longitudinal family data.

    Science.gov (United States)

    Balliu, Brunilda; Uh, Hae-Won; Tsonaka, Roula; Boehringer, Stefan; Helmer, Quinta; Houwing-Duistermaat, Jeanine J

    2014-01-01

    In this analysis, we investigate the contributions that linkage-based methods, such as identical-by-descent mapping, can make to association mapping to identify rare variants in next-generation sequencing data. First, we identify regions in which cases share more segments identical-by-descent around a putative causal variant than do controls. Second, we use a two-stage mixed-effect model approach to summarize the single-nucleotide polymorphism data within each region and include them as covariates in the model for the phenotype. We assess the impact of linkage disequilibrium in determining identical-by-descent states between individuals by using markers with and without linkage disequilibrium for the first part and the impact of imputation in testing for association by using imputed genome-wide association studies or raw sequence markers for the second part. We apply the method to next-generation sequencing longitudinal family data from Genetic Association Workshop 18 and identify a significant region at chromosome 3: 40249244-41025167 (p-value = 2.3 × 10(-3)).

  16. Ultra-deep sequencing reveals high prevalence and broad structural diversity of hepatitis B surface antigen mutations in a global population.

    Science.gov (United States)

    Gencay, Mikael; Hübner, Kirsten; Gohl, Peter; Seffner, Anja; Weizenegger, Michael; Neofytos, Dionysios; Batrla, Richard; Woeste, Andreas; Kim, Hyon-Suk; Westergaard, Gaston; Reinsch, Christine; Brill, Eva; Thu Thuy, Pham Thi; Hoang, Bui Huu; Sonderup, Mark; Spearman, C Wendy; Pabinger, Stephan; Gautier, Jérémie; Brancaccio, Giuseppina; Fasano, Massimo; Santantonio, Teresa; Gaeta, Giovanni B; Nauck, Markus; Kaminski, Wolfgang E

    2017-01-01

    The diversity of the hepatitis B surface antigen (HBsAg) has a significant impact on the performance of diagnostic screening tests and the clinical outcome of hepatitis B infection. Neutralizing or diagnostic antibodies against the HBsAg are directed towards its highly conserved major hydrophilic region (MHR), in particular towards its "a" determinant subdomain. Here, we explored, on a global scale, the genetic diversity of the HBsAg MHR in a large, multi-ethnic cohort of randomly selected subjects with HBV infection from four continents. A total of 1553 HBsAg positive blood samples of subjects originating from 20 different countries across Africa, America, Asia and central Europe were characterized for amino acid variation in the MHR. Using highly sensitive ultra-deep sequencing, we found 72.8% of the successfully sequenced subjects (n = 1391) demonstrated amino acid sequence variation in the HBsAg MHR. This indicates that the global variation frequency in the HBsAg MHR is threefold higher than previously reported. The majority of the amino acid mutations were found in the HBV genotypes B (28.9%) and C (25.4%). Collectively, we identified 345 distinct amino acid mutations in the MHR. Among these, we report 62 previously unknown mutations, which extends the worldwide pool of currently known HBsAg MHR mutations by 22%. Importantly, topological analysis identified the "a" determinant upstream flanking region as the structurally most diverse subdomain of the HBsAg MHR. The highest prevalence of "a" determinant region mutations was observed in subjects from Asia, followed by the African, American and European cohorts, respectively. Finally, we found that more than half (59.3%) of all HBV subjects investigated carried multiple MHR mutations. Together, this worldwide ultra-deep sequencing based genotyping study reveals that the global prevalence and structural complexity of variation in the hepatitis B surface antigen have, to date, been significantly underappreciated.

  17. ThinkHazard!: an open-source, global tool for understanding hazard information

    Science.gov (United States)

    Fraser, Stuart; Jongman, Brenden; Simpson, Alanna; Nunez, Ariel; Deparday, Vivien; Saito, Keiko; Murnane, Richard; Balog, Simone

    2016-04-01

    Rapid and simple access to added-value natural hazard and disaster risk information is a key issue for various stakeholders of the development and disaster risk management (DRM) domains. Accessing available data often requires specialist knowledge of heterogeneous data, which are often highly technical and can be difficult for non-specialists in DRM to find and exploit. Thus, availability, accessibility and processing of these information sources are crucial issues, and an important reason why many development projects suffer significant impacts from natural hazards. The World Bank's Global Facility for Disaster Reduction and Recovery (GFDRR) is currently developing a new open-source tool to address this knowledge gap: ThinkHazard! The main aim of the ThinkHazard! project is to develop an analytical tool dedicated to facilitating improvements in knowledge and understanding of natural hazards among non-specialists in DRM. It also aims at providing users with relevant guidance and information on handling the threats posed by the natural hazards present in a chosen location. Furthermore, all aspects of this tool will be open and transparent, in order to give users enough information to understand its operational principles. In this presentation, we will explain the technical approach behind the tool, which translates state-of-the-art probabilistic natural hazard data into understandable hazard classifications and practical recommendations. We will also demonstrate the functionality of the tool, and discuss limitations from a scientific as well as an operational perspective.

  18. Drug pricing and reimbursement information management: processes and decision making in the global economy.

    Science.gov (United States)

    Tsourougiannis, Dimitrios

    2017-01-01

    Background : Cost-containment initiatives are re-shaping the pharmaceutical business environment and affecting market access as well as pricing and reimbursement decisions. Effective price management procedures are too complex to accomplish manually. Prior to February 2013, price management within Astellas Pharma Europe Ltd was done manually using an Excel database. The system was labour intensive, slow to update, and prone to error. An innovative web-based pricing information management system was developed to address the shortcomings of the previous system. Development : A secure web-based system for submitting, reviewing and approving pricing requests was designed to: track all pricing applications and approval status; update approved pricing information automatically; provide fixed and customizable reports of pricing information; collect pricing and reimbursement rules from each country; validate pricing and reimbursement rules monthly. Several sequential phases of development emphasized planning, time schedules, target dates, budgets and implementation of the entire system. A test system was used to pilot the electronic (e)-pricing system with three affiliates (four users) in February 2013. Outcomes : The web-based system was introduced in March 2013, currently has about 227 active users globally and comprises more than 1000 presentations of 150 products. The overall benefits of switching from a manual to an e-pricing system were immediate and highly visible in terms of efficiency, transparency, reliability and compliance. Conclusions : The e-pricing system has improved the efficiency, reliability, compliance, transparency and ease of access to multinational drug pricing and approval information.

  19. Application of the accident management information needs methodology to a severe accident sequence

    International Nuclear Information System (INIS)

    Ward, L.W.; Hanson, D.J.; Nelson, W.R.; Solberg, D.E.

    1989-01-01

    The U.S. Nuclear Regulatory Commission is conducting an accident management research program that emphasizes the use of severe accident research to enhance the ability of plant operating personnel to effectively manage severe accidents. Hence, it is necessary to ensure that the plant instrumentation and information systems adequately provide this information to the operating staff during accident conditions. A methodology to identify and assess the information needs of the operating staff of a nuclear power plant during a severe accident has been developed. The methodology identifies (a) the information needs of the plant personnel during a wide range of accident conditions, (b) the existing plant measurements capable of supplying these information needs and minor additions to instrument and display systems that would enhance management capabilities, (c) measurement capabilities and limitations during severe accident conditions, and (d) areas in which the information systems could mislead plant personnel

  20. Application of the accident management information needs methodology to a severe accident sequence

    Energy Technology Data Exchange (ETDEWEB)

    Ward, L.W.; Hanson, D.J.; Nelson, W.R. (Idaho National Engineering Laboratory, Idaho Falls (USA)); Solberg, D.E. (Nuclear Regulatory Commission, Washington, DC (USA))

    1989-11-01

    The U.S. Nuclear Regulatory Commission is conducting an accident management research program that emphasizes the use of severe accident research to enhance the ability of plant operating personnel to effectively manage severe accidents. Hence, it is necessary to ensure that the plant instrumentation and information systems adequately provide this information to the operating staff during accident conditions. A methodology to identify and assess the information needs of the operating staff of a nuclear power plant during a severe accident has been developed. The methodology identifies (a) the information needs of the plant personnel during a wide range of accident conditions, (b) the existing plant measurements capable of supplying these information needs and minor additions to instrument and display systems that would enhance management capabilities, (c) measurement capabilities and limitations during severe accident conditions, and (d) areas in which the information systems could mislead plant personnel.

  1. 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.

  2. Socio-Economic Correlates of Information Security Threats and Controls in Global Financial Services Industry: An Analysis

    OpenAIRE

    Princely Ifinedo

    2015-01-01

    Threats to data and information assets of Global Financial Services Industry (GFSI) are ever-present; such problems, if not well understood, could lead to huge negative impact. To some extent, the environment where a business operates does matter for its success. This study presents information about the relationships between selected socio-economic factors and information security threats and controls in the financial services industry. Essentially, it seeks to enrich the information provide...

  3. El desarrollo en la agenda global. Análisis del informe del PNUD de 2005

    Directory of Open Access Journals (Sweden)

    Mercedes Alcaniz

    2012-03-01

    Full Text Available El artículo presenta  en primer lugar un breve recorrido histórico sobre la dinámica de las teorías del desarrollo y sus más recientes aportaciones, señalando que el concepto de desarrollo es heredero de la idea ilustrada europea de progreso y que esta  idea se ha expandido a lo largo del planeta. En segundo lugar, se hace referencia a la inclusión de la idea de desarrollo en la agenda global; las Naciones Unidas asume que es una responsabilidad de la comunidad internacional y crea para ello organismos especializados para su implementación. Finalmente, se exponen los resultados del último informe del PNUD, Programa de las Naciones Unidas para el Desarrollo, sobre la situación de los diversos Estados con respecto al desarrollo humano mostrando las desigualdades y brechas entre unos países y otros. The development of  the global agenda. An analysis of the 2005 UNDP report. Firstly, the article briefly traces the history of the dynamics of development theories and their most recent contributions, indicating that the concept of development is heir to the European enlightenment idea of "progress" and that this idea has spread all over the planet. Secondly, the inclusion of the idea of development on the global agenda is also mentioned, with the United Nations assuming that this is a responsibility of the international community and thus creating specialised organisations to implement it. Finally, we explain the results of the latest United Nations Development Programme (UNPD Report on the human development situation in several countries, showing inequalities and gaps between States.

  4. Transcranial magnetic stimulation-induced global propagation of transient phase resetting associated with directional information flow

    Directory of Open Access Journals (Sweden)

    Masahiro eKawasaki

    2014-03-01

    Full Text Available Electroencephalogram (EEG phase synchronization analyses can reveal large-scale communication between distant brain areas. However, it is not possible to identify the directional information flow between distant areas using conventional phase synchronization analyses. In the present study, we applied transcranial magnetic stimulation (TMS to the occipital area in subjects who were resting with their eyes closed, and analyzed the spatial propagation of transient TMS-induced phase resetting by using the transfer entropy (TE, to quantify the causal and directional flow of information. The time-frequency EEG analysis indicated that the theta (5 Hz phase locking factor (PLF reached its highest value at the distant area (the motor area in this study, with a time lag that followed the peak of the transient PLF enhancements of the TMS-targeted area at the TMS onset. PPI (phase-preservation index analyses demonstrated significant phase resetting at the TMS-targeted area and distant area. Moreover, the TE from the TMS-targeted area to the distant area increased clearly during the delay that followed TMS onset. Interestingly, the time lags were almost coincident between the PLF and TE results (152 vs. 165 ms, which provides strong evidence that the emergence of the delayed PLF reflects the causal information flow. Such tendencies were observed only in the higher-intensity TMS condition, and not in the lower-intensity or sham TMS conditions. Thus, TMS may manipulate large-scale causal relationships between brain areas in an intensity-dependent manner. We demonstrated that single-pulse TMS modulated global phase dynamics and directional information flow among synchronized brain networks. Therefore, our results suggest that single-pulse TMS can manipulate both incoming and outgoing information in the TMS-targeted area associated with functional changes.

  5. FCJ-198 New International Information Order (NIIO Revisited: Global Algorithmic Governance and Neocolonialism

    Directory of Open Access Journals (Sweden)

    Danny Butt

    2016-03-01

    Full Text Available The field of Internet governance has been dominated by Euro-American actors and has largely resisted consideration of a holistic and integrative rights-based agenda, confining itself to narrow discussions on the technical stability of Internet Protocol resources and debates about nation-state involvement in multistakeholder governance of those resources. In light of the work of Edward Snowden documenting the close relationship between government security agencies and dominant social media platforms, this paper revisits the relevance of the New International Information Order (NIIO, a conceptualisation of the global politics of information described at the 1973 Fourth Summit Conference of the Non-Aligned Movement of nations in Algiers. This paper argues that critical analysis of the oligopolistic structure of “platforms” and their algorithmic forms of governance can build a more inclusive movement toward social justice by extending the NIIO framework’s emphasis on decolonisation, collective ownership of strategic information resources, and documentation of powerful transnational entities.

  6. Lessons learned in building a global information network on chemicals (GINC)

    International Nuclear Information System (INIS)

    Kaminuma, Tsuguchika

    2005-01-01

    The Global Information Network on Chemicals (GINC) was a project to construct a worldwide information network linking international, national, and other organizations working for the safe management of chemicals. Proposed in 1993, the project started the next year and lasted almost 10 years. It was begun as a joint project of World Health Organization (WHO), International Labor Organization (ILO), and United Nations Environment Program (UNEP), and later endorsed by the Intergovernmental Forum on Chemical Safety (IFCS). Asia, particularly East Asia and the Pacific islands, was chosen as the feasibility study region. The author's group then at the National Institute of Health Sciences (NIHS) of Japan led this initiative and hosted numerous meetings. At these meetings, tutorial sessions for communicating chemical safety expertise and emerging new information technologies relevant to the safe management of chemicals were offered. Our experience with this project, particularly the Web-based system and the tutorial sessions, may be of use to others involved with Web-based instruction and the training of chemical safety specialists from both developed and developing countries

  7. A Proteomic Workflow Using High-Throughput De Novo Sequencing Towards Complementation of Genome Information for Improved Comparative Crop Science.

    Science.gov (United States)

    Turetschek, Reinhard; Lyon, David; Desalegn, Getinet; Kaul, Hans-Peter; Wienkoop, Stefanie

    2016-01-01

    The proteomic study of non-model organisms, such as many crop plants, is challenging due to the lack of comprehensive genome information. Changing environmental conditions require the study and selection of adapted cultivars. Mutations, inherent to cultivars, hamper protein identification and thus considerably complicate the qualitative and quantitative comparison in large-scale systems biology approaches. With this workflow, cultivar-specific mutations are detected from high-throughput comparative MS analyses, by extracting sequence polymorphisms with de novo sequencing. Stringent criteria are suggested to filter for confidential mutations. Subsequently, these polymorphisms complement the initially used database, which is ready to use with any preferred database search algorithm. In our example, we thereby identified 26 specific mutations in two cultivars of Pisum sativum and achieved an increased number (17 %) of peptide spectrum matches.

  8. Measuring global oil trade dependencies: An application of the point-wise mutual information method

    International Nuclear Information System (INIS)

    Kharrazi, Ali; Fath, Brian D.

    2016-01-01

    Oil trade is one of the most vital networks in the global economy. In this paper, we analyze the 1998–2012 oil trade networks using the point-wise mutual information (PMI) method and determine the pairwise trade preferences and dependencies. Using examples of the USA's trade partners, this research demonstrates the usefulness of the PMI method as an additional methodological tool to evaluate the outcomes from countries' decisions to engage in preferred trading partners. A positive PMI value indicates trade preference where trade is larger than would be expected. For example, in 2012 the USA imported 2,548.7 kbpd despite an expected 358.5 kbpd of oil from Canada. Conversely, a negative PMI value indicates trade dis-preference where the amount of trade is smaller than what would be expected. For example, the 15-year average of annual PMI between Saudi Arabia and the U.S.A. is −0.130 and between Russia and the USA −1.596. We reflect the three primary reasons of discrepancies between actual and neutral model trade can be related to position, price, and politics. The PMI can quantify the political success or failure of trade preferences and can more accurately account temporal variation of interdependencies. - Highlights: • We analyzed global oil trade networks using the point-wise mutual information method. • We identified position, price, & politics as drivers of oil trade preference. • The PMI method is useful in research on complex trade networks and dependency theory. • A time-series analysis of PMI can track dependencies & evaluate policy decisions.

  9. iDNA at Sea: Recovery of Whale Shark (Rhincodon typus Mitochondrial DNA Sequences from the Whale Shark Copepod (Pandarus rhincodonicus Confirms Global Population Structure

    Directory of Open Access Journals (Sweden)

    Mark Meekan

    2017-12-01

    Full Text Available The whale shark (Rhincodon typus is an iconic and endangered species with a broad distribution spanning warm-temperate and tropical oceans. Effective conservation management of the species requires an understanding of the degree of genetic connectivity among populations, which is hampered by the need for sampling that involves invasive techniques. Here, the feasibility of minimally-invasive sampling was explored by isolating and sequencing whale shark DNA from a commensal or possibly parasitic copepod, Pandarus rhincodonicus that occurs on the skin of the host. We successfully recovered mitochondrial control region DNA sequences (~1,000 bp of the host via DNA extraction and polymerase chain reaction from whole copepod specimens. DNA sequences obtained from multiple copepods collected from the same shark exhibited 100% sequence similarity, suggesting a persistent association of copepods with individual hosts. Newly-generated mitochondrial haplotypes of whale shark hosts derived from the copepods were included in an analysis of the genetic structure of the global population of whale sharks (644 sequences; 136 haplotypes. Our results supported those of previous studies and suggested limited genetic structuring across most of the species range, but the presence of a genetically unique and potentially isolated population in the Atlantic Ocean. Furthermore, we recovered the mitogenome and nuclear ribosomal genes of a whale shark using a shotgun sequencing approach on copepod tissue. The recovered mitogenome is the third mitogenome reported for the species and the first from the Mozambique population. Our invertebrate DNA (iDNA approach could be used to better understand the population structure of whale sharks, particularly in the Atlantic Ocean, and also for genetic analyses of other elasmobranchs parasitized by pandarid copepods.

  10. Controlling the structure of sequence-defined poly(phosphodiester)s for optimal MS/MS reading of digital information.

    Science.gov (United States)

    Amalian, J-A; Al Ouahabi, A; Cavallo, G; König, N F; Poyer, S; Lutz, J-F; Charles, L

    2017-11-01

    Digital polymers are monodisperse chains with a controlled sequence of co-monomers, defined as letters of an alphabet, and are used to store information at the molecular level. Reading such messages is hence a sequencing task that can be efficiently achieved by tandem mass spectrometry. To improve their readability, structure of sequence-controlled synthetic polymers can be optimized, based on considerations regarding their fragmentation behavior. This strategy is described here for poly(phosphodiester)s, which were synthesized as monodisperse chains with more than 100 units but exhibited extremely complex dissociation spectra. In these polymers, two repeating units that differ by a simple H/CH 3 variation were defined as the 0 and 1 bit of the ASCII code and spaced by a phosphate moiety. They were readily ionized in negative ion mode electrospray but dissociated via cleavage at all phosphate bonds upon collisional activation. Although allowing a complete sequence coverage of digital poly(phosphodiester)s, this fragmentation behavior was not efficient for macromolecules with more than 50 co-monomers, and data interpretation was very tedious. The structure of these polymers was then modified by introducing alkoxyamine linkages at appropriate location throughout the chain. A first design consisted of placing these low dissociation energy bonds between each monomeric bit: while cleavage of this sole bond greatly simplified MS/MS spectra, efficient sequencing was limited to chains with up to about 50 units. In contrast, introduction of alkoxyamine bonds between each byte (i.e. a set of eight co-monomers) was a more successful strategy. Long messages (so far, up to 8 bytes) could be read in MS 3 experiments, where single-byte containing fragments released during the first activation stage were further dissociated for sequencing. The whole sequence of such byte-truncated poly(phosphodiester)s could be easily re-constructed based on a mass tagging system which permits

  11. Amino acid and nucleotide recurrence in aligned sequences: synonymous substitution patterns in association with global and local base compositions.

    Science.gov (United States)

    Nishizawa, M; Nishizawa, K

    2000-10-01

    The tendency for repetitiveness of nucleotides in DNA sequences has been reported for a variety of organisms. We show that the tendency for repetitive use of amino acids is widespread and is observed even for segments conserved between human and Drosophila melanogaster at the level of >50% amino acid identity. This indicates that repetitiveness influences not only the weakly constrained segments but also those sequence segments conserved among phyla. Not only glutamine (Q) but also many of the 20 amino acids show a comparable level of repetitiveness. Repetitiveness in bases at codon position 3 is stronger for human than for D.melanogaster, whereas local repetitiveness in intron sequences is similar between the two organisms. While genes for immune system-specific proteins, but not ancient human genes (i.e. human homologs of Escherichia coli genes), have repetitiveness at codon bases 1 and 2, repetitiveness at codon base 3 for these groups is similar, suggesting that the human genome has at least two mechanisms generating local repetitiveness. Neither amino acid nor nucleotide repetitiveness is observed beyond the exon boundary, denying the possibility that such repetitiveness could mainly stem from natural selection on mRNA or protein sequences. Analyses of mammalian sequence alignments show that while the 'between gene' GC content heterogeneity, which is linked to 'isochores', is a principal factor associated with the bias in substitution patterns in human, 'within gene' heterogeneity in nucleotide composition is also associated with such bias on a more local scale. The relationship amongst the various types of repetitiveness is discussed.

  12. Medical Information Exchange: Pattern of Global Mobile Messenger Usage among Otolaryngologists.

    Science.gov (United States)

    Siegal, Gil; Dagan, Elad; Wolf, Michael; Duvdevani, Shay; Alon, Eran E

    2016-11-01

    Information technology has revolutionized health care. However, the development of dedicated mobile health software has been lagging, leading to the use of general mobile applications to fill in the void. The use of such applications has several legal, ethical, and regulatory implications. We examined the experience and practices governing the usage of a global mobile messenger application (WhatsApp) for mobile health purposes in a national cohort of practicing otolaryngologists in Israel, a known early adaptor information technology society. Cross-sectional data were collected from practicing otolaryngologists and otolaryngology residents via self-administered questionnaire. The questionnaire was composed of a demographic section, a section surveying the practices of mobile application use, mobile health application use, and knowledge regarding institutional policies governing the transmission of medical data. The sample included 22 otolaryngology residents and 47 practicing otolaryngologists. Of the physicians, 83% worked in academic centers, and 88% and 40% of the physicians who worked in a hospital setting or a community clinic used WhatsApp for medical use, respectively. Working with residents increased the medical usage of WhatsApp from 50% to 91% (P = .006). Finally, 72% were unfamiliar with any institutional policy regarding the transfer of medical information by personal smartphones. Mobile health is becoming an integral part of modern medical systems, improving accessibility, efficiency, and possibly quality of medical care. The need to incorporate personal mobile devices in the overall information technology standards, guidelines, and regulation is becoming more acute. Nonetheless, practices must be properly instituted to prevent unwanted consequences. © American Academy of Otolaryngology—Head and Neck Surgery Foundation 2016.

  13. Personal efficacy, the information environment, and attitudes toward global warming and climate change in the United States.

    Science.gov (United States)

    Kellstedt, Paul M; Zahran, Sammy; Vedlitz, Arnold

    2008-02-01

    Despite the growing scientific consensus about the risks of global warming and climate change, the mass media frequently portray the subject as one of great scientific controversy and debate. And yet previous studies of the mass public's subjective assessments of the risks of global warming and climate change have not sufficiently examined public informedness, public confidence in climate scientists, and the role of personal efficacy in affecting global warming outcomes. By examining the results of a survey on an original and representative sample of Americans, we find that these three forces-informedness, confidence in scientists, and personal efficacy-are related in interesting and unexpected ways, and exert significant influence on risk assessments of global warming and climate change. In particular, more informed respondents both feel less personally responsible for global warming, and also show less concern for global warming. We also find that confidence in scientists has unexpected effects: respondents with high confidence in scientists feel less responsible for global warming, and also show less concern for global warming. These results have substantial implications for the interaction between scientists and the public in general, and for the public discussion of global warming and climate change in particular.

  14. PulseNet International: Vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance.

    NARCIS (Netherlands)

    Nadon, Celine; Van Walle, Ivo; Gerner-Smidt, Peter; Campos, Josefina; Chinen, Isabel; Concepcion-Acevedo, Jeniffer; Gilpin, Brent; Smith, Anthony M; Man Kam, Kai; Perez, Enrique; Trees, Eija; Kubota, Kristy; Takkinen, Johanna; Nielsen, Eva Møller; Carleton, Heather

    2017-01-01

    PulseNet International is a global network dedicated to laboratory-based surveillance for food-borne diseases. The network comprises the national and regional laboratory networks of Africa, Asia Pacific, Canada, Europe, Latin America and the Caribbean, the Middle East, and the United States. The

  15. Diversity and Genome Analysis of Australian and Global Oilseed Brassica napus L. Germplasm Using Transcriptomics and Whole Genome Re-sequencing

    Directory of Open Access Journals (Sweden)

    M. Michelle Malmberg

    2018-04-01

    Full Text Available Intensive breeding of Brassica napus has resulted in relatively low diversity, such that B. napus would benefit from germplasm improvement schemes that sustain diversity. As such, samples representative of global germplasm pools need to be assessed for existing population structure, diversity and linkage disequilibrium (LD. Complexity reduction genotyping-by-sequencing (GBS methods, including GBS-transcriptomics (GBS-t, enable cost-effective screening of a large number of samples, while whole genome re-sequencing (WGR delivers the ability to generate large numbers of unbiased genomic single nucleotide polymorphisms (SNPs, and identify structural variants (SVs. Furthermore, the development of genomic tools based on whole genomes representative of global oilseed diversity and orientated by the reference genome has substantial industry relevance and will be highly beneficial for canola breeding. As recent studies have focused on European and Chinese varieties, a global diversity panel as well as a substantial number of Australian spring types were included in this study. Focusing on industry relevance, 633 varieties were initially genotyped using GBS-t to examine population structure using 61,037 SNPs. Subsequently, 149 samples representative of global diversity were selected for WGR and both data sets used for a side-by-side evaluation of diversity and LD. The WGR data was further used to develop genomic resources consisting of a list of 4,029,750 high-confidence SNPs annotated using SnpEff, and SVs in the form of 10,976 deletions and 2,556 insertions. These resources form the basis of a reliable and repeatable system allowing greater integration between canola genomics studies, with a strong focus on breeding germplasm and industry applicability.

  16. Successfully Changing the Landscape of Information Distribution: Extension Food Website Reaches People Locally and Globally

    Directory of Open Access Journals (Sweden)

    Alice Henneman

    2016-02-01

    Full Text Available The goal of the Food website was to develop Internet-based content that was relevant and reached the general public and multiplier groups, such as educators, health professionals, and media outlets. The purpose of this paper was to examine whether a multi-modal approach to information delivery through increases in and changes to content, electronic mailing list creation, and social media posting impacted user access, traffic channels, and referrals from 2010 to 2014. When comparing 2010-2011 versus 2013-2014, there was a 150% increase in total pageviews, 197% increase in unique pageviews, and a 39% increase in average time spent on a page. Since 2010, the website had over 5.2 million total pageviews, 3.1 million sessions, and 2.6 million users. In 2014, top social media referrals included Pinterest, Facebook, LinkedIn, and Twitter. Age of visitors ranged from 18 to 65+, with 45% being 18-34 years old. Approximately 70% were female. Visitors came from 229 countries/territories and 18,237 different cities. The website connects Nebraska and the world to the exciting food research and information generated at the University of Nebraska-Lincoln and is playing an increasingly important role in shaping the future of food in the local and global community.

  17. Neisseria gonorrhoeae Sequence Typing for Antimicrobial Resistance, a Novel Antimicrobial Resistance Multilocus Typing Scheme for Tracking Global Dissemination of N. gonorrhoeae Strains.

    Science.gov (United States)

    Demczuk, W; Sidhu, S; Unemo, M; Whiley, D M; Allen, V G; Dillon, J R; Cole, M; Seah, C; Trembizki, E; Trees, D L; Kersh, E N; Abrams, A J; de Vries, H J C; van Dam, A P; Medina, I; Bharat, A; Mulvey, M R; Van Domselaar, G; Martin, I

    2017-05-01

    A curated Web-based user-friendly sequence typing tool based on antimicrobial resistance determinants in Neisseria gonorrhoeae was developed and is publicly accessible (https://ngstar.canada.ca). The N. gonorrhoeae Sequence Typing for Antimicrobial Resistance (NG-STAR) molecular typing scheme uses the DNA sequences of 7 genes ( penA , mtrR , porB , ponA , gyrA , parC , and 23S rRNA) associated with resistance to β-lactam antimicrobials, macrolides, or fluoroquinolones. NG-STAR uses the entire penA sequence, combining the historical nomenclature for penA types I to XXXVIII with novel nucleotide sequence designations; the full mtrR sequence and a portion of its promoter region; portions of ponA , porB , gyrA , and parC ; and 23S rRNA sequences. NG-STAR grouped 768 isolates into 139 sequence types (STs) ( n = 660) consisting of 29 clonal complexes (CCs) having a maximum of a single-locus variation, and 76 NG-STAR STs ( n = 109) were identified as unrelated singletons. NG-STAR had a high Simpson's diversity index value of 96.5% (95% confidence interval [CI] = 0.959 to 0.969). The most common STs were NG-STAR ST-90 ( n = 100; 13.0%), ST-42 and ST-91 ( n = 45; 5.9%), ST-64 ( n = 44; 5.72%), and ST-139 ( n = 42; 5.5%). Decreased susceptibility to azithromycin was associated with NG-STAR ST-58, ST-61, ST-64, ST-79, ST-91, and ST-139 ( n = 156; 92.3%); decreased susceptibility to cephalosporins was associated with NG-STAR ST-90, ST-91, and ST-97 ( n = 162; 94.2%); and ciprofloxacin resistance was associated with NG-STAR ST-26, ST-90, ST-91, ST-97, ST-150, and ST-158 ( n = 196; 98.0%). All isolates of NG-STAR ST-42, ST-43, ST-63, ST-81, and ST-160 ( n = 106) were susceptible to all four antimicrobials. The standardization of nomenclature associated with antimicrobial resistance determinants through an internationally available database will facilitate the monitoring of the global dissemination of antimicrobial-resistant N. gonorrhoeae strains. © Crown copyright 2017.

  18. Phylogenetic assessment of global Suillus ITS sequences supports morphologically defined species and reveals synonymous and undescribed taxa.

    Science.gov (United States)

    Nguyen, Nhu H; Vellinga, Else C; Bruns, Thomas D; Kennedy, Peter G

    The genus Suillus represents one of the most recognizable groups of mushrooms in conifer forests throughout the Northern Hemisphere. Although for decades the genus has been relatively well defined morphologically, previous molecular phylogenetic assessments have provided important yet preliminary insights into its evolutionary history. We present the first large-scale phylogenetic study of the boundaries of each species in the genus Suillus based on the most current internal transcribed spacer (ITS) barcode sequences available inPUBLIC databases, as well as sequencing of 224 vouchered specimens and cultures, 15 of which were type specimens from North America. We found that species boundaries delimited by morphological data are broadly congruent with those based on ITS sequences. However, some species appear to have been described several times under different names, several species groups cannot be resolved by ITS sequences alone, and undescribed taxa are apparent, especially in Asia. Therefore, we elevated S. tomentosus var. discolor to S. discolor; proposed synonymies of S. neoalbidipes with S. glandulosipes, S. borealis with S. brunnescens, Boletus serotinus and B. solidipes with Suillus elbensis, S. lactifluus with S. granulatus, S. himalayensis with S. americanus; and proposed usage of the names S. clintonianus in the place of the North American S. grevillei, S. weaverae for North American S. granulatus, S. ampliporus in the place of the North American S. cavipes, and S. elbensis in place of the North American S. viscidus. We showed that the majority of Suillus species have strong affinities for particular host genera. Although deep node support was low, geographic differentiation was apparent, with species from North America, Eurasia, and Asia often forming their own clades. Collectively, this comprehensive genus-level phylogenetic integration of currently available Suillus ITS molecular data and metadata will aid future taxonomic and ecological work on an

  19. 1H NMR studies of plastocyanin from Scenedesmus obliquus: Complete sequence-specific assignment, secondary structure analysis, and global fold

    International Nuclear Information System (INIS)

    Moore, J.M.; Chazin, W.J.; Wright, P.E.; Powls, R.

    1988-01-01

    Two-dimensional 1 H NMR methods have been used to make sequence-specific resonance assignments for the 97 amino acid residues of the plastocyanin from the green alga Scenedesmus obliquus. Assignments were obtained for all backbone protons and the majority of the side-chain protons. Spin system identification relied heavily on the observation of relayed connectivities to the backbone amide proton. Sequence-specific assignments were made by using the sequential assignment procedure. During this process, an extra valine residue was identified that had not been detected in the original amino acid sequence. Elements of regular secondary structure were identified from characteristic NOE connectivities between backbone protons, coupling constant values, and the observation of slowly exchanging amide protons. The protein in solution contains eight β-strands, one short segment of helix, five reverse turns, and five loops. The β-strands may be arranged into two βsheets on the basis of extensive cross-strand NOE connectivities. The chain-folding topology determined from the NMR experiments is that of a Greek key β-barrel and is similar to that observed for French bean plastocyanin in solution and poplar plastocyanin in the crystalline state. While the overall structures are similar, several differences in local structure between the S. obliquus and higher plant plastocyanins have been identified

  20. Magnifying visual target information and the role of eye movements in motor sequence learning.

    Science.gov (United States)

    Massing, Matthias; Blandin, Yannick; Panzer, Stefan

    2016-01-01

    An experiment investigated the influence of eye movements on learning a simple motor sequence task when the visual display was magnified. The task was to reproduce a 1300 ms spatial-temporal pattern of elbow flexions and extensions. The spatial-temporal pattern was displayed in front of the participants. Participants were randomly assigned to four groups differing on eye movements (free to use their eyes/instructed to fixate) and the visual display (small/magnified). All participants had to perform a pre-test, an acquisition phase, a delayed retention test, and a transfer test. The results indicated that participants in each practice condition increased their performance during acquisition. The participants who were permitted to use their eyes in the magnified visual display outperformed those who were instructed to fixate on the magnified visual display. When a small visual display was used, the instruction to fixate induced no performance decrements compared to participants who were permitted to use their eyes during acquisition. The findings demonstrated that a spatial-temporal pattern can be learned without eye movements, but being permitting to use eye movements facilitates the response production when the visual angle is increased. Copyright © 2015 Elsevier B.V. All rights reserved.

  1. The Benefits and Limitations of Crowdsourced Information for Rapid Damage Assessment of Global Earthquakes

    Science.gov (United States)

    Bossu, R.; Landès, M.; Roussel, F.

    2017-12-01

    The Internet has fastened the collection of felt reports and macroseismic data after global earthquakes. At the European-Mediterranean Seismological Centre (EMSC), where the traditional online questionnaires have been replace by thumbnail-based questionnaires, an average of half of the reports are collected within 10 minutes of an earthquake's occurrence. In regions where EMSC is well identified this goes down to 5 min. The user simply specifies the thumbnail corresponding to observed effects erasing languages barriers and improving collection via small smartphone screens. A previous study has shown that EMSC data is well correlated with "Did You Feel It" (DYFI) data and 3 independent, manually collected datasets. The efficiency and rapidity of felt report collection through thumbnail-based questionnaires does not necessarily mean that they offer a complete picture of the situation for all intensities values, especially the higher ones. There are several potential limitations. Demographics probably play a role but so might eyewitnesses' behaviors: it is probably not their priority to report when their own safety and that of their loved ones is at stake. We propose to test this hypothesis on EMSC felt reports and to extend the study to LastQuake smartphone application uses. LastQuake is a free smartphone app providing very rapid information on felt earthquakes. There are currently 210 000 active users around the world covering almost every country except for a few ones in Sub-Saharan Africa. Along with felt reports we also analyze the characteristics of LastQuake app launches. For both composite datasets created from 108 earthquakes, we analyze the rapidity of eyewitnesses' reaction and how it changes with intensity values and surmise how they reflect different types of behaviors. We will show the intrinsic limitations of crowdsourced information for rapid situation awareness. More importantly, we will show in which cases the lack of crowdsourced information could

  2. A Global User-Driven Model for Tile Prefetching in Web Geographical Information Systems.

    Science.gov (United States)

    Pan, Shaoming; Chong, Yanwen; Zhang, Hang; Tan, Xicheng

    2017-01-01

    A web geographical information system is a typical service-intensive application. Tile prefetching and cache replacement can improve cache hit ratios by proactively fetching tiles from storage and replacing the appropriate tiles from the high-speed cache buffer without waiting for a client's requests, which reduces disk latency and improves system access performance. Most popular prefetching strategies consider only the relative tile popularities to predict which tile should be prefetched or consider only a single individual user's access behavior to determine which neighbor tiles need to be prefetched. Some studies show that comprehensively considering all users' access behaviors and all tiles' relationships in the prediction process can achieve more significant improvements. Thus, this work proposes a new global user-driven model for tile prefetching and cache replacement. First, based on all users' access behaviors, a type of expression method for tile correlation is designed and implemented. Then, a conditional prefetching probability can be computed based on the proposed correlation expression mode. Thus, some tiles to be prefetched can be found by computing and comparing the conditional prefetching probability from the uncached tiles set and, similarly, some replacement tiles can be found in the cache buffer according to multi-step prefetching. Finally, some experiments are provided comparing the proposed model with other global user-driven models, other single user-driven models, and other client-side prefetching strategies. The results show that the proposed model can achieve a prefetching hit rate in approximately 10.6% ~ 110.5% higher than the compared methods.

  3. Human Capital Response to Globalization: Education and Information Technology in India

    Science.gov (United States)

    Shastry, Gauri Kartini

    2012-01-01

    Recent studies suggest that globalization increases inequality, by increasing skilled wage premiums in developing countries. This effect may be mitigated, however, if human capital responds to global opportunities. I study how the impact of globalization varies across Indian districts with different costs of learning English. Linguistic diversity…

  4. Antarctica and Global Environmental Change - Lessons from the Past Inform Climate Change Policy Today

    Science.gov (United States)

    Dunbar, R. B.; Scientific Team Of Odp Drilling Leg 318; Andrill Science Team

    2011-12-01

    Antarctic's continental ice, sea ice, and the broader Southern Ocean form a coupled and complex climate system that interacts in important yet poorly understood ways with the low and mid-latitudes. Because of its unusual sovereignty status and the fact that there is no indigenous human population, information about climate change in Antarctica penetrates the policy world less readily than findings from other regions. Yet, Antarctica's potential to impact climate change globally is disproportionately large. Vulnerable portions of the ice sheet may contribute up to 3 to 5 meters of sea level rise in the coming centuries, including significant amounts within the next 50 years. Loss of sea ice and other changes in the Southern Ocean may reduce oceanic uptake of excess atmospheric carbon dioxide, exacerbating global warming worldwide. Antarctica's impact on the Southern Hemisphere wind field is now well-established, contributing to ongoing decadal-scale perturbations in continental precipitation as well as major reorganizations of Southern Ocean food chains. Recent scientific drilling programs in the Ross Sea and off Wilkes Land, Antarctica, provide valuable insights into past climatic and biogeochemical change in Antarctica, insights of great relevance to international and national climate change policy. In this paper, we discuss polar amplification, sea level variability coupled to Antarctic ice volume, and response timescales as seen through the lens of past climate change. One key result emerging from multiple drilling programs is recognition of unanticipated dynamism in the Antarctic ice sheet during portions of the Pliocene (at a time with pCO2 levels equivalent to those anticipated late this century) as well as during "super-interglacials" of the Pleistocene. Evidence for substantially warmer ocean temperatures and reduced sea ice cover at these times suggests that polar amplification of natural climate variability, even under scenarios of relative small amounts

  5. 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.

  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. The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences

    Science.gov (United States)

    Portales-Casamar, Elodie; Arenillas, David; Lim, Jonathan; Swanson, Magdalena I.; Jiang, Steven; McCallum, Anthony; Kirov, Stefan; Wasserman, Wyeth W.

    2009-01-01

    The PAZAR database unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. The flexible PAZAR schema permits the representation of diverse information derived from experiments ranging from biochemical protein–DNA binding to cellular reporter gene assays. Data collections can be made available to the public, or restricted to specific system users. The data ‘boutiques’ within the shopping-mall-inspired system facilitate the analysis of genomics data and the creation of predictive models of gene regulation. Since its initial release, PAZAR has grown in terms of data, features and through the addition of an associated package of software tools called the ORCA toolkit (ORCAtk). ORCAtk allows users to rapidly develop analyses based on the information stored in the PAZAR system. PAZAR is available at http://www.pazar.info. ORCAtk can be accessed through convenient buttons located in the PAZAR pages or via our website at http://www.cisreg.ca/ORCAtk. PMID:18971253

  8. Acceptability of, and Information Needs Regarding, Next-Generation Sequencing in People Tested for Hereditary Cancer: A Qualitative Study.

    Science.gov (United States)

    Meiser, Bettina; Storey, Ben; Quinn, Veronica; Rahman, Belinda; Andrews, Lesley

    2016-04-01

    Next generation sequencing (NGS) for patients at risk of hereditary cancer syndromes can also identify non-cancer related mutations, as well as variants of unknown significance. This study aimed to determine what benefits and shortcomings patients perceive in relation to NGS, as well as their interest and information preferences in regards to such testing. Eligible patients had previously received inconclusive results from clinical mutation testing for cancer susceptibility. Semi-structured telephone interviews were subjected to qualitative analysis guided by the approach developed by Miles and Huberman. The majority of the 19 participants reported they would be interested in panel/genomic testing. Advantages identified included that it would enable better preparation and allow implementation of individualized preventative strategies, with few disadvantages mentioned. Almost all participants said they would want all results, not just those related to their previous diagnosis. Participants felt that a face-to-face discussion supplemented by an information booklet would be the best way to convey information and achieve informed consent. All participants wanted their information stored and reviewed in accordance with new developments. Although the findings indicate strong interest among these individuals, it seems that the consent process, and the interpretation and communication of results will be areas that will require revision to meet the needs of patients.

  9. Massively parallel sequencing of 165 ancestry informative SNPs in two Chinese Tibetan-Burmese minority ethnicities.

    Science.gov (United States)

    Wang, Zheng; He, Guanglin; Luo, Tao; Zhao, Xueying; Liu, Jing; Wang, Mengge; Zhou, Di; Chen, Xu; Li, Chengtao; Hou, Yiping

    2018-05-01

    The Tibeto-Burman language, one subfamily of the Sino-Tibetan languages, is spoken by over 60 million people all over East Asia. Yet the ethnic origin and genetic architecture of Tibeto-Burman speaking populations remain largely unexplored. In the present study, 169 Chinese individuals from Tibeto-Burman speaking populations (two ethnic groups: Tibetan and Yi) in four different geographic regions in western China were analyzed using the Precision ID Ancestry Panel (165 AISNPs) and the Ion PGM System. The performance and corresponding forensic statistical parameters of this AISNPs panel were investigated. Comprehensive population genetic comparisons (143 populations based on Kidd' SNPs, 92 populations on the basis of Seldin' SNPs and 31 populations based on the Precision ID Ancestry Panel) and ancestry inference were further performed. Sequencing performance demonstrated that the Precision ID Ancestry Panel is effective and robust. Forensic characteristics suggested that this panel not only can be used for ancestry estimation of Tibeto-Burman populations but also for individual identification. Tibetan and Yi shared a common genetic ancestry origin but experienced the complex history of gene flow, local adaptation, and isolation, and constructed the specific genetic landscape of human genetic diversity of Highlander and Lowlander populations. Tibetan-Burman populations and other East Asian populations showed sufficient genetic difference and could be distinguished into three distinct groups. Furthermore, analysis of population structure revealed that significant genetic difference was existed inter-continent populations and strong genetic affinity was observed within-continent populations. Additional population-specific AISNPs and a relatively more comprehensive database with sufficient reference population data remain necessary to get better-scale resolution within a geographically proximate populations in East Asia. Copyright © 2018 Elsevier B.V. All rights

  10. Integrating Global Open Geo-Information for Major Disaster Assessment: A Case Study of the Myanmar Flood

    Directory of Open Access Journals (Sweden)

    Suju Li

    2017-07-01

    Full Text Available Major disasters typically impact large areas, cause considerable damages, and result in significant human and economic losses. The timely and accurate estimation of impacts and damages is essential to better understand disaster conditions and to support emergency response operations. Geo-information drawn from various sources at multi spatial-temporal scales can be used for disaster assessments through a synthesis of hazard, exposure, and post disaster information based on pertinent approaches. Along with the increased availability of open sourced data and cooperation initiatives, more global scale geo-information, including global land cover datasets, has been produced and can be integrated with other information for disaster dynamic damage assessment (e.g., impact estimation immediately after a disaster occurs, physical damage assessment during the emergency response stage, and comprehensive assessment following an emergency response. Residential areas and arable lands affected by the flood disaster occurring from July to August 2015 in Myanmar were assessed based on satellite images, GlobeLand30 data, and other global open sourced information as a study case. The results show that integrating global open geo-information could serve as a practical and efficient means of assessing damage resulting from major disasters worldwide, especially at the early emergency response stage.

  11. Global MLST of Salmonella Typhi Revisited in Post-Genomic Era: Genetic conservation, Population Structure and Comparative genomics of rare sequence types

    Directory of Open Access Journals (Sweden)

    Kien-Pong eYap

    2016-03-01

    Full Text Available Typhoid fever, caused by Salmonella enterica serovar Typhi, remains an important public health burden in Southeast Asia and other endemic countries. Various genotyping methods have been applied to study the genetic variations of this human-restricted pathogen. Multilocus Sequence Typing (MLST is one of the widely accepted methods, and recently, there is a growing interest in the re-application of MLST in the post-genomic era. In this study, we provide the global MLST distribution of S. Typhi utilizing both publicly available 1,826 S. Typhi genome sequences in addition to performing conventional MLST on S. Typhi strains isolated from various endemic regions spanning over a century. Our global MLST analysis confirms the predominance of two sequence types (ST1 and ST2 co-existing in the endemic regions. Interestingly, S. Typhi strains with ST8 are currently confined within the African continent. Comparative genomic analyses of ST8 and other rare STs with genomes of ST1/ST2 revealed unique mutations in important virulence genes such as flhB, sipC and tviD that may explain the variations that differentiate between seemingly successful (widespread and unsuccessful (poor dissemination S. Typhi populations. Large scale whole-genome phylogeny demonstrated evidence of phylogeographical structuring and showed that ST8 may have diverged from the earlier ancestral population of ST1 and ST2, which later lost some of its fitness advantages, leading to poor worldwide dissemination. In response to the unprecedented increase in genomic data, this study demonstrates and highlights the utility of large-scale genome-based MLST as a quick and effective approach to narrow the scope of in-depth comparative genomic analysis and consequently provide new insights into the fine scale of pathogen evolution and population structure.

  12. Enrichment and genome sequence of the group I.1a ammonia-oxidizing Archaeon "Ca. Nitrosotenuis uzonensis" representing a clade globally distributed in thermal habitats.

    Directory of Open Access Journals (Sweden)

    Elena V Lebedeva

    Full Text Available The discovery of ammonia-oxidizing archaea (AOA of the phylum Thaumarchaeota and the high abundance of archaeal ammonia monooxygenase subunit A encoding gene sequences in many environments have extended our perception of nitrifying microbial communities. Moreover, AOA are the only aerobic ammonia oxidizers known to be active in geothermal environments. Molecular data indicate that in many globally distributed terrestrial high-temperature habits a thaumarchaeotal lineage within the Nitrosopumilus cluster (also called "marine" group I.1a thrives, but these microbes have neither been isolated from these systems nor functionally characterized in situ yet. In this study, we report on the enrichment and genomic characterization of a representative of this lineage from a thermal spring in Kamchatka. This thaumarchaeote, provisionally classified as "Candidatus Nitrosotenuis uzonensis", is a moderately thermophilic, non-halophilic, chemolithoautotrophic ammonia oxidizer. The nearly complete genome sequence (assembled into a single scaffold of this AOA confirmed the presence of the typical thaumarchaeotal pathways for ammonia oxidation and carbon fixation, and indicated its ability to produce coenzyme F420 and to chemotactically react to its environment. Interestingly, like members of the genus Nitrosoarchaeum, "Candidatus N. uzonensis" also possesses a putative artubulin-encoding gene. Genome comparisons to related AOA with available genome sequences confirmed that the newly cultured AOA has an average nucleotide identity far below the species threshold and revealed a substantial degree of genomic plasticity with unique genomic regions in "Ca. N. uzonensis", which potentially include genetic determinants of ecological niche differentiation.

  13. Enrichment and genome sequence of the group I.1a ammonia-oxidizing Archaeon "Ca. Nitrosotenuis uzonensis" representing a clade globally distributed in thermal habitats.

    Science.gov (United States)

    Lebedeva, Elena V; Hatzenpichler, Roland; Pelletier, Eric; Schuster, Nathalie; Hauzmayer, Sandra; Bulaev, Aleksandr; Grigor'eva, Nadezhda V; Galushko, Alexander; Schmid, Markus; Palatinszky, Marton; Le Paslier, Denis; Daims, Holger; Wagner, Michael

    2013-01-01

    The discovery of ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota and the high abundance of archaeal ammonia monooxygenase subunit A encoding gene sequences in many environments have extended our perception of nitrifying microbial communities. Moreover, AOA are the only aerobic ammonia oxidizers known to be active in geothermal environments. Molecular data indicate that in many globally distributed terrestrial high-temperature habits a thaumarchaeotal lineage within the Nitrosopumilus cluster (also called "marine" group I.1a) thrives, but these microbes have neither been isolated from these systems nor functionally characterized in situ yet. In this study, we report on the enrichment and genomic characterization of a representative of this lineage from a thermal spring in Kamchatka. This thaumarchaeote, provisionally classified as "Candidatus Nitrosotenuis uzonensis", is a moderately thermophilic, non-halophilic, chemolithoautotrophic ammonia oxidizer. The nearly complete genome sequence (assembled into a single scaffold) of this AOA confirmed the presence of the typical thaumarchaeotal pathways for ammonia oxidation and carbon fixation, and indicated its ability to produce coenzyme F420 and to chemotactically react to its environment. Interestingly, like members of the genus Nitrosoarchaeum, "Candidatus N. uzonensis" also possesses a putative artubulin-encoding gene. Genome comparisons to related AOA with available genome sequences confirmed that the newly cultured AOA has an average nucleotide identity far below the species threshold and revealed a substantial degree of genomic plasticity with unique genomic regions in "Ca. N. uzonensis", which potentially include genetic determinants of ecological niche differentiation.

  14. Summary of global warming uncertainties and the value of information: An analysis using CETA

    International Nuclear Information System (INIS)

    Peck, S.C.

    1994-01-01

    The authors investigate the sensitivity of optimal carbon control strategies to parameters of the Carbon Emissions Trajectory Assessment (CETA) Model, and they use CETA in a simple decision tree framework to estimate the value of information about global warming uncertainties. They find that if an optimal control policy is used under uncertainty, the eventual resolution of uncertainty has high value relative to current research budgets, and resolving uncertainty about the costs of warming is nearly as important as resolving uncertainty about the extent of warming. In addition, the authors find that there is not a high premium on immediate resolution of uncertainty, if resolution would otherwise occur within, say, twenty years; this implies that time is available to plan and execute a carefully designed research program. On the other hand, they find that if the real-world political process would result in a suboptimal control policy being chosen under uncertainty, and this choice could be prevented by early resolution of uncertainty, the benefit of early resolution may be as much as three orders of magnitude greater

  15. Temporal Patterns of Happiness and Information in a Global Social Network: Hedonometrics and Twitter

    Science.gov (United States)

    Dodds, Peter Sheridan; Harris, Kameron Decker; Kloumann, Isabel M.; Bliss, Catherine A.; Danforth, Christopher M.

    2011-01-01

    Individual happiness is a fundamental societal metric. Normally measured through self-report, happiness has often been indirectly characterized and overshadowed by more readily quantifiable economic indicators such as gross domestic product. Here, we examine expressions made on the online, global microblog and social networking service Twitter, uncovering and explaining temporal variations in happiness and information levels over timescales ranging from hours to years. Our data set comprises over 46 billion words contained in nearly 4.6 billion expressions posted over a 33 month span by over 63 million unique users. In measuring happiness, we construct a tunable, real-time, remote-sensing, and non-invasive, text-based hedonometer. In building our metric, made available with this paper, we conducted a survey to obtain happiness evaluations of over 10,000 individual words, representing a tenfold size improvement over similar existing word sets. Rather than being ad hoc, our word list is chosen solely by frequency of usage, and we show how a highly robust and tunable metric can be constructed and defended. PMID:22163266

  16. Global warming uncertainties and the value of information: an analysis using CETA

    International Nuclear Information System (INIS)

    Peck, S.C.; Teisberg, T.J.

    1993-01-01

    This paper investigated the sensitivity of optimal carbon control strategies to parameters of the Carbon Emissions Trajectory Assessment (CETA) Model, and CETA is used in a simple decision tree framework to estimate the value of information about global warming uncertainties. We find that if an optimal control policy is used under uncertainty, the eventual resolution of uncertainty has high value relative to current research budgets, and resolving uncertainty about the costs of warming is nearly as important as resolving uncertainty about the extent of warming. In addition, we find that there is not a high premium on immediate resolution of uncertainty, if resolution would otherwise occur within, say, twenty years; this implies that time is available to plan and execute a carefully designed research program. On the other hand, we find that if the real world political process would result in a suboptimal control policy being chosen under uncertainty, and this choice could be prevented by early resolution of uncertainty, the benefit of early resolution may be as much as three orders of magnitude greater. 26 refs., 11 figs., 8 tabs

  17. Transdisciplinary Challenges for Sustainable Management of Mediterranean Landscapes in the Global Information Society

    Directory of Open Access Journals (Sweden)

    Zev Naveh

    2009-11-01

    Full Text Available The present chaotic transformation from the industrial to the global information society is accelerating the ecological, social and economic unsustainability. The rapidly growing unsustainable, fossil energy powered urbanindustrial technosphere and their detrimental impacts on nature and human well-being are threatening the solar energy powered natural and seminatural biosphere landscapes and their vital ecosystem services. A sustainability revolution is therefore urgently needed, requiring a shift from the „fossil age“ to the „solar age“ of a new world economy, coupled with more sustainable lifestyles and consumption patterns. The sustainable future of viable multifunctional biosphere landscapes of the Mediterranean Region and elsewhere and their biological and cultural richness can only be ensured by a post-industrial symbiosis between nature and human society. For this purpose a mindset shift of scientists and professionals from narrow disciplinarity to transdisciplinarity is necessary, dealing with holistic land use planning and management, in close cooperation with land users and stakeholders. To conserve and restore the rapidly vanishing and degrading Mediterranean uplands and highest biological ecological and cultural landscape ecodiversity, their dynamic homeorhetic flow equilibrium, has to be maintained by continuing or simulating all anthropogenic processes of grazing, browsing by wild and domesticated ungulates. Catastrophic wildfires can be prevented only by active fire and fuel management, converting highly inflammable pine forests and dense shrub thickets into floristically enriched, multi- layered open woodlands and recreation forests.

  18. Validation of an hourly resolved global aerosol model in answer to solar electricity generation information needs

    Directory of Open Access Journals (Sweden)

    M. Schroedter-Homscheidt

    2013-04-01

    Full Text Available Solar energy applications need global aerosol optical depth (AOD information to derive historic surface solar irradiance databases from geostationary meteorological satellites reaching back to the 1980's. This paper validates the MATCH/DLR model originating in the climate community against AERONET ground measurements. Hourly or daily mean AOD model output is evaluated individually for all stations in Europe, Africa and the Middle East – an area highly interesting for solar energy applications being partly dominated by high aerosol loads. Overall, a bias of 0.02 and a root-mean-square error (RMSE of 0.23 are found for daily mean AOD values, while the RMSE increases to 0.28 for hourly mean AOD values. Large differences between various regions and stations are found providing a feedback loop for the aerosol modelling community. The difference in using daily means versus hourly resolved modelling with respect to hourly resolved observations is evaluated. Nowadays state-of-the-art in solar resource assessment relies on monthly turbidity or AOD climatologies while at least hourly resolved irradiance time series are needed by the solar sector. Therefore, the contribution of higher temporally modelled AOD is evaluated.

  19. Note on difference spectra for fast extraction of global image information.

    CSIR Research Space (South Africa)

    Van Wyk, BJ

    2007-06-01

    Full Text Available FOR FAST EXTRACTION OF GLOBAL IMAGE INFORMATION. B.J van Wyk* M.A. van Wyk* and F. van den Bergh** * c29c55c48c51c46c4bc03 c36c52c58c57c4bc03 c24c49c55c4cc46c44c51c03 c37c48c46c4bc51c4cc46c44c4fc03 c2cc51c56c57c4cc57c58c57c48c03 c4cc51c03 c28c4fc48c...46c57c55c52c51c4cc46c56c03 c0bc29cb6c36c24c37c2cc28c0cc03 c44c57c03 c57c4bc48c03 c37c56c4bc5ac44c51c48c03 c38c51c4cc59c48c55c56c4cc57c5cc03 c52c49c03 Technology, Private Bag X680, Pretoria 0001. ** Remote Sensing Research Group, Meraka Institute...

  20. Global epidemiology of capsular group W meningococcal disease (1970-2015): Multifocal emergence and persistence of hypervirulent sequence type (ST)-11 clonal complex.

    Science.gov (United States)

    Mustapha, Mustapha M; Marsh, Jane W; Harrison, Lee H

    2016-03-18

    Following an outbreak in Mecca Saudi Arabia in 2000, meningococcal strains expressing capsular group W (W) emerged as a major cause of invasive meningococcal disease (IMD) worldwide. The Saudi Arabian outbreak strain (Hajj clone) belonging to the ST-11 clonal complex (cc11) is similar to W cc11 causing occasional sporadic disease before 2000. Since 2000, W cc11 has caused large meningococcal disease epidemics in the African meningitis belt and endemic disease in South America, Europe and China. Traditional molecular epidemiologic typing suggested that a majority of current W cc11 burden represented global spread of the Hajj clone. However, recent whole genome sequencing (WGS) analyses revealed significant genetic heterogeneity among global W cc11 strains. While continued spread of the Hajj clone occurs in the Middle East, the meningitis belt and South Africa have co-circulation of the Hajj clone and other unrelated W cc11 strains. Notably, South America, the UK, and France share a genetically distinct W cc11 strain. Other W lineages persist in low numbers in Europe, North America and the meningitis belt. In summary, WGS is helping to unravel the complex genomic epidemiology of group W meningococcal strains. Wider application of WGS and strengthening of global IMD surveillance is necessary to monitor the continued evolution of group W lineages. Copyright © 2016 Elsevier Ltd. All rights reserved.

  1. An information-theoretic approach to the modeling and analysis of whole-genome bisulfite sequencing data.

    Science.gov (United States)

    Jenkinson, Garrett; Abante, Jordi; Feinberg, Andrew P; Goutsias, John

    2018-03-07

    DNA methylation is a stable form of epigenetic memory used by cells to control gene expression. Whole genome bisulfite sequencing (WGBS) has emerged as a gold-standard experimental technique for studying DNA methylation by producing high resolution genome-wide methylation profiles. Statistical modeling and analysis is employed to computationally extract and quantify information from these profiles in an effort to identify regions of the genome that demonstrate crucial or aberrant epigenetic behavior. However, the performance of most currently available methods for methylation analysis is hampered by their inability to directly account for statistical dependencies between neighboring methylation sites, thus ignoring significant information available in WGBS reads. We present a powerful information-theoretic approach for genome-wide modeling and analysis of WGBS data based on the 1D Ising model of statistical physics. This approach takes into account correlations in methylation by utilizing a joint probability model that encapsulates all information available in WGBS methylation reads and produces accurate results even when applied on single WGBS samples with low coverage. Using the Shannon entropy, our approach provides a rigorous quantification of methylation stochasticity in individual WGBS samples genome-wide. Furthermore, it utilizes the Jensen-Shannon distance to evaluate differences in methylation distributions between a test and a reference sample. Differential performance assessment using simulated and real human lung normal/cancer data demonstrate a clear superiority of our approach over DSS, a recently proposed method for WGBS data analysis. Critically, these results demonstrate that marginal methods become statistically invalid when correlations are present in the data. This contribution demonstrates clear benefits and the necessity of modeling joint probability distributions of methylation using the 1D Ising model of statistical physics and of

  2. KNOWLEDGE AND INFORMATION – NEW FACTORS OF PRODUCTION IN THE CONTEXT OF GLOBALIZATION

    Directory of Open Access Journals (Sweden)

    Mirela Alina COCALIA (CRĂCIUN

    2015-02-01

    Full Text Available The present article has as a starting point the phenomenon of globalization, so debated worldwide today. Along this work, we have tried offer a departure point, motivated of what the phenomenon of globalization means in economical context. Thus, we debate problems of major interest like: acceptances of the word “globalization”, multiple influences exerted by globalization over the proper nations and the way in which the specific economical and geographic area is marked by the phenomenon of globalization in the same time.

  3. Systematic Review on Global Epidemiology of Methicillin-Resistant Staphylococcus pseudintermedius: Inference of Population Structure from Multilocus Sequence Typing Data

    DEFF Research Database (Denmark)

    dos Santos, Teresa Pires; Damborg, Peter; Moodley, Arshnee

    2016-01-01

    Background and rationale: Methicillin-resistant Staphylococcus pseudintermedius (MRSP) is a major cause of infections in dogs, also posing a zoonotic risk to humans. This systematic review aimed to determine the global epidemiology of MRSP and provide new insights into the population structure...... the MLST database for this species. Analysis of MLST data was performed with eBURST and ClonalFrame, and the proportion of MRSP isolates resistant to selected antimicrobial drugs was determined for the most predominant clonal complexes. Results: Fifty-eight studies published over the last 10 years were....... In Europe, CC258, which is more frequently susceptible to enrofloxacin and aminoglycosides, and more frequently resistant to sulphonamides/trimethoprim than CC71, is increasingly reported in various countries. CC68, previously described as the epidemic North American clone, is frequently reported...

  4. To assess and control global change in agriculture through ecosystem models integrated into geographic information systems

    International Nuclear Information System (INIS)

    Ponti, L.; Iannetta, M.; Gutierrez, A.P.

    2015-01-01

    The transfer of ENEA PBDM (physiologically based demographic models) GIS technology, represents an opportunity to address global change in agriculture on an ecological basis in a local context, be able to provide European governmental agencies the necessary scientific basis for developing effective policies for adaptation to global change, including climate change [it

  5. Information exchange in global logistics chains : An application for model-based auditing,

    NARCIS (Netherlands)

    Veenstra, A.W.; Hulstijn, J.; Christiaanse, R.M.J.; Tan, Y.

    2013-01-01

    An integrated data pipeline has been proposed to meet requirements for visibility, supervision and control in global supply chains. How can data integration be used for risk assessment, monitoring and control in global supply chains? We argue that concepts from model-based auditing can be used to

  6. Voice over Internet Protocol (VoIP) Technology as a Global Learning Tool: Information Systems Success and Control Belief Perspectives

    Science.gov (United States)

    Chen, Charlie C.; Vannoy, Sandra

    2013-01-01

    Voice over Internet Protocol- (VoIP) enabled online learning service providers struggling with high attrition rates and low customer loyalty issues despite VoIP's high degree of system fit for online global learning applications. Effective solutions to this prevalent problem rely on the understanding of system quality, information quality, and…

  7. Developing Information Services and Tools to Access and Evaluate Data Quality in Global Satellite-based Precipitation Products

    Science.gov (United States)

    Liu, Z.; Shie, C. L.; Meyer, D. J.

    2017-12-01

    Global satellite-based precipitation products have been widely used in research and applications around the world. Compared to ground-based observations, satellite-based measurements provide precipitation data on a global scale, especially in remote continents and over oceans. Over the years, satellite-based precipitation products have evolved from single sensor and single algorithm to multi-sensors and multi-algorithms. As a result, many satellite-based precipitation products have been enhanced such as spatial and temporal coverages. With inclusion of ground-based measurements, biases of satellite-based precipitation products have been significantly reduced. However, data quality issues still exist and can be caused by many factors such as observations, satellite platform anomaly, algorithms, production, calibration, validation, data services, etc. The NASA Goddard Earth Sciences (GES) Data and Information Services Center (DISC) is home to NASA global precipitation product archives including the Tropical Rainfall Measuring Mission (TRMM), the Global Precipitation Measurement (GPM), as well as other global and regional precipitation products. Precipitation is one of the top downloaded and accessed parameters in the GES DISC data archive. Meanwhile, users want to easily locate and obtain data quality information at regional and global scales to better understand how precipitation products perform and how reliable they are. As data service providers, it is necessary to provide an easy access to data quality information, however, such information normally is not available, and when it is available, it is not in one place and difficult to locate. In this presentation, we will present challenges and activities at the GES DISC to address precipitation data quality issues.

  8. Intelligent Access to Sequence and Structure Databases (IASSD) - an interface for accessing information from major web databases.

    Science.gov (United States)

    Ganguli, Sayak; Gupta, Manoj Kumar; Basu, Protip; Banik, Rahul; Singh, Pankaj Kumar; Vishal, Vineet; Bera, Abhisek Ranjan; Chakraborty, Hirak Jyoti; Das, Sasti Gopal

    2014-01-01

    With the advent of age of big data and advances in high throughput technology accessing data has become one of the most important step in the entire knowledge discovery process. Most users are not able to decipher the query result that is obtained when non specific keywords or a combination of keywords are used. Intelligent access to sequence and structure databases (IASSD) is a desktop application for windows operating system. It is written in Java and utilizes the web service description language (wsdl) files and Jar files of E-utilities of various databases such as National Centre for Biotechnology Information (NCBI) and Protein Data Bank (PDB). Apart from that IASSD allows the user to view protein structure using a JMOL application which supports conditional editing. The Jar file is freely available through e-mail from the corresponding author.

  9. The Global Framework for Providing Information about Volcanic-Ash Hazards to International Air Navigation

    Science.gov (United States)

    Romero, R. W.; Guffanti, M.

    2009-12-01

    The International Civil Aviation Organization (ICAO) created the International Airways Volcano Watch (IAVW) in 1987 to establish a requirement for international dissemination of information about airborne ash hazards to safe air navigation. The IAVW is a set of operational protocols and guidelines that member countries agree to follow in order to implement a global, multi-faceted program to support the strategy of ash-cloud avoidance. Under the IAVW, the elements of eruption reporting, ash-cloud detecting, and forecasting expected cloud dispersion are coordinated to culminate in warnings sent to air traffic controllers, dispatchers, and pilots about the whereabouts of ash clouds. Nine worldwide Volcanic Ash Advisory Centers (VAAC) established under the IAVW have the responsibility for detecting the presence of ash in the atmosphere, primarily by looking at imagery from civilian meteorological satellites, and providing advisories about the location and movement of ash clouds to aviation meteorological offices and other aviation users. Volcano Observatories also are a vital part of the IAVW, as evidenced by the recent introduction of a universal message format for reporting the status of volcanic activity, including precursory unrest, to aviation users. Since 2003, the IAVW has been overseen by a standing group of scientific, technical, and regulatory experts that assists ICAO in the development of standards and other regulatory material related to volcanic ash. Some specific problems related to the implementation of the IAVW include: the lack of implementation of SIGMET (warning to aircraft in flight) provisions and delayed notifications of volcanic eruptions. Expected future challenges and developments involve the improvement in early notifications of volcanic eruptions, the consolidation of the issuance of SIGMETs, and the possibility of determining a “safe” concentration of volcanic ash.

  10. In the search for the low-complexity sequences in prokaryotic and eukaryotic genomes: how to derive a coherent picture from global and local entropy measures

    Energy Technology Data Exchange (ETDEWEB)

    Acquisti, Claudia; Allegrini, Paolo E-mail: allegrip@ilc.cnr.it; Bogani, Patrizia; Buiatti, Marcello; Catanese, Elena; Fronzoni, Leone; Grigolini, Paolo; Mersi, Giuseppe; Palatella, Luigi

    2004-04-01

    We investigate on a possible way to connect the presence of low-complexity sequences (LCS) in DNA genomes and the non-stationary properties of base correlations. Under the hypothesis that these variations signal a change in the DNA function, we use a new technique, called non-stationarity entropic index (NSEI) method, and we prove that this technique is an efficient way to detect functional changes with respect to a random baseline. The remarkable aspect is that NSEI does not imply any training data or fitting parameter, the only arbitrarity being the choice of a marker in the sequence. We make this choice on the basis of biological information about LCS distributions in genomes. We show that there exists a correlation between changing the amount in LCS and the ratio of long- to short-range correlation.

  11. In the search for the low-complexity sequences in prokaryotic and eukaryotic genomes: how to derive a coherent picture from global and local entropy measures

    Science.gov (United States)

    Acquisti, Claudia; Allegrini, Paolo; Bogani, Patrizia; Buiatti, Marcello; Catanese, Elena; Fronzoni, Leone; Grigolini, Paolo; Mersi, Giuseppe; Palatella, Luigi

    2004-04-01

    We investigate on a possible way to connect the presence of Low-Complexity Sequences (LCS) in DNA genomes and the nonstationary properties of base correlations. Under the hypothesis that these variations signal a change in the DNA function, we use a new technique, called Non-Stationarity Entropic Index (NSEI) method, and we prove that this technique is an efficient way to detect functional changes with respect to a random baseline. The remarkable aspect is that NSEI does not imply any training data or fitting parameter, the only arbitrarity being the choice of a marker in the sequence. We make this choice on the basis of biological information about LCS distributions in genomes. We show that there exists a correlation between changing the amount in LCS and the ratio of long- to short-range correlation.

  12. In the search for the low-complexity sequences in prokaryotic and eukaryotic genomes: how to derive a coherent picture from global and local entropy measures

    International Nuclear Information System (INIS)

    Acquisti, Claudia; Allegrini, Paolo; Bogani, Patrizia; Buiatti, Marcello; Catanese, Elena; Fronzoni, Leone; Grigolini, Paolo; Mersi, Giuseppe; Palatella, Luigi

    2004-01-01

    We investigate on a possible way to connect the presence of low-complexity sequences (LCS) in DNA genomes and the non-stationary properties of base correlations. Under the hypothesis that these variations signal a change in the DNA function, we use a new technique, called non-stationarity entropic index (NSEI) method, and we prove that this technique is an efficient way to detect functional changes with respect to a random baseline. The remarkable aspect is that NSEI does not imply any training data or fitting parameter, the only arbitrarity being the choice of a marker in the sequence. We make this choice on the basis of biological information about LCS distributions in genomes. We show that there exists a correlation between changing the amount in LCS and the ratio of long- to short-range correlation

  13. Developing a framework to assess the cost-effectiveness of COMPARE -A global platform for the exchange of sequence-based pathogen data

    DEFF Research Database (Denmark)

    Alleweldt, F.; Kara, Sami; Osinski, A.

    2017-01-01

    Analysing the genomic data of pathogens with the help of next-generation sequencing (NGS) is an increasingly important part of disease outbreak investigations and helps guide responses. While this technology has already been successfully employed to elucidate and control disease outbreaks, wider...... implementation of NGS also depends on its cost-effectiveness. COMPARE - short for 'Collaborative Management Platform for detection and Analyses of (Re-) emerging and foodborne outbreaks' - is a major project, funded by the European Union, to develop a global platform for sharing and analysing NGS data...... and thereby improve the rapid identification, containment and mitigation of emerging infectious diseases and foodborne outbreaks. This article introduces the project and presents the results of a review of the literature, composed of previous relevant cost-benefit and cost-effectiveness analyses. The authors...

  14. Deep sequencing of Brachypodium small RNAs at the global genome level identifies microRNAs involved in cold stress response

    Directory of Open Access Journals (Sweden)

    Chong Kang

    2009-09-01

    Full Text Available Abstract Background MicroRNAs (miRNAs are endogenous small RNAs having large-scale regulatory effects on plant development and stress responses. Extensive studies of miRNAs have only been performed in a few model plants. Although miRNAs are proved to be involved in plant cold stress responses, little is known for winter-habit monocots. Brachypodium distachyon, with close evolutionary relationship to cool-season cereals, has recently emerged as a novel model plant. There are few reports of Brachypodium miRNAs. Results High-throughput sequencing and whole-genome-wide data mining led to the identification of 27 conserved miRNAs, as well as 129 predicted miRNAs in Brachypodium. For multiple-member conserved miRNA families, their sizes in Brachypodium were much smaller than those in rice and Populus. The genome organization of miR395 family in Brachypodium was quite different from that in rice. The expression of 3 conserved miRNAs and 25 predicted miRNAs showed significant changes in response to cold stress. Among these miRNAs, some were cold-induced and some were cold-suppressed, but all the conserved miRNAs were up-regulated under cold stress condition. Conclusion Our results suggest that Brachypodium miRNAs are composed of a set of conserved miRNAs and a large proportion of non-conserved miRNAs with low expression levels. Both kinds of miRNAs were involved in cold stress response, but all the conserved miRNAs were up-regulated, implying an important role for cold-induced miRNAs. The different size and genome organization of miRNA families in Brachypodium and rice suggest that the frequency of duplication events or the selection pressure on duplicated miRNAs are different between these two closely related plant species.

  15. Assess and control global change in agriculture through ecosystem models integrated in geographic information systems

    International Nuclear Information System (INIS)

    Ponti, Luigi; Gutierrez, Andrew Paul; Iannetta, Massimo

    2015-01-01

    ENEA has created, in collaboration with the University of California at Berkeley, the Global Change Biology project that, for the first time, has made available in Europe a technology that can be It used to interpret and effectively manage change Global agriculture. The aim of the project was to provide tools to summarize, manage and analyze data Ecological on the effects of global change in agricultural systems, using traditional Mediterranean crops (Eg. Vineyards and olive) as model systems (http: // cordis.europa.eu/project/rcn/89728_en.html). [it

  16. Managing Identifiers for Elements of Provenance of the Third National Climate Assessment in the Global Change Information System (Invited)

    Science.gov (United States)

    Tilmes, C.; Aulenbach, S.; Duggan, B.; Goldstein, J.

    2013-12-01

    A Federal Advisory Committee (The "National Climate Assessment and Development Advisory Committee" or NCADAC) has overseen the development of a draft climate report that after extensive review will be considered by the Federal Government in the Third National Climate Assessment (NCA). This comprehensive report (1) Integrates, evaluates, and interprets the findings of the Program and discusses the scientific uncertainties associated with such findings; (2) Analyzes the effects of global change on the natural environment, agriculture, energy production and use, land and water resources, transportation, human health and welfare, human social systems, and biological diversity; and (3) Analyzes current trends in global change, both human-induced and natural, and projects major trends for the subsequent 25 to 100 years. The U.S. Global Change Program (USGCRP), composed of the 13 federal agencies most concerned with global change, is building a Global Change Information System (GCIS) that will ultimately organize access to all of the research, data, and information about global change from across the system. A prototype of the system has been constructed that captures and presents all of the elements of provenance of the NCA through a coherent data model and friendly front end web site. This work will focus on the globally unique and persistent identifiers used to reference and organize those items. These include externally referenced items, such as DOIs used by scientific journal publishers for research articles or by agencies as dataset identifiers, as well as our own internal approach to identifiers, our overall data model and experiences managing persistent identifiers within the GCIS.

  17. World Summit on the Information Society finding the best use of a global asset

    CERN Multimedia

    2003-01-01

    "The first global summit on bridging the digital divide between rich and poor countries - the first meeting of its kind - convened in Geneva last week as governments struggled to agree on what they wanted to achieve" (2 pages)

  18. PINGU: PredIction of eNzyme catalytic residues usinG seqUence information.

    Directory of Open Access Journals (Sweden)

    Priyadarshini P Pai

    Full Text Available Identification of catalytic residues can help unveil interesting attributes of enzyme function for various therapeutic and industrial applications. Based on their biochemical roles, the number of catalytic residues and sequence lengths of enzymes vary. This article describes a prediction approach (PINGU for such a scenario. It uses models trained using physicochemical properties and evolutionary information of 650 non-redundant enzymes (2136 catalytic residues in a support vector machines architecture. Independent testing on 200 non-redundant enzymes (683 catalytic residues in predefined prediction settings, i.e., with non-catalytic per catalytic residue ranging from 1 to 30, suggested that the prediction approach was highly sensitive and specific, i.e., 80% or above, over the incremental challenges. To learn more about the discriminatory power of PINGU in real scenarios, where the prediction challenge is variable and susceptible to high false positives, the best model from independent testing was used on 60 diverse enzymes. Results suggested that PINGU was able to identify most catalytic residues and non-catalytic residues properly with 80% or above accuracy, sensitivity and specificity. The effect of false positives on precision was addressed in this study by application of predicted ligand-binding residue information as a post-processing filter. An overall improvement of 20% in F-measure and 0.138 in Correlation Coefficient with 16% enhanced precision could be achieved. On account of its encouraging performance, PINGU is hoped to have eventual applications in boosting enzyme engineering and novel drug discovery.

  19. Informed consent for exome sequencing research in families with genetic disease: the emerging issue of incidental findings.

    Science.gov (United States)

    Bergner, Amanda L; Bollinger, Juli; Raraigh, Karen S; Tichnell, Crystal; Murray, Brittney; Blout, Carrie Lynn; Telegrafi, Aida Bytyci; James, Cynthia A

    2014-11-01

    Genomic sequencing technology is increasingly used in genetic research. Studies of informed consent for exome and genome sequencing (ES/GS) research have largely involved hypothetical scenarios or healthy individuals enrolling in population-based studies. Studies have yet to explore the consent experiences of adults with inherited disease. We conducted a qualitative interview study of 15 adults recently enrolled in a large-scale ES/GS study (11 affected adults, four parents of affected children). Our study had two goals: (1) to explore three theoretical barriers to consent for ES/GS research (interpretive/technical complexity, possibility of incidental findings, and risks of loss of privacy); and (2) to explore how interviewees experienced the consent process. Interviewees could articulate study goals and processes, describe incidental findings, discuss risks of privacy loss, and reflect on their consent experience. Few expected the study would identify the genetic cause of their condition. All elected to receive incidental findings. Interviewees acknowledged paying little attention to potential implications of incidental findings in light of more pressing goals of supporting research regarding their own medical conditions. Interviewees suggested that experience living with a genetic condition prepared them to adjust to incidental findings. Interviewees also expressed little concern about loss of confidentiality of study data. Some experienced the consent process as very long. None desired reconsent prior to return of study results. Families with inherited disease likely would benefit from a consent process in which study risks and benefits were discussed in the context of prior experiences with genetic research and genetic disease. © 2014 Wiley Periodicals, Inc.

  20. Global Complexity: Information, Chaos, and Control at ASIS 1996 Annual Meeting.

    Science.gov (United States)

    Jacob, M. E. L.

    1996-01-01

    Discusses proceedings of the 1996 ASIS (American Society for Information Science) annual meeting in Baltimore (Maryland), including chaos theory; electronic universities; distance education; intellectual property, including information privacy on the Internet; the need for leadership in libraries and information centers; information warfare and…

  1. Stochastic process of pragmatic information for 2D spiral wave turbulence in globally and locally coupled Alief-Panfilov oscillators

    Science.gov (United States)

    Kuwahara, Jun; Miyata, Hajime; Konno, Hidetoshi

    2017-09-01

    Recently, complex dynamics of globally coupled oscillators have been attracting many researcher's attentions. In spite of their numerous studies, their features of nonlinear oscillator systems with global and local couplings in two-dimension (2D) are not understood fully. The paper focuses on 2D states of coherent, clustered and chaotic oscillation especially under the effect of negative global coupling (NGC) in 2D Alief-Panfilov model. It is found that the tuning NGC can cause various new coupling-parameter dependency on the features of oscillations. Then quantitative characterization of various states of oscillations (so called spiral wave turbulence) is examined by using the pragmatic information (PI) which have been utilized in analyzing multimode laser, solar activity and neuronal systems. It is demonstrated that the dynamics of the PI for various oscillations can be characterized successfully by the Hyper-Gamma stochastic process.

  2. Feasibility of integrating other federal information systems into the Global Network of Environment and Technology, GNET{reg_sign}

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1998-05-01

    The Global Environment and Technology Enterprise (GETE) of the Global Environment and Technology Foundation (GETF) has been tasked by the US Department of Energy`s (DOE), Federal Energy Technology Center (FETC) to assist in reducing DOE`s cost for the Global Network of Environment and Technology (GNET{reg_sign}). As part of this task, GETE is seeking federal partners to invest in GNET{reg_sign}. The authors are also seeking FETC`s commitment to serve as GNET`s federal agency champion promoting the system to potential agency partners. This report assesses the benefits of partnering with GNET{reg_sign} and provides recommendations for identifying and integrating other federally funded (non-DOE) environmental information management systems into GNET{reg_sign}.

  3. Information Seeking about Global Climate Change among Adolescents: The Role of Risk Perceptions, Efficacy Beliefs and Parental Influences

    Science.gov (United States)

    Mead, Erin; Roser-Renouf, Connie; Rimal, Rajiv N.; Flora, June A.; Maibach, Edward W.; Leiserowitz, Anthony

    2012-01-01

    Global climate change is likely to have significant impacts on public health. Effective communication is critical to informing public decision making and behavior to mitigate climate change. An effective method of audience segmentation, the risk perception attitude (RPA) framework has been previously tested with other health behaviors and classifies people into 4 groups on the basis of their perceptions of risk and beliefs about personal efficacy. The 4 groups – indifference (low risk, weak efficacy), proactive (low risk, strong efficacy), avoidance (high risk, weak efficacy), and responsive (high risk, strong efficacy) – are hypothesized to differ in their self-protective behaviors and in their motivations to seek information. In this paper, we extend the RPA framework in two ways. First, we use it at the household level to determine whether parental classifications into the 4 groups are associated with their teenage children’s classification into the same 4 groups. Second, we predict adolescent information-seeking behaviors on the basis of their and their parents’ membership in the 4 RPA groups. Results (N = 523 parent-adolescent pairs) indicated that parental membership in the 4 RPA groups was significantly associated with children’s membership in the same 4 groups. Furthermore, the RPA framework was a significant predictor of adolescent information-seeking: those in the responsive and avoidance groups sought more information on climate change than the indifference group. Family communication on global warming was positively associated with adolescents’ information-seeking. Implications for interventions are discussed. PMID:22866024

  4. Understanding Information Technology Investment Decision-Making in the Context of Hotel Global Distribution Systems: a Multiple-Case Study

    OpenAIRE

    Connolly, Daniel J.

    1999-01-01

    UNDERSTANDING INFORMATION TECHNOLOGY INVESTMENT DECISION-MAKING IN THE CONTEXT OF HOTEL GLOBAL DISTRIBUTION SYSTEMS: A MULTIPLE-CASE STUDY by Daniel J. Connolly Dr. Michael D. Olsen, Chair Department of Hospitality and Tourism Management ABSTRACT This study investigates what three large, multinational hospitality companies do in practice when evaluating and making IT investment decisions. This study was launched in an attempt to 1) learn more about ...

  5. Mapping global surface water inundation dynamics using synergistic information from SMAP, AMSR2 and Landsat

    Science.gov (United States)

    Du, J.; Kimball, J. S.; Galantowicz, J. F.; Kim, S.; Chan, S.; Reichle, R. H.; Jones, L. A.; Watts, J. D.

    2017-12-01

    A method to monitor global land surface water (fw) inundation dynamics was developed by exploiting the enhanced fw sensitivity of L-band (1.4 GHz) passive microwave observations from the Soil Moisture Active Passive (SMAP) mission. The L-band fw (fwLBand) retrievals were derived using SMAP H-polarization brightness temperature (Tb) observations and predefined L-band reference microwave emissivities for water and land endmembers. Potential soil moisture and vegetation contributions to the microwave signal were represented from overlapping higher frequency Tb observations from AMSR2. The resulting fwLBand global record has high temporal sampling (1-3 days) and 36-km spatial resolution. The fwLBand annual averages corresponded favourably (R=0.84, pretrievals showed favourable classification accuracy for water (commission error 31.84%; omission error 28.08%) and land (commission error 0.82%; omission error 0.99%) and seasonal wet and dry periods when compared to independent water maps derived from Landsat-8 imagery. The new fwLBand algorithms and continuing SMAP and AMSR2 operations provide for near real-time, multi-scale monitoring of global surface water inundation dynamics, potentially benefiting hydrological monitoring, flood assessments, and global climate and carbon modeling.

  6. Using Models to Inform Policy: Insights from Modeling the Complexities of Global Polio Eradication

    Science.gov (United States)

    Thompson, Kimberly M.

    Drawing on over 20 years of experience modeling risks in complex systems, this talk will challenge SBP participants to develop models that provide timely and useful answers to critical policy questions when decision makers need them. The talk will include reflections on the opportunities and challenges associated with developing integrated models for complex problems and communicating their results effectively. Dr. Thompson will focus the talk largely on collaborative modeling related to global polio eradication and the application of system dynamics tools. After successful global eradication of wild polioviruses, live polioviruses will still present risks that could potentially lead to paralytic polio cases. This talk will present the insights of efforts to use integrated dynamic, probabilistic risk, decision, and economic models to address critical policy questions related to managing global polio risks. Using a dynamic disease transmission model combined with probabilistic model inputs that characterize uncertainty for a stratified world to account for variability, we find that global health leaders will face some difficult choices, but that they can take actions that will manage the risks effectively. The talk will emphasize the need for true collaboration between modelers and subject matter experts, and the importance of working with decision makers as partners to ensure the development of useful models that actually get used.

  7. Information processing speed as a mediator between psychosocial stress and global cognition in older adults.

    Science.gov (United States)

    Foong, Hui F; Hamid, Tengku A; Ibrahim, Rahimah; Haron, Sharifah A

    2018-01-01

    The link between psychosocial stress and cognitive function is complex, and previous studies have indicated that it may be mediated by processing speed. Therefore, the main aim of this study was to examine whether processing speed mediates the association between psychosocial stress and global cognition in older adults. Moreover, the moderating role of gender in this model is examined as well. The study included 2322 community-dwelling older adults in Malaysia who were randomly selected through a multistage proportional cluster random sampling technique. Global cognition construct was measured by the Mini-Mental State Examination and Montreal Cognitive Assessment; psychosocial stress construct was measured by perceived stress, depression, loneliness, and neuroticism; and processing speed was assessed by the Digit Symbol Substitution Test. Structural equation modelling was used to analyze the mediation and moderation tests. Processing speed was found to partially mediate the relationship between psychosocial stress and global cognition (β in the direct model = -0.15, P cognition was found to be significant in men only, whereas the association between processing speed and global cognition was significant in men and women. Psychosocial stress may increase the likelihood that older adults will experience poor processing capacity, which could reduce their higher level cognition. Results indicate that there is a need to develop processing capacity intervention programmes for psychologically distressed older adults to prevent them from suffering cognitive decline. © 2018 Japanese Psychogeriatric Society.

  8. Librarians Lead the Growth of Information Literacy and Global Digital Citizens

    Science.gov (United States)

    Crockett, Lee Watanabe

    2018-01-01

    Librarians are leaders in growing global digital citizens. The libraries of the future are more than just housing centers for books and media. They are invigorating meeting places and communities where truly meaningful learning and discovery take place. As technology has transformed reading and learning, it has also transformed the vision of the…

  9. Globalization, social exclusion and work : with special reference to informal employment and gender

    OpenAIRE

    Carr, Marilyn; Chen, Martha

    2004-01-01

    Looks at three different patterns that limit competitiveness: a) questionable working conditions in export processing zones or within global value chains that are driven by a foreign or multinational enterprise; b) exclusion of self-employed from the internal governance process of the chain; c) import-flooding putting domestic sectors at a disadvantage. Makes policy recommendations for more favourable inclusion opportunities.

  10. EDUCATION IN GLOBAL INFORMATION-COMMUNICATION AND ANTHROPOGENIC ENVIRONMENT: NEW OPPORTUNITIES AND LIMITS

    Directory of Open Access Journals (Sweden)

    Sergey F. Sergeev

    2013-01-01

    Full Text Available The article answers the question of how to use global anthropogenic environments in order to create effective educational environment. We demonstrate both technological and didactic abilities and limits of modern environment-based technologies, and provide a new approach to the educational environment creation. 

  11. 75 FR 60068 - Global Free Flow of Information on the Internet

    Science.gov (United States)

    2010-09-29

    ... Recognizing the vital importance of the Internet to U.S. prosperity, education and political and cultural life... of modern consumer, business, political and educational activity. Between 1999 and 2007, the United... traditional notions of jurisdiction, venue and choice of law evolving as services are offered on a global...

  12. Combining A Priori Knowledge and Sensor Information for Updating the Global Position of an Autonomous Vehicle

    NARCIS (Netherlands)

    Zivkovic, Z.; Schoute, Albert L.; van der Heijden, Ferdinand; van Amerongen, J.; Jonker, B.; Regtien, P.P.L; Stramigioli, S.

    The problem of updating the global position of an autonomous vehicle is considered. An iterative procedure is proposed to fit a map to a set of noisy measurements. The procedure is inspired by a non-parametric procedure for probability density function mode searching. We show how this could be used

  13. Interviewing Key Informants: Strategic Planning for a Global Public Health Management Program

    Science.gov (United States)

    Kun, Karen E.; Kassim, Anisa; Howze, Elizabeth; MacDonald, Goldie

    2013-01-01

    The Centers for Disease Control and Prevention's Sustainable Management Development Program (SMDP) partners with low- and middle-resource countries to develop management capacity so that effective global public health programs can be implemented and better health outcomes can be achieved. The program's impact however, was variable. Hence, there…

  14. Relevance of soil and terrain information in studies of major global issues

    NARCIS (Netherlands)

    Bindraban, P.S.; Batjes, N.H.; Leenaars, J.G.B.; Bai, Z.G.

    2010-01-01

    The Carbon Benefits Project (CBP) is working to produce a standardized system for Global Environmental Facility (GEF) and other sustainable land management (SLM) projects to measure, monitor and model carbon stock changes and greenhouse gas (GHG) emissions. The project builds on existing C-inventory

  15. Information Exchange in Global Logistics Chains : An application for Model-based Auditing (abstract)

    NARCIS (Netherlands)

    Veenstra, A.W.; Hulstijn, J.; Christiaanse, R.; Tan, Y.

    2013-01-01

    An integrated data pipeline has been proposed to meet requirements for supply chain visibility and control. How can data integration be used for risk assessment, monitoring and control in global supply chains? We argue that concepts from model-based auditing can be used to model the ‘ideal’ flow of

  16. Government restrictions to the right to information in the modern globalized world

    Directory of Open Access Journals (Sweden)

    T. S. Korshun

    2014-11-01

    Ukraine, with its powerful intellectual potential is obliged to provide the widest right to access to information for all citizens. Legislation should provide the maximum assistance for the free flow of information. The fundamental rejection of attempts to monopolize information technology has become another very important issue.

  17. Genetic differentiation between fake abalone and genuine Haliotis species using the forensically informative nucleotide sequencing (FINS) method.

    Science.gov (United States)

    Ha, Wai Y; Reid, David G; Kam, Wan L; Lau, Yuk Y; Sham, Wing C; Tam, Silvia Y K; Sin, Della W M; Mok, Chuen S

    2011-05-25

    Abalones ( Haliotis species) are a popular delicacy and commonly preserved in dried form either whole or in slices or small pieces for consumption in Asian countries. Driven by the huge profit from trading abalones, dishonest traders may substitute other molluscan species for processed abalone, of which the morphological characteristics are frequently lost in the processed form. For protection of consumer rights and law enforcement against fraud, there is a need for an effective methodology to differentiate between fake and genuine abalone. This paper describes a method (validated according to the international forensic guidelines provided by SWGDAM) for the identification of fake abalone species using forensically informative nucleotide sequence (FINS) analysis. A study of the local market revealed that many claimed "abalone slice" samples on sale are not genuine. The fake abalone samples were found to be either volutids of the genus Cymbium (93%) or the muricid Concholepas concholepas (7%). This is the first report of Cymbium species being used for the preparation and sale as "abalone" in dried sliced form in Hong Kong.

  18. Lncident: A Tool for Rapid Identification of Long Noncoding RNAs Utilizing Sequence Intrinsic Composition and Open Reading Frame Information

    Directory of Open Access Journals (Sweden)

    Siyu Han

    2016-01-01

    Full Text Available More and more studies have demonstrated that long noncoding RNAs (lncRNAs play critical roles in diversity of biological process and are also associated with various types of disease. How to rapidly identify lncRNAs and messenger RNA is the fundamental step to uncover the function of lncRNAs identification. Here, we present a novel method for rapid identification of lncRNAs utilizing sequence intrinsic composition features and open reading frame information based on support vector machine model, named as Lncident (LncRNAs identification. The 10-fold cross-validation and ROC curve are used to evaluate the performance of Lncident. The main advantage of Lncident is high speed without the loss of accuracy. Compared with the exiting popular tools, Lncident outperforms Coding-Potential Calculator, Coding-Potential Assessment Tool, Coding-Noncoding Index, and PLEK. Lncident is also much faster than Coding-Potential Calculator and Coding-Noncoding Index. Lncident presents an outstanding performance on microorganism, which offers a great application prospect to the analysis of microorganism. In addition, Lncident can be trained by users’ own collected data. Furthermore, R package and web server are simultaneously developed in order to maximize the convenience for the users. The R package “Lncident” can be easily installed on multiple operating system platforms, as long as R is supported.

  19. The politics of agenda setting at the global level: key informant interviews regarding the International Labour Organization Decent Work Agenda.

    Science.gov (United States)

    Di Ruggiero, Erica; Cohen, Joanna E; Cole, Donald C

    2014-07-01

    Global labour markets continue to undergo significant transformations resulting from socio-political instability combined with rises in structural inequality, employment insecurity, and poor working conditions. Confronted by these challenges, global institutions are providing policy guidance to protect and promote the health and well-being of workers. This article provides an account of how the International Labour Organization's Decent Work Agenda contributes to the work policy agendas of the World Health Organization and the World Bank. This qualitative study involved semi-structured interviews with representatives from three global institutions--the International Labour Organization (ILO), the World Health Organization and the World Bank. Of the 25 key informants invited to participate, 16 took part in the study. Analysis for key themes was followed by interpretation using selected agenda setting theories. Interviews indicated that through the Decent Work Agenda, the International Labour Organization is shaping the global policy narrative about work among UN agencies, and that the pursuit of decent work and the Agenda were perceived as important goals with the potential to promote just policies. The Agenda was closely linked to the World Health Organization's conception of health as a human right. However, decent work was consistently identified by World Bank informants as ILO terminology in contrast to terms such as job creation and job access. The limited evidence base and its conceptual nature were offered as partial explanations for why the Agenda has yet to fully influence other global institutions. Catalytic events such as the economic crisis were identified as creating the enabling conditions to influence global work policy agendas. Our evidence aids our understanding of how an issue like decent work enters and stays on the policy agendas of global institutions, using the Decent Work Agenda as an illustrative example. Catalytic events and policy

  20. The politics of agenda setting at the global level: key informant interviews regarding the International Labour Organization Decent Work Agenda

    Science.gov (United States)

    2014-01-01

    Background Global labour markets continue to undergo significant transformations resulting from socio-political instability combined with rises in structural inequality, employment insecurity, and poor working conditions. Confronted by these challenges, global institutions are providing policy guidance to protect and promote the health and well-being of workers. This article provides an account of how the International Labour Organization’s Decent Work Agenda contributes to the work policy agendas of the World Health Organization and the World Bank. Methods This qualitative study involved semi-structured interviews with representatives from three global institutions – the International Labour Organization (ILO), the World Health Organization and the World Bank. Of the 25 key informants invited to participate, 16 took part in the study. Analysis for key themes was followed by interpretation using selected agenda setting theories. Results Interviews indicated that through the Decent Work Agenda, the International Labour Organization is shaping the global policy narrative about work among UN agencies, and that the pursuit of decent work and the Agenda were perceived as important goals with the potential to promote just policies. The Agenda was closely linked to the World Health Organization’s conception of health as a human right. However, decent work was consistently identified by World Bank informants as ILO terminology in contrast to terms such as job creation and job access. The limited evidence base and its conceptual nature were offered as partial explanations for why the Agenda has yet to fully influence other global institutions. Catalytic events such as the economic crisis were identified as creating the enabling conditions to influence global work policy agendas. Conclusions Our evidence aids our understanding of how an issue like decent work enters and stays on the policy agendas of global institutions, using the Decent Work Agenda as an illustrative

  1. INFORMATION TECHNOLOGY CAPACITIES AND THE BORN GLOBAL COMPANIES DOI: 10.5585/riae.v8i1.1629

    Directory of Open Access Journals (Sweden)

    María Soledad Etchebarne López

    2009-08-01

    Full Text Available International business transactions have increased in recent years, triggered by the opening up of markets and the development of information technologies and communications, especially in the cases of small and medium enterprises. In this context, a new type of company is emerging: the so-called 'born global' companies. These organizations have an international profile since their birth, and have not gone through the traditional evolutionary pattern of internationalization.  This article describes the theories that explain this new phenomenon, the main features of these new companies and their relationship with information technology (IT, which allows them to generate competitive advantages when entering the international market.

  2. The New Global Information Economy: Implications and Recommendations for Service-Oriented Architectures (SOAs)

    Science.gov (United States)

    2005-06-01

    thinking to view themselves much like a metropolitan chamber of commerce would view their industrial capabilities, as a part of an evolving global...powerful and influential than top down control. This worldview implies that “cities” must develop the equivalent of the traditional “ chamber of commerce ” that...aggregate capabilities just as a metropolitan chamber of commerce would promote the capabilities of their city.10 We advise DoD to work aggressively to

  3. The Flood, the Channels and the Dykes: Managing Legal Information in a Globalized and Digital World

    OpenAIRE

    Breuker, J.; Casanovas, P.; Klein, M.C.A.; Francesconi, E.; Breuker, J.; Casanovas, P.; Klein, M.C.A.; Francesconi, E.

    2008-01-01

    Information search and retrieval are part of daily routines of the legal profession. Lawyers, judges, prosecutors, and legal clerks usually access a number of electronic resources to browse, search, select, or update legal contents. Legal databases have currently become large digital libraries where the tasks related to information-seeking may sometimes be cumbersome. Adding semantics to support information search may provide significant results in terms of efficiency, efficacy, and user sati...

  4. A genetic algorithm for finding good balanced sequences in a customer assignment problem with no state information

    NARCIS (Netherlands)

    Hordijk, W.; Hordijk, A.; Heidergott, B.F.

    2015-01-01

    In this paper, we study the control problem of optimal assignment of tasks to servers in a multi-server queue with inhomogeneous servers. In order to improve the performance of the system, we use a periodic deterministic sequence of job assignments to servers called a billiard sequence. We then use

  5. Ultrascalable Techniques Applied to the Global Intelligence Community Information Awareness Common Operating Picture (IA COP)

    National Research Council Canada - National Science Library

    Valdes, Alfonso; Kadte, Jim

    2005-01-01

    The focus of this research is to develop detection, correlation, and representation approaches to address the needs of the Intelligence Community Information Awareness Common Operating Picture (IA COP...

  6. Electronic processing of informed consents in a global pharmaceutical company environment.

    Science.gov (United States)

    Vishnyakova, Dina; Gobeill, Julien; Oezdemir-Zaech, Fatma; Kreim, Olivier; Vachon, Therese; Clade, Thierry; Haenning, Xavier; Mikhailov, Dmitri; Ruch, Patrick

    2014-01-01

    We present an electronic capture tool to process informed consents, which are mandatory recorded when running a clinical trial. This tool aims at the extraction of information expressing the duration of the consent given by the patient to authorize the exploitation of biomarker-related information collected during clinical trials. The system integrates a language detection module (LDM) to route a document into the appropriate information extraction module (IEM). The IEM is based on language-specific sets of linguistic rules for the identification of relevant textual facts. The achieved accuracy of both the LDM and IEM is 99%. The architecture of the system is described in detail.

  7. Optimizing multiple sequence alignments using a genetic algorithm based on three objectives: structural information, non-gaps percentage and totally conserved columns.

    Science.gov (United States)

    Ortuño, Francisco M; Valenzuela, Olga; Rojas, Fernando; Pomares, Hector; Florido, Javier P; Urquiza, Jose M; Rojas, Ignacio

    2013-09-01

    Multiple sequence alignments (MSAs) are widely used approaches in bioinformatics to carry out other tasks such as structure predictions, biological function analyses or phylogenetic modeling. However, current tools usually provide partially optimal alignments, as each one is focused on specific biological features. Thus, the same set of sequences can produce different alignments, above all when sequences are less similar. Consequently, researchers and biologists do not agree about which is the most suitable way to evaluate MSAs. Recent evaluations tend to use more complex scores including further biological features. Among them, 3D structures are increasingly being used to evaluate alignments. Because structures are more conserved in proteins than sequences, scores with structural information are better suited to evaluate more distant relationships between sequences. The proposed multiobjective algorithm, based on the non-dominated sorting genetic algorithm, aims to jointly optimize three objectives: STRIKE score, non-gaps percentage and totally conserved columns. It was significantly assessed on the BAliBASE benchmark according to the Kruskal-Wallis test (P algorithm also outperforms other aligners, such as ClustalW, Multiple Sequence Alignment Genetic Algorithm (MSA-GA), PRRP, DIALIGN, Hidden Markov Model Training (HMMT), Pattern-Induced Multi-sequence Alignment (PIMA), MULTIALIGN, Sequence Alignment Genetic Algorithm (SAGA), PILEUP, Rubber Band Technique Genetic Algorithm (RBT-GA) and Vertical Decomposition Genetic Algorithm (VDGA), according to the Wilcoxon signed-rank test (P 0.05) with the advantage of being able to use less structures. Structural information is included within the objective function to evaluate more accurately the obtained alignments. The source code is available at http://www.ugr.es/~fortuno/MOSAStrE/MO-SAStrE.zip.

  8. Urban Environmental Education for Global Transformation Initiatives - Integrating Information and Communication Systems for Urban Sustainability in 2050.

    Science.gov (United States)

    Chaudhari, K.

    2017-12-01

    The Urban population of developing countries is predicted to rise from one third in 1990 to over 50% by 2025. In 1950 the world's total urban population was 734 million, of whom 448 million were living in developed countries and remaining 286 were in developing region. The total population on earth is predicted to increase by more than one billion people within the next 15 years, reaching 8.5 billion in 2030, and to increase further to 9.7 billion in 2050 and 11.2 billion by 2100. Looking at the ever increasing urbanization.In 2016, an estimated 54.5 per cent of the world's populations inhabited in urban region. By 2030, urban areas are projected to shelter 60 per cent of people worldwide and one in every three people will live in cities with at least half a million inhabitants.On the basis of these figures and other global trends, it would appear that Africa and Asia will have the highest share of world's urban growth in next 25 years, resulting consideration rise of large number of metropolitan cities and towns. Therefore issues related to urban climate change will be important for socio economic development for urban transformation through environmental sustainability.The information and communication systems plays an important role in achieving the social sustainability through environmental sustainability for urban transformation. This presentation aims to start the Global initiatives on the problem identifications in environment education for global transformation, education for socio-economic and environmental sustainability due to urbanization in 2050 to investigate problems related to social-economic risks and management issues resulting from urbanization to aid mitigation planning in globalized world and to educate scientists and local populations to form a basis for sustainable solutions in environment learning.The presentation aims to assess the potential of information and communication technology for environment education,both within different

  9. Integrating information systems : linking global business goals to local database applications

    NARCIS (Netherlands)

    Dignum, F.P.M.; Houben, G.J.P.M.

    1999-01-01

    This paper describes a new approach to design modern information systems that offer an integrated access to the data and knowledge that is available in local applications. By integrating the local data management activities into one transparent information distribution process, modern organizations

  10. Comprehensive two-dimensional gel protein databases offer a global approach to the analysis of human cells: the transformed amnion cells (AMA) master database and its link to genome DNA sequence data

    DEFF Research Database (Denmark)

    Celis, J E; Gesser, B; Rasmussen, H H

    1990-01-01

    , mitochondria, Golgi, ribosomes, intermediate filaments, microfilaments and microtubules), levels in fetal human tissues, partial protein sequences (containing information on 48 human proteins microsequenced so far), cell cycle-regulated proteins, proteins sensitive to interferons alpha, beta, and gamma, heat...

  11. 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.

  12. The information metric on the moduli space of instantons with global symmetries

    Directory of Open Access Journals (Sweden)

    Emanuel Malek

    2016-02-01

    Full Text Available In this note we revisit Hitchin's prescription [1] of the Fisher metric as a natural measure on the moduli space of instantons that encodes the space–time symmetries of a classical field theory. Motivated by the idea of the moduli space of supersymmetric instantons as an emergent space in the sense of the gauge/gravity duality, we extend the prescription to encode also global symmetries of the underlying theory. We exemplify our construction with the instanton solution of the CPN sigma model on R2.

  13. Reading out neural populations: shared variability, global fluctuations and information processing

    OpenAIRE

    Romero Arandia, Iñigo

    2017-01-01

    Entendre l'origen i la funció de l'activitat de poblacions neuronals, i com aquesta activitat es relaciona amb els estímuls sensorials, les decisions o les accions motores és un gran repte per les neurociències. En aquest treball hem analitzat l'activitat de desenes de neurones enregistrades a l'escorça visual primària de micos mentre se'ls presentaven escletxes sinusoïdals en diferents orientacions. Hem trobat que les fluctuacions globals de la xarxa mesurades mitjançant l'...

  14. The roles of information technology in global chain supply: a multiple case study of multinational companies of China

    Science.gov (United States)

    He, Mao; Duan, Wanchun

    2007-12-01

    Nowadays many Chinese companies have being becoming more and more international. Therefore, these Chinese companies have to face global supply chains rather than the former domestic ones. The use of information technology (IT) is considered a prerequisite for the effective control of today's complex global supply chains. Based on empirical data from 10 multinational companies of China, this paper presents a classification of the ways in which companies use IT in SCM, and examines the drivers for these different utilization types. According to the findings of this research, the purposes of using of IT in SCM can be divided into 1) transaction processing, 2) supply chain planning and collaboration, and 3) order tracking and delivery coordination. The findings further suggest that the drivers between these three uses of IT in SCM differ.

  15. Information Assurance Technologies for the Global Command and Control System (GCCS) Leading Edge Services (LES)

    National Research Council Canada - National Science Library

    O'Brien, Richard

    2001-01-01

    ... (LES) program was sponsored by DARPA's Information Systems Office. This report describes the different technology areas the program encompassed, summarized the major achievements of the program, and documents lessons learned and open issues...

  16. The New Global Information Economy: Implications and Recommendations for Service-Oriented Architectures (SOAs)

    National Research Council Canada - National Science Library

    Bass, Tim; Donahue, William

    2005-01-01

    ... to fast changing mission and business needs. The large-scale service-oriented architectures that DoD planners envision are designed to lower barriers to dynamic information sharing and improve content quality, quantity and propriety...

  17. The New Global Information Economy: Implications and Recommendations for Service-Oriented Architectures (SOAs)

    National Research Council Canada - National Science Library

    Bass, Tim; Donahue, William

    2005-01-01

    Service-oriented architecture (SOA), a term often used today in conjunction with net-centric operations, implies that existing and future DoD information capabilities will be engineered to publish product and/or service offerings...

  18. Visual working memory for global, object, and part-based information.

    Science.gov (United States)

    Patterson, Michael D; Bly, Benjamin Martin; Porcelli, Anthony J; Rypma, Bart

    2007-06-01

    We investigated visual working memory for novel objects and parts of novel objects. After a delay period, participants showed strikingly more accurate performance recognizing a single whole object than the parts of that object. This bias to remember whole objects, rather than parts, persisted even when the division between parts was clearly defined and the parts were disconnected from each other so that, in order to remember the single whole object, the participants needed to mentally combine the parts. In addition, the bias was confirmed when the parts were divided by color. These experiments indicated that holistic perceptual-grouping biases are automatically used to organize storage in visual working memory. In addition, our results suggested that the bias was impervious to top-down consciously directed control, because when task demands were manipulated through instruction and catch trials, the participants still recognized whole objects more quickly and more accurately than their parts. This bias persisted even when the whole objects were novel and the parts were familiar. We propose that visual working memory representations depend primarily on the global configural properties of whole objects, rather than part-based representations, even when the parts themselves can be clearly perceived as individual objects. This global configural bias beneficially reduces memory load on a capacity-limited system operating in a complex visual environment, because fewer distinct items must be remembered.

  19. How information technology can help sustainability and aid in combating global warming[ACI SP-234-44

    Energy Technology Data Exchange (ETDEWEB)

    Kondratova, I.L.; Goldfarb, I. [National Research Council of Canada, Ottawa, ON (Canada). Inst. for Information Technology

    2006-07-01

    This presentation addressed the need to reduce the environmental impact of concrete production. Unit based carbon dioxide emissions in cement production vary from 0.73 to 0.99 kg carbon dioxide per kg of cement. As such, annual cement manufacturing contributes significantly to global warming. The challenge facing the concrete industry regarding sustainable growth was discussed. It was suggested that sustainable development in the cement industry can be accomplished not only by making an industry wide shift to conservation of energy and materials, but by making greater use of the Internet for information technology on sustainable construction materials such as lightweight aggregates and lightweight concrete. The paper outlined the evolution of various methods of disseminating research results on the durability of concrete at the United States Army Corps of Engineers Treat Island marine exposure site. The results indicated that structural lightweight and semi-lightweight concrete provides long-term durability in a marine environment. It was noted that knowledge utilization includes technology transfer, information dissemination and utilization, research utilization, innovation, and organizational change. The paper emphasized the use of web portals as a tool for improving access to practical information on a full range of sustainable industry practices, products and resources. These tools allow side-by side comparison of testing results for different concrete mixtures and support decision-making on the choice of environmentally sound and durable concrete. The authors demonstrated by advantages of using modern information technology tools by suggesting that with the development of a full scale Portal, the Expanded Shale, Clay, and Slate Institute (ESCSI) could become a global source of credible information and expertise in the area of lightweight concrete. As such ESCSI could be in a position to influence innovation and technology transfer to the industry. The paper

  20. AIM satellite-based research bridges the unique scientific aspects of the mission to informal education programs globally

    Science.gov (United States)

    Robinson, D.; Maggi, B.

    2003-04-01

    The Education and Public Outreach (EPO) component of the satellite-based research mission "Aeronomy of Ice In the Mesosphere" (AIM) will bridge the unique scientific aspects of the mission to informal education organizations. The informal education materials developed by the EPO will utilize AIM data and educate the public about the environmental implications associated with the data. This will assist with creating a scientifically literate workforce and in developing a citizenry capable of making educated decisions related to environmental policies and laws. The objective of the AIM mission is to understand the mechanisms that cause Polar Mesospheric Clouds (PMCs) to form, how their presence affects the atmosphere, and how change in the atmosphere affects them. PMCs are sometimes known as Noctilucent Clouds (NLCs) because of their visibility during the night from appropriate locations. The phenomenon of PMCs is an observable indicator of global change, a concern to all citizens. Recent sightings of these clouds over populated regions have compelled AIM educators to expand informal education opportunities to communities worldwide. Collaborations with informal organizations include: Museums/Science Centers; NASA Sun-Earth Connection Forum; Alaska Native Ways of Knowing Project; Amateur Noctilucent Cloud Observers Organization; National Parks Education Programs; After School Science Clubs; Public Broadcasting Associations; and National Public Radio. The Native Ways of Knowing Project is an excellent example of informal collaboration with the AIM EPO. This Alaska based project will assist native peoples of the state with photographing NLCs for the EPO website. It will also aid the EPO with developing materials for informal organizations that incorporate traditional native knowledge and science, related to the sky. Another AIM collaboration that will offer citizens lasting informal education opportunities is the one established with the United States National Parks

  1. The “Commodification” of Knowledge in the Global Information Society

    Directory of Open Access Journals (Sweden)

    Peter Fleissner

    2009-11-01

    Possible strategies on how to go on from now are presented, among them the struggle and on-going resistance of the European Parliament on the one hand, against the European Commission and the European Patent Office on the other, also the movements of open source/free software and the ideas of copyleft to create new rules for information goods.

  2. GlobePort Faces Global Business Challenges--Assessing the Organizational Side of Information Systems Projects

    Science.gov (United States)

    Ghosh, Biswadip

    2011-01-01

    Published studies have reported that Information System (IS) projects succeed or fail based on how effectively the organizational issues were understood and addressed in the specification, development and implementation stages of the project. This is particularly true in the design and delivery of Inter-Organizational Systems (IOS) that can affect…

  3. 2015 Global Information Technology Report: Consequences on Knowledge Management in Higher Education Institutions in Nigeria

    Science.gov (United States)

    Ololube, Nwachukwu Prince; Agbor, Comfort Nkogho; Major, Nanighe Baldwin; Agabi, Chinyere O.; Wali, Worlu I.

    2016-01-01

    This research is a continuation of a theoretical review that evaluated ICT Policy Outcomes for National Development in relation to Networked Readiness Index (NRI) and the impact it has on knowledge integration and management in higher education institutions in Nigeria. A new dawn in information technology (IT) has initiated new trends in…

  4. The Flood, the Channels and the Dykes: Managing Legal Information in a Globalized and Digital World

    NARCIS (Netherlands)

    Breuker, J.; Casanovas, P.; Klein, M.C.A.; Francesconi, E.; Breuker, J.; Casanovas, P.; Klein, M.C.A.; Francesconi, E.

    2008-01-01

    Information search and retrieval are part of daily routines of the legal profession. Lawyers, judges, prosecutors, and legal clerks usually access a number of electronic resources to browse, search, select, or update legal contents. Legal databases have currently become large digital libraries where

  5. Global publication trends in the Health Information and Libraries Journal, 2014-2015.

    Science.gov (United States)

    Murphy, Jeannette

    2016-03-01

    In an age when health science librarians are encouraged to engage in research, it is worth considering how international the published literature is. This article analyses the authorship of articles in Health Information & Libraries Journal over a 1-year period, to determine the country of the authors who were published. JM. © 2016 Health Libraries Group.

  6. Management Education for Archivists, Information Managers, and Librarians: Is There a Global Core?

    Science.gov (United States)

    Evans, G. Edward

    1984-01-01

    Reports on an analysis of 35 American management textbooks that identifies 17 core concepts for management courses for information professionals. Each concept--accountability, accounting, authority, budgeting, change/innovation/creativity, communication, controlling, decision making, delegation and organization, ethics, fiscal management,…

  7. 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.

  8. The role of new information technology meeting the global need and gap of education in pediatric surgery.

    Science.gov (United States)

    Ure, Benno; Zoeller, Christoph; Lacher, Martin

    2015-06-01

    Traditionally, pediatric surgical education consisted of exposure to patients, textbooks, lectures, team-based education, congresses, and workshops. Over the last decades, however, new information technology (IT) and the internet revolutionized the sharing of information and communication. IT has become relevant in particular for the younger generation of pediatric surgeons. Today, gaps in children's health and the quality of pediatric surgical education persist between countries and regions. Advances in health care are not shared equitably. The use of IT for resource libraries, teleconferences, virtual symposiums, and telementoring has great potential in closing this gap and meeting the global needs for pediatric surgical education. This article focuses on the potential role of IT in this respect. Copyright © 2015 Elsevier Inc. All rights reserved.

  9. The implications of megatrends in information and communication technology and transportation for changes in global physical activity.

    Science.gov (United States)

    Pratt, Michael; Sarmiento, Olga L; Montes, Felipe; Ogilvie, David; Marcus, Bess H; Perez, Lilian G; Brownson, Ross C

    2012-07-21

    Physical inactivity accounts for more than 3 million deaths per year, most from non-communicable diseases in low-income and middle-income countries. We used reviews of physical activity interventions and a simulation model to examine how megatrends in information and communication technology and transportation directly and indirectly affect levels of physical activity across countries of low, middle, and high income. The model suggested that the direct and potentiating eff ects of information and communication technology, especially mobile phones, are nearly equal in magnitude to the mean eff ects of planned physical activity interventions. The greatest potential to increase population physical activity might thus be in creation of synergistic policies in sectors outside health including communication and transportation. However, there remains a glaring mismatch between where studies on physical activity interventions are undertaken and where the potential lies in low-income and middle-income countries for population-level effects that will truly affect global health.

  10. Mobile geonet: Anywhere, global and secure access to your geographic oriented information

    International Nuclear Information System (INIS)

    Denizot, Laurent

    2001-01-01

    Today, the mobile technology has set up devices and communication architectures which change the way to work and improve efficiency and interactivity. EADS Matra Systems and Information is involved into these changes and develops a generic technology, mobile geonet, which brings these new means to improve the link between people who works together. Mobile geonet is a framework to develop mobile applications with a high security level and geographic capabilities. It is based on fully networked technologies (intranet/extranet/internet). It uses common mobile devices, enhanced by localisation and communication add-ons, like GPS, GSM or satellite phones modules. All the information processed and produced by upstream activities is stored in the DB GEO database system. These can be reports, maps, satellite images, structured information, points of interest and anything else with an potential geographic component. The role of the ASP (Application Service Provider) is to integrate existing applications or provide new ones. These applications are activated whether server-side, to mine, prepare and encode data or client-side to decode, present or interact in particular means with the user. The applications and data are disseminated through an extranet server. A particular interest of distributing the client applications by the ASP is the deployment cost on all mobile and fixed terminals, which is very small, because it is automatically downloaded for each upgrade. The communication layer aims at delivering applications up to the mobile device and permits the data exchange between the mobile device and the central data repository. Different means can be used: GSM network, internet or satellite communications. The applications are adapted to the available bandwidth, especially when image parts are downloaded. The mobile device is chosen on the shelf, depending of the requirements of the application. The computer can be a very small Pocket PC or a typical portable PC. For

  11. Drug pricing and reimbursement information management: processes and decision making in the global economy

    OpenAIRE

    Tsourougiannis, Dimitrios

    2017-01-01

    ABSTRACT Background: Cost-containment initiatives are re-shaping the pharmaceutical business environment and affecting market access as well as pricing and reimbursement decisions. Effective price management procedures are too complex to accomplish manually. Prior to February 2013, price management within Astellas Pharma Europe Ltd was done manually using an Excel database. The system was labour intensive, slow to update, and prone to error. An innovative web-based pricing information managem...

  12. Successfully Changing the Landscape of Information Distribution: Extension Food Website Reaches People Locally and Globally

    OpenAIRE

    Alice Henneman; Lisa Franzen-Castle; Kayla Colgrove; Vishal Singh

    2016-01-01

    The goal of the Food website was to develop Internet-based content that was relevant and reached the general public and multiplier groups, such as educators, health professionals, and media outlets. The purpose of this paper was to examine whether a multi-modal approach to information delivery through increases in and changes to content, electronic mailing list creation, and social media posting impacted user access, traffic channels, and referrals from 2010 to 2014. When comparing 2010-2011 ...

  13. [Global analysis of the readability of the informed consent forms used in public hospitals of Spain].

    Science.gov (United States)

    Mariscal-Crespo, M I; Coronado-Vázquez, M V; Ramirez-Durán, M V

    To analyse the readability of informed consent forms (ICF) used in Public Hospitals throughout Spain, with the aim of checking their function of providing comprehensive information to people who are making any health decision no matter where they are in Spain. A descriptive study was performed on a total of 11,339 ICF received from all over Spanish territory, of which 1617 ICF were collected from 4 web pages of Health Portal and the rest (9722) were received through email and/or telephone contact from March 2012 to February 2013. The readability level was studied using the Inflesz tool. A total of 372 ICF were selected and analysed using simple random sampling. The Inflesz scale and the Flesch-Szigriszt index were used to analyse the readability. The readability results showed that 62.4% of the ICF were rated as a "little difficult", the 23.4% as "normal", and the 13.4% were rated as "very difficult". The highest readability means using the Flesch index were scored in Andalusia with a mean of 56.99 (95% CI; 55.42-58.57) and Valencia with a mean of 51.93 (95% CI; 48.4-55.52). The lowest readability means were in Galicia with a mean of 40.77 (95% CI; 9.83-71.71) and Melilla, mean=41.82 (95% CI; 35.5-48.14). The readability level of Spanish informed consent forms must be improved because their scores using readability tools could not be classified in normal scales. Furthermore, there was very wide variability among Spanish ICF, which showed a lack of equity in information access among Spanish citizens. Copyright © 2017 SECA. Publicado por Elsevier España, S.L.U. All rights reserved.

  14. The Global Opioid Policy Initiative: a wealth of information, but what is next?

    Science.gov (United States)

    Scholten, Willem

    2014-03-01

    Recently, the outcomes were published of the Global Opioid Policy Initiative, evaluating the availability, cost of opioid medicines and the regulatory barriers that are possibly impeding access for the management of cancer pain in developing countries. Other studies have shown that the vast majority of the world population has no access to opioid analgesics. This study shows by country which opioid medicines are available, what they cost to the patient, and investigates the presence of barriers for access to these medicines. Data from the project will be an important resource for those who advocate for improved access to opioid analgesics. Yet, like so often, many more aspects of inadequate opioid analgesic consumption require exploration and reporting, including legislative barriers. The last publication on the project is a "What's next?" that is over focusing on palliative care, forgetting that outside palliative care is also a huge need for opioid analgesics in moderate and severe pain. While promoting access to palliative care and pain management, their recognition as a human right by UN bodies would be of great help. Moreover, WHO's Access to Controlled Medicines Programme, could be an important programme to support the countries in making these improvements.

  15. Impact of credit information on the banks stability: Global experience and lessons for Ukraine

    Directory of Open Access Journals (Sweden)

    Inna Bielova

    2016-05-01

    Full Text Available A quality of the credit portfolio is one of the most important factors of banking system reliability. It is obviously, that there is a direct relationship between this indicator and financial stability of the bank. In turn, the quality of the loan portfolio depends on many factors that are investigated in scientific and educational literature. In this paper, we propose to focus on a group of factors of credit risk that are connected with the availability of information about the borrower. The low efficiency of the national system of collecting information about borrowers in Ukraine in comparison with foreign models was confirmed by the quantitative analysis. This tendency cases the high level of credit risks and low financial stability level of domestic banks. It is necessary to make active efforts on improving the effectiveness of credit bureaus in Ukraine by establishing public credit registry and also to focus on solving other problems associated with the collection and use of information about borrowers

  16. Global sensitivity analysis of water age and temperature for informing salmonid disease management

    Science.gov (United States)

    Javaheri, Amir; Babbar-Sebens, Meghna; Alexander, Julie; Bartholomew, Jerri; Hallett, Sascha

    2018-06-01

    Many rivers in the Pacific Northwest region of North America are anthropogenically manipulated via dam operations, leading to system-wide impacts on hydrodynamic conditions and aquatic communities. Understanding how dam operations alter abiotic and biotic variables is important for designing management actions. For example, in the Klamath River, dam outflows could be manipulated to alter water age and temperature to reduce risk of parasite infections in salmon by diluting or altering viability of parasite spores. However, sensitivity of water age and temperature to the riverine conditions such as bathymetry can affect outcomes from dam operations. To examine this issue in detail, we conducted a global sensitivity analysis of water age and temperature to a comprehensive set of hydraulics and meteorological parameters in the Klamath River, California, where management of salmonid disease is a high priority. We applied an analysis technique, which combined Latin-hypercube and one-at-a-time sampling methods, and included simulation runs with the hydrodynamic numerical model of the Lower Klamath. We found that flow rate and bottom roughness were the two most important parameters that influence water age. Water temperature was more sensitive to inflow temperature, air temperature, solar radiation, wind speed, flow rate, and wet bulb temperature respectively. Our results are relevant for managers because they provide a framework for predicting how water within 'high infection risk' sections of the river will respond to dam water (low infection risk) input. Moreover, these data will be useful for prioritizing the use of water age (dilution) versus temperature (spore viability) under certain contexts when considering flow manipulation as a method to reduce risk of infection and disease in Klamath River salmon.

  17. Shigella isolates from the global enteric multicenter study inform vaccine development.

    Science.gov (United States)

    Livio, Sofie; Strockbine, Nancy A; Panchalingam, Sandra; Tennant, Sharon M; Barry, Eileen M; Marohn, Mark E; Antonio, Martin; Hossain, Anowar; Mandomando, Inacio; Ochieng, John B; Oundo, Joseph O; Qureshi, Shahida; Ramamurthy, Thandavarayan; Tamboura, Boubou; Adegbola, Richard A; Hossain, Mohammed Jahangir; Saha, Debasish; Sen, Sunil; Faruque, Abu Syed Golam; Alonso, Pedro L; Breiman, Robert F; Zaidi, Anita K M; Sur, Dipika; Sow, Samba O; Berkeley, Lynette Y; O'Reilly, Ciara E; Mintz, Eric D; Biswas, Kousick; Cohen, Dani; Farag, Tamer H; Nasrin, Dilruba; Wu, Yukun; Blackwelder, William C; Kotloff, Karen L; Nataro, James P; Levine, Myron M

    2014-10-01

    Shigella, a major diarrheal disease pathogen worldwide, is the target of vaccine development. The Global Enteric Multicenter Study (GEMS) investigated burden and etiology of moderate-to-severe diarrheal disease in children aged Shigella was 1 of the 4 most common pathogens across sites and age strata. GEMS Shigella serotypes are reviewed to guide vaccine development. Subjects' stool specimens/rectal swabs were transported to site laboratories in transport media and plated onto xylose lysine desoxycholate and MacConkey agar. Suspect Shigella colonies were identified by biochemical tests and agglutination with antisera. Shigella isolates were shipped to the GEMS Reference Laboratory (Baltimore, MD) for confirmation and serotyping of S. flexneri; one-third of isolates were sent to the Centers for Disease Control and Prevention for quality control. Shigella dysenteriae and S. boydii accounted for 5.0% and 5.4%, respectively, of 1130 Shigella case isolates; S. flexneri comprised 65.9% and S. sonnei 23.7%. Five serotypes/subserotypes comprised 89.4% of S. flexneri, including S. flexneri 2a, S. flexneri 6, S. flexneri 3a, S. flexneri 2b, and S. flexneri 1b. A broad-spectrum Shigella vaccine must protect against S. sonnei and 15 S. flexneri serotypes/subserotypes. A quadrivalent vaccine with O antigens from S. sonnei, S. flexneri 2a, S. flexneri 3a, and S. flexneri 6 can provide broad direct coverage against these most common serotypes and indirect coverage against all but 1 (rare) remaining subserotype through shared S. flexneri group antigens. © The Author 2014. Published by Oxford University Press on behalf of the Infectious Diseases Society of America.

  18. Freedom of information and abuse of media in the process of globalization

    OpenAIRE

    Milan Palevic; Srdjan Djordjevic

    2013-01-01

    Freedom of speech is considered to be one of the basic human rights and is included as an indisputable in all major international conventions and national laws. Due to the role they play in informing the public and creating public opinion, mass media and journalists are often said to be the "fourth power" in the society. Indeed, the media have increased their capacity in material, technical and personnel agenda, so that today they can independently, or, in alliance with a broader factor of po...

  19. International Cyber Incident Repository System: Information Sharing on a Global Scale

    Energy Technology Data Exchange (ETDEWEB)

    Joyce, Amanda L.; Evans, PhD, Nathaniel; Tanzman, Edward A.; Israeli, Daniel

    2017-02-02

    According to the 2016 Internet Security Threat Report, the largest number of cyber attacks were recorded last year (2015), reaching a total of 430 million incidents throughout the world. As the number of cyber incidents increases, the need for information and intelligence sharing increases, as well. This fairly large increase in cyber incidents is driving the need for an international cyber incident data reporting system. The goal of the cyber incident reporting system is to make available shared and collected information about cyber events among participating international parties. In its 2014 report, Insurance Industry Working Session Readout Report-Insurance for CyberRelated Critical Infrastructure Loss: Key Issues, on the outcomes of a working session on cyber insurance, the U.S. Department of Homeland Security observed that “many participants cited the need for a secure method through which organizations could pool and share cyber incident information” and noted that one underwriter emphasized the importance of internationally harmonized data taxonomies. This cyber incident data reporting system could benefit all nations that take part in reporting incidents to provide a more common operating picture. In addition, this reporting system could allow for trending and anticipated attacks and could potentially benefit participating members by enabling them to get in front of potential attacks. The purpose of this paper is to identify options for consideration for such a system in fostering cooperative cyber defense.

  20. Toward Soil Spatial Information Systems (SSIS) for global modeling and ecosystem management

    Science.gov (United States)

    Baumgardner, Marion F.

    1995-01-01

    The general objective is to conduct research to contribute toward the realization of a world soils and terrain (SOTER) database, which can stand alone or be incorporated into a more complete and comprehensive natural resources digital information system. The following specific objectives are focussed on: (1) to conduct research related to (a) translation and correlation of different soil classification systems to the SOTER database legend and (b) the inferfacing of disparate data sets in support of the SOTER Project; (2) to examine the potential use of AVHRR (Advanced Very High Resolution Radiometer) data for delineating meaningful soils and terrain boundaries for small scale soil survey (range of scale: 1:250,000 to 1:1,000,000) and terrestrial ecosystem assessment and monitoring; and (3) to determine the potential use of high dimensional spectral data (220 reflectance bands with 10 m spatial resolution) for delineating meaningful soils boundaries and conditions for the purpose of detailed soil survey and land management.

  1. An analysis of Vigimed, a global e-mail system for the exchange of pharmacovigilance information.

    Science.gov (United States)

    Johansson, Kristina; Olsson, Sten; Hellman, Björn; Meyboom, Ronald H B

    2007-01-01

    The Internet provides novel ways for communication and data exchange between national regulators. One innovation was the introduction of Vigimed, an e-mail discussion forum for national pharmacovigilance centres (NPCs). We reviewed a sample of Vigimed messages to learn more about this new tool and about the problems encountered in everyday pharmacovigilance and how these are handled. We analysed the contents of 100 subsequent questions and the corresponding responses as stored in the Vigimed datafile. To the 100 questions circulated through Vigimed, 575 answers were received; mean number of answers per question 6, range 0-20. Fifty-five (77%) of the 71 collaborating countries and 88 (43%) of the 204 individuals who had access in the study period had submitted at least one question or answer. These countries were in all parts of the world and in various phases of development. A total of 38% of the questions concerned the regulatory status of a drug; 30% safety issues; 13% regulatory actions under consideration; and 10% drug use-related problems (more than one category possible). Of the questions, 89% concerned established drugs; 11% were classified as new. A total of 90% of the questions concerned specific active substances or drug groups. Of the drugs, 73% were classified as 'orthodox' and 9% as herbal; 4% were vaccines and 4% excipients. Emerging drug groups (anatomical therapeutic chemical codes) were NSAIDs and analgesics (M01, N02), antibacterials (J01), antiobesity drugs (A08), psychotropic drugs (N05) and antihistamines (R06). NPCs operate in a restricted environment and there is little published information about the daily practices and experiences at NPCs. Our study concerned a sample in a limited period in time. In the meantime, the use of Vigimed has greatly expanded. The data in the Vigimed records are subjected to confidentiality in regard to the identities of countries, staff members, drug products and pharmaceutical companies, which limits the

  2. The use of mycobacterial interspersed repetitive unit typing and whole genome sequencing to inform tuberculosis prevention and control activities.

    Science.gov (United States)

    Gilbert, Gwendolyn L; Sintchenko, Vitali

    2013-07-01

    Molecular strain typing of Mycobacterium tuberculosis has been possible for only about 20 years; it has significantly improved our understanding of the evolution and epidemiology of Mycobacterium tuberculosis and tuberculosis disease. Mycobacterial interspersed repetitive unit typing, based on 24 variable number tandem repeat unit loci, is highly discriminatory, relatively easy to perform and interpret and is currently the most widely used molecular typing system for tuberculosis surveillance. Nevertheless, clusters identified by mycobacterial interspersed repetitive unit typing sometimes cannot be confirmed or adequately defined by contact tracing and additional methods are needed. Recently, whole genome sequencing has been used to identify single nucleotide polymorphisms and other mutations, between genotypically indistinguishable isolates from the same cluster, to more accurately trace transmission pathways. Rapidly increasing speed and quality and reduced costs will soon make large scale whole genome sequencing feasible, combined with the use of sophisticated bioinformatics tools, for epidemiological surveillance of tuberculosis.

  3. A Globally Distributed System for Job, Data, and Information Handling for High Energy Physics

    Energy Technology Data Exchange (ETDEWEB)

    Garzoglio, Gabriele [DePaul Univ., Chicago, IL (United States)

    2006-01-13

    The computing infrastructures of the modern high energy physics experiments need to address an unprecedented set of requirements. The collaborations consist of hundreds of members from dozens of institutions around the world and the computing power necessary to analyze the data produced surpasses already the capabilities of any single computing center. A software infrastructure capable of seamlessly integrating dozens of computing centers around the world, enabling computing for a large and dynamical group of users, is of fundamental importance for the production of scientific results. Such a computing infrastructure is called a computational grid. The SAM-Grid offers a solution to these problems for CDF and DZero, two of the largest high energy physics experiments in the world, running at Fermilab. The SAM-Grid integrates standard grid middleware, such as Condor-G and the Globus Toolkit, with software developed at Fermilab, organizing the system in three major components: data handling, job handling, and information management. This dissertation presents the challenges and the solutions provided in such a computing infrastructure.

  4. Medical image registration by combining global and local information: a chain-type diffeomorphic demons algorithm

    International Nuclear Information System (INIS)

    Liu, Xiaozheng; Yuan, Zhenming; Zhu, Junming; Xu, Dongrong

    2013-01-01

    The demons algorithm is a popular algorithm for non-rigid image registration because of its computational efficiency and simple implementation. The deformation forces of the classic demons algorithm were derived from image gradients by considering the deformation to decrease the intensity dissimilarity between images. However, the methods using the difference of image intensity for medical image registration are easily affected by image artifacts, such as image noise, non-uniform imaging and partial volume effects. The gradient magnitude image is constructed from the local information of an image, so the difference in a gradient magnitude image can be regarded as more reliable and robust for these artifacts. Then, registering medical images by considering the differences in both image intensity and gradient magnitude is a straightforward selection. In this paper, based on a diffeomorphic demons algorithm, we propose a chain-type diffeomorphic demons algorithm by combining the differences in both image intensity and gradient magnitude for medical image registration. Previous work had shown that the classic demons algorithm can be considered as an approximation of a second order gradient descent on the sum of the squared intensity differences. By optimizing the new dissimilarity criteria, we also present a set of new demons forces which were derived from the gradients of the image and gradient magnitude image. We show that, in controlled experiments, this advantage is confirmed, and yields a fast convergence. (paper)

  5. Measuring the global information society - explaining digital inequality by economic level and education standard

    Science.gov (United States)

    Ünver, H.

    2017-02-01

    A main focus of this research paper is to investigate on the explanation of the ‘digital inequality’ or ‘digital divide’ by economic level and education standard of about 150 countries worldwide. Inequality regarding GDP per capita, literacy and the so-called UN Education Index seem to be important factors affecting ICT usage, in particular Internet penetration, mobile phone usage and also mobile Internet services. Empirical methods and (multivariate) regression analysis with linear and non-linear functions are useful methods to measure some crucial factors of a country or culture towards becoming information and knowledge based society. Overall, the study concludes that the convergence regarding ICT usage proceeds worldwide faster than the convergence in terms of economic wealth and education in general. The results based on a large data analysis show that the digital divide is declining over more than a decade between 2000 and 2013, since more people worldwide use mobile phones and the Internet. But a high digital inequality explained to a significant extent by the functional relation between technology penetration rates, education level and average income still exists. Furthermore it supports the actions of countries at UN/G20/OECD level for providing ICT access to all people for a more balanced world in context of sustainable development by postulating that policymakers need to promote comprehensive education worldwide by means of using ICT.

  6. A study of archaeal enzymes involved in polar lipid synthesis linking amino acid sequence information, genomic contexts and lipid composition

    Directory of Open Access Journals (Sweden)

    Hiromi Daiyasu

    2005-01-01

    Full Text Available Cellular membrane lipids, of which phospholipids are the major constituents, form one of the characteristic features that distinguish Archaea from other organisms. In this study, we focused on the steps in archaeal phospholipid synthetic pathways that generate polar lipids such as archaetidylserine, archaetidylglycerol, and archaetidylinositol. Only archaetidylserine synthase (ASS, from Methanothermobacter thermautotrophicus, has been experimentally identified. Other enzymes have not been fully examined. Through database searching, we detected many archaeal hypothetical proteins that show sequence similarity to members of the CDP alcohol phosphatidyltransferase family, such as phosphatidylserine synthase (PSS, phosphatidylglycerol synthase (PGS and phosphatidylinositol synthase (PIS derived from Bacteria and Eukarya. The archaeal hypothetical proteins were classified into two groups, based on the sequence similarity. Members of the first group, including ASS from M. thermautotrophicus, were closely related to PSS. The rough agreement between PSS homologue distribution within Archaea and the experimentally identified distribution of archaetidylserine suggested that the hypothetical proteins are ASSs. We found that an open reading frame (ORF tends to be adjacent to that of ASS in the genome, and that the order of the two ORFs is conserved. The sequence similarity of phosphatidylserine decarboxylase to the product of the ORF next to the ASS gene, together with the genomic context conservation, suggests that the ORF encodes archaetidylserine decarboxylase, which may transform archaetidylserine to archaetidylethanolamine. The second group of archaeal hypothetical proteins was related to PGS and PIS. The members of this group were subjected to molecular phylogenetic analysis, together with PGSs and PISs and it was found that they formed two distinct clusters in the molecular phylogenetic tree. The distribution of members of each cluster within Archaea

  7. Macro-Logistics Decision Factors and Information Measures for Scanning Global (Supply Chain) Environments in International Location Choice

    DEFF Research Database (Denmark)

    Kinra, Aseem

    2012-01-01

    and strategic forecasting needs in relation to international risks. This may be done within the context of decision support systems that aid in global site location and other supply chain design problems. In contrast to solely utilizing widely-accepted environmental scanning indexes, managers may......value chains and supply chain management. This scope is usually accompanied by uncertainty to organisations, especially for the cross-border value chain with geographically dispersed operations and activities, and poses environmental complexity in the form of risks and costs that organisations need...... that pose constraints to international supply chain flows, and describe international uncertainty for firms. A catalogue of 187 information measures that aid in decisions on each relevant factor is also identified. The findings may be used by managers in different industry contexts for their scanning...

  8. Global Mapping of Transcription Factor Binding Sites by Sequencing Chromatin Surrogates: a Perspective on Experimental Design, Data Analysis, and Open Problems.

    Science.gov (United States)

    Wei, Yingying; Wu, George; Ji, Hongkai

    2013-05-01

    Mapping genome-wide binding sites of all transcription factors (TFs) in all biological contexts is a critical step toward understanding gene regulation. The state-of-the-art technologies for mapping transcription factor binding sites (TFBSs) couple chromatin immunoprecipitation (ChIP) with high-throughput sequencing (ChIP-seq) or tiling array hybridization (ChIP-chip). These technologies have limitations: they are low-throughput with respect to surveying many TFs. Recent advances in genome-wide chromatin profiling, including development of technologies such as DNase-seq, FAIRE-seq and ChIP-seq for histone modifications, make it possible to predict in vivo TFBSs by analyzing chromatin features at computationally determined DNA motif sites. This promising new approach may allow researchers to monitor the genome-wide binding sites of many TFs simultaneously. In this article, we discuss various experimental design and data analysis issues that arise when applying this approach. Through a systematic analysis of the data from the Encyclopedia Of DNA Elements (ENCODE) project, we compare the predictive power of individual and combinations of chromatin marks using supervised and unsupervised learning methods, and evaluate the value of integrating information from public ChIP and gene expression data. We also highlight the challenges and opportunities for developing novel analytical methods, such as resolving the one-motif-multiple-TF ambiguity and distinguishing functional and non-functional TF binding targets from the predicted binding sites. The online version of this article (doi:10.1007/s12561-012-9066-5) contains supplementary material, which is available to authorized users.

  9. Networking of research information on global environment protection technologies; Chikyu kankyo taisaku gijutsu no kenkyu joho network jigyo

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1999-03-01

    Networking is being executed with an objective of exchanging information on global environment technologies at an international level. In order to further promote the information exchange, and to make web sites user-friendly, fiscal 1998 has performed structuring a thesis renewal system. As a result of structuring the thesis renewal system, researchers can use the system as using a word processor by inputting data from a terminal in their laboratories. The data can also be made into a data base nearly semi-automatically. In addition to reducing time loss, delay and input errors because of re-entry, the researchers can make the data into a database on nearly a real time basis, and can provide their own theses to any part of the world through Internet. With regard to retaining Internet security, the security software having been introduced last year was renewed. In addition, detailed status such as daily access has become possible of identification as a result of introducing the net intellect. (NEDO)

  10. Global Land Data Assimilation System (GLDAS) Products, Services and Application from NASA Hydrology Data and Information Services Center (HDISC)

    Science.gov (United States)

    Fang, Hongliang; Beaudoing, Hiroko K.; Rodell, matthew; Teng, William L.; Vollmer, Bruce E.

    2009-01-01

    The Global Land Data Assimilation System (GLDAS) is generating a series of land surface state (e.g., soil moisture and surface temperature) and flux (e.g., evaporation and sensible heat flux) products simulated by four land surface models (CLM, Mosaic, Noah and VIC). These products are now accessible at the Hydrology Data and Information Services Center (HDISC), a component of the NASA Goddard Earth Sciences Data and Information Services Center (GES DISC). Current data holdings include a set of 1.0 degree resolution data products from the four models, covering 1979 to the present; and a 0.25 degree data product from the Noah model, covering 2000 to the present. The products are in Gridded Binary (GRIB) format and can be accessed through a number of interfaces. Users can search the products through keywords and perform on-the-fly spatial and parameter subsetting and format conversion of selected data. More advanced visualization, access and analysis capabilities will be available in the future. The long term GLDAS data are used to develop climatology of water cycle components and to explore the teleconnections of droughts and pluvial.

  11. Information Communication Technology, State building, and Globalization in the 21st Century: Regional Frameworks for Emerging State Assistance

    National Research Council Canada - National Science Library

    Reese, Justin Y

    2008-01-01

    .... Globalization has modified the essential role of the nation-state towards managing global flows of resource, capital, and populations rather than, as in the past, presiding over distinct national economies...

  12. SU-F-E-14: Global Radiation Oncology Education and Training in Medical Physics Powered by Information and Communication Technologies

    International Nuclear Information System (INIS)

    Ngwa, W; Sajo, E; Ngoma, T; Dachi, J; Julius Mwaiselage, J; Kenton, O; Avery, S

    2016-01-01

    Purpose: Recent publications have highlighted the potential of Information and Communication Technologies (ICTs) to catalyze collaborations in cancer care, research and education in global radiation oncology. This work reports on the use of ICTs for global Medical Physics education and training across three countries: USA, Tanzania and Kuwait Methods: An online education platform was established by Radiation Oncology Faculty from Harvard Medical School, and the University of Pennsylvania with integrated Medical Physics Course modules accessible to trainees in Tanzania via partnership with the Muhimbili University of Health and Allied Sciences, and the Ocean Road Cancer Institute. The course modules incorporated lectures covering Radiation Therapy Physics with videos, discussion board, assessments and grade center. Faculty at Harvard Medical School and the University of Massachusetts Lowell also employed weekly Skype meetings to train/mentor three graduate students, living out-of-state and in Kuwait for up to 9 research credits per semester for over two semesters towards obtaining their graduate degrees Results: Students were able to successfully access the Medical Physics course modules and participate in learning activities, online discussion boards, and assessments. Other instructors could also access/co-teach the course modules from USA and Tanzania. Meanwhile all three graduate students with remote training via Skype and email made major progress in their graduate training with each one of them submitting their research results as abstracts to be presented at the 2016 AAPM conference. One student has also published her work already and all three are developing these abstracts for publication in peer-reviewed journals. Conclusion: Altogether, this work highlights concrete examples/model on how ICTs can be used for capacity building in Medical Physics across continents, for both education and research training needed for Masters/PhD degrees. The developed modules

  13. SU-F-E-14: Global Radiation Oncology Education and Training in Medical Physics Powered by Information and Communication Technologies

    Energy Technology Data Exchange (ETDEWEB)

    Ngwa, W [Harvard Medical School, Boston, MA (United States); University Massachusetts Lowell, Lowell, MA (United States); Sajo, E [University Massachusetts Lowell, Lowell, MA (United States); Ngoma, T [Muhimbili University of Health and Allied Sciences, Dar Es Salaam, TA (Tanzania, United Republic of); Dachi, J; Julius Mwaiselage, J [Ocean Road Cancer Institute, Dar Es Salaam (Tanzania, United Republic of); Kenton, O [University of Pennsylvania, Philadelphia, Pennsylvania (United States); Avery, S [University of Pennsylvania, Sicklerville, NJ (United States)

    2016-06-15

    Purpose: Recent publications have highlighted the potential of Information and Communication Technologies (ICTs) to catalyze collaborations in cancer care, research and education in global radiation oncology. This work reports on the use of ICTs for global Medical Physics education and training across three countries: USA, Tanzania and Kuwait Methods: An online education platform was established by Radiation Oncology Faculty from Harvard Medical School, and the University of Pennsylvania with integrated Medical Physics Course modules accessible to trainees in Tanzania via partnership with the Muhimbili University of Health and Allied Sciences, and the Ocean Road Cancer Institute. The course modules incorporated lectures covering Radiation Therapy Physics with videos, discussion board, assessments and grade center. Faculty at Harvard Medical School and the University of Massachusetts Lowell also employed weekly Skype meetings to train/mentor three graduate students, living out-of-state and in Kuwait for up to 9 research credits per semester for over two semesters towards obtaining their graduate degrees Results: Students were able to successfully access the Medical Physics course modules and participate in learning activities, online discussion boards, and assessments. Other instructors could also access/co-teach the course modules from USA and Tanzania. Meanwhile all three graduate students with remote training via Skype and email made major progress in their graduate training with each one of them submitting their research results as abstracts to be presented at the 2016 AAPM conference. One student has also published her work already and all three are developing these abstracts for publication in peer-reviewed journals. Conclusion: Altogether, this work highlights concrete examples/model on how ICTs can be used for capacity building in Medical Physics across continents, for both education and research training needed for Masters/PhD degrees. The developed modules

  14. Zimbabwe's Human Resources for health Information System (ZHRIS)-an assessment in the context of establishing a global standard.

    Science.gov (United States)

    Waters, Keith P; Zuber, Alexandra; Simbini, Tungamirirai; Bangani, Zwashe; Krishnamurthy, Ramesh S

    2017-04-01

    There have been numerous global calls to action to utilize human resources information systems (HRIS) to improve the availability and quality of data for strengthening the regulation and deployment of health workers. However, with no normative guidance in existence, the development of HRIS has been inconsistent and lacking in standardization, hindering the availability and use of data for health workforce planning and decision making (Riley et al., 2012). CDC and WHO partnered with the Ministry of Health in several countries to conduct HRIS functional requirements analyses and establish a Minimum Data Set (MDS) of elements essential for a global standard HRIS. As a next step, CDC advanced a study to examine the alignment of one of the HRIS it supports (in Zimbabwe) against this MDS. For this study, we created a new data collection and analysis tool to assess the extent to which Zimbabwe's CDC-supported HRIS was aligned with the WHO MDS. We performed systematic "gap analyses" in order to make prioritized recommendations for addressing the gaps, with the aim of improving the availability and quality of data on Zimbabwe's health workforce. The majority of the data elements outlined in the WHO MDS were present in the ZHRIS databases, though they were found to be missing various applicable elements. The lack of certain elements could impede functions such as health worker credential verification or equitable in-service training allocation. While the HRIS MDS treats all elements equally, our assessment revealed that not all the elements have equal significance when it comes to data utilization. Further, some of the HRIS MDS elements exceeded the current needs of regulatory bodies and the Ministry of Health and Child Care (MOHCC) in Zimbabwe. The preliminary findings of this study helped inspire the development of a more recent HRH Registry MDS subset, which is a shorter list of priority data elements recommended as a global standard for HRIS. The field-tested assessment

  15. A Framework for Effective Assessment of Model-based Projections of Biodiversity to Inform the Next Generation of Global Conservation Targets

    Science.gov (United States)

    Myers, B.; Beard, T. D.; Weiskopf, S. R.; Jackson, S. T.; Tittensor, D.; Harfoot, M.; Senay, G. B.; Casey, K.; Lenton, T. M.; Leidner, A. K.; Ruane, A. C.; Ferrier, S.; Serbin, S.; Matsuda, H.; Shiklomanov, A. N.; Rosa, I.

    2017-12-01

    Biodiversity and ecosystems services underpin political targets for the conservation of biodiversity; however, previous incarnations of these biodiversity-related targets have not relied on integrated model based projections of possible outcomes based on climate and land use change. Although a few global biodiversity models are available, most biodiversity models lie along a continuum of geography and components of biodiversity. Model-based projections of the future of global biodiversity are critical to support policymakers in the development of informed global conservation targets, but the scientific community lacks a clear strategy for integrating diverse data streams in developing, and evaluating the performance of, such biodiversity models. Therefore, in this paper, we propose a framework for ongoing testing and refinement of model-based projections of biodiversity trends and change, by linking a broad variety of biodiversity models with data streams generated by advances in remote sensing, coupled with new and emerging in-situ observation technologies to inform development of essential biodiversity variables, future global biodiversity targets, and indicators. Our two main objectives are to (1) develop a framework for model testing and refining projections of a broad range of biodiversity models, focusing on global models, through the integration of diverse data streams and (2) identify the realistic outputs that can be developed and determine coupled approaches using remote sensing and new and emerging in-situ observations (e.g., metagenomics) to better inform the next generation of global biodiversity targets.

  16. 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...

  17. Development of Highly Informative Genome-Wide Single Sequence Repeat Markers for Breeding Applications in Sesame and Construction of a Web Resource: SisatBase

    Directory of Open Access Journals (Sweden)

    Komivi Dossa

    2017-08-01

    Full Text Available The sequencing of the full nuclear genome of sesame (Sesamum indicum L. provides the platform for functional analyses of genome components and their application in breeding programs. Although the importance of microsatellites markers or simple sequence repeats (SSR in crop genotyping, genetics, and breeding applications is well established, only a little information exist concerning SSRs at the whole genome level in sesame. In addition, SSRs represent a suitable marker type for sesame molecular breeding in developing countries where it is mainly grown. In this study, we identified 138,194 genome-wide SSRs of which 76.5% were physically mapped onto the 13 pseudo-chromosomes. Among these SSRs, up to three primers pairs were supplied for 101,930 SSRs and used to in silico amplify the reference genome together with two newly sequenced sesame accessions. A total of 79,957 SSRs (78% were polymorphic between the three genomes thereby suggesting their promising use in different genomics-assisted breeding applications. From these polymorphic SSRs, 23 were selected and validated to have high polymorphic potential in 48 sesame accessions from different growing areas of Africa. Furthermore, we have developed an online user-friendly database, SisatBase (http://www.sesame-bioinfo.org/SisatBase/, which provides free access to SSRs data as well as an integrated platform for functional analyses. Altogether, the reference SSR and SisatBase would serve as useful resources for genetic assessment, genomic studies, and breeding advancement in sesame, especially in developing countries.

  18. 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

  19. Dynamic change of global and local information processing in propofol-induced loss and recovery of consciousness.

    Directory of Open Access Journals (Sweden)

    Martin M Monti

    Full Text Available Whether unique to humans or not, consciousness is a central aspect of our experience of the world. The neural fingerprint of this experience, however, remains one of the least understood aspects of the human brain. In this paper we employ graph-theoretic measures and support vector machine classification to assess, in 12 healthy volunteers, the dynamic reconfiguration of functional connectivity during wakefulness, propofol-induced sedation and loss of consciousness, and the recovery of wakefulness. Our main findings, based on resting-state fMRI, are three-fold. First, we find that propofol-induced anesthesia does not bear differently on long-range versus short-range connections. Second, our multi-stage design dissociated an initial phase of thalamo-cortical and cortico-cortical hyperconnectivity, present during sedation, from a phase of cortico-cortical hypoconnectivity, apparent during loss of consciousness. Finally, we show that while clustering is increased during loss of consciousness, as recently suggested, it also remains significantly elevated during wakefulness recovery. Conversely, the characteristic path length of brain networks (i.e., the average functional distance between any two regions of the brain appears significantly increased only during loss of consciousness, marking a decrease of global information-processing efficiency uniquely associated with unconsciousness. These findings suggest that propofol-induced loss of consciousness is mainly tied to cortico-cortical and not thalamo-cortical mechanisms, and that decreased efficiency of information flow is the main feature differentiating the conscious from the unconscious brain.

  20. Comprehensive global amino acid sequence analysis of PB1F2 protein of influenza A H5N1 viruses and the influenza A virus subtypes responsible for the 20th‐century pandemics

    Science.gov (United States)

    Pasricha, Gunisha; Mishra, Akhilesh C.; Chakrabarti, Alok K.

    2012-01-01

    Please cite this paper as: Pasricha et al. (2012) Comprehensive global amino acid sequence analysis of PB1F2 protein of influenza A H5N1 viruses and the Influenza A virus subtypes responsible for the 20th‐century pandemics. Influenza and Other Respiratory Viruses 7(4), 497–505. Background  PB1F2 is the 11th protein of influenza A virus translated from +1 alternate reading frame of PB1 gene. Since the discovery, varying sizes and functions of the PB1F2 protein of influenza A viruses have been reported. Selection of PB1 gene segment in the pandemics, variable size and pleiotropic effect of PB1F2 intrigued us to analyze amino acid sequences of this protein in various influenza A viruses. Methods  Amino acid sequences for PB1F2 protein of influenza A H5N1, H1N1, H2N2, and H3N2 subtypes were obtained from Influenza Research Database. Multiple sequence alignments of the PB1F2 protein sequences of the aforementioned subtypes were used to determine the size, variable and conserved domains and to perform mutational analysis. Results  Analysis showed that 96·4% of the H5N1 influenza viruses harbored full‐length PB1F2 protein. Except for the 2009 pandemic H1N1 virus, all the subtypes of the 20th‐century pandemic influenza viruses contained full‐length PB1F2 protein. Through the years, PB1F2 protein of the H1N1 and H3N2 viruses has undergone much variation. PB1F2 protein sequences of H5N1 viruses showed both human‐ and avian host‐specific conserved domains. Global database of PB1F2 protein revealed that N66S mutation was present only in 3·8% of the H5N1 strains. We found a novel mutation, N84S in the PB1F2 protein of 9·35% of the highly pathogenic avian influenza H5N1 influenza viruses. Conclusions  Varying sizes and mutations of the PB1F2 protein in different influenza A virus subtypes with pandemic potential were obtained. There was genetic divergence of the protein in various hosts which highlighted the host‐specific evolution of the virus

  1. Informing policy to protect coastal coral reefs: insight from a global review of reducing agricultural pollution to coastal ecosystems.

    Science.gov (United States)

    Kroon, Frederieke J; Schaffelke, Britta; Bartley, Rebecca

    2014-08-15

    The continuing degradation of coral reefs has serious consequences for the provision of ecosystem goods and services to local and regional communities. While climate change is considered the most serious risk to coral reefs, agricultural pollution threatens approximately 25% of the total global reef area with further increases in sediment and nutrient fluxes projected over the next 50 years. Here, we aim to inform coral reef management using insights learned from management examples that were successful in reducing agricultural pollution to coastal ecosystems. We identify multiple examples reporting reduced fluxes of sediment and nutrients at end-of-river, and associated declines in nutrient concentrations and algal biomass in receiving coastal waters. Based on the insights obtained, we recommend that future protection of coral reef ecosystems demands policy focused on desired ecosystem outcomes, targeted regulatory approaches, up-scaling of watershed management, and long-term maintenance of scientifically robust monitoring programs linked with adaptive management. Crown Copyright © 2014. Published by Elsevier Ltd. All rights reserved.

  2. UN Committee on Global Geospatial Information Management: Insediato il Comitato delle Nazioni Unite sulla gestione dell’informazione geospaziale

    Directory of Open Access Journals (Sweden)

    Mauro Salvemini

    2012-04-01

    Full Text Available L’iniziativa delle Nazioni Unite volta alla formazione di un comitato di esperti nella gestione della informazione geografica, già presentata in questa rubrica in un precedente numero, ha fatto un passo avanti definitivo con l’incontro di Seoul dello scorso ottobre. The  United  Nations  Committee  of  Experts on Global Geospatial Information Manage-ment,  established  by  ECOSOC  on  27  July 2011 as the official UN consultative mechanism  on  GGIM,  has  convened  its  inaugural  meeting  on  26  October  2011  in  Seoul, Republic  of  Korea.  The  inaugural  meeting has  brought  together  experts  from  Member States and observers from international organizations  to  adopt  the  Terms  of  Refer-ence of the Committee, review the Rules of Procedure of the Committee, and discuss its contribution to Rio+20 Conference as well as an inventory of critical issues to be addressed by the Committee in its future sessions

  3. How Should Global Fund Use Value-for-Money Information to Sustain its Investments in Graduating Countries?

    Directory of Open Access Journals (Sweden)

    Kitti Kanpirom

    2017-09-01

    Full Text Available It has been debated whether the Global Fund (GF, which is supporting the implementation of programs on the prevention and control of HIV/AIDS, tuberculosis (TB and malaria, should consider the value-for-money (VFM for programs/interventions that they are supporting. In this paper, we critically analyze the uses of economic information for GF programs, not only to ensure accountability to their donors but also to support country governments in continuing investment in cost-effective interventions initiated by the GF despite the discontinuation of financial support after graduation. We demonstrate that VFM is not a static property of interventions and may depend on program start-up cost, economies of scales, the improvement of effectiveness and efficiency of providers once the program develops, and acceptance and adherence of the target population. Interventions that are cost-ineffective in the beginning may become cost-effective in later stages. We consider recent GF commitments towards value for money and recommend that the GF supports interventions with proven cost-effectiveness from program initiation as well as interventions that may be cost-effective afterwards. Thus, the GF and country governments should establish mechanisms to monitor cost-effectiveness of interventions invested over time.

  4. Characterization of the Kenaf (Hibiscus cannabinus) Global Transcriptome Using Illumina Paired-End Sequencing and Development of EST-SSR Markers

    Science.gov (United States)

    Li, Hui; Li, Defang; Chen, Anguo; Tang, Huijuan; Li, Jianjun; Huang, Siqi

    2016-01-01

    Kenaf (Hibiscus cannabinus L.) is an economically important natural fiber crop grown worldwide. However, only 20 expressed tag sequences (ESTs) for kenaf are available in public databases. The aim of this study was to develop large-scale simple sequence repeat (SSR) markers to lay a solid foundation for the construction of genetic linkage maps and marker-assisted breeding in kenaf. We used Illumina paired-end sequencing technology to generate new EST-simple sequences and MISA software to mine SSR markers. We identified 71,318 unigenes with an average length of 1143 nt and annotated these unigenes using four different protein databases. Overall, 9324 complementary pairs were designated as EST-SSR markers, and their quality was validated using 100 randomly selected SSR markers. In total, 72 primer pairs reproducibly amplified target amplicons, and 61 of these primer pairs detected significant polymorphism among 28 kenaf accessions. Thus, in this study, we have developed large-scale SSR markers for kenaf, and this new resource will facilitate construction of genetic linkage maps, investigation of fiber growth and development in kenaf, and also be of value to novel gene discovery and functional genomic studies. PMID:26960153

  5. A global meta-analysis of Tuber ITS rDNA sequences: species diversity, host associations and long-distance dispersal

    Science.gov (United States)

    Gregory M. Bonito; Andrii P. Gryganskyi; James M. Trappe; Rytas. Vilgalys

    2010-01-01

    Truffles (Tuber) are ectomycorrhizal fungi characterized by hypogeous fruitbodies. Their biodiversity, host associations and geographical distributions are not well documented. ITS rDNA sequences of Tuber are commonly recovered from molecular surveys of fungal communities, but most remain insufficiently identified making it...

  6. Characterization of the Kenaf (Hibiscus cannabinus) Global Transcriptome Using Illumina Paired-End Sequencing and Development of EST-SSR Markers.

    Science.gov (United States)

    Li, Hui; Li, Defang; Chen, Anguo; Tang, Huijuan; Li, Jianjun; Huang, Siqi

    2016-01-01

    Kenaf (Hibiscus cannabinus L.) is an economically important natural fiber crop grown worldwide. However, only 20 expressed tag sequences (ESTs) for kenaf are available in public databases. The aim of this study was to develop large-scale simple sequence repeat (SSR) markers to lay a solid foundation for the construction of genetic linkage maps and marker-assisted breeding in kenaf. We used Illumina paired-end sequencing technology to generate new EST-simple sequences and MISA software to mine SSR markers. We identified 71,318 unigenes with an average length of 1143 nt and annotated these unigenes using four different protein databases. Overall, 9324 complementary pairs were designated as EST-SSR markers, and their quality was validated using 100 randomly selected SSR markers. In total, 72 primer pairs reproducibly amplified target amplicons, and 61 of these primer pairs detected significant polymorphism among 28 kenaf accessions. Thus, in this study, we have developed large-scale SSR markers for kenaf, and this new resource will facilitate construction of genetic linkage maps, investigation of fiber growth and development in kenaf, and also be of value to novel gene discovery and functional genomic studies.

  7. Global Earth Observation System of Systems: Characterizing Uncertainties of Space- based Measurements and Earth System Models Informing Decision Tools

    Science.gov (United States)

    Birk, R. J.; Frederick, M.

    2006-05-01

    The Global Earth Observation System of Systems (GEOSS) framework identifies the benefits of systematically and scientifically networking the capacity of organizations and systems into solutions that benefit nine societal benefit areas. The U.S. Integrated Earth Observation System (IEOS), the U.S. contribution to the GEOSS, focuses on near-term, mid-term, and long-term opportunities to establish integrated system solutions based on capacities and capabilities of member agencies and affiliations. Scientists at NASA, NOAA, DOE, NSF and other U.S. agencies are evolving the predictive capacity of models of Earth processes based on space-based, airborne and surface-based instruments and their measurements. NASA research activities include advancing the power and accessibility of computational resources (i.e. Project Columbia) to enable robust science data analysis, modeling, and assimilation techniques to rapidly advance. The integration of the resulting observations and predictions into decision support tools require characterization of the accuracies of a range of input measurements includes temperature and humidity profiles, wind speed, ocean height, sea surface temperature, and atmospheric constituents that are measured globally by U.S. deployed spacecraft. These measurements are stored in many data formats on many different information systems with widely varying accessibility and have processes whose documentation ranges from extremely detailed to very minimal. Integrated and interdisciplinary modeling (enabled by the Earth System Model Framework) enable the types of ensemble analysis that are useful for decision processes associated with energy management, public health risk assessments, and optimizing transportation safety and efficiency. Interdisciplinary approaches challenge systems integrators (both scientists and engineers) to expand beyond the traditional boundaries of particular disciplines to develop, verify and validate, and ultimately benchmark the

  8. Bridging Innovation and Outreach to Overcome Global Gaps in Radiation Oncology Through Information and Communication Tools, Trainee Advancement, Engaging Industry, Attention to Ethical Challenges, and Political Advocacy.

    Science.gov (United States)

    Dad, Luqman; Royce, Trevor J; Morris, Zachary; Moran, Meena; Pawlicki, Todd; Khuntia, Deepak; Hardenbergh, Patricia; Cummings, Bernard; Mayr, Nina; Hu, Kenneth

    2017-04-01

    An evolving paradigm in global outreach in radiation oncology has been the implementation of a more region-specific, needs-based approach to help close the gap in radiation services to low- and middle-income countries through the use of innovative tools in information and communication technology. This report highlights 4 information and communication technology tools in action today: (1) the NCCN Framework for Resource Stratification of NCCN guidelines, (2) ASTRO e-Contouring, (3) i.treatsafely.org, and (4) ChartRounds.com. We also render special consideration to matters related to global outreach that we believe require distinct attention to help us meet the goals established by the 2011 United Nations׳ Declaration on noncommunicable diseases: (1) trainee advancement toward careers in global health, (2) ethical challenges of international outreach, (3) critical importance of political advocacy, and (4) collaboration with Industry. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. Roles of repetitive sequences

    Energy Technology Data Exchange (ETDEWEB)

    Bell, G.I.

    1991-12-31

    The DNA of higher eukaryotes contains many repetitive sequences. The study of repetitive sequences is important, not only because many have important biological function, but also because they provide information on genome organization, evolution and dynamics. In this paper, I will first discuss some generic effects that repetitive sequences will have upon genome dynamics and evolution. In particular, it will be shown that repetitive sequences foster recombination among, and turnover of, the elements of a genome. I will then consider some examples of repetitive sequences, notably minisatellite sequences and telomere sequences as examples of tandem repeats, without and with respectively known function, and Alu sequences as an example of interspersed repeats. Some other examples will also be considered in less detail.

  10. Development of Information and Knowledge Architectures and an Associated Framework and Methodology for System Management of a Global Reserve Currency

    Science.gov (United States)

    Cardullo, Mario W.

    2013-01-01

    The global financial system appears to be heading for a major financial crisis. This crisis is being driven by a growing global debt. This crisis is not limited to nations that are heavily in debt such as Greece, Spain, Portugal, Ireland, Italy or Cyprus but to such others as the United States. While there has been a great deal of emphasis on…

  11. A novel genome-information content-based statistic for genome-wide association analysis designed for next-generation sequencing data.

    Science.gov (United States)

    Luo, Li; Zhu, Yun; Xiong, Momiao

    2012-06-01

    The genome-wide association studies (GWAS) designed for next-generation sequencing data involve testing association of genomic variants, including common, low frequency, and rare variants. The current strategies for association studies are well developed for identifying association of common variants with the common diseases, but may be ill-suited when large amounts of allelic heterogeneity are present in sequence data. Recently, group tests that analyze their collective frequency differences between cases and controls shift the current variant-by-variant analysis paradigm for GWAS of common variants to the collective test of multiple variants in the association analysis of rare variants. However, group tests ignore differences in genetic effects among SNPs at different genomic locations. As an alternative to group tests, we developed a novel genome-information content-based statistics for testing association of the entire allele frequency spectrum of genomic variation with the diseases. To evaluate the performance of the proposed statistics, we use large-scale simulations based on whole genome low coverage pilot data in the 1000 Genomes Project to calculate the type 1 error rates and power of seven alternative statistics: a genome-information content-based statistic, the generalized T(2), collapsing method, multivariate and collapsing (CMC) method, individual χ(2) test, weighted-sum statistic, and variable threshold statistic. Finally, we apply the seven statistics to published resequencing dataset from ANGPTL3, ANGPTL4, ANGPTL5, and ANGPTL6 genes in the Dallas Heart Study. We report that the genome-information content-based statistic has significantly improved type 1 error rates and higher power than the other six statistics in both simulated and empirical datasets.

  12. PROMIS GH (Patient-Reported Outcomes Measurement Information System Global Health) Scale in Stroke: A Validation Study.

    Science.gov (United States)

    Katzan, Irene L; Lapin, Brittany

    2018-01-01

    The International Consortium for Health Outcomes Measurement recently included the 10-item PROMIS GH (Patient-Reported Outcomes Measurement Information System Global Health) scale as part of their recommended Standard Set of Stroke Outcome Measures. Before collection of PROMIS GH is broadly implemented, it is necessary to assess its performance in the stroke population. The objective of this study was to evaluate the psychometric properties of PROMIS GH in patients with ischemic stroke and intracerebral hemorrhage. PROMIS GH and 6 PROMIS domain scales measuring same/similar constructs were electronically collected on 1102 patients with ischemic and hemorrhagic strokes at various stages of recovery from their stroke who were seen in a cerebrovascular clinic from October 12, 2015, through June 2, 2017. Confirmatory factor analysis was performed to evaluate the adequacy of 2-factor structure of component scores. Test-retest reliability and convergent validity of PROMIS GH items and component scores were assessed. Discriminant validity and responsiveness were compared between PROMIS GH and PROMIS domain scales measuring the same or related constructs. Analyses were repeated stratified by stroke subtype and modified Rankin Scale score validity was good with significant correlations between all PROMIS GH items and PROMIS domain scales ( P 0.5) was demonstrated for 8 of the 10 PROMIS GH items. Reliability and validity remained consistent across stroke subtype and disability level (modified Rankin Scale, <2 versus ≥2). PROMIS GH exhibits acceptable performance in patients with stroke. Our findings support International Consortium for Health Outcomes Measurement recommendation to use PROMIS GH as part of the standard set of outcome measures in stroke. © 2017 American Heart Association, Inc.

  13. Supporting the Evaluation and Implementation of Musculoskeletal Models of Care: A Globally Informed Framework for Judging Readiness and Success.

    Science.gov (United States)

    Briggs, Andrew M; Jordan, Joanne E; Jennings, Matthew; Speerin, Robyn; Bragge, Peter; Chua, Jason; Woolf, Anthony D; Slater, Helen

    2017-04-01

    To develop a globally informed framework to evaluate readiness for implementation and success after implementation of musculoskeletal models of care (MOCs). Three phases were undertaken: 1) a qualitative study with 27 Australian subject matter experts (SMEs) to develop a draft framework; 2) an eDelphi study with an international panel of 93 SMEs across 30 nations to evaluate face validity, and refine and establish consensus on the framework components; and 3) translation of the framework into a user-focused resource and evaluation of its acceptability with the eDelphi panel. A comprehensive evaluation framework was developed for judging the readiness and success of musculoskeletal MOCs. The framework consists of 9 domains, with each domain containing a number of themes underpinned by detailed elements. In the first Delphi round, scores of "partly agree" or "completely agree" with the draft framework ranged 96.7%-100%. In the second round, "essential" scores ranged 58.6%-98.9%, resulting in 14 of 34 themes being classified as essential. SMEs strongly agreed or agreed that the final framework was useful (98.8%), usable (95.1%), credible (100%) and appealing (93.9%). Overall, 96.3% strongly supported or supported the final structure of the framework as it was presented, while 100%, 96.3%, and 100% strongly supported or supported the content within the readiness, initiating implementation, and success streams, respectively. An empirically derived framework to evaluate the readiness and success of musculoskeletal MOCs was strongly supported by an international panel of SMEs. The framework provides an important internationally applicable benchmark for the development, implementation, and evaluation of musculoskeletal MOCs. © 2016, American College of Rheumatology.

  14. Sequence variants in the bovine silent information regulator 6, their linkage and their associations with body measurements and carcass quality traits in Qinchuan cattle.

    Science.gov (United States)

    Gui, Linsheng; Jiang, Bijie; Zhang, Yaran; Zan, Linsen

    2015-03-15

    Silent information regulator 6 (SIRT6) belongs to the family of class III nicotinamide adenine dinucleotide (NAD)-dependent deacetylase and plays an essential role in DNA repair and metabolism. This study was conducted to detect potential polymorphisms of the bovine SIRT6 gene and explore their relationships with body measurement and carcass quality in Qinchuan cattle. Four sequence variants (SVs) were identified in intron 6, exon 7, exon 9, and 3' UTR, via sequencing technology conducted in 468 individual Qinchuan cattle. Eleven different haplotypes were identified, of which two major haplotypes had a frequency of 45.7% (-CACT-) and 14.8% (-CGTC-). Three SVs (SV2, SV3 and SV4) were significantly associated with some of the body measurements and carcass quality traits (P<0.05 or P<0.01), and the H2H7 (CC-GA-TT-TC) diplotype had better performance than other combinations. Our results suggest that some polymorphisms in SIRT6 are associated with production traits and may be used as candidates for marker-assisted selection (MAS) and management in beef cattle breeding programs. Copyright © 2015 Elsevier B.V. All rights reserved.

  15. 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.

  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

    2010-01-01

    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

  17. 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.

  18. Divide and conquer: enriching environmental sequencing data.

    Directory of Open Access Journals (Sweden)

    Anne Bergeron

    2007-09-01

    Full Text Available In environmental sequencing projects, a mix of DNA from a whole microbial community is fragmented and sequenced, with one of the possible goals being to reconstruct partial or complete genomes of members of the community. In communities with high diversity of species, a significant proportion of the sequences do not overlap any other fragment in the sample. This problem will arise not only in situations with a relatively even distribution of many species, but also when the community in a particular environment is routinely dominated by the same few species. In the former case, no genomes may be assembled at all, while in the latter case a few dominant species in an environment will always be sequenced at high coverage to the detriment of coverage of the greater number of sparse species.Here we show that, with the same global sequencing effort, separating the species into two or more sub-communities prior to sequencing can yield a much higher proportion of sequences that can be assembled. We first use the Lander-Waterman model to show that, if the expected percentage of singleton sequences is higher than 25%, then, under the uniform distribution hypothesis, splitting the community is always a wise choice. We then construct simulated microbial communities to show that the results hold for highly non-uniform distributions. We also show that, for the distributions considered in the experiments, it is possible to estimate quite accurately the relative diversity of the two sub-communities.Given the fact that several methods exist to split microbial communities based on physical properties such as size, density, surface biochemistry, or optical properties, we strongly suggest that groups involved in environmental sequencing, and expecting high diversity, consider splitting their communities in order to maximize the information content of their sequencing effort.

  19. The complete genome sequence of Escherichia coli EC958: a high quality reference sequence for the globally disseminated multidrug resistant E. coli O25b:H4-ST131 clone.

    Directory of Open Access Journals (Sweden)

    Brian M Forde

    Full Text Available Escherichia coli ST131 is now recognised as a leading contributor to urinary tract and bloodstream infections in both community and clinical settings. Here we present the complete, annotated genome of E. coli EC958, which was isolated from the urine of a patient presenting with a urinary tract infection in the Northwest region of England and represents the most well characterised ST131 strain. Sequencing was carried out using the Pacific Biosciences platform, which provided sufficient depth and read-length to produce a complete genome without the need for other technologies. The discovery of spurious contigs within the assembly that correspond to site-specific inversions in the tail fibre regions of prophages demonstrates the potential for this technology to reveal dynamic evolutionary mechanisms. E. coli EC958 belongs to the major subgroup of ST131 strains that produce the CTX-M-15 extended spectrum β-lactamase, are fluoroquinolone resistant and encode the fimH30 type 1 fimbrial adhesin. This subgroup includes the Indian strain NA114 and the North American strain JJ1886. A comparison of the genomes of EC958, JJ1886 and NA114 revealed that differences in the arrangement of genomic islands, prophages and other repetitive elements in the NA114 genome are not biologically relevant and are due to misassembly. The availability of a high quality uropathogenic E. coli ST131 genome provides a reference for understanding this multidrug resistant pathogen and will facilitate novel functional, comparative and clinical studies of the E. coli ST131 clonal lineage.

  20. Discovery of global genomic re-organization based on comparison of two newly sequenced rice mitochondrial genomes with cytoplasmic male sterility-related genes

    Directory of Open Access Journals (Sweden)

    Yamada Mari

    2010-03-01

    Full Text Available Abstract Background Plant mitochondrial genomes are known for their complexity, and there is abundant evidence demonstrating that this organelle is important for plant sexual reproduction. Cytoplasmic male sterility (CMS is a phenomenon caused by incompatibility between the nucleus and mitochondria that has been discovered in various plant species. As the exact sequence of steps leading to CMS has not yet been revealed, efforts should be made to elucidate the factors underlying the mechanism of this important trait for crop breeding. Results Two CMS mitochondrial genomes, LD-CMS, derived from Oryza sativa L. ssp. indica (434,735 bp, and CW-CMS, derived from Oryza rufipogon Griff. (559,045 bp, were newly sequenced in this study. Compared to the previously sequenced Nipponbare (Oryza sativa L. ssp. japonica mitochondrial genome, the presence of 54 out of 56 protein-encoding genes (including pseudo-genes, 22 tRNA genes (including pseudo-tRNAs, and three rRNA genes was conserved. Two other genes were not present in the CW-CMS mitochondrial genome, and one of them was present as part of the newly identified chimeric ORF, CW-orf307. At least 12 genomic recombination events were predicted between the LD-CMS mitochondrial genome and Nipponbare, and 15 between the CW-CMS genome and Nipponbare, and novel genetic structures were formed by these genomic rearrangements in the two CMS lines. At least one of the genomic rearrangements was completely unique to each CMS line and not present in 69 rice cultivars or 9 accessions of O. rufipogon. Conclusion Our results demonstrate novel mitochondrial genomic rearrangements that are unique in CMS cytoplasm, and one of the genes that is unique in the CW mitochondrial genome, CW-orf307, appeared to be the candidate most likely responsible for the CW-CMS event. Genomic rearrangements were dynamic in the CMS lines in comparison with those of rice cultivars, suggesting that 'death' and possible 'birth' processes of the

  1. Whole exome sequencing of a consanguineous family identifies the possible modifying effect of a globally rare AK5 allelic variant in celiac disease development among Saudi patients.

    Directory of Open Access Journals (Sweden)

    Jumana Yousuf Al-Aama

    Full Text Available Celiac disease (CD, a multi-factorial auto-inflammatory disease of the small intestine, is known to occur in both sporadic and familial forms. Together HLA and Non-HLA genes can explain up to 50% of CD's heritability. In order to discover the missing heritability due to rare variants, we have exome sequenced a consanguineous Saudi family presenting CD in an autosomal recessive (AR pattern. We have identified a rare homozygous insertion c.1683_1684insATT, in the conserved coding region of AK5 gene that showed classical AR model segregation in this family. Sequence validation of 200 chromosomes each of sporadic CD cases and controls, revealed that this extremely rare (EXac MAF 0.000008 mutation is highly penetrant among general Saudi populations (MAF is 0.62. Genotype and allelic distribution analysis have indicated that this AK5 (c.1683_1684insATT mutation is negatively selected among patient groups and positively selected in the control group, in whom it may modify the risk against CD development [p<0.002]. Our observation gains additional support from computational analysis which predicted that Iso561 insertion shifts the existing H-bonds between 400th and 556th amino acid residues lying near the functional domain of adenylate kinase. This shuffling of amino acids and their H-bond interactions is likely to disturb the secondary structure orientation of the polypeptide and induces the gain-of-function in nucleoside phosphate kinase activity of AK5, which may eventually down-regulates the reactivity potential of CD4+ T-cells against gluten antigens. Our study underlines the need to have population-specific genome databases to avoid false leads and to identify true candidate causal genes for the familial form of celiac disease.

  2. Comprehensive global amino acid sequence analysis of PB1F2 protein of influenza A H5N1 viruses and the influenza A virus subtypes responsible for the 20th-century pandemics.

    Science.gov (United States)

    Pasricha, Gunisha; Mishra, Akhilesh C; Chakrabarti, Alok K

    2013-07-01

    PB1F2 is the 11th protein of influenza A virus translated from +1 alternate reading frame of PB1 gene. Since the discovery, varying sizes and functions of the PB1F2 protein of influenza A viruses have been reported. Selection of PB1 gene segment in the pandemics, variable size and pleiotropic effect of PB1F2 intrigued us to analyze amino acid sequences of this protein in various influenza A viruses. Amino acid sequences for PB1F2 protein of influenza A H5N1, H1N1, H2N2, and H3N2 subtypes were obtained from Influenza Research Database. Multiple sequence alignments of the PB1F2 protein sequences of the aforementioned subtypes were used to determine the size, variable and conserved domains and to perform mutational analysis. Analysis showed that 96·4% of the H5N1 influenza viruses harbored full-length PB1F2 protein. Except for the 2009 pandemic H1N1 virus, all the subtypes of the 20th-century pandemic influenza viruses contained full-length PB1F2 protein. Through the years, PB1F2 protein of the H1N1 and H3N2 viruses has undergone much variation. PB1F2 protein sequences of H5N1 viruses showed both human- and avian host-specific conserved domains. Global database of PB1F2 protein revealed that N66S mutation was present only in 3·8% of the H5N1 strains. We found a novel mutation, N84S in the PB1F2 protein of 9·35% of the highly pathogenic avian influenza H5N1 influenza viruses. Varying sizes and mutations of the PB1F2 protein in different influenza A virus subtypes with pandemic potential were obtained. There was genetic divergence of the protein in various hosts which highlighted the host-specific evolution of the virus. However, studies are required to correlate this sequence variability with the virulence and pathogenicity. © 2012 John Wiley & Sons Ltd.

  3. Sequence co-evolutionary information is a natural partner to minimally-frustrated models of biomolecular dynamics [version 1; referees: 3 approved

    Directory of Open Access Journals (Sweden)

    Jeffrey K Noel

    2016-01-01

    Full Text Available Experimentally derived structural constraints have been crucial to the implementation of computational models of biomolecular dynamics. For example, not only does crystallography provide essential starting points for molecular simulations but also high-resolution structures permit for parameterization of simplified models. Since the energy landscapes for proteins and other biomolecules have been shown to be minimally frustrated and therefore funneled, these structure-based models have played a major role in understanding the mechanisms governing folding and many functions of these systems. Structural information, however, may be limited in many interesting cases. Recently, the statistical analysis of residue co-evolution in families of protein sequences has provided a complementary method of discovering residue-residue contact interactions involved in functional configurations. These functional configurations are often transient and difficult to capture experimentally. Thus, co-evolutionary information can be merged with that available for experimentally characterized low free-energy structures, in order to more fully capture the true underlying biomolecular energy landscape.

  4. The Need for Clinical Decision Support Integrated with the Electronic Health Record for the Clinical Application of Whole Genome Sequencing Information

    Directory of Open Access Journals (Sweden)

    Brandon M. Welch

    2013-12-01

    Full Text Available Whole genome sequencing (WGS is rapidly approaching widespread clinical application. Technology advancements over the past decade, since the first human genome was decoded, have made it feasible to use WGS for clinical care. Future advancements will likely drive down the price to the point wherein WGS is routinely available for care. However, were this to happen today, most of the genetic information available to guide clinical care would go unused due to the complexity of genetics, limited physician proficiency in genetics, and lack of genetics professionals in the clinical workforce. Furthermore, these limitations are unlikely to change in the future. As such, the use of clinical decision support (CDS to guide genome-guided clinical decision-making is imperative. In this manuscript, we describe the barriers to widespread clinical application of WGS information, describe how CDS can be an important tool for overcoming these barriers, and provide clinical examples of how genome-enabled CDS can be used in the clinical setting.

  5. Fast convergence of spike sequences to periodic patterns in recurrent networks

    International Nuclear Information System (INIS)

    Jin, Dezhe Z.

    2002-01-01

    The dynamical attractors are thought to underlie many biological functions of recurrent neural networks. Here we show that stable periodic spike sequences with precise timings are the attractors of the spiking dynamics of recurrent neural networks with global inhibition. Almost all spike sequences converge within a finite number of transient spikes to these attractors. The convergence is fast, especially when the global inhibition is strong. These results support the possibility that precise spatiotemporal sequences of spikes are useful for information encoding and processing in biological neural networks

  6. Microarrays for global expression constructed with a low redundancy set of 27,500 sequenced cDNAs representing an array of developmental stages and physiological conditions of the soybean plant

    Directory of Open Access Journals (Sweden)

    Retzel Ernest

    2004-09-01

    Full Text Available Abstract Background Microarrays are an important tool with which to examine coordinated gene expression. Soybean (Glycine max is one of the most economically valuable crop species in the world food supply. In order to accelerate both gene discovery as well as hypothesis-driven research in soybean, global expression resources needed to be developed. The applications of microarray for determining patterns of expression in different tissues or during conditional treatments by dual labeling of the mRNAs are unlimited. In addition, discovery of the molecular basis of traits through examination of naturally occurring variation in hundreds of mutant lines could be enhanced by the construction and use of soybean cDNA microarrays. Results We report the construction and analysis of a low redundancy 'unigene' set of 27,513 clones that represent a variety of soybean cDNA libraries made from a wide array of source tissue and organ systems, developmental stages, and stress or pathogen-challenged plants. The set was assembled from the 5' sequence data of the cDNA clones using cluster analysis programs. The selected clones were then physically reracked and sequenced at the 3' end. In order to increase gene discovery from immature cotyledon libraries that contain abundant mRNAs representing storage protein gene families, we utilized a high density filter normalization approach to preferentially select more weakly expressed cDNAs. All 27,513 cDNA inserts were amplified by polymerase chain reaction. The amplified products, along with some repetitively spotted control or 'choice' clones, were used to produce three 9,728-element microarrays that have been used to examine tissue specific gene expression and global expression in mutant isolines. Conclusions Global expression studies will be greatly aided by the availability of the sequence-validated and low redundancy cDNA sets described in this report. These cDNAs and ESTs represent a wide array of developmental

  7. Distributed team cohesion – not an oxymoron. The impact of information and communications technologies on teamness in globally distributed IT projects

    Directory of Open Access Journals (Sweden)

    Olga Stawnicza

    2015-01-01

    Full Text Available Globally distributed IT projects are common practice in today’s globalized world. Typically, project team members’ work on interdependent tasks, with a common goal to be achieved as one team. However, being split between multiple locations impedes communication among team members and hampers the development of trust. Information and communications media enable communication between geographically distributed project team members and help to create and maintain trust within project units. Communication and trust are particularly significant for fostering a feeling of oneness among project team members. Oneness, also referred to as “teamness”, is repeatedly mentioned as one of the challenges facing global project teams. However, prior literature on teamness is very scarce and its importance is underrepresented. This research contributes to the field in two ways. First, the theoretical study based on a systematic literature review examines available evidence of teamness in globally distributed projects. Secondly, an empirical study based on interviews conducted with global project managers fills the current gap in literature on the link between use of ICT and establishing a sense of team unity. This paper draws practitioners’ attention to the importance of striving for teamness in spite of the geographical distance that exists between project team members.

  8. Analysis of the Main Access Municipal Project Free and Free Internet in Public Squares: Digital Inclusion in the Present Corporate Information Globalized

    Directory of Open Access Journals (Sweden)

    Anderson Nogueira Oliveira

    2015-12-01

    Full Text Available The present study has as its theme the role of municipalities in the current global information society. So it has the general objective analysis on the free access to the internet in public places as a means of digital inclusion, with such spaces known as digital o hotspots squares. In this case we will present concepts, definitions and brief historical development of the objects of study of this research, namely, globalization, the information society and digital inclusion. We emphasize that this research will analyze recent data on internet access in Brazil, and will check the key municipal projects freely and free internet access in public squares. For this research we use the hypothetical-deductive method by the methodology of analysis of books, scientific papers and official data by renamed institutions to present a scientifically valid conclusion.

  9. Allele Re-sequencing Technologies

    DEFF Research Database (Denmark)

    Byrne, Stephen; Farrell, Jacqueline Danielle; Asp, Torben

    2013-01-01

    The development of next-generation sequencing technologies has made sequencing an affordable approach for detection of genetic variations associated with various traits. However, the cost of whole genome re-sequencing still remains too high to be feasible for many plant species with large...... alternative to whole genome re-sequencing to identify causative genetic variations in plants. One challenge, however, will be efficient bioinformatics strategies for data handling and analysis from the increasing amount of sequence information....

  10. Global Earth Structure Recovery from State-of-the-art Models of the Earth's Gravity Field and Additional Geophysical Information

    NARCIS (Netherlands)

    Hamayun, H.

    2014-01-01

    Currently, a tremendous improvement is observed in the accuracy and spatial resolution of global Earth’s gravity field models. This improvement is achieved due to using various new data, including those from satellite gravimetry missions (CHAMP, GRACE, and GOCE); terrestrial and airborne gravity

  11. Does Research Information Meet the Needs of Stakeholders? Exploring Evidence Selection in the Global Management of Invasive Species

    Science.gov (United States)

    Bayliss, Helen R.; Wilcox, Andrew; Stewart, Gavin B.; Randall, Nicola P.

    2012-01-01

    This study explored factors affecting information selection by international stakeholders working with invasive species. Despite differences in information requirements between groups, all stakeholders demonstrated a clear preference for free, easily accessible online information, and predominantly used internet search engines and specialist…

  12. A qualitative content analysis of global health engagements in Peacekeeping and Stability Operations Institute's stability operations lessons learned and information management system.

    Science.gov (United States)

    Nang, Roberto N; Monahan, Felicia; Diehl, Glendon B; French, Daniel

    2015-04-01

    Many institutions collect reports in databases to make important lessons-learned available to their members. The Uniformed Services University of the Health Sciences collaborated with the Peacekeeping and Stability Operations Institute to conduct a descriptive and qualitative analysis of global health engagements (GHEs) contained in the Stability Operations Lessons Learned and Information Management System (SOLLIMS). This study used a summative qualitative content analysis approach involving six steps: (1) a comprehensive search; (2) two-stage reading and screening process to identify first-hand, health-related records; (3) qualitative and quantitative data analysis using MAXQDA, a software program; (4) a word cloud to illustrate word frequencies and interrelationships; (5) coding of individual themes and validation of the coding scheme; and (6) identification of relationships in the data and overarching lessons-learned. The individual codes with the most number of text segments coded included: planning, personnel, interorganizational coordination, communication/information sharing, and resources/supplies. When compared to the Department of Defense's (DoD's) evolving GHE principles and capabilities, the SOLLIMS coding scheme appeared to align well with the list of GHE capabilities developed by the Department of Defense Global Health Working Group. The results of this study will inform practitioners of global health and encourage additional qualitative analysis of other lessons-learned databases. Reprint & Copyright © 2015 Association of Military Surgeons of the U.S.

  13. Dynamic Sequence Assignment.

    Science.gov (United States)

    1983-12-01

    D-136 548 DYNAMIIC SEQUENCE ASSIGNMENT(U) ADVANCED INFORMATION AND 1/2 DECISION SYSTEMS MOUNTAIN YIELW CA C A 0 REILLY ET AL. UNCLSSIIED DEC 83 AI/DS...I ADVANCED INFORMATION & DECISION SYSTEMS Mountain View. CA 94040 84 u ,53 V,..’. Unclassified _____ SCURITY CLASSIFICATION OF THIS PAGE REPORT...reviews some important heuristic algorithms developed for fas- ter solution of the sequence assignment problem. 3.1. DINAMIC MOGRAMUNIG FORMULATION FOR

  14. Establishment of the National Nuclear Regulatory Portal (NNRP) as the key element of the Global Nuclear Safety and Security Network and Regulatory Network (GNSSN/RegNet) for sharing of nuclear safety information and knowledge among the Global Expert Community

    International Nuclear Information System (INIS)

    Kuvshinnikov, A.V.

    2011-01-01

    The Global Nuclear Safety and Security Network (GNSSN) implements the concept of the Global Nuclear Safety and Security Framework (GNSSF) as outlined in INSAG 21. This is the framework of instruments and resources for achieving and maintaining worldwide a high level of safety and security at nuclear facilities and activities as stated in SF-1 and supporting safety standards or recommendations such as INSAG-12. National efforts are and should be augmented by the activities of a variety of international enterprises that facilitate safety and security. The IAEA standard GS-R-3 requires that information and knowledge is managed as a resource. Further strengthening of GNSSN in particular regulatory networking as intended by GNSSN/RegNet has to be based on current national priorities, on existing regional and thematic networks and on the established mechanisms of international co-operation as presented for example on the websites of the IAEA or the OECD-NEA. Current design and operation of RegNet are flexible enough to accommodate differences in national and international approaches and practices and to facilitate exchange and cooperation on regulatory matters. The main role of GNSSN/RegNet is sharing knowledge and bringing people together to enhance and promote nuclear safety and security. The objectives of GNSSN/RegNet: enhancing safety and security by international cooperation, sharing information and best practices, enabling adequate access to relevant safety and security information and promoting the dissemination of this information, implementing active collaboration in the relevant areas related to safety and security, such as joint projects, peer reviews, enabling synergies among existing networks and initiatives, informing the public on the relevant safety and security areas and the related international collaboration. In the RegNet part of the GNSSN exist the National Nuclear Regulatory Portal (NNRP) which is on one hand a part of the global RegNet and on the

  15. Development of an Experimental African Drought Monitoring and Seasonal Forecasting System: A First Step towards a Global Drought Information System

    Science.gov (United States)

    Wood, E. F.; Chaney, N.; Sheffield, J.; Yuan, X.

    2012-12-01

    forecasts are bias corrected, downscaled and used as inputs to the VIC LSM as well as forecasts based on ESP and CPC official seasonal outlook. For Africa, data from a combination of remote sensing (TMPA-based precipitation, land cover characteristics) and GFS analysis fields (temperature and wind) are used to monitor drought using our soil moisture drought index as well as 1, 3 and and 6-month SPI. River discharge is also estimated at over 900 locations. Seasonal forecasts have been developed using CFSv2 climate forecasts following the approaches used over CONUS. We will discuss the performance of the system to evaluate the depiction of drought over various scales, from regional to the African continent, and over a number of years to capture multiple drought events. Furthermore, the hindcasts from the seasonal drought forecast system are analyzed to assess the ability of seasonal climate models to detect drought on-set and its recovery. Finally, we will discuss whether our ADM provides a pathway to a Global Drought Information System, a goal of the WCRP Drought Task Force.

  16. 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...

  17. 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

  18. Sequence assembly

    DEFF Research Database (Denmark)

    Scheibye-Alsing, Karsten; Hoffmann, S.; Frankel, Annett Maria

    2009-01-01

    Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies and...... in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at: http://genome.ku.dk/resources/assembly/methods.html....

  19. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  20. A global network for the control of snail-borne disease using satellite surveillance and geographic information systems.

    Science.gov (United States)

    Malone, J B; Bergquist, N R; Huh, O K; Bavia, M E; Bernardi, M; El Bahy, M M; Fuentes, M V; Kristensen, T K; McCarroll, J C; Yilma, J M; Zhou, X N

    2001-04-27

    At a team residency sponsored by the Rockefeller Foundation in Bellagio, Italy, 10-14 April 2000 an organizational plan was conceived to create a global network of collaborating health workers and earth scientists dedicated to the development of computer-based models that can be used for improved control programs for schistosomiasis and other snail-borne diseases of medical and veterinary importance. The models will be assembled using GIS methods, global climate model data, sensor data from earth observing satellites, disease prevalence data, the distribution and abundance of snail hosts, and digital maps of key environmental factors that affect development and propagation of snail-borne disease agents. A work plan was developed for research collaboration and data sharing, recruitment of new contributing researchers, and means of access of other medical scientists and national control program managers to GIS models that may be used for more effective control of snail-borne disease. Agreement was reached on the use of compatible GIS formats, software, methods and data resources, including the definition of a 'minimum medical database' to enable seamless incorporation of results from each regional GIS project into a global model. The collaboration plan calls for linking a 'central resource group' at the World Health Organization, the Food and Agriculture Organization, Louisiana State University and the Danish Bilharziasis Laboratory with regional GIS networks to be initiated in Eastern Africa, Southern Africa, West Africa, Latin America and Southern Asia. An Internet site, www.gnosisGIS.org, (GIS Network On Snail-borne Infections with special reference to Schistosomiasis), has been initiated to allow interaction of team members as a 'virtual research group'. When completed, the site will point users to a toolbox of common resources resident on computers at member organizations, provide assistance on routine use of GIS health maps in selected national disease control

  1. WE-G-BRD-02: Characterizing Information Loss in a Sparse-Sampling-Based Dynamic MRI Sequence (k-T BLAST) for Lung Motion Monitoring

    International Nuclear Information System (INIS)

    Arai, T; Nofiele, J; Sawant, A

    2015-01-01

    Purpose: Rapid MRI is an attractive, non-ionizing tool for soft-tissue-based monitoring of respiratory motion in thoracic and abdominal radiotherapy. One big challenge is to achieve high temporal resolution while maintaining adequate spatial resolution. K-t BLAST, sparse-sampling and reconstruction sequence based on a-priori information represents a potential solution. In this work, we investigated how much “true” motion information is lost as a-priori information is progressively added for faster imaging. Methods: Lung tumor motions in superior-inferior direction obtained from ten individuals were replayed into an in-house, MRI-compatible, programmable motion platform (50Hz refresh and 100microns precision). Six water-filled 1.5ml tubes were placed on it as fiducial markers. Dynamic marker motion within a coronal slice (FOV: 32×32cm"2, resolution: 0.67×0.67mm"2, slice-thickness: 5mm) was collected on 3.0T body scanner (Ingenia, Philips). Balanced-FFE (TE/TR: 1.3ms/2.5ms, flip-angle: 40degrees) was used in conjunction with k-t BLAST. Each motion was repeated four times as four k-t acceleration factors 1, 2, 5, and 16 (corresponding frame rates were 2.5, 4.7, 9.8, and 19.1Hz, respectively) were compared. For each image set, one average motion trajectory was computed from six marker displacements. Root mean square error (RMS) was used as a metric of spatial accuracy where measured trajectories were compared to original data. Results: Tumor motion was approximately 10mm. The mean(standard deviation) of respiratory rates over ten patients was 0.28(0.06)Hz. Cumulative distributions of tumor motion frequency spectra (0–25Hz) obtained from the patients showed that 90% of motion fell on 3.88Hz or less. Therefore, the frame rate must be a double or higher for accurate monitoring. The RMS errors over patients for k-t factors of 1, 2, 5, and 16 were.10(.04),.17(.04), .21(.06) and.26(.06)mm, respectively. Conclusions: K-t factor of 5 or higher can cover the high

  2. Communications, Immunization, and Polio Vaccines: Lessons From a Global Perspective on Generating Political Will, Informing Decision-Making and Planning, and Engaging Local Support.

    Science.gov (United States)

    Menning, Lisa; Garg, Gaurav; Pokharel, Deepa; Thrush, Elizabeth; Farrell, Margaret; Kodio, Frederic Kunjbe; Veira, Chantal Laroche; Wanyoike, Sarah; Malik, Suleman; Patel, Manish; Rosenbauer, Oliver

    2017-07-01

    The requirements under objective 2 of the Polio Eradication and Endgame Strategic Plan 2013-2018-to introduce at least 1 dose of inactivated poliomyelitis vaccine (IPV); withdraw oral poliomyelitis vaccine (OPV), starting with the type 2 component; and strengthen routine immunization programs-set an ambitious series of targets for countries. Effective implementation of IPV introduction and the switch from trivalent OPV (containing types 1, 2, and 3 poliovirus) to bivalent OPV (containing types 1 and 3 poliovirus) called for intense global communications and coordination on an unprecedented scale from 2014 to 2016, involving global public health technical agencies and donors, vaccine manufacturers, World Health Organization and United Nations Children's Fund regional offices, and national governments. At the outset, the new program requirements were perceived as challenging to communicate, difficult to understand, unrealistic in terms of timelines, and potentially infeasible for logistical implementation. In this context, a number of core areas of work for communications were established: (1) generating awareness and political commitment via global communications and advocacy; (2) informing national decision-making, planning, and implementation; and (3) in-country program communications and capacity building, to ensure acceptance of IPV and continued uptake of OPV. Central to the communications function in driving progress for objective 2 was its ability to generate a meaningful policy dialogue about polio vaccines and routine immunization at multiple levels. This included efforts to facilitate stakeholder engagement and ownership, strengthen coordination at all levels, and ensure an iterative process of feedback and learning. This article provides an overview of the global efforts and challenges in successfully implementing the communications activities to support objective 2. Lessons from the achievements by countries and partners will likely be drawn upon when

  3. In silico site-directed mutagenesis informs species-specific predictions of chemical susceptibility derived from the Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool

    Science.gov (United States)

    The Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool was developed to address needs for rapid, cost effective methods of species extrapolation of chemical susceptibility. Specifically, the SeqAPASS tool compares the primary sequence (Level 1), functiona...

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

    NARCIS (Netherlands)

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

    1993-01-01

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

  5. Informal roles within eSport teams : a content analysis of the game 'Counter-Strike: Global Offensive

    OpenAIRE

    Drenthe, Rolf

    2016-01-01

    Informal roles are roles that are not formally prescribed by a group or organization and are being established through group interaction that takes place among group members. Previous literature has identified twelve roles within traditional sport, however to date limited research has been done within the field of role development within competitive computer gaming (eSports). The purpose of the present study was to explore the informal roles within the eSport setting and i...

  6. The Japanese Experience of the NameExoWorlds Competition: Translating Official Information into Japanese to Enable Domestic Groups to Participate in a Global Event

    Science.gov (United States)

    Usuda-Sato, K.; Iizuka, R.; Yamaoka, H.; Handa, T.

    2018-02-01

    Translation of information from English is an essential step toward ensuring the involvement of non-English speakers in global events. The NameExoWorlds competition, led by the International Astronomical Union (IAU), was held from 9 July 2014 to 15 December 2015. It was a unique event that invited the public to name celestial bodies. In Japan, language acts as a significant barrier for amateur astronomers and school students to participate in global events hosted in English. To address this concern, we established a domestic working group to set up a Japanese website and provided a translation of the IAU's official site for the NameExoWorlds competition. We also developed additional original information in Japanese when needed and sent announcements to a mailing lists of astronomy societies in Japan. As a result, 28% of the registered groups and 47% of proposals for names were from Japan, making Japan the most active country for these stages of the competition. After the competition had ended, we carried out a survey in the Japanese astronomy community and received 124 responses. We found that most of the Japanese participants referred to our official Japanese website in order to overcome the language barrier and participate in the competition. This article explores our work of translating the competition information into Japanese and our evaluation of the impact of this action on the uptake by Japanese astronomy enthusiasts.

  7. Globalization, the Information Society and New Crimes : the Challenge for the XXI Century / Mondialisation, société de l’information et crimes nouveaux : le défi du 21ème siècle

    Directory of Open Access Journals (Sweden)

    Viano Emilio

    2012-08-01

    Full Text Available This paper examines in depth the current phenomenon of globalization and its trends; its impact, positive or negative which is the cornerstone of the current restructuring of the global economy; the nature and consequences of the globalization of trade and financial services; the operations and impact of the multinationals; and the hierarchy of countries based on their relative importance in the global economy, and its consequences. The paper then distinguishes between real and virtual globalization and its impact on economic growth; its inclusive and exclusive dynamics and their consequences for individual and corporate economic actors. The paper then addresses the information society, a phenomenon that accompanies and significantly facilitates globalization through drastic and significant improvements in communications and transport. The Internet and electronic devices used for massive surveillance, the collection of personal information, and the systematic erosion of privacy - the Internet as Panopticon – are also examined.Finally, the paper analyzes the vulnerability of the global information society to crime, especially economic and identity theft crimes, ironically facilitated especially by its global and inter-connected nature. Even the global improvement in the financial conditions of most people worldwide, creating more wealth and economic well being, has negative, and at times criminal, repercussions, impacting especially indigenous or vulnerable populations, fauna and flora. Most illustrative examples of these criminal trends are trafficking in people, endangered species, animal organs and products, antiquities, art and various types of counterfeiting. In conclusion there is a clear and close connection between globalization, the information society, criminal behavior and a society’s ability to effectively protect itself from piracy and the violations of a country’s laws and treaties.Ce document examine en profondeur le ph

  8. Organizing Global IS Management to Meet Competitive Challenges: Experiences from the Pharmaceutical Industry

    OpenAIRE

    Bettina Schwarzer

    1995-01-01

    Despite the widely acknowledged importance information technology plays in multinational corporations, many companies lack an understanding of when and how to (re)organize global IS management. The issues of timing and organization of global IS management, however, seem to be of utmost importance in a company’s attempt to implement a new, global business strategy. Based on three case studies from the pharmaceutical industry, this paper analyzes the sequence in which business strategy, organ...

  9. Major multinational food and beverage companies and informal sector contributions to global food consumption: implications for nutrition policy

    Directory of Open Access Journals (Sweden)

    Yach Derek

    2011-08-01

    Full Text Available Abstract Background In recent years, 10 major multinational food and beverage companies have worked together within the International Food and Beverage Alliance (IFBA to increase their commitments to public health. Current IFBA commitments include initiatives to improve the nutrition quality of products and how these products are advertised to children. The impact and magnitude of IFBA member contributions to the total market share of packaged foods and beverages consumed remain incompletely understood, however. Methods In order to evaluate this impact, we examined packaged food and soft drink company shares provided by Euromonitor, an international independent market analysis company. Packaged foods include baby food, bakery, canned/preserved food, chilled/processed food, confectionery, dairy, dried processed food, frozen processed food, ice cream, meal replacement, noodles, oils and fats, pasta, ready meals, sauces, dressings and condiments, snack bars, soup, spreads, and sweet and savoury snacks. Soft drinks include carbonates, packaged fruit/vegetable juice, bottled water, functional drinks, concentrates, ready-to-drink tea, ready-to-drink coffee and Asian specialty drinks. We calculated the market shares for IFBA companies, globally and within nine countries--the US, China, India, Egypt, South Africa, Brazil, Mexico, Turkey and the UK. Results Worldwide, the top ten packaged food companies account for 15.2% of sales, with each individual company contributing less than 3.3%. The top ten soft drink companies account for 52.3% of sales worldwide; Coca-Cola and PepsiCo lead with 25.9% and 11.5% of sales, respectively. Conclusions Although the top ten soft drink companies account for half of global sales, the top ten packaged food companies account for only a small proportion of market share with most individual companies contributing less than 3.3% each. Major multinational companies need to be joined by the myriad of small- and medium

  10. Major multinational food and beverage companies and informal sector contributions to global food consumption: implications for nutrition policy

    Science.gov (United States)

    2011-01-01

    Background In recent years, 10 major multinational food and beverage companies have worked together within the International Food and Beverage Alliance (IFBA) to increase their commitments to public health. Current IFBA commitments include initiatives to improve the nutrition quality of products and how these products are advertised to children. The impact and magnitude of IFBA member contributions to the total market share of packaged foods and beverages consumed remain incompletely understood, however. Methods In order to evaluate this impact, we examined packaged food and soft drink company shares provided by Euromonitor, an international independent market analysis company. Packaged foods include baby food, bakery, canned/preserved food, chilled/processed food, confectionery, dairy, dried processed food, frozen processed food, ice cream, meal replacement, noodles, oils and fats, pasta, ready meals, sauces, dressings and condiments, snack bars, soup, spreads, and sweet and savoury snacks. Soft drinks include carbonates, packaged fruit/vegetable juice, bottled water, functional drinks, concentrates, ready-to-drink tea, ready-to-drink coffee and Asian specialty drinks. We calculated the market shares for IFBA companies, globally and within nine countries--the US, China, India, Egypt, South Africa, Brazil, Mexico, Turkey and the UK. Results Worldwide, the top ten packaged food companies account for 15.2% of sales, with each individual company contributing less than 3.3%. The top ten soft drink companies account for 52.3% of sales worldwide; Coca-Cola and PepsiCo lead with 25.9% and 11.5% of sales, respectively. Conclusions Although the top ten soft drink companies account for half of global sales, the top ten packaged food companies account for only a small proportion of market share with most individual companies contributing less than 3.3% each. Major multinational companies need to be joined by the myriad of small- and medium-sized enterprises in developing and

  11. Major multinational food and beverage companies and informal sector contributions to global food consumption: implications for nutrition policy.

    Science.gov (United States)

    Alexander, Eleanore; Yach, Derek; Mensah, George A

    2011-08-01

    In recent years, 10 major multinational food and beverage companies have worked together within the International Food and Beverage Alliance (IFBA) to increase their commitments to public health. Current IFBA commitments include initiatives to improve the nutrition quality of products and how these products are advertised to children. The impact and magnitude of IFBA member contributions to the total market share of packaged foods and beverages consumed remain incompletely understood, however. In order to evaluate this impact, we examined packaged food and soft drink company shares provided by Euromonitor, an international independent market analysis company. Packaged foods include baby food, bakery, canned/preserved food, chilled/processed food, confectionery, dairy, dried processed food, frozen processed food, ice cream, meal replacement, noodles, oils and fats, pasta, ready meals, sauces, dressings and condiments, snack bars, soup, spreads, and sweet and savoury snacks. Soft drinks include carbonates, packaged fruit/vegetable juice, bottled water, functional drinks, concentrates, ready-to-drink tea, ready-to-drink coffee and Asian specialty drinks. We calculated the market shares for IFBA companies, globally and within nine countries--the US, China, India, Egypt, South Africa, Brazil, Mexico, Turkey and the UK. Worldwide, the top ten packaged food companies account for 15.2% of sales, with each individual company contributing less than 3.3%. The top ten soft drink companies account for 52.3% of sales worldwide; Coca-Cola and PepsiCo lead with 25.9% and 11.5% of sales, respectively. Although the top ten soft drink companies account for half of global sales, the top ten packaged food companies account for only a small proportion of market share with most individual companies contributing less than 3.3% each. Major multinational companies need to be joined by the myriad of small- and medium-sized enterprises in developing and implementing programs to improve the

  12. Building capacity for information and communication technology use in global health research and training in China: a qualitative study among Chinese health sciences faculty members.

    Science.gov (United States)

    Wang, Jie; Abdullah, Abu S; Ma, Zhenyu; Fu, Hua; Huang, Kaiyong; Yu, Hongping; Wang, Jiaji; Cai, Le; He, Huimin; Xiao, Jian; Quintiliani, Lisa; Friedman, Robert H; Yang, Li

    2017-06-28

    The demand to use information and communications technology (ICT) in education and research has grown fast among researchers and educators working in global health. However, access to ICT resources and the capacity to use them in global health research remains limited among developing country faculty members. In order to address the global health needs and to design an ICT-related training course, we herein explored the Chinese health science faculty members' perceptions and learning needs for ICT use. Nine focus groups discussions (FGDs) were conducted during December 2015 to March 2016, involving 63 faculty members working in areas of health sciences from six universities in China. All FGDs were audio recorded and analysed thematically. The findings suggest that the understandings of ICT were not clear among many researchers; some thought that the concept of ICT was too wide and ambiguous. Most participants were able to cite examples of ICT application in their research and teaching activities. Positive attitudes and high needs of ICT use and training were common among most participants. Recommendations for ICT training included customised training programmes focusing on a specific specialty, maintaining a balance between theories and practical applications, more emphasis on the application of ICT, and skills in finding the required information from the bulk information available in the internet. Suggestions regarding the format and offering of training included short training programmes, flexible timing, lectures with practicum opportunities, and free of charge or with very minimal cost to the participants. Two participants suggested the linking of ICT-related training courses with faculty members' year-end assessment and promotion. This study among health sciences faculty members in China demonstrated a high level of need and interest in learning about ICT use in research and training. The results have important implications for the design and implementation of

  13. Sequence History Update Tool

    Science.gov (United States)

    Khanampompan, Teerapat; Gladden, Roy; Fisher, Forest; DelGuercio, Chris

    2008-01-01

    The Sequence History Update Tool performs Web-based sequence statistics archiving for Mars Reconnaissance Orbiter (MRO). Using a single UNIX command, the software takes advantage of sequencing conventions to automatically extract the needed statistics from multiple files. This information is then used to populate a PHP database, which is then seamlessly formatted into a dynamic Web page. This tool replaces a previous tedious and error-prone process of manually editing HTML code to construct a Web-based table. Because the tool manages all of the statistics gathering and file delivery to and from multiple data sources spread across multiple servers, there is also a considerable time and effort savings. With the use of The Sequence History Update Tool what previously took minutes is now done in less than 30 seconds, and now provides a more accurate archival record of the sequence commanding for MRO.

  14. The Need to Adapt to New Financial Accounting Technologies Information in the Context of Global Economic Crisis

    Directory of Open Access Journals (Sweden)

    Enrique BONSON-PONTE

    2010-12-01

    Full Text Available Today, accounting is a necessity and not a desire. Concerns for the improvement of accounting practices are necessary, especially in Romania, where these activities are strengthened with the progress of the Romanian economy integration into the structures of the European Union. This paper carried an objective analysis of how the web report is now being made by financial and accounting information, presents the disadvantages of this approach to reporting introduced, but the potential benefits that could be created by the rapid adoption of international standards for reporting financial information website, too. At the same time, the paper tries to create new opportunities as soon as possible regarding the adoption of intelligent technologies, which, coupled with language Web reporting financial information.

  15. 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

  16. The implications of megatrends in information and communication technology and transportation for changes in global physical activity

    DEFF Research Database (Denmark)

    Pratt, Michael; Sarmiento, Olga L; Montes, Felipe

    2012-01-01

    Physical inactivity accounts for more than 3 million deaths per year, most from non-communicable diseases in low-income and middle-income countries. We used reviews of physical activity interventions and a simulation model to examine how megatrends in information and communication technology and ...

  17. Globalization, Information and Communication Technologies (ICTs) and Open/Distance Learning in Nigeria: Trends, Issues and Solution

    Science.gov (United States)

    Olusola, Akande Joshua; Alaba, Sofowora Olaniyi

    2011-01-01

    The main thrust of this paper is to discuss the development of open and distance education in Nigeria and the major manifestations of the use of information and communication technologies (ICTs) in education in open and distance learning. This study further discusses the importance and use of ICTs in open and distance learning in making education…

  18. Pairwise Sequence Alignment Library

    Energy Technology Data Exchange (ETDEWEB)

    2015-05-20

    Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprint that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, a novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.

  19. The Evolution of Global Politics

    Directory of Open Access Journals (Sweden)

    George Moldeski

    1995-08-01

    Full Text Available The rise and decline of world powers has attracted much scholarly attention in recent years. The theory of long cycles answers parsimoniously the question: why, in the past half millenium, have Portugal, the Dutch Republic, Britain (twice, and the United States risen to global leadership while others have failed to do so? This accounts for the success, or failure, of individual states, but to explain the entire sequence we need to employ an evolutionary paradigm that proposes that each of these long cycles is one mechanism in a spectrum of global evolutionary processes. The leadership succession is an intermediate stage in the evolution og global politics, whose next likely major phase, reaching a high point later in the 21st century, will be the gradual absorption of the informal role of global leadership, when embedded in a democratic community, into a network of more formal positions within an emerging global organization of a federalist character. The conditions of that process can now be specified.

  20. Center for Environmental Information's Ninth International Conference on Global Energy Strategies : Living with Restricted Greenhouse Gas Emissions

    CERN Document Server

    1993-01-01

    The world is getting warmer. Among scientists concerned with global climate change this is the broad consensus. How fast and by how much, are questions which cannot be answered quantitatively, but the probability of rising temperatures must be faced in a prudent manner - there is enough certainty of change so that we must anticipate and prepare before irreparable damage is done to our world. Even if it isn't going to be as bad as some people think, the actions we propose will benefit the earth and give us a kind of insurance. The root of the change is population growth, and its attendant demand for energy. While the developed world expects to hold future emissions relatively steady, the developing countries, where population growth is most rampant, will expand the use of energy as they aspire to a better quality of life. H greater energy use is inevitable it behooves us to produce that energy in the least objectionable manner, and to produce it where the cost is lowest in dollars, GNP, and environmental chang...