Science.gov

Sample records for additional biological information

  1. Herpetofauna of the Beni Biological Station Biosphere Reserve, Amazonian Bolivia: Additional information, and current knowledge in context

    USGS Publications Warehouse

    Middendorf, G.; Reynolds, R.; Herrera-MacBryde, Olga; Dallmeier, Francisco; MacBryde, Bruce; Cominskey, James A.; Miranda, Carmen

    2000-01-01

    Previous collections in the Departamento del Beni in tropical Bolivia only hinted at high levels of herpetological biodiversity (Fugler 1986, 1988; de la Riva 1990a; Fugler and de la Riva 1990). Fieldwork (totaling 48 days) in July-August 1988 and September 1987 (dry seasons) and November-December 1990 (wet season) has resulted in collection and identification of 401 amphibian and reptilian specimens from the general area of the Beni Biological Station's (EBB) headquarters at El Porvenir. These collections represent 33 amphibian and 17 reptilian species in 29 genera (14 amphibian, 15 reptilian). The inventory of herpetofauna scientifically documented to occur in the Departamento del Beni is considered to have been increased by 6 amphibian and 10 reptilian species. Specimens that could not be definitively identified (reflecting taxonomic uncertainty and/or probably species new to science) include 3 amphibian species (anurans) and 2 reptilian species (snakes). The EBB harbors the richest savanna for anuran species known in South America.

  2. Biological Information Signal Processor

    NASA Technical Reports Server (NTRS)

    Chow, Edward T.; Peterson, John C.; Yoo, Michael M.

    1993-01-01

    Biological Information Signal Processor (BISP) is computing system analyzing data on deoxyribonucleic acid (DNA) sequences for molecular genetic analysis. Includes coprocessors, specialized microprocessors complementing present and future computers by performing rapidly most-time-consuming DNA-sequence-analyzing functions, establishing relationships (alignments) between both global sequences and defining patterns in multiple sequences. Also includes state-of-art software and data-base systems on both conventional and parallel computer systems to augment analytical abilities of developmental coprocessors.

  3. Additive manufacturing of biologically-inspired materials.

    PubMed

    Studart, André R

    2016-01-21

    Additive manufacturing (AM) technologies offer an attractive pathway towards the fabrication of functional materials featuring complex heterogeneous architectures inspired by biological systems. In this paper, recent research on the use of AM approaches to program the local chemical composition, structure and properties of biologically-inspired materials is reviewed. A variety of structural motifs found in biological composites have been successfully emulated in synthetic systems using inkjet-based, direct-writing, stereolithography and slip casting technologies. The replication in synthetic systems of design principles underlying such structural motifs has enabled the fabrication of lightweight cellular materials, strong and tough composites, soft robots and autonomously shaping structures with unprecedented properties and functionalities. Pushing the current limits of AM technologies in future research should bring us closer to the manufacturing capabilities of living organisms, opening the way for the digital fabrication of advanced materials with superior performance, lower environmental impact and new functionalities.

  4. 16 CFR 1102.16 - Additional information.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Content Requirements § 1102.16 Additional... in the Database any additional information it determines to be in the public interest,...

  5. 16 CFR 1102.16 - Additional information.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Content Requirements § 1102.16 Additional... in the Database any additional information it determines to be in the public interest,...

  6. 16 CFR 1102.16 - Additional information.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Content Requirements § 1102.16 Additional... in the Database any additional information it determines to be in the public interest,...

  7. Evolution, Entropy, & Biological Information

    ERIC Educational Resources Information Center

    Peterson, Jacob

    2014-01-01

    A logical question to be expected from students: "How could life develop, that is, change, evolve from simple, primitive organisms into the complex forms existing today, while at the same time there is a generally observed decline and disorganization--the second law of thermodynamics?" The explanations in biology textbooks relied upon by…

  8. The meaning of biological information.

    PubMed

    Koonin, Eugene V

    2016-03-13

    Biological information encoded in genomes is fundamentally different from and effectively orthogonal to Shannon entropy. The biologically relevant concept of information has to do with 'meaning', i.e. encoding various biological functions with various degree of evolutionary conservation. Apart from direct experimentation, the meaning, or biological information content, can be extracted and quantified from alignments of homologous nucleotide or amino acid sequences but generally not from a single sequence, using appropriately modified information theoretical formulae. For short, information encoded in genomes is defined vertically but not horizontally. Informally but substantially, biological information density seems to be equivalent to 'meaning' of genomic sequences that spans the entire range from sharply defined, universal meaning to effective meaninglessness. Large fractions of genomes, up to 90% in some plants, belong within the domain of fuzzy meaning. The sequences with fuzzy meaning can be recruited for various functions, with the meaning subsequently fixed, and also could perform generic functional roles that do not require sequence conservation. Biological meaning is continuously transferred between the genomes of selfish elements and hosts in the process of their coevolution. Thus, in order to adequately describe genome function and evolution, the concepts of information theory have to be adapted to incorporate the notion of meaning that is central to biology.

  9. The meaning of biological information

    PubMed Central

    Koonin, Eugene V.

    2016-01-01

    Biological information encoded in genomes is fundamentally different from and effectively orthogonal to Shannon entropy. The biologically relevant concept of information has to do with ‘meaning’, i.e. encoding various biological functions with various degree of evolutionary conservation. Apart from direct experimentation, the meaning, or biological information content, can be extracted and quantified from alignments of homologous nucleotide or amino acid sequences but generally not from a single sequence, using appropriately modified information theoretical formulae. For short, information encoded in genomes is defined vertically but not horizontally. Informally but substantially, biological information density seems to be equivalent to ‘meaning’ of genomic sequences that spans the entire range from sharply defined, universal meaning to effective meaninglessness. Large fractions of genomes, up to 90% in some plants, belong within the domain of fuzzy meaning. The sequences with fuzzy meaning can be recruited for various functions, with the meaning subsequently fixed, and also could perform generic functional roles that do not require sequence conservation. Biological meaning is continuously transferred between the genomes of selfish elements and hosts in the process of their coevolution. Thus, in order to adequately describe genome function and evolution, the concepts of information theory have to be adapted to incorporate the notion of meaning that is central to biology. PMID:26857678

  10. 16 CFR 1102.16 - Additional information.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE (Eff. Jan. 10, 2011) Content Requirements... notices, the CPSC shall include in the Database any additional information it determines to be in...

  11. Information Visualization for Biological Data.

    PubMed

    Czauderna, Tobias; Schreiber, Falk

    2017-01-01

    Visualization is a powerful method to present and explore a large amount of data. It is increasingly important in the life sciences and is used for analyzing different types of biological data, such as structural information, high-throughput data, and biochemical networks. This chapter gives a brief introduction to visualization methods for bioinformatics, presents two commonly used techniques in detail, and discusses a graphical standard for biological networks and cellular processes.

  12. Uniform Additivity in Classical and Quantum Information

    NASA Astrophysics Data System (ADS)

    Cross, Andrew; Li, Ke; Smith, Graeme

    2017-01-01

    Information theory quantifies the optimal rates of resource interconversions, usually in terms of entropies. However, nonadditivity often makes evaluating entropic formulas intractable. In a few auspicious cases, additivity allows a full characterization of optimal rates. We study uniform additivity of formulas, which is easily evaluated and captures all known additive quantum formulas. Our complete characterization of uniform additivity exposes an intriguing new additive quantity and identifies a remarkable coincidence—the classical and quantum uniformly additive functions with one auxiliary variable are identical.

  13. 10 CFR 810.14 - Additional information.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 10 Energy 4 2011-01-01 2011-01-01 false Additional information. 810.14 Section 810.14 Energy DEPARTMENT OF ENERGY ASSISTANCE TO FOREIGN ATOMIC ENERGY ACTIVITIES § 810.14 Additional information. The Department of Energy may at any time require a person engaging in any generally or specifically...

  14. 10 CFR 810.14 - Additional information.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 10 Energy 4 2010-01-01 2010-01-01 false Additional information. 810.14 Section 810.14 Energy DEPARTMENT OF ENERGY ASSISTANCE TO FOREIGN ATOMIC ENERGY ACTIVITIES § 810.14 Additional information. The Department of Energy may at any time require a person engaging in any generally or specifically...

  15. 12 CFR 1010.116 - Additional information.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 12 Banks and Banking 8 2013-01-01 2013-01-01 false Additional information. 1010.116 Section 1010.116 Banks and Banking BUREAU OF CONSUMER FINANCIAL PROTECTION LAND REGISTRATION (REGULATION J) Reporting Requirements § 1010.116 Additional information. (a) Property Owners' Association. (1) Will there be a property owners' association for...

  16. 12 CFR 1010.116 - Additional information.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 12 Banks and Banking 8 2014-01-01 2014-01-01 false Additional information. 1010.116 Section 1010.116 Banks and Banking BUREAU OF CONSUMER FINANCIAL PROTECTION LAND REGISTRATION (REGULATION J) Reporting Requirements § 1010.116 Additional information. (a) Property Owners' Association. (1) Will there be a property owners' association for...

  17. The problems of biological information.

    PubMed

    Ball, Philip

    2016-03-13

    The discovery of genetic encoding in the DNA molecule, and its mode of translation into protein structures, secured the modern view of biology as an information science. But it remains unclear what kind of information science it is. The all-too-ready analogy with computer programs stored on spools of magnetic tape has been hard to relinquish, even while the complexity of information storage and flow in the cell has become ever more apparent. To understand how life is sustained and evolves through encoding and processing of information, new ideas are now required, within which genetic encoding in DNA seems likely to provide only one part of a much broader and more profound puzzle. In particular, it seems likely that the emerging picture will need to take a more subtle view of causation, context and meaning in the orchestrated, hierarchical processes that make life possible.

  18. Information and Knowledge in Biology

    PubMed Central

    2007-01-01

    The second law of thermodynamics accounts for irreversibility of processes in the universe. As a statement about increasing disorder, it also plays a central role in creating order. Structuring is a way of how to increase the rate of dissipation of matter and energy. This is the reason why chemical reactions on Earth have produced a profusion of structures. Chemical structures with particularly high stability, maintained by continual dissipation, are designated, somewhat arbitrarily, as living systems. To preserve stability, organisms are unceasingly performing ontic work, assisted by epistemic work. Biological evolution is a progressing process of knowledge acquisition (cognition) and, correspondingly, of growth of complexity. The acquired knowledge represents epistemic complexity. Biological species are the main “bookkeepers” of acquired knowledge, with individual members of the species functioning as “explorers” of novelty. Science, a human species-specific mode of acquiring knowledge, abounds in metaphors no less than art. In the postgenomic era, the metaphor of information, along with the related metaphor of selfish genes, may need reconsideration and/or complementation. The world of great complexity, which is becoming the focus of studies of contemporary biology, may require—similarly as is the case of quantum physics—descriptions based on the principle of complementarity. Embodied knowledge, molecular engine, ontic and epistemic work, and triggering may become parts of a new conceptual armory. PMID:19516970

  19. 24 CFR 1710.116 - Additional information.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 24 Housing and Urban Development 5 2014-04-01 2014-04-01 false Additional information. 1710.116 Section 1710.116 Housing and Urban Development Regulations Relating to Housing and Urban Development... URBAN DEVELOPMENT (INTERSTATE LAND SALES REGISTRATION PROGRAM) LAND REGISTRATION Reporting...

  20. 24 CFR 1710.216 - Additional information.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 24 Housing and Urban Development 5 2014-04-01 2014-04-01 false Additional information. 1710.216 Section 1710.216 Housing and Urban Development Regulations Relating to Housing and Urban Development... URBAN DEVELOPMENT (INTERSTATE LAND SALES REGISTRATION PROGRAM) LAND REGISTRATION Reporting...

  1. 18 CFR 5.21 - Additional information.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 18 Conservation of Power and Water Resources 1 2012-04-01 2012-04-01 false Additional information. 5.21 Section 5.21 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT OF ENERGY REGULATIONS UNDER THE FEDERAL POWER ACT INTEGRATED LICENSE APPLICATION PROCESS §...

  2. 18 CFR 5.21 - Additional information.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 18 Conservation of Power and Water Resources 1 2010-04-01 2010-04-01 false Additional information. 5.21 Section 5.21 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT OF ENERGY REGULATIONS UNDER THE FEDERAL POWER ACT INTEGRATED LICENSE APPLICATION PROCESS §...

  3. 18 CFR 5.21 - Additional information.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 18 Conservation of Power and Water Resources 1 2013-04-01 2013-04-01 false Additional information. 5.21 Section 5.21 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT OF ENERGY REGULATIONS UNDER THE FEDERAL POWER ACT INTEGRATED LICENSE APPLICATION PROCESS §...

  4. 18 CFR 5.21 - Additional information.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 18 Conservation of Power and Water Resources 1 2011-04-01 2011-04-01 false Additional information. 5.21 Section 5.21 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT OF ENERGY REGULATIONS UNDER THE FEDERAL POWER ACT INTEGRATED LICENSE APPLICATION PROCESS §...

  5. 18 CFR 5.21 - Additional information.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 18 Conservation of Power and Water Resources 1 2014-04-01 2014-04-01 false Additional information. 5.21 Section 5.21 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT OF ENERGY REGULATIONS UNDER THE FEDERAL POWER ACT INTEGRATED LICENSE APPLICATION PROCESS §...

  6. 24 CFR 1710.116 - Additional information.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 24 Housing and Urban Development 5 2013-04-01 2013-04-01 false Additional information. 1710.116 Section 1710.116 Housing and Urban Development Regulations Relating to Housing and Urban Development (Continued) OFFICE OF ASSISTANT SECRETARY FOR HOUSING-FEDERAL HOUSING COMMISSIONER, DEPARTMENT OF HOUSING AND URBAN DEVELOPMENT (INTERSTATE LAND...

  7. 27 CFR 41.197 - Additional information.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ..., § 41.197 was revised, effective Aug. 26, 2013 through Aug. 26, 2016. ... 27 Alcohol, Tobacco Products and Firearms 2 2014-04-01 2014-04-01 false Additional information. 41.197 Section 41.197 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE...

  8. 18 CFR 33.10 - Additional information.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 18 Conservation of Power and Water Resources 1 2010-04-01 2010-04-01 false Additional information. 33.10 Section 33.10 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT OF ENERGY REGULATIONS UNDER THE FEDERAL POWER ACT APPLICATIONS UNDER FEDERAL POWER ACT SECTION...

  9. [Information about phosphorus additives and nutritional counseling].

    PubMed

    Kido, Shinsuke; Nomura, Kengo; Sasaki, Shohei; Shiozaki, Yuji; Segawa, Hiroko; Tatsumi, Sawako

    2012-10-01

    Hyperphosphatemia is a common disorder in patients with chronic kidney disease (CKD) , and may result in hyperparathyroidism and renal osteodystrophy. Hyperphosphatemia also may contribute to deterioration vascular calcification and increase mortality. Hence, correction and prevention of hyperphosphatemia is a main component of the management of CKD. This goal is usually approached both by administering phosphorus binders and by restricting dietary phosphorus (P) intake. Dietary intake of phosphorus (P) is derived largely from foods with high protein content or food additives and is an important determinant of P balance in patient with CKD. Food additives (PO4) can dramatically increase the amount of P consumed in the daily diet, especially because P is more readily absorbed in its inorganic form. In addition, information about the P content and type in prepared foods is often unavailable or misleading. Therefore, during dietary counseling of patients with CKD, we recommended that they consider both the absolute dietary P content and the P-to-protein ratio of foods and meals including food additives.

  10. Information Theory in Biology after 18 Years

    ERIC Educational Resources Information Center

    Johnson, Horton A.

    1970-01-01

    Reviews applications of information theory to biology, concluding that they have not proved very useful. Suggests modifications and extensions to increase the biological relevance of the theory, and speculates about applications in quantifying cell proliferation, chemical homeostasis and aging. (EB)

  11. 47 CFR 25.111 - Additional information.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... Service (BSS) in Appendix 30 of the ITU Radio Regulations (RR) and associated feeder-link plans in Appendix 30A of the ITU RR, if the system has technical characteristics differing from those specified in... provide the Commission with the information required by Appendix 4 of the ITU RR for advance...

  12. 47 CFR 25.111 - Additional information.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) COMMON CARRIER SERVICES SATELLITE COMMUNICATIONS... Administrations. (c) In the Direct Broadcast Satellite service, applicants and licensees shall also provide the Commission with all information it requires in order to modify the Appendix 30 Broadcasting-Satellite...

  13. 47 CFR 25.111 - Additional information.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) COMMON CARRIER SERVICES SATELLITE COMMUNICATIONS... Administrations. (c) In the Direct Broadcast Satellite service, applicants and licensees shall also provide the Commission with all information it requires in order to modify the Appendix 30 Broadcasting-Satellite...

  14. 47 CFR 25.111 - Additional information.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) COMMON CARRIER SERVICES SATELLITE COMMUNICATIONS... Administrations. (c) In the Direct Broadcast Satellite service, applicants and licensees shall also provide the Commission with all information it requires in order to modify the Appendix 30 Broadcasting-Satellite...

  15. Promoting Information Competency in Biological Psychology

    PubMed Central

    Freberg, Laura A.; Brosnan-Watters, Gayle

    2005-01-01

    Information competency refers to skills that allow a student to identify appropriate sources of information, evaluate information critically, and use it ethically. Although the sudden increase of information available in electronic form has stimulated interest in information competency, the basic principles apply to all sources of information, including print. Information competency is especially critical in biological psychology. New discoveries in the neurosciences are featured every day by the mainstream media. As a society, we are being asked to make informed decisions about increasingly complex concepts, as in the case of the recent California proposition regarding stem cell research. Ideally, our students will become community leaders who will help shape these and other policy decisions, but the assumption of this role requires skills that extend long after the completion of a particular course or degree. Because of the perceived complexity of biological psychology, students new to the discipline may be reluctant to venture out into the experimental literature. A variety of activities are presented here that will build student confidence and shape information competency. Although these exercises can be used in a variety of disciplines, they are particularly well suited to biological psychology. The various exercises lend themselves to different levels of student expertise. Many of the exercises are quite appropriate for all levels and abilities, including graduate level students. As a bonus, these activities involve students in writing about biological psychology, providing a foundation for the writing of formal term papers or research reports. PMID:23492841

  16. Information technology developments within the national biological information infrastructure

    USGS Publications Warehouse

    Cotter, G.; Frame, M.T.

    2000-01-01

    Looking out an office window or exploring a community park, one can easily see the tremendous challenges that biological information presents the computer science community. Biological information varies in format and content depending whether or not it is information pertaining to a particular species (i.e. Brown Tree Snake), or a specific ecosystem, which often includes multiple species, land use characteristics, and geospatially referenced information. The complexity and uniqueness of each individual species or ecosystem do not easily lend themselves to today's computer science tools and applications. To address the challenges that the biological enterprise presents the National Biological Information Infrastructure (NBII) (http://www.nbii.gov) was established in 1993. The NBII is designed to address these issues on a National scale within the United States, and through international partnerships abroad. This paper discusses current computer science efforts within the National Biological Information Infrastructure Program and future computer science research endeavors that are needed to address the ever-growing issues related to our Nation's biological concerns.

  17. Biological Information as Set-Based Complexity

    PubMed Central

    Galas, David J.; Nykter, Matti; Carter, Gregory W.; Price, Nathan D.; Shmulevich, Ilya

    2010-01-01

    Summary It is not obvious what fraction of all the potential information residing in the molecules and structures of living systems is significant or meaningful to the system. Sets of random sequences or identically repeated sequences, for example, would be expected to contribute little or no useful information to a cell. This issue of quantitation of information is important since the ebb and flow of biologically significant information is essential to our quantitative understanding of biological function and evolution. Motivated specifically by these problems of biological information, we propose here a class of measures to quantify the contextual nature of the information in sets of objects, based on Kolmogorov's intrinsic complexity. Such measures discount both random and redundant information and are inherent in that they do not require a defined state space to quantify the information. The maximization of this new measure, which can be formulated in terms of the universal information distance, appears to have several useful and interesting properties, some of which we illustrate with examples. PMID:27857450

  18. Towards a Biologically Informed Primary School Practice

    ERIC Educational Resources Information Center

    Silcock, Peter

    2008-01-01

    The various ways "nature" and "nurture" interact to shape school pupils' lives are examined from the perspective of recent biologically informed studies. The idea of a highly predictive, genetically based inheritance is strikingly upheld by research in infancy and early childhood. Research evidence also shows how pupil…

  19. Optimizing information flow in biological networks

    NASA Astrophysics Data System (ADS)

    Bialek, William

    2009-03-01

    The generation of physicists who turned to the phenomena of life in the 1930s realized that to understand these phenomena one would need to track not just the flow of energy (as in inanimate systems) but also the flow of information. It would take more than a decade before Shannon provided the tools to formalize this intuition, making precise the connection between entropy and information. Since Shannon, many investigators have explored the possibility that biological mechanisms are selected to maximize the efficiency with which information is transmitted or represented, subject to fundamental physical constraints. I will survey these efforts, emphasizing that the same principles are being used in thinking about biological systems at very different levels of organization, from bacteria to brains. Although sometimes submerged under concerns about particular systems, the idea that information flow is optimized provides us with a candidate for a real theory of biological networks, rather than just a collection of parameterized models. I will try to explain why I think the time is right to focus on this grand theoretical goal, pointing to some key open problems and opportunities for connection to emerging experiments.

  20. 10 CFR 71.39 - Requirement for additional information.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 10 Energy 2 2010-01-01 2010-01-01 false Requirement for additional information. 71.39 Section 71.39 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) PACKAGING AND TRANSPORTATION OF RADIOACTIVE MATERIAL Application for Package Approval § 71.39 Requirement for additional information. The...

  1. 78 FR 75568 - Notice of Request for Additional Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-12

    ... From the Federal Register Online via the Government Publishing Office FEDERAL MARITIME COMMISSION Notice of Request for Additional Information The Commission gives notice that it has formally requested that the parties to the below listed agreement provide additional information pursuant to 46 U.S.C. 40304(d). This action prevents the...

  2. 29 CFR 502.44 - Additional information, if required.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... ENFORCEMENT OF CONTRACTUAL OBLIGATIONS FOR TEMPORARY ALIEN AGRICULTURAL WORKERS ADMITTED UNDER SECTION 218 OF... Administrative Law Judge's Decision § 502.44 Additional information, if required. Where the ARB has determined...

  3. 29 CFR 502.44 - Additional information, if required.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... ENFORCEMENT OF CONTRACTUAL OBLIGATIONS FOR TEMPORARY ALIEN AGRICULTURAL WORKERS ADMITTED UNDER SECTION 218 OF... Administrative Law Judge's Decision § 502.44 Additional information, if required. Where the ARB has determined...

  4. 29 CFR 502.44 - Additional information, if required.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... ENFORCEMENT OF CONTRACTUAL OBLIGATIONS FOR TEMPORARY ALIEN AGRICULTURAL WORKERS ADMITTED UNDER SECTION 218 OF... Administrative Law Judge's Decision § 502.44 Additional information, if required. Where the ARB has determined...

  5. 29 CFR 502.44 - Additional information, if required.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... ENFORCEMENT OF CONTRACTUAL OBLIGATIONS FOR TEMPORARY ALIEN AGRICULTURAL WORKERS ADMITTED UNDER SECTION 218 OF... Administrative Law Judge's Decision § 502.44 Additional information, if required. Where the ARB has determined...

  6. 29 CFR 502.44 - Additional information, if required.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... ENFORCEMENT OF CONTRACTUAL OBLIGATIONS FOR TEMPORARY ALIEN AGRICULTURAL WORKERS ADMITTED UNDER SECTION 218 OF... Administrative Law Judge's Decision § 502.44 Additional information, if required. Where the ARB has determined...

  7. Trienamine catalyzed asymmetric synthesis and biological investigation of a cytochalasin B-inspired compound collection† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c5ob02272j Click here for additional data file.

    PubMed Central

    Sellstedt, Magnus; Schwalfenberg, Melanie; Ziegler, Slava; Antonchick, Andrey P.

    2016-01-01

    Due to their enhanced metabolic needs many cancers need a sufficient supply of glucose, and novel inhibitors of glucose import are in high demand. Cytochalasin B (CB) is a potent natural glucose import inhibitor which also impairs the actin cytoskeleton leading to undesired toxicity. With a view to identifying selective glucose import inhibitors we have developed an enantioselective trienamine catalyzed synthesis of a CB-inspired compound collection. Biological analysis revealed that indeed actin impairment can be distinguished from glucose import inhibition and led to the identification of the first selective glucose import inhibitor based on the basic structural architecture of cytochalasin B. PMID:26606903

  8. 21 CFR 71.4 - Samples; additional information.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 1 2013-04-01 2013-04-01 false Samples; additional information. 71.4 Section 71.4 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL COLOR... samples of the color additive, articles used as components thereof, or of the food, drug, or cosmetic...

  9. 21 CFR 71.4 - Samples; additional information.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 1 2012-04-01 2012-04-01 false Samples; additional information. 71.4 Section 71.4 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL COLOR... samples of the color additive, articles used as components thereof, or of the food, drug, or cosmetic...

  10. Information theory applications for biological sequence analysis.

    PubMed

    Vinga, Susana

    2014-05-01

    Information theory (IT) addresses the analysis of communication systems and has been widely applied in molecular biology. In particular, alignment-free sequence analysis and comparison greatly benefited from concepts derived from IT, such as entropy and mutual information. This review covers several aspects of IT applications, ranging from genome global analysis and comparison, including block-entropy estimation and resolution-free metrics based on iterative maps, to local analysis, comprising the classification of motifs, prediction of transcription factor binding sites and sequence characterization based on linguistic complexity and entropic profiles. IT has also been applied to high-level correlations that combine DNA, RNA or protein features with sequence-independent properties, such as gene mapping and phenotype analysis, and has also provided models based on communication systems theory to describe information transmission channels at the cell level and also during evolutionary processes. While not exhaustive, this review attempts to categorize existing methods and to indicate their relation with broader transversal topics such as genomic signatures, data compression and complexity, time series analysis and phylogenetic classification, providing a resource for future developments in this promising area.

  11. Quantum information and the problem of mechanisms of biological evolution.

    PubMed

    Melkikh, Alexey V

    2014-01-01

    One of the most important conditions for replication in early evolution is the de facto elimination of the conformational degrees of freedom of the replicators, the mechanisms of which remain unclear. In addition, realistic evolutionary timescales can be established based only on partially directed evolution, further complicating this issue. A division of the various evolutionary theories into two classes has been proposed based on the presence or absence of a priori information about the evolving system. A priori information plays a key role in solving problems in evolution. Here, a model of partially directed evolution, based on the learning automata theory, which includes a priori information about the fitness space, is proposed. A potential repository of such prior information is the states of biologically important molecules. Thus, the need for extended evolutionary synthesis is discussed. Experiments to test the hypothesis of partially directed evolution are proposed.

  12. 25 CFR 227.7 - Additional information from applicant.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 25 Indians 1 2011-04-01 2011-04-01 false Additional information from applicant. 227.7 Section 227.7 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR ENERGY AND MINERALS LEASING OF CERTAIN LANDS IN WIND RIVER INDIAN RESERVATION, WYOMING, FOR OIL AND GAS MINING How to Acquire...

  13. 25 CFR 227.7 - Additional information from applicant.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 25 Indians 1 2012-04-01 2011-04-01 true Additional information from applicant. 227.7 Section 227.7 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR ENERGY AND MINERALS LEASING OF CERTAIN LANDS IN WIND RIVER INDIAN RESERVATION, WYOMING, FOR OIL AND GAS MINING How to Acquire Leases §...

  14. 25 CFR 227.7 - Additional information from applicant.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 25 Indians 1 2010-04-01 2010-04-01 false Additional information from applicant. 227.7 Section 227.7 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR ENERGY AND MINERALS LEASING OF CERTAIN LANDS IN WIND RIVER INDIAN RESERVATION, WYOMING, FOR OIL AND GAS MINING How to Acquire...

  15. 25 CFR 215.17 - Additional information required.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 25 Indians 1 2013-04-01 2013-04-01 false Additional information required. 215.17 Section 215.17 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR ENERGY AND MINERALS LEAD AND ZINC MINING... interested in lead and zinc mining leases, or land under the jurisdiction of the Quapaw Indian Agency,...

  16. 38 CFR 39.3 - Decisionmakers, notifications, and additional information.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2010-07-01 2010-07-01 false Decisionmakers, notifications, and additional information. 39.3 Section 39.3 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS (CONTINUED) AID TO STATES FOR ESTABLISHMENT, EXPANSION, AND IMPROVEMENT...

  17. 25 CFR 227.7 - Additional information from applicant.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 25 Indians 1 2013-04-01 2013-04-01 false Additional information from applicant. 227.7 Section 227.7 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR ENERGY AND MINERALS LEASING OF CERTAIN LANDS IN WIND RIVER INDIAN RESERVATION, WYOMING, FOR OIL AND GAS MINING How to Acquire...

  18. 25 CFR 227.7 - Additional information from applicant.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 25 Indians 1 2014-04-01 2014-04-01 false Additional information from applicant. 227.7 Section 227.7 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR ENERGY AND MINERALS LEASING OF CERTAIN LANDS IN WIND RIVER INDIAN RESERVATION, WYOMING, FOR OIL AND GAS MINING How to Acquire...

  19. 21 CFR 207.31 - Additional drug listing information.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 4 2014-04-01 2014-04-01 false Additional drug listing information. 207.31 Section 207.31 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) DRUGS: GENERAL REGISTRATION OF PRODUCERS OF DRUGS AND LISTING OF DRUGS IN COMMERCIAL...

  20. 21 CFR 207.31 - Additional drug listing information.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 4 2011-04-01 2011-04-01 false Additional drug listing information. 207.31 Section 207.31 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) DRUGS: GENERAL REGISTRATION OF PRODUCERS OF DRUGS AND LISTING OF DRUGS IN COMMERCIAL...

  1. 21 CFR 207.31 - Additional drug listing information.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 4 2012-04-01 2012-04-01 false Additional drug listing information. 207.31 Section 207.31 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) DRUGS: GENERAL REGISTRATION OF PRODUCERS OF DRUGS AND LISTING OF DRUGS IN COMMERCIAL...

  2. 29 CFR 2570.39 - Opportunities to submit additional information.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 29 Labor 9 2010-07-01 2010-07-01 false Opportunities to submit additional information. 2570.39 Section 2570.39 Labor Regulations Relating to Labor (Continued) EMPLOYEE BENEFITS SECURITY ADMINISTRATION, DEPARTMENT OF LABOR ADMINISTRATION AND ENFORCEMENT UNDER THE EMPLOYEE RETIREMENT INCOME SECURITY ACT OF...

  3. 29 CFR 2570.39 - Opportunities to submit additional information.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 29 Labor 9 2013-07-01 2013-07-01 false Opportunities to submit additional information. 2570.39 Section 2570.39 Labor Regulations Relating to Labor (Continued) EMPLOYEE BENEFITS SECURITY ADMINISTRATION, DEPARTMENT OF LABOR ADMINISTRATION AND ENFORCEMENT UNDER THE EMPLOYEE RETIREMENT INCOME SECURITY ACT OF...

  4. 29 CFR 2570.39 - Opportunities to submit additional information.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 29 Labor 9 2012-07-01 2012-07-01 false Opportunities to submit additional information. 2570.39 Section 2570.39 Labor Regulations Relating to Labor (Continued) EMPLOYEE BENEFITS SECURITY ADMINISTRATION, DEPARTMENT OF LABOR ADMINISTRATION AND ENFORCEMENT UNDER THE EMPLOYEE RETIREMENT INCOME SECURITY ACT OF...

  5. 43 CFR 3922.30 - Application-Additional information.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 43 Public Lands: Interior 2 2014-10-01 2014-10-01 false Application-Additional information. 3922.30 Section 3922.30 Public Lands: Interior Regulations Relating to Public Lands (Continued) BUREAU OF LAND MANAGEMENT, DEPARTMENT OF THE INTERIOR MINERALS MANAGEMENT (3000) OIL SHALE LEASING...

  6. 43 CFR 3922.30 - Application-Additional information.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 43 Public Lands: Interior 2 2011-10-01 2011-10-01 false Application-Additional information. 3922.30 Section 3922.30 Public Lands: Interior Regulations Relating to Public Lands (Continued) BUREAU OF LAND MANAGEMENT, DEPARTMENT OF THE INTERIOR RANGE MANAGEMENT (4000) OIL SHALE LEASING...

  7. 43 CFR 3922.30 - Application-Additional information.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 43 Public Lands: Interior 2 2012-10-01 2012-10-01 false Application-Additional information. 3922.30 Section 3922.30 Public Lands: Interior Regulations Relating to Public Lands (Continued) BUREAU OF LAND MANAGEMENT, DEPARTMENT OF THE INTERIOR MINERALS MANAGEMENT (3000) OIL SHALE LEASING...

  8. 43 CFR 3922.30 - Application-Additional information.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 43 Public Lands: Interior 2 2013-10-01 2013-10-01 false Application-Additional information. 3922.30 Section 3922.30 Public Lands: Interior Regulations Relating to Public Lands (Continued) BUREAU OF LAND MANAGEMENT, DEPARTMENT OF THE INTERIOR MINERALS MANAGEMENT (3000) OIL SHALE LEASING...

  9. 46 CFR 535.606 - Requests for additional information.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 46 Shipping 9 2010-10-01 2010-10-01 false Requests for additional information. 535.606 Section 535.606 Shipping FEDERAL MARITIME COMMISSION REGULATIONS AFFECTING OCEAN SHIPPING IN FOREIGN COMMERCE OCEAN COMMON CARRIER AND MARINE TERMINAL OPERATOR AGREEMENTS SUBJECT TO THE SHIPPING ACT OF 1984...

  10. Prions: Protein assemblies that convey biological information

    PubMed Central

    Sanders, David W.; Kaufman, Sarah K.; Holmes, Brandon B.; Diamond, Marc I.

    2016-01-01

    Prions derived from the prion protein (PrP) were first characterized as infectious agents that transmit pathology between individuals. However, the majority of cases of neurodegeneration caused by PrP prions occur sporadically. Proteins that self-assemble as cross-beta sheet amyloids are a defining pathological feature of infectious prion disorders and all major age-associated neurodegenerative diseases. In fact, multiple non-infectious proteins exhibit properties of template-driven self-assembly that are strikingly similar to PrP. Evidence suggests that like PrP, many proteins form aggregates that propagate between cells and convert cognate monomer into ordered assemblies. We now recognize that numerous proteins assemble into macromolecular complexes as part of normal physiology, some of which are self-amplifying. This review highlights similarities among infectious and non-infectious neurodegenerative diseases associated with prions, emphasizing the normal and pathogenic roles of higher-order protein assemblies. We propose that studies of the structural and cellular biology of pathological vs. physiological aggregates will be mutually informative. PMID:26844828

  11. Towards quantum simulations of biological information flow.

    PubMed

    Dorner, Ross; Goold, John; Vedral, Vlatko

    2012-08-06

    Recent advances in the spectroscopy of biomolecules have highlighted the possibility of quantum coherence playing an active role in biological energy transport. The revelation that quantum coherence can survive in the hot and wet environment of biology has generated a lively debate across both the physics and biology communities. In particular, it remains unclear to what extent non-trivial quantum effects are used in biology and what advantage, if any, they afford. We propose an analogue quantum simulator, based on currently available techniques in ultra-cold atom physics, to study a model of energy and electron transport based on the Holstein Hamiltonian. By simulating the salient aspects of a biological system in a tunable laboratory set-up, we hope to gain insight into the validity of several theoretical models of biological quantum transport in a variety of relevant parameter regimes.

  12. Censored data treatment using additional information in intelligent medical systems

    NASA Astrophysics Data System (ADS)

    Zenkova, Z. N.

    2015-11-01

    Statistical procedures are a very important and significant part of modern intelligent medical systems. They are used for proceeding, mining and analysis of different types of the data about patients and their diseases; help to make various decisions, regarding the diagnosis, treatment, medication or surgery, etc. In many cases the data can be censored or incomplete. It is a well-known fact that censorship considerably reduces the efficiency of statistical procedures. In this paper the author makes a brief review of the approaches which allow improvement of the procedures using additional information, and describes a modified estimation of an unknown cumulative distribution function involving additional information about a quantile which is known exactly. The additional information is used by applying a projection of a classical estimator to a set of estimators with certain properties. The Kaplan-Meier estimator is considered as an estimator of the unknown cumulative distribution function, the properties of the modified estimator are investigated for a case of a single right censorship by means of simulations.

  13. The use of information theory in evolutionary biology.

    PubMed

    Adami, Christoph

    2012-05-01

    Information is a key concept in evolutionary biology. Information stored in a biological organism's genome is used to generate the organism and to maintain and control it. Information is also that which evolves. When a population adapts to a local environment, information about this environment is fixed in a representative genome. However, when an environment changes, information can be lost. At the same time, information is processed by animal brains to survive in complex environments, and the capacity for information processing also evolves. Here, I review applications of information theory to the evolution of proteins and to the evolution of information processing in simulated agents that adapt to perform a complex task.

  14. A synthetic biology approach to understanding cellular information processing

    PubMed Central

    Riccione, Katherine A; Smith, Robert P; Lee, Anna J; You, Lingchong

    2012-01-01

    The survival of cells and organisms requires proper responses to environmental signals. These responses are governed by cellular networks, which serve to process diverse environmental cues. Biological networks often contain recurring network topologies called ‘motifs’. It has been recognized that the study of such motifs allows one to predict the response of a biological network, and thus cellular behavior. However, studying a single motif in complete isolation of all other network motifs in a natural setting is difficult. Synthetic biology has emerged as a powerful approach to understanding the dynamic properties of network motifs. In addition to testing existing theoretical predictions, construction and analysis of synthetic gene circuits has led to the discovery of novel motif dynamics such as how the combination of simple motifs can lead to autonomous dynamics or how noise in transcription and translation can affect the dynamics of a motif. Here, we review developments in synthetic biology as they pertain to increasing our understanding of cellular information processing. We highlight several types of dynamic behaviors that diverse motifs can generate, including the control of input/output responses, the generation of autonomous spatial and temporal dynamics, as well as the influence of noise in motif dynamics and cellular behavior. PMID:23411668

  15. Biological Information Processing in Single Microtubules

    DTIC Science & Technology

    2014-03-05

    single Microtubule Google Mountain view campus, workshop on quantum biology 22 October 2010 3. Paul Davies Beyond Center at Arizona State University...Phoenix) Phoenix, workshop on quantum biology and cancer research, Experimental studies on single microtubule, 25-27 October 2010, Tempe, Arizona...State University, USA 4. Quantum aspects of microtubule: Direct experimental evidence for the existence of quantum states in microtubule, Towards a

  16. 21 CFR 607.31 - Additional blood product listing information.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ..., the Director of the Center for Biologics Evaluation and Research may require submission of the..., upon request made by the Director of the Center for Biologics Evaluation and Research for good cause, a... Director of the Center for Biologics Evaluation and Research that it is necessary to carry out the...

  17. 21 CFR 607.31 - Additional blood product listing information.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ..., the Director of the Center for Biologics Evaluation and Research may require submission of the..., upon request made by the Director of the Center for Biologics Evaluation and Research for good cause, a... Director of the Center for Biologics Evaluation and Research that it is necessary to carry out the...

  18. 21 CFR 607.31 - Additional blood product listing information.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ..., the Director of the Center for Biologics Evaluation and Research may require submission of the..., upon request made by the Director of the Center for Biologics Evaluation and Research for good cause, a... Director of the Center for Biologics Evaluation and Research that it is necessary to carry out the...

  19. 21 CFR 607.31 - Additional blood product listing information.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ..., the Director of the Center for Biologics Evaluation and Research may require submission of the..., upon request made by the Director of the Center for Biologics Evaluation and Research for good cause, a... Director of the Center for Biologics Evaluation and Research that it is necessary to carry out the...

  20. 21 CFR 607.31 - Additional blood product listing information.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ..., the Director of the Center for Biologics Evaluation and Research may require submission of the..., upon request made by the Director of the Center for Biologics Evaluation and Research for good cause, a... Director of the Center for Biologics Evaluation and Research that it is necessary to carry out the...

  1. Biological Information Processing in Single Microtubules

    DTIC Science & Technology

    2011-08-20

    electronic properties of a single Microtubule Google Mountain view campus, workshop on quantum biology 22 October 2010 http://www.youtube.com/watch?v...Chemists, Tsukuba, Japan March 1-3, (2011) 3. Quantum aspects of microtubule: Direct experimental evidence for the existence of quantum states in...microtubule, Towards a science of consciousness May 2-8 (2011), Sweden 4. Electromagnetic energy of cells and microtubule: how microtubule research will

  2. Modeling information flow in biological networks.

    PubMed

    Kim, Yoo-Ah; Przytycki, Jozef H; Wuchty, Stefan; Przytycka, Teresa M

    2011-06-01

    Large-scale molecular interaction networks are being increasingly used to provide a system level view of cellular processes. Modeling communications between nodes in such huge networks as information flows is useful for dissecting dynamical dependences between individual network components. In the information flow model, individual nodes are assumed to communicate with each other by propagating the signals through intermediate nodes in the network. In this paper, we first provide an overview of the state of the art of research in the network analysis based on information flow models. In the second part, we describe our computational method underlying our recent work on discovering dysregulated pathways in glioma. Motivated by applications to inferring information flow from genotype to phenotype in a very large human interaction network, we generalized previous approaches to compute information flows for a large number of instances and also provided a formal proof for the method.

  3. New scaling relation for information transfer in biological networks

    PubMed Central

    Kim, Hyunju; Davies, Paul; Walker, Sara Imari

    2015-01-01

    We quantify characteristics of the informational architecture of two representative biological networks: the Boolean network model for the cell-cycle regulatory network of the fission yeast Schizosaccharomyces pombe (Davidich et al. 2008 PLoS ONE 3, e1672 (doi:10.1371/journal.pone.0001672)) and that of the budding yeast Saccharomyces cerevisiae (Li et al. 2004 Proc. Natl Acad. Sci. USA 101, 4781–4786 (doi:10.1073/pnas.0305937101)). We compare our results for these biological networks with the same analysis performed on ensembles of two different types of random networks: Erdös–Rényi and scale-free. We show that both biological networks share features in common that are not shared by either random network ensemble. In particular, the biological networks in our study process more information than the random networks on average. Both biological networks also exhibit a scaling relation in information transferred between nodes that distinguishes them from random, where the biological networks stand out as distinct even when compared with random networks that share important topological properties, such as degree distribution, with the biological network. We show that the most biologically distinct regime of this scaling relation is associated with a subset of control nodes that regulate the dynamics and function of each respective biological network. Information processing in biological networks is therefore interpreted as an emergent property of topology (causal structure) and dynamics (function). Our results demonstrate quantitatively how the informational architecture of biologically evolved networks can distinguish them from other classes of network architecture that do not share the same informational properties. PMID:26701883

  4. How to retrieve additional information from the multiplicity distributions

    NASA Astrophysics Data System (ADS)

    Wilk, Grzegorz; Włodarczyk, Zbigniew

    2017-01-01

    Multiplicity distributions (MDs) P(N) measured in multiparticle production processes are most frequently described by the negative binomial distribution (NBD). However, with increasing collision energy some systematic discrepancies have become more and more apparent. They are usually attributed to the possible multi-source structure of the production process and described using a multi-NBD form of the MD. We investigate the possibility of keeping a single NBD but with its parameters depending on the multiplicity N. This is done by modifying the widely known clan model of particle production leading to the NBD form of P(N). This is then confronted with the approach based on the so-called cascade-stochastic formalism which is based on different types of recurrence relations defining P(N). We demonstrate that a combination of both approaches allows the retrieval of additional valuable information from the MDs, namely the oscillatory behavior of the counting statistics apparently visible in the high energy data.

  5. Biological Information Document, Radioactive Liquid Waste Treatment Facility

    SciTech Connect

    Biggs, J.

    1995-12-31

    This document is intended to act as a baseline source material for risk assessments which can be used in Environmental Assessments and Environmental Impact Statements. The current Radioactive Liquid Waste Treatment Facility (RLWTF) does not meet current General Design Criteria for Non-reactor Nuclear Facilities and could be shut down affecting several DOE programs. This Biological Information Document summarizes various biological studies that have been conducted in the vicinity of new Proposed RLWTF site and an Alternative site. The Proposed site is located on Mesita del Buey, a mess top, and the Alternative site is located in Mortandad Canyon. The Proposed Site is devoid of overstory species due to previous disturbance and is dominated by a mixture of grasses, forbs, and scattered low-growing shrubs. Vegetation immediately adjacent to the site is a pinyon-juniper woodland. The Mortandad canyon bottom overstory is dominated by ponderosa pine, willow, and rush. The south-facing slope was dominated by ponderosa pine, mountain mahogany, oak, and muhly. The north-facing slope is dominated by Douglas fir, ponderosa pine, and oak. Studies on wildlife species are limited in the vicinity of the proposed project and further studies will be necessary to accurately identify wildlife populations and to what extent they utilize the project area. Some information is provided on invertebrates, amphibians and reptiles, and small mammals. Additional species information from other nearby locations is discussed in detail. Habitat requirements exist in the project area for one federally threatened wildlife species, the peregrine falcon, and one federal candidate species, the spotted bat. However, based on surveys outside of the project area but in similar habitats, these species are not expected to occur in either the Proposed or Alternative RLWTF sites. Habitat Evaluation Procedures were used to evaluate ecological functioning in the project area.

  6. Does information theory explain biological evolution?

    NASA Astrophysics Data System (ADS)

    Battail, G.

    1997-11-01

    It is suggested that Dawkins' model of evolution needs error-correction coding in the genome replication process. Nested coding is moreover assumed. Consequences of these hypotheses are drawn using fundamental results of information theory. Genome replication is dealt with independently of phenotype encoding, which pertains to semantics. The proposed hypotheses enable explaining facts of genetics and evolution, including the existence of redundant DNA (the introns), the observed correlation between the rate of mutations on the one hand, the genome length and the redundancy rate on the other hand, the discreteness of species and the trend of eukaryotes evolution towards complexity.

  7. Lehrman's dictum: information and explanation in developmental biology.

    PubMed

    Griffiths, Paul E

    2013-01-01

    The integration of concepts from evolutionary developmental biology, such as the homology concept, into developmental psychobiology has great potential. However, evolutionary developmental biology is an attempt to integrate evolutionary and developmental explanation and developmental psychobiology has traditionally been concerned to avoid conflating these two kinds of explanation. This article examines a recent attempt to explain development in terms of "inherited information." The resulting explanation is an evolutionary explanation of development of a kind typical of evolutionary developmental biology. But its proponent mistakes it for an actual developmental explanation. Any integration of evolutionary developmental biology and developmental psychobiology should pay close attention to longstanding concerns about conflating evolutionary and developmental explanations.

  8. Nano and Biological Technology Panel: Quantum Information Science

    DTIC Science & Technology

    2008-12-03

    Electrical Engineering & Telecommunications The University of New South Wales Nano and Biological Technology Panel: Quantum Information Science 26th US Army...Technology Panel: Quantum Information Science 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER 5e. TASK...Business School Summary – Quantum Information Science • Quantum information technologies now a reality • First impacts will be secure communications

  9. Is Information a proper observable for biological organization?

    PubMed Central

    Longo, G.; Miquel, P.-A.; Sonnenschein, C.; Soto, A. M.

    2014-01-01

    In the last century, jointly with the advent of computers, mathematical theories of information were developed. Shortly thereafter, during the ascent of molecular biology, the concept of information was rapidly transferred into biology at large. Several philosophers and biologists have argued against adopting this concept based on epistemological and ontological arguments, and also, because it encouraged genetic determinism. While the theories of elaboration and transmission of information are valid mathematical theories, their own logic and implicit causal structure make them inimical to biology, and because of it, their applications have and are hindering the development of a sound theory of organisms. Our analysis concentrates on the development of information theories in mathematics and on the differences between these theories regarding the relationship among complexity, information and entropy. PMID:22796169

  10. 31 CFR 26.5 - Upgrades and additional environmental information.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ..., such environmental information from the MDB (e.g., environmental chapters from project feasibility studies or environmental data sheets) which contains this environmental analysis. The MDB Office...

  11. Building Better Biology Undergraduates through Information Literacy Integration

    ERIC Educational Resources Information Center

    Winterman, Brian

    2009-01-01

    Biology undergraduates at Indiana University have often been expected to find information for course exercises or written reports, but the skills necessary to do so are not taught consistently in the curriculum. Other efforts described in the literature have been successful in teaching information literacy skills, but not always in a way that is…

  12. The National Biological Information Infrastructure: Coming of age

    USGS Publications Warehouse

    Cotter, G.; Frame, M.; Sepic, R.; Zolly, L.

    2000-01-01

    Coordinated by the US Geological Survey, the National Biological Information Infrastructure (NBII) is a Web-based system that provides increased access to data and information on the nation's biological resources. The NBII can be viewed from a variety of perspectives. This article - an individual case study and not a broad survey with extensive references to the literature - addresses the structure of the NBII related to thematic sections, infrastructure sections and place-based sections, and other topics such as the Integrated Taxonomic Information System (one of our more innovative tools) and the development of our controlled vocabulary.

  13. 76 FR 34639 - Notice of Proposed Additional Information Collection: Advisory Committee and Research and...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-14

    ... Notice of Proposed Additional Information Collection: Advisory Committee and Research and Promotion... approved information collection of the Advisory Committee and Research and Promotion Background Information... . SUPPLEMENTARY INFORMATION: Title: Advisory Committee and Research and Promotion Background Information....

  14. Teaching information literacy skills to sophomore-level biology majors.

    PubMed

    Thompson, Leigh; Blankinship, Lisa Ann

    2015-05-01

    Many undergraduate students lack a sound understanding of information literacy. The skills that comprise information literacy are particularly important when combined with scientific writing for biology majors as they are the foundation skills necessary to complete upper-division biology course assignments, better train students for research projects, and prepare students for graduate and professional education. To help undergraduate biology students develop and practice information literacy and scientific writing skills, a series of three one-hour hands-on library sessions, discussions, and homework assignments were developed for Biological Literature, a one-credit, one-hour-per-week, required sophomore-level course. The embedded course librarian developed a learning exercise that reviewed how to conduct database and web searches, the difference between primary and secondary sources, source credibility, and how to access articles through the university's databases. Students used the skills gained in the library training sessions for later writing assignments including a formal lab report and annotated bibliography. By focusing on improving information literacy skills as well as providing practice in scientific writing, Biological Literature students are better able to meet the rigors of upper-division biology courses and communicate research findings in a more professional manner.

  15. Teaching Information Literacy Skills to Sophomore-Level Biology Majors

    PubMed Central

    Thompson, Leigh; Blankinship, Lisa Ann

    2015-01-01

    Many undergraduate students lack a sound understanding of information literacy. The skills that comprise information literacy are particularly important when combined with scientific writing for biology majors as they are the foundation skills necessary to complete upper-division biology course assignments, better train students for research projects, and prepare students for graduate and professional education. To help undergraduate biology students develop and practice information literacy and scientific writing skills, a series of three one-hour hands-on library sessions, discussions, and homework assignments were developed for Biological Literature, a one-credit, one-hour-per-week, required sophomore-level course. The embedded course librarian developed a learning exercise that reviewed how to conduct database and web searches, the difference between primary and secondary sources, source credibility, and how to access articles through the university’s databases. Students used the skills gained in the library training sessions for later writing assignments including a formal lab report and annotated bibliography. By focusing on improving information literacy skills as well as providing practice in scientific writing, Biological Literature students are better able to meet the rigors of upper-division biology courses and communicate research findings in a more professional manner. PMID:25949754

  16. 10 CFR 1.3 - Sources of additional information.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... fall within an exemption to the Act's openness requirement and the Commission also has determined that... availability of NRC records under the Freedom of Information Act and Privacy Act of 1974 may be obtained...

  17. Additives

    NASA Technical Reports Server (NTRS)

    Smalheer, C. V.

    1973-01-01

    The chemistry of lubricant additives is discussed to show what the additives are chemically and what functions they perform in the lubrication of various kinds of equipment. Current theories regarding the mode of action of lubricant additives are presented. The additive groups discussed include the following: (1) detergents and dispersants, (2) corrosion inhibitors, (3) antioxidants, (4) viscosity index improvers, (5) pour point depressants, and (6) antifouling agents.

  18. 77 FR 39573 - Additional Identifying Information Associated With Persons Whose Property and Interests in...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-07-03

    ... Office of Foreign Assets Control Additional Identifying Information Associated With Persons Whose... Treasury's Office of Foreign Assets Control (``OFAC'') is publishing additional indentifying information... on June 1, 2012. FOR FURTHER INFORMATION CONTACT: Assistant Director, Sanctions...

  19. Information Literacy in Biology Education: An Example from an Advanced Cell Biology Course

    ERIC Educational Resources Information Center

    Porter, John R.

    2005-01-01

    Information literacy skills are critically important for the undergraduate biology student. The ability to find, understand, evaluate, and use information, whether from the scientific literature or from Web resources, is essential for a good understanding of a topic and for the conduct of research. A project in which students receive information…

  20. 40 CFR 141.154 - Required additional health information.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... Hotline (800-426-4791). (b) Ending in the report due by July 1, 2001, a system which detects arsenic at... system that detects arsenic above 0.005 mg/L and up to and including 0.010 mg/L: (1) Must include in its report a short informational statement about arsenic, using language such as: While your drinking...

  1. 40 CFR 141.154 - Required additional health information.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... Hotline (800-426-4791). (b) Ending in the report due by July 1, 2001, a system which detects arsenic at... system that detects arsenic above 0.005 mg/L and up to and including 0.010 mg/L: (1) Must include in its report a short informational statement about arsenic, using language such as: While your drinking...

  2. 40 CFR 141.154 - Required additional health information.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... consultation with the Primacy Agency. (c) A system which detects nitrate at levels above 5 mg/l, but below the MCL: (1) Must include a short informational statement about the impacts of nitrate on children using language such as: Nitrate in drinking water at levels above 10 ppm is a health risk for infants of...

  3. 40 CFR 141.154 - Required additional health information.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... consultation with the Primacy Agency. (c) A system which detects nitrate at levels above 5 mg/l, but below the MCL: (1) Must include a short informational statement about the impacts of nitrate on children using language such as: Nitrate in drinking water at levels above 10 ppm is a health risk for infants of...

  4. 40 CFR 141.154 - Required additional health information.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... consultation with the Primacy Agency. (c) A system which detects nitrate at levels above 5 mg/l, but below the MCL: (1) Must include a short informational statement about the impacts of nitrate on children using language such as: Nitrate in drinking water at levels above 10 ppm is a health risk for infants of...

  5. Meaningful auditory information enhances perception of visual biological motion.

    PubMed

    Arrighi, Roberto; Marini, Francesco; Burr, David

    2009-04-30

    Robust perception requires efficient integration of information from our various senses. Much recent electrophysiology points to neural areas responsive to multisensory stimulation, particularly audiovisual stimulation. However, psychophysical evidence for functional integration of audiovisual motion has been ambiguous. In this study we measure perception of an audiovisual form of biological motion, tap dancing. The results show that the audio tap information interacts with visual motion information, but only when in synchrony, demonstrating a functional combination of audiovisual information in a natural task. The advantage of multimodal combination was better than the optimal maximum likelihood prediction.

  6. SNP Markers as Additional Information to Resolve Complex Kinship Cases

    PubMed Central

    Pontes, M. Lurdes; Fondevila, Manuel; Laréu, Maria Victoria; Medeiros, Rui

    2015-01-01

    Summary Background DNA profiling with sets of highly polymorphic autosomal short tandem repeat (STR) markers has been applied in various aspects of human identification in forensic casework for nearly 20 years. However, in some cases of complex kinship investigation, the information provided by the conventionally used STR markers is not enough, often resulting in low likelihood ratio (LR) calculations. In these cases, it becomes necessary to increment the number of loci under analysis to reach adequate LRs. Recently, it has been proposed that single nucleotide polymorphisms (SNPs) could be used as a supportive tool to STR typing, eventually even replacing the methods/markers now employed. Methods In this work, we describe the results obtained in 7 revised complex paternity cases when applying a battery of STRs, as well as 52 human identification SNPs (SNPforID 52plex identification panel) using a SNaPshot methodology followed by capillary electrophoresis. Results Our results show that the analysis of SNPs, as complement to STR typing in forensic casework applications, would at least increase by a factor of 4 total PI values and correspondent Essen-Möller's W value. Conclusions We demonstrated that SNP genotyping could be a key complement to STR information in challenging casework of disputed paternity, such as close relative individualization or complex pedigrees subject to endogamous relations. PMID:26733770

  7. Quantum Information Biology: From Information Interpretation of Quantum Mechanics to Applications in Molecular Biology and Cognitive Psychology

    NASA Astrophysics Data System (ADS)

    Asano, Masanari; Basieva, Irina; Khrennikov, Andrei; Ohya, Masanori; Tanaka, Yoshiharu; Yamato, Ichiro

    2015-10-01

    We discuss foundational issues of quantum information biology (QIB)—one of the most successful applications of the quantum formalism outside of physics. QIB provides a multi-scale model of information processing in bio-systems: from proteins and cells to cognitive and social systems. This theory has to be sharply distinguished from "traditional quantum biophysics". The latter is about quantum bio-physical processes, e.g., in cells or brains. QIB models the dynamics of information states of bio-systems. We argue that the information interpretation of quantum mechanics (its various forms were elaborated by Zeilinger and Brukner, Fuchs and Mermin, and D' Ariano) is the most natural interpretation of QIB. Biologically QIB is based on two principles: (a) adaptivity; (b) openness (bio-systems are fundamentally open). These principles are mathematically represented in the framework of a novel formalism— quantum adaptive dynamics which, in particular, contains the standard theory of open quantum systems.

  8. Information science and technology developments within the National Biological Information Infrastructure

    USGS Publications Warehouse

    Frame, M.T.; Cotter, G.; Zolly, L.; Little, J.

    2002-01-01

    Whether your vantage point is that of an office window or a national park, your view undoubtedly encompasses a rich diversity of life forms, all carefully studied or managed by some scientist, resource manager, or planner. A few simple calculations - the number of species, their interrelationships, and the many researchers studying them - and you can easily see the tremendous challenges that the resulting biological data presents to the information and computer science communities. Biological information varies in format and content: it may pertain to a particular species or an entire ecosystem; it can contain land use characteristics, and geospatially referenced information. The complexity and uniqueness of each individual species or ecosystem do not easily lend themselves to today's computer science tools and applications. To address the challenges that the biological enterprise presents, the National Biological Information Infrastructure (NBII) (http://www.nbii.gov) was established in 1993 on the recommendation of the National Research Council (National Research Council 1993). The NBII is designed to address these issues on a national scale, and through international partnerships. This paper discusses current information and computer science efforts within the National Biological Information Infrastructure Program, and future computer science research endeavors that are needed to address the ever-growing issues related to our nation's biological concerns. ?? 2003 by The Haworth Press, Inc. All rights reserved.

  9. 78 FR 77119 - Proposed Information Collection Request; Comment Request; Regulation of Fuels and Fuel Additives...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-20

    ... AGENCY Proposed Information Collection Request; Comment Request; Regulation of Fuels and Fuel Additives: 2011 Renewable Fuel Standards-- Petition for International Aggregate Compliance Approach AGENCY... to submit an information collection request (ICR), ``Regulation of Fuels and Fuel Additives:...

  10. Construction of a Linux based chemical and biological information system.

    PubMed

    Molnár, László; Vágó, István; Fehér, András

    2003-01-01

    A chemical and biological information system with a Web-based easy-to-use interface and corresponding databases has been developed. The constructed system incorporates all chemical, numerical and textual data related to the chemical compounds, including numerical biological screen results. Users can search the database by traditional textual/numerical and/or substructure or similarity queries through the web interface. To build our chemical database management system, we utilized existing IT components such as ORACLE or Tripos SYBYL for database management and Zope application server for the web interface. We chose Linux as the main platform, however, almost every component can be used under various operating systems.

  11. Methods of information geometry in computational system biology (consistency between chemical and biological evolution).

    PubMed

    Astakhov, Vadim

    2009-01-01

    Interest in simulation of large-scale metabolic networks, species development, and genesis of various diseases requires new simulation techniques to accommodate the high complexity of realistic biological networks. Information geometry and topological formalisms are proposed to analyze information processes. We analyze the complexity of large-scale biological networks as well as transition of the system functionality due to modification in the system architecture, system environment, and system components. The dynamic core model is developed. The term dynamic core is used to define a set of causally related network functions. Delocalization of dynamic core model provides a mathematical formalism to analyze migration of specific functions in biosystems which undergo structure transition induced by the environment. The term delocalization is used to describe these processes of migration. We constructed a holographic model with self-poetic dynamic cores which preserves functional properties under those transitions. Topological constraints such as Ricci flow and Pfaff dimension were found for statistical manifolds which represent biological networks. These constraints can provide insight on processes of degeneration and recovery which take place in large-scale networks. We would like to suggest that therapies which are able to effectively implement estimated constraints, will successfully adjust biological systems and recover altered functionality. Also, we mathematically formulate the hypothesis that there is a direct consistency between biological and chemical evolution. Any set of causal relations within a biological network has its dual reimplementation in the chemistry of the system environment.

  12. Exploring the Possible Use of Information Barriers for future Biological Weapons Verification Regimes

    SciTech Connect

    Luke, S J

    2011-12-20

    genetic information associated with the various pathogens. In addition, it has been determined that a suitable information barrier could be applied to this technology when the verification regime has been defined. Finally, the report posits a path forward for additional development of information barriers in a biological weapons verification regime. This path forward has shown that a new analysis approach coined as Information Loss Analysis might need to be pursued so that a numerical understanding of how information can be lost in specific measurement systems can be achieved.

  13. Information in the Biosphere: Biological and Digital Worlds.

    PubMed

    Gillings, Michael R; Hilbert, Martin; Kemp, Darrell J

    2016-03-01

    Evolution has transformed life through key innovations in information storage and replication, including RNA, DNA, multicellularity, and culture and language. We argue that the carbon-based biosphere has generated a cognitive system (humans) capable of creating technology that will result in a comparable evolutionary transition. Digital information has reached a similar magnitude to information in the biosphere. It increases exponentially, exhibits high-fidelity replication, evolves through differential fitness, is expressed through artificial intelligence (AI), and has facility for virtually limitless recombination. Like previous evolutionary transitions, the potential symbiosis between biological and digital information will reach a critical point where these codes could compete via natural selection. Alternatively, this fusion could create a higher-level superorganism employing a low-conflict division of labor in performing informational tasks.

  14. 30 CFR 75.1200-1 - Additional information on mine map.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 30 Mineral Resources 1 2014-07-01 2014-07-01 false Additional information on mine map. 75.1200-1... SAFETY AND HEALTH MANDATORY SAFETY STANDARDS-UNDERGROUND COAL MINES Maps § 75.1200-1 Additional information on mine map. Additional information required to be shown on mine maps under § 75.1200...

  15. 30 CFR 75.1200-1 - Additional information on mine map.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Additional information on mine map. 75.1200-1... SAFETY AND HEALTH MANDATORY SAFETY STANDARDS-UNDERGROUND COAL MINES Maps § 75.1200-1 Additional information on mine map. Additional information required to be shown on mine maps under § 75.1200...

  16. Methods of information theory and algorithmic complexity for network biology.

    PubMed

    Zenil, Hector; Kiani, Narsis A; Tegnér, Jesper

    2016-03-01

    We survey and introduce concepts and tools located at the intersection of information theory and network biology. We show that Shannon's information entropy, compressibility and algorithmic complexity quantify different local and global aspects of synthetic and biological data. We show examples such as the emergence of giant components in Erdös-Rényi random graphs, and the recovery of topological properties from numerical kinetic properties simulating gene expression data. We provide exact theoretical calculations, numerical approximations and error estimations of entropy, algorithmic probability and Kolmogorov complexity for different types of graphs, characterizing their variant and invariant properties. We introduce formal definitions of complexity for both labeled and unlabeled graphs and prove that the Kolmogorov complexity of a labeled graph is a good approximation of its unlabeled Kolmogorov complexity and thus a robust definition of graph complexity.

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

    ERIC Educational Resources Information Center

    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…

  18. Information Literacy in Biology Education: An Example from an Advanced Cell Biology Course

    PubMed Central

    2005-01-01

    Information literacy skills are critically important for the undergraduate biology student. The ability to find, understand, evaluate, and use information, whether from the scientific literature or from Web resources, is essential for a good understanding of a topic and for the conduct of research. A project in which students receive information literacy instruction and then proceed to select, update, and write about a current research topic in an upper-level cell biology course is described. Students research the chosen topic using paper and electronic resources, generate a list of relevant articles, prepare abstracts based on papers read, and, finally, prepare a “state-of-the-art” paper on the topic. This approach, which extends over most of one semester, has resulted in a number of well-researched and well-written papers that incorporate some of the latest research in cell biology. The steps in this project have also led to students who are prepared to address future projects on new and complex topics. The project is part of an undergraduate course in cell biology, but parts of the assignments can be modified to fit a variety of subject areas and levels. PMID:16341261

  19. Linking genes to literature: text mining, information extraction, and retrieval applications for biology

    PubMed Central

    Krallinger, Martin; Valencia, Alfonso; Hirschman, Lynette

    2008-01-01

    Efficient access to information contained in online scientific literature collections is essential for life science research, playing a crucial role from the initial stage of experiment planning to the final interpretation and communication of the results. The biological literature also constitutes the main information source for manual literature curation used by expert-curated databases. Following the increasing popularity of web-based applications for analyzing biological data, new text-mining and information extraction strategies are being implemented. These systems exploit existing regularities in natural language to extract biologically relevant information from electronic texts automatically. The aim of the BioCreative challenge is to promote the development of such tools and to provide insight into their performance. This review presents a general introduction to the main characteristics and applications of currently available text-mining systems for life sciences in terms of the following: the type of biological information demands being addressed; the level of information granularity of both user queries and results; and the features and methods commonly exploited by these applications. The current trend in biomedical text mining points toward an increasing diversification in terms of application types and techniques, together with integration of domain-specific resources such as ontologies. Additional descriptions of some of the systems discussed here are available on the internet . PMID:18834499

  20. EUCLIS--an information system for circadian systems biology.

    PubMed

    Batista, R T B; Ramirez, D B; Santos, R D; del Rosario, M C I; Mendoza, E R

    2007-09-01

    A major barrier to progress in systems biology is the absence of suitable infrastructure for data and software integration, which would enable working biologists to use and manipulate the techniques directly. We describe the incremental development of key components of such an infrastructure for a research community focused on a specific (but important) biological system. EUCLOCK combines the expertise of 34 chronobiology laboratories from 29 institutions in 11 European countries in a 5-year effort to understand how circadian clocks are synchronised to their specific cyclic environment (entrainment). We envision that the EUCLOCK Information System (EUCLIS) will subsequently evolve to support the worldwide chronobiology community. The architecture of EUCLIS integrates a database for circadian systems biology, containing modules for experimental data (Clock Experiments) and models (Clock Models) with a digital library (Clock KnowledgeBase) for the research community. The digital library paradigm is superior to the simple 'access' or 'mining' as well as the 'data warehouse' approaches currently used in other systems as it provides a flexible framework for community information needs and the potential to use emerging reference models and standards, which will enable easier integration with other systems in the future. The main Clock KnowledgeBase components for EUCLIS V1.0, Clock Genes and Clock Library, are described in detail. An important aspect this work will need to address in the future is the integration of the database and digital library management functions.

  1. Two faces of entropy and information in biological systems.

    PubMed

    Mitrokhin, Yuriy

    2014-10-21

    The article attempts to overcome the well-known paradox of contradictions between the emerging biological organization and entropy production in biological systems. It is assumed that quality, speculative correlation between entropy and antientropy processes taking place both in the past and today in the metabolic and genetic cellular systems may be perfectly authorized for adequate description of the evolution of biological organization. So far as thermodynamic entropy itself cannot compensate for the high degree of organization which exists in the cell, we discuss the mode of conjunction of positive entropy events (mutations) in the genetic systems of the past generations and the formation of organized structures of current cells. We argue that only the information which is generated in the conditions of the information entropy production (mutations and other genome reorganization) in genetic systems of the past generations provides the physical conjunction of entropy and antientropy processes separated from each other in time generations. It is readily apparent from the requirements of the Second law of thermodynamics.

  2. Quantum Information Biology: From Theory of Open Quantum Systems to Adaptive Dynamics

    NASA Astrophysics Data System (ADS)

    Asano, Masanari; Basieva, Irina; Khrennikov, Andrei; Ohya, Masanori; Tanaka, Yoshiharu; Yamato, Ichiro

    This chapter reviews quantum(-like) information biology (QIB). Here biology is treated widely as even covering cognition and its derivatives: psychology and decision making, sociology, and behavioral economics and finances. QIB provides an integrative description of information processing by bio-systems at all scales of life: from proteins and cells to cognition, ecological and social systems. Mathematically QIB is based on the theory of adaptive quantum systems (which covers also open quantum systems). Ideologically QIB is based on the quantum-like (QL) paradigm: complex bio-systems process information in accordance with the laws of quantum information and probability. This paradigm is supported by plenty of statistical bio-data collected at all bio-scales. QIB re ects the two fundamental principles: a) adaptivity; and, b) openness (bio-systems are fundamentally open). In addition, quantum adaptive dynamics provides the most generally possible mathematical representation of these principles.

  3. Oryzabase. An integrated biological and genome information database for rice.

    PubMed

    Kurata, Nori; Yamazaki, Yukiko

    2006-01-01

    The aim of Oryzabase is to create a comprehensive view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information (http://www.shigen.nig.ac.jp/rice/oryzabase/top/top.jsp). The database contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. The anatomical description of rice development is unique and is the first known representation for rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. The systematic presentation of a large number of rice mutant and mutant trait genes is indispensable, as is description of research in wild strains, core collections, and their detailed characterization. Several genetic, physical, and expression maps with full genome and cDNA sequences are also combined with biological data in Oryzabase. These datasets, when pooled together, could provide a useful tool for gaining greater knowledge about the life cycle of rice, the relationship between phenotype and gene function, and rice genetic diversity. For exchanging community information, Oryzabase publishes the Rice Genetics Newsletter organized by the Rice Genetics Cooperative and provides a mailing service, rice-e-net/rice-net.

  4. Biological Information Transfer Beyond the Genetic Code: The Sugar Code

    NASA Astrophysics Data System (ADS)

    Gabius, H.-J.

    In the era of genetic engineering, cloning, and genome sequencing the focus of research on the genetic code has received an even further accentuation in the public eye. In attempting, however, to understand intra- and intercellular recognition processes comprehensively, the two biochemical dimensions established by nucleic acids and proteins are not sufficient to satisfactorily explain all molecular events in, for example, cell adhesion or routing. The consideration of further code systems is essential to bridge this gap. A third biochemical alphabet forming code words with an information storage capacity second to no other substance class in rather small units (words, sentences) is established by monosaccharides (letters). As hardware oligosaccharides surpass peptides by more than seven orders of magnitude in the theoretical ability to build isomers, when the total of conceivable hexamers is calculated. In addition to the sequence complexity, the use of magnetic resonance spectroscopy and molecular modeling has been instrumental in discovering that even small glycans can often reside in not only one but several distinct low-energy conformations (keys). Intriguingly, conformers can display notably different capacities to fit snugly into the binding site of nonhomologous receptors (locks). This process, experimentally verified for two classes of lectins, is termed "differential conformer selection." It adds potential for shifts of the conformer equilibrium to modulate ligand properties dynamically and reversibly to the well-known changes in sequence (including anomeric positioning and linkage points) and in pattern of substitution, for example, by sulfation. In the intimate interplay with sugar receptors (lectins, enzymes, and antibodies) the message of coding units of the sugar code is deciphered. Their recognition will trigger postbinding signaling and the intended biological response. Knowledge about the driving forces for the molecular rendezvous, i

  5. EFFECT OF NITROGEN AND METAL ADDITIONS ON NITROGEN FIXATION ACTIVITY IN BIOLOGICAL SOIL CRUSTS

    NASA Astrophysics Data System (ADS)

    Alexander, K.; Lui, D.; Anbar, A. D.; Garcia-Pichel, F.; Hartnett, H. E.

    2009-12-01

    Biological soil crusts (BSCs) are diverse consortia of microorganisms that live in intimate association with soils in arid environments. Also called cryptogamic or microbiotic crusts, these communities can include cyanobacteria, algae, heterotrophic bacteria, fungi, lichens, and mosses. Together, these organisms provide many services to their surrounding ecosystems, including reduction of water runoff, promotion of water infiltration, and prevention of soil erosion. The cyanobacteria and algae also provide fixed carbon (C) to the soil through photosynthesis, and because atmospheric deposition of nitrogen (N) in arid environments is low, the major input of biologically available N comes from cyanobacteria capable of converting nitrogen gas (N2) to ammonium (NH4+). Biological soil crusts are easily destroyed by livestock grazing, motor vehicle travel, and many forms of recreational and agricultural land use. Loss of BSC cover can leave the soil vulnerable to intense erosion that can remove the nutrients necessary to sustain plant and animal life, thus accelerating the process of desertification. In order to preserve existing crusts and encourage the development of new crusts, it is crucial to understand the nutrient requirements of metabolism and growth in these microbial communities. This study investigated the affect of nitrogen and metal additions on N2-fixation activity in cyanobacterially-dominated crusts from the Colorado Plateau near Moab, Utah. Although N2-fixation has been studied in this system before, the affect of nutrient additions on N2-fixation activity has not been documented. The goal of this work was to understand how N and metal supplementation affects crust N metabolism. Three experiments were conducted to observe how N2-fixation activity changed with the addition of N, molybdenum (Mo), and vanadium (V). Molybdenum and vanadium were chosen because they are most commonly found at the active site of the enzyme nitrogenase, the molecule responsible

  6. Revealing biological information using data structuring and automated learning.

    PubMed

    Mohorianu, Irina; Moulton, Vincent

    2010-11-01

    The intermediary steps between a biological hypothesis, concretized in the input data, and meaningful results, validated using biological experiments, commonly employ bioinformatics tools. Starting with storage of the data and ending with a statistical analysis of the significance of the results, every step in a bioinformatics analysis has been intensively studied and the resulting methods and models patented. This review summarizes the bioinformatics patents that have been developed mainly for the study of genes, and points out the universal applicability of bioinformatics methods to other related studies such as RNA interference. More specifically, we overview the steps undertaken in the majority of bioinformatics analyses, highlighting, for each, various approaches that have been developed to reveal details from different perspectives. First we consider data warehousing, the first task that has to be performed efficiently, optimizing the structure of the database, in order to facilitate both the subsequent steps and the retrieval of information. Next, we review data mining, which occupies the central part of most bioinformatics analyses, presenting patents concerning differential expression, unsupervised and supervised learning. Last, we discuss how networks of interactions of genes or other players in the cell may be created, which help draw biological conclusions and have been described in several patents.

  7. Genes are information, so information theory is coming to the aid of evolutionary biology.

    PubMed

    Sherwin, William B

    2015-11-01

    Speciation is central to evolutionary biology, and to elucidate it, we need to catch the early genetic changes that set nascent taxa on their path to species status (Via 2009). That challenge is difficult, of course, for two chief reasons: (i) serendipity is required to catch speciation in the act; and (ii) after a short time span with lingering gene flow, differentiation may be low and/or embodied only in rare alleles that are difficult to sample. In this issue of Molecular Ecology Resources, Smouse et al. (2015) have noted that optimal assessment of differentiation within and between nascent species should be robust to these challenges, and they identified a measure based on Shannon's information theory that has many advantages for this and numerous other tasks. The Shannon measure exhibits complete additivity of information at different levels of subdivision. Of all the family of diversity measures ('0' or allele counts, '1' or Shannon, '2' or heterozygosity, F(ST) and related metrics) Shannon's measure comes closest to weighting alleles by their frequencies. For the Shannon measure, rare alleles that represent early signals of nascent speciation are neither down-weighted to the point of irrelevance, as for level 2 measures, nor up-weighted to overpowering importance, as for level 0 measures (Chao et al. 2010, )2015. Shannon measures have a long history in population genetics, dating back to Shannon's PhD thesis in 1940 (Crow 2001), but have received only sporadic attention, until a resurgence of interest in the last ten years, as reviewed briefly by Smouse et al. (2015).

  8. Rapid Recovery of Cyanobacterial Pigments in Desiccated Biological Soil Crusts following Addition of Water

    PubMed Central

    Abed, Raeid M. M.; Polerecky, Lubos; Al-Habsi, Amal; Oetjen, Janina; Strous, Marc; de Beer, Dirk

    2014-01-01

    We examined soil surface colour change to green and hydrotaxis following addition of water to biological soil crusts using pigment extraction, hyperspectral imaging, microsensors and 13C labeling experiments coupled to matrix-assisted laser desorption and ionization time of flight-mass spectrometry (MALD-TOF MS). The topsoil colour turned green in less than 5 minutes following water addition. The concentrations of chlorophyll a (Chl a), scytonemin and echinenon rapidly increased in the top <1 mm layer while in the deeper layer, their concentrations remained low. Hyperspectral imaging showed that, in both wet and dehydrated crusts, cyanobacteria formed a layer at a depth of 0.2–0.4 mm and this layer did not move upward after wetting. 13C labeling experiments and MALDI TOF analysis showed that Chl a was already present in the desiccated crusts and de novo synthesis of this molecule started only after 2 days of wetting due to growth of cyanobacteria. Microsensor measurements showed that photosynthetic activity increased concomitantly with the increase of Chl a, and reached a maximum net rate of 92 µmol m−2 h−1 approximately 2 hours after wetting. We conclude that the colour change of soil crusts to green upon water addition was not due to hydrotaxis but rather to the quick recovery and reassembly of pigments. Cyanobacteria in crusts can maintain their photosynthetic apparatus intact even under prolonged periods of desiccation with the ability to resume their photosynthetic activities within minutes after wetting. PMID:25375172

  9. Rapid recovery of cyanobacterial pigments in desiccated biological soil crusts following addition of water.

    PubMed

    Abed, Raeid M M; Polerecky, Lubos; Al-Habsi, Amal; Oetjen, Janina; Strous, Marc; de Beer, Dirk

    2014-01-01

    We examined soil surface colour change to green and hydrotaxis following addition of water to biological soil crusts using pigment extraction, hyperspectral imaging, microsensors and 13C labeling experiments coupled to matrix-assisted laser desorption and ionization time of flight-mass spectrometry (MALD-TOF MS). The topsoil colour turned green in less than 5 minutes following water addition. The concentrations of chlorophyll a (Chl a), scytonemin and echinenon rapidly increased in the top <1 mm layer while in the deeper layer, their concentrations remained low. Hyperspectral imaging showed that, in both wet and dehydrated crusts, cyanobacteria formed a layer at a depth of 0.2-0.4 mm and this layer did not move upward after wetting. 13C labeling experiments and MALDI TOF analysis showed that Chl a was already present in the desiccated crusts and de novo synthesis of this molecule started only after 2 days of wetting due to growth of cyanobacteria. Microsensor measurements showed that photosynthetic activity increased concomitantly with the increase of Chl a, and reached a maximum net rate of 92 µmol m-2 h-1 approximately 2 hours after wetting. We conclude that the colour change of soil crusts to green upon water addition was not due to hydrotaxis but rather to the quick recovery and reassembly of pigments. Cyanobacteria in crusts can maintain their photosynthetic apparatus intact even under prolonged periods of desiccation with the ability to resume their photosynthetic activities within minutes after wetting.

  10. Informational Aspects of Isotopic Diversity in Biology and Medicine

    NASA Astrophysics Data System (ADS)

    Berezin, Alexander A.

    2004-10-01

    Use of stable and radioactive isotopes in biology and medicine is intensive, yet informational aspects of isotopes as such are largely neglected (A.A.Berezin, J.Theor.Biol.,1992). Classical distinguishability (``labelability'') of isotopes allows for pattern generation dynamics. Quantum mechanically advantages of isotopicity (diversity of stable isotopes) arise from (almost perfect) degeneracy of various isotopic configurations; this in turn allows for isotopic sweeps (hoppings) by resonance neutron tunneling (Eccles mechanism). Isotopic variations of de Broglie wavelength affect quantum tunneling, diffusivity, magnetic interactions (e.g. by Lorentz force), etc. Ergodicity principle (all isoenergetic states are eventually accessed) implies possibility of fast scanning of library of morphogenetic patterns (cf metaphors of universal ``Platonic'' Library of Patterns: e.g. J.L.Borges, R.Sheldrake) with subsequent Darwinian reinforcement (e.g. by targeted mutations) of evolutionary advantageous patterns and structures. Isotopic shifts in organisms, from viruses and protozoa to mammalians, (e.g. DNA with enriched or depleted C-13) are tools to elucidate possible informational (e.g. Shannon entropy) role of isotopicity in genetic (e.g. evolutionary and morphological), dynamical (e.g. physiological and neurological) as well as medical (e.g. carcinogenesis, aging) aspects of biology and medicine.

  11. 49 CFR 260.25 - Additional information for Applicants not having a credit rating.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... prospective traffic base; (3) System-wide plans to maintain equipment and rights-of-way at current or improved... 49 Transportation 4 2014-10-01 2014-10-01 false Additional information for Applicants not having a... Financial Assistance § 260.25 Additional information for Applicants not having a credit rating....

  12. 49 CFR 260.25 - Additional information for Applicants not having a credit rating.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... prospective traffic base; (3) System-wide plans to maintain equipment and rights-of-way at current or improved... 49 Transportation 4 2013-10-01 2013-10-01 false Additional information for Applicants not having a... Financial Assistance § 260.25 Additional information for Applicants not having a credit rating....

  13. 16 CFR 2.20 - Petitions for review of requests for additional information or documentary material.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... additional information or documentary material. 2.20 Section 2.20 Commercial Practices FEDERAL TRADE... material, or recommend such modification to the responsible Assistant Director of the Bureau of Competition... investigation. A request for additional information or documentary material may be modified only in...

  14. 47 CFR 25.111 - Additional information and ITU cost recovery.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 47 Telecommunication 2 2014-10-01 2014-10-01 false Additional information and ITU cost recovery....111 Additional information and ITU cost recovery. (a) The Commission may request from any party at any... interference caused by radio stations authorized by other Administrations is guaranteed unless ITU...

  15. 49 CFR 260.25 - Additional information for Applicants not having a credit rating.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 4 2010-10-01 2010-10-01 false Additional information for Applicants not having a... Financial Assistance § 260.25 Additional information for Applicants not having a credit rating. Each application submitted by Applicants not having a recent credit rating from one or more nationally...

  16. 33 CFR 148.107 - What additional information may be required?

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... What additional information may be required? (a) The Commandant (CG-5), in coordination with MARAD, may... analysis, explanation, or other information he or she deems necessary. (b) The Commandant (CG-5) may... (CG-5) may set a deadline for receiving the information. (1) If the applicant states that the...

  17. 33 CFR 148.107 - What additional information may be required?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... What additional information may be required? (a) The Commandant (CG-5), in coordination with MARAD, may... analysis, explanation, or other information he or she deems necessary. (b) The Commandant (CG-5) may... (CG-5) may set a deadline for receiving the information. (1) If the applicant states that the...

  18. 78 FR 74218 - Imposition of Additional Sanctions on Syria Under the Chemical and Biological Weapons Control and...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-10

    ... Imposition of Additional Sanctions on Syria Under the Chemical and Biological Weapons Control and Warfare... chemical weapons in violation of international law or lethal chemical weapons against its own nationals... the Chemical and Biological Weapons Control and Warfare Elimination Act of 1991, 22 U.S.C. 5604(a)...

  19. Biological, ecological, conservation and legal information for all species and subspecies of Australian bird

    NASA Astrophysics Data System (ADS)

    Garnett, Stephen T.; Duursma, Daisy E.; Ehmke, Glenn; Guay, Patrick-Jean; Stewart, Alistair; Szabo, Judit K.; Weston, Michael A.; Bennett, Simon; Crowley, Gabriel M.; Drynan, David; Dutson, Guy; Fitzherbert, Kate; Franklin, Donald C.

    2015-11-01

    We introduce a dataset of biological, ecological, conservation and legal information for every species and subspecies of Australian bird, 2056 taxa or populations in total. Version 1 contains 230 fields grouped under the following headings: Taxonomy & nomenclature, Phylogeny, Australian population status, Conservation status, Legal status, Distribution, Morphology, Habitat, Food, Behaviour, Breeding, Mobility and Climate metrics. It is envisaged that the dataset will be updated periodically with new data for existing fields and the addition of new fields. The dataset has already had, and will continue to have applications in Australian and international ornithology, especially those that require standard information for a large number of taxa.

  20. Biological, ecological, conservation and legal information for all species and subspecies of Australian bird

    PubMed Central

    Garnett, Stephen T.; Duursma, Daisy E.; Ehmke, Glenn; Guay, Patrick-Jean; Stewart, Alistair; Szabo, Judit K.; Weston, Michael A.; Bennett, Simon; Crowley, Gabriel M.; Drynan, David; Dutson, Guy; Fitzherbert, Kate; Franklin, Donald C.

    2015-01-01

    We introduce a dataset of biological, ecological, conservation and legal information for every species and subspecies of Australian bird, 2056 taxa or populations in total. Version 1 contains 230 fields grouped under the following headings: Taxonomy & nomenclature, Phylogeny, Australian population status, Conservation status, Legal status, Distribution, Morphology, Habitat, Food, Behaviour, Breeding, Mobility and Climate metrics. It is envisaged that the dataset will be updated periodically with new data for existing fields and the addition of new fields. The dataset has already had, and will continue to have applications in Australian and international ornithology, especially those that require standard information for a large number of taxa. PMID:26594379

  1. 75 FR 77645 - Agency Information Collection Activities; Proposed Collection; Comment Request; Color Additive...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-13

    ... Collection; Comment Request; Color Additive Certification Requests and Recordkeeping AGENCY: Food and Drug... certification of color additives manufactured for use in foods, drugs, cosmetics or medical devices in the... of information technology. Color Additive Certification Requests and Recordkeeping--21 CFR Part...

  2. PREFACE: Complex Networks: from Biology to Information Technology

    NASA Astrophysics Data System (ADS)

    Barrat, A.; Boccaletti, S.; Caldarelli, G.; Chessa, A.; Latora, V.; Motter, A. E.

    2008-06-01

    The field of complex networks is one of the most active areas in contemporary statistical physics. Ten years after seminal work initiated the modern study of networks, interest in the field is in fact still growing, as indicated by the ever increasing number of publications in network science. The reason for such a resounding success is most likely the simplicity and broad significance of the approach that, through graph theory, allows researchers to address a variety of different complex systems within a common framework. This special issue comprises a selection of contributions presented at the workshop 'Complex Networks: from Biology to Information Technology' held in July 2007 in Pula (Cagliari), Italy as a satellite of the general conference STATPHYS23. The contributions cover a wide range of problems that are currently among the most important questions in the area of complex networks and that are likely to stimulate future research. The issue is organised into four sections. The first two sections describe 'methods' to study the structure and the dynamics of complex networks, respectively. After this methodological part, the issue proceeds with a section on applications to biological systems. The issue closes with a section concentrating on applications to the study of social and technological networks. The first section, entitled Methods: The Structure, consists of six contributions focused on the characterisation and analysis of structural properties of complex networks: The paper Motif-based communities in complex networks by Arenas et al is a study of the occurrence of characteristic small subgraphs in complex networks. These subgraphs, known as motifs, are used to define general classes of nodes and their communities by extending the mathematical expression of the Newman-Girvan modularity. The same line of research, aimed at characterising network structure through the analysis of particular subgraphs, is explored by Bianconi and Gulbahce in Algorithm

  3. Improvement of dairy manufacture effluent anaerobic digestion with biological waste addition using a Chinese dome digester.

    PubMed

    Jihen, Toumi; Hassib, Bouallagui; Moktar, Hamdi; Said, Nouira

    2010-05-01

    Anaerobic co-digestion of dairy manufacture effluent (DME) and biological waste (BW) was investigated at various DME/BW ratios using laboratory batch digesters. The biogas yield ranged 0.34-0.88l biogas g(-1) volatile solids (VS) removed. The highest VS reductions of 58% and 62% were obtained for DME/BW ratios of 60:40% and 80:20%, respectively. Results were used to operate a pilot-scale digester of 5m(3). The highest biogas yield of 0.48lg(-1) VS removed was obtained at an organic loading rate (OLR) of 1.64gVSl(-1)d(-1) corresponding to a DME/BW ratio of 80:20%. This could be mainly attributed to the higher biodegradability of DME and the correction of the C:N ratio by the addition of the BW. The N, P and K contents were increased significantly in the TS of the digestate to be around 6.8%, 0.64% and 1.26%, respectively.

  4. Biological responses of a simulated marine food chain to lead addition.

    PubMed

    Soto-Jiménez, Martín F; Arellano-Fiore, Claudia; Rocha-Velarde, Ruth; Jara-Marini, Martín E; Ruelas-Inzunza, Jorge; Voltolina, Domenico; Frías-Espericueta, Martín G; Quintero-Alvarez, Jesús M; Páez-Osuna, Federico

    2011-07-01

    This investigation sought to assess the biological responses to Pb along a simplified four-level food chain, from the primary producer, the microalgae Tetraselmis suecica, grown in a control medium with < 1 µg/L of Pb and exposed to a sublethal dose (20 µg/L of Pb) and used as the base of a simulated food chain, through the primary-, secondary-, and tertiary-level consumers, namely, the brine shrimp, Artemia franciscana; the white-leg shrimp, Litopenaeus vannamei; and the grunt fish, Haemulon scudderi, respectively. Growth of Pb-exposed T. suecica was 40% lower than that of the control cultures, and survival of A. franciscana fed this diet was 25 to 30% lower than the control. No differences in the growth rates of Pb-exposed and control shrimp and fish and no gross morphological changes were evident in the exposed specimens. However, the exposed shrimp and fish had 20 and 15% higher mortalities than their controls, respectively. In addition, behavioral alterations were observed in exposed shrimp and fish, including reduction in food consumption or cessation of feeding, breathing air out of the water, reduction of motility, and erratic swimming. The negative correlation between Pb concentration in whole body of shrimp and fish and Fulton's condition factor suggested also that the exposed organisms were stressed because of Pb accumulation.

  5. LinkProt: a database collecting information about biological links

    PubMed Central

    Dabrowski-Tumanski, Pawel; Jarmolinska, Aleksandra I.; Niemyska, Wanda; Rawdon, Eric J.; Millett, Kenneth C.; Sulkowska, Joanna I.

    2017-01-01

    Protein chains are known to fold into topologically complex shapes, such as knots, slipknots or complex lassos. This complex topology of the chain can be considered as an additional feature of a protein, separate from secondary and tertiary structures. Moreover, the complex topology can be defined also as one additional structural level. The LinkProt database (http://linkprot.cent.uw.edu.pl) collects and displays information about protein links — topologically non-trivial structures made by up to four chains and complexes of chains (e.g. in capsids). The database presents deterministic links (with loops closed, e.g. by two disulfide bonds), links formed probabilistically and macromolecular links. The structures are classified according to their topology and presented using the minimal surface area method. The database is also equipped with basic tools which allow users to analyze the topology of arbitrary (bio)polymers. PMID:27794552

  6. Defense Health Care: Additional Information Needed about Mental Health Provider Staffing Needs

    DTIC Science & Technology

    2015-01-01

    DEFENSE HEALTH CARE Additional Information Needed about Mental Health Provider Staffing Needs Report to the...REPORT TYPE 3. DATES COVERED 00-00-2015 to 00-00-2015 4. TITLE AND SUBTITLE Defense Health Care: Additional Information Needed about Mental ...Z39-18 Page i GAO-15-184 DOD Mental Health Staffing Letter 1 Background 4 DOD and the Military Services Have Increased the

  7. 78 FR 52803 - Agency Information Collection Activities; Submission for OMB Review; Comment Request; Additional...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-26

    ... OMB under the PRA and displays a currently valid OMB Control Number. In addition, notwithstanding any... collection of information that does not display a valid Control Number. See 5 CFR 1320.5(a) and 1320.6. The DOL obtains OMB approval for this information collection under Control Number 1218-0237....

  8. Dynamic phases in control and information processing biological circuits

    NASA Astrophysics Data System (ADS)

    Vaikuntanathan, Suriyanarayanan

    2015-03-01

    Recent work using the mathematical framework of large deviation theory has shown that fluctuations about the steady state can have a particularly rich structure even in extremely simple non-equilibrium systems [Phys. Rev. E. 89, 062108, 2014]. In certain instances the fluctuations can encode the presence of a dynamical phase with properties distinct from those of the steady state of the system. The transition between these two regimes is akin to a first order thermodynamic phase transition. Specifically, it implies an extreme sensitivity of the system to changes in certain sets of parameters. I will show that such dynamical phase transitions can serve as a general organizing principle to understand biological circuits that are involved in information processing and control. I will focus on two specific examples: adaptation control in E. coli chemotaxis and ultra sensitive response of the E. coli flagella motor, to illustrate these calculations. This work also elucidates the role played by energy dissipation in ensuring control and suggests general guidelines for the construction of robust non equilibrium circuits that perform various specified functions.

  9. "The Dose Makes the Poison": Informing Consumers About the Scientific Risk Assessment of Food Additives.

    PubMed

    Bearth, Angela; Cousin, Marie-Eve; Siegrist, Michael

    2016-01-01

    Intensive risk assessment is required before the approval of food additives. During this process, based on the toxicological principle of "the dose makes the poison,ˮ maximum usage doses are assessed. However, most consumers are not aware of these efforts to ensure the safety of food additives and are therefore sceptical, even though food additives bring certain benefits to consumers. This study investigated the effect of a short video, which explains the scientific risk assessment and regulation of food additives, on consumers' perceptions and acceptance of food additives. The primary goal of this study was to inform consumers and enable them to construct their own risk-benefit assessment and make informed decisions about food additives. The secondary goal was to investigate whether people have different perceptions of food additives of artificial (i.e., aspartame) or natural origin (i.e., steviolglycoside). To attain these research goals, an online experiment was conducted on 185 Swiss consumers. Participants were randomly assigned to either the experimental group, which was shown a video about the scientific risk assessment of food additives, or the control group, which was shown a video about a topic irrelevant to the study. After watching the video, the respondents knew significantly more, expressed more positive thoughts and feelings, had less risk perception, and more acceptance than prior to watching the video. Thus, it appears that informing consumers about complex food safety topics, such as the scientific risk assessment of food additives, is possible, and using a carefully developed information video is a successful strategy for informing consumers.

  10. Beware the tail that wags the dog: informal and formal models in biology

    PubMed Central

    Gunawardena, Jeremy

    2014-01-01

    Informal models have always been used in biology to guide thinking and devise experiments. In recent years, formal mathematical models have also been widely introduced. It is sometimes suggested that formal models are inherently superior to informal ones and that biology should develop along the lines of physics or economics by replacing the latter with the former. Here I suggest to the contrary that progress in biology requires a better integration of the formal with the informal. PMID:25368417

  11. Integrating Information in Biological Ontologies and Molecular Networks to Infer Novel Terms

    PubMed Central

    Li, Le; Yip, Kevin Y.

    2016-01-01

    Currently most terms and term-term relationships in Gene Ontology (GO) are defined manually, which creates cost, consistency and completeness issues. Recent studies have demonstrated the feasibility of inferring GO automatically from biological networks, which represents an important complementary approach to GO construction. These methods (NeXO and CliXO) are unsupervised, which means 1) they cannot use the information contained in existing GO, 2) the way they integrate biological networks may not optimize the accuracy, and 3) they are not customized to infer the three different sub-ontologies of GO. Here we present a semi-supervised method called Unicorn that extends these previous methods to tackle the three problems. Unicorn uses a sub-tree of an existing GO sub-ontology as training part to learn parameters in integrating multiple networks. Cross-validation results show that Unicorn reliably inferred the left-out parts of each specific GO sub-ontology. In addition, by training Unicorn with an old version of GO together with biological networks, it successfully re-discovered some terms and term-term relationships present only in a new version of GO. Unicorn also successfully inferred some novel terms that were not contained in GO but have biological meanings well-supported by the literature.Availability: Source code of Unicorn is available at http://yiplab.cse.cuhk.edu.hk/unicorn/. PMID:27976738

  12. Additives-biological activities of tin-containing polymers bonded to noncarbons

    SciTech Connect

    Carraher, C.; Butler, C.; Foster, V.; Pandya, B.; Sterling, D.

    1993-12-31

    Organotin-containing polymers serve as effective additives to a silicon-based sealant, latex coating and talc exhibiting inhibition to tested bacteria and fungi. These polymers are candidates for uses a paint additives, sealant and caulk additives and within talc as an epidermal treatment.

  13. 24 CFR 1710.200 - Instructions for Statement of Record, Additional Information and Documentation.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 24 Housing and Urban Development 5 2014-04-01 2014-04-01 false Instructions for Statement of Record, Additional Information and Documentation. 1710.200 Section 1710.200 Housing and Urban Development Regulations Relating to Housing and Urban Development (Continued) OFFICE OF ASSISTANT SECRETARY FOR...

  14. 10 CFR 52.158 - Contents of application; additional technical information.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 10 Energy 2 2014-01-01 2014-01-01 false Contents of application; additional technical information. 52.158 Section 52.158 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) LICENSES, CERTIFICATIONS, AND APPROVALS FOR NUCLEAR POWER PLANTS Manufacturing Licenses § 52.158 Contents of application;...

  15. 10 CFR 52.158 - Contents of application; additional technical information.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 10 Energy 2 2013-01-01 2013-01-01 false Contents of application; additional technical information. 52.158 Section 52.158 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) LICENSES, CERTIFICATIONS, AND APPROVALS FOR NUCLEAR POWER PLANTS Manufacturing Licenses § 52.158 Contents of application;...

  16. 10 CFR 52.158 - Contents of application; additional technical information.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 10 Energy 2 2012-01-01 2012-01-01 false Contents of application; additional technical information. 52.158 Section 52.158 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) LICENSES, CERTIFICATIONS, AND APPROVALS FOR NUCLEAR POWER PLANTS Manufacturing Licenses § 52.158 Contents of application;...

  17. 10 CFR 52.158 - Contents of application; additional technical information.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 10 Energy 2 2010-01-01 2010-01-01 false Contents of application; additional technical information. 52.158 Section 52.158 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) LICENSES, CERTIFICATIONS, AND APPROVALS FOR NUCLEAR POWER PLANTS Manufacturing Licenses § 52.158 Contents of application;...

  18. 10 CFR 52.158 - Contents of application; additional technical information.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 10 Energy 2 2011-01-01 2011-01-01 false Contents of application; additional technical information. 52.158 Section 52.158 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) LICENSES, CERTIFICATIONS, AND APPROVALS FOR NUCLEAR POWER PLANTS Manufacturing Licenses § 52.158 Contents of application;...

  19. 16 CFR 803.20 - Requests for additional information or documentary material.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 16 Commercial Practices 1 2010-01-01 2010-01-01 false Requests for additional information or documentary material. 803.20 Section 803.20 Commercial Practices FEDERAL TRADE COMMISSION RULES, REGULATIONS, STATEMENTS AND INTERPRETATIONS UNDER THE HART-SCOTT-RODINO ANTITRUST IMPROVEMENTS ACT OF 1976...

  20. 16 CFR 803.20 - Requests for additional information or documentary material.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 16 Commercial Practices 1 2013-01-01 2013-01-01 false Requests for additional information or documentary material. 803.20 Section 803.20 Commercial Practices FEDERAL TRADE COMMISSION RULES, REGULATIONS, STATEMENTS AND INTERPRETATIONS UNDER THE HART-SCOTT-RODINO ANTITRUST IMPROVEMENTS ACT OF 1976...

  1. 16 CFR 803.20 - Requests for additional information or documentary material.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 16 Commercial Practices 1 2014-01-01 2014-01-01 false Requests for additional information or documentary material. 803.20 Section 803.20 Commercial Practices FEDERAL TRADE COMMISSION RULES, REGULATIONS, STATEMENTS AND INTERPRETATIONS UNDER THE HART-SCOTT-RODINO ANTITRUST IMPROVEMENTS ACT OF 1976...

  2. 16 CFR 803.21 - Additional information shall be supplied within reasonable time.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 16 Commercial Practices 1 2010-01-01 2010-01-01 false Additional information shall be supplied within reasonable time. 803.21 Section 803.21 Commercial Practices FEDERAL TRADE COMMISSION RULES, REGULATIONS, STATEMENTS AND INTERPRETATIONS UNDER THE HART-SCOTT-RODINO ANTITRUST IMPROVEMENTS ACT OF...

  3. 16 CFR 803.21 - Additional information shall be supplied within reasonable time.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 16 Commercial Practices 1 2013-01-01 2013-01-01 false Additional information shall be supplied within reasonable time. 803.21 Section 803.21 Commercial Practices FEDERAL TRADE COMMISSION RULES, REGULATIONS, STATEMENTS AND INTERPRETATIONS UNDER THE HART-SCOTT-RODINO ANTITRUST IMPROVEMENTS ACT OF...

  4. 16 CFR 803.21 - Additional information shall be supplied within reasonable time.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 16 Commercial Practices 1 2011-01-01 2011-01-01 false Additional information shall be supplied within reasonable time. 803.21 Section 803.21 Commercial Practices FEDERAL TRADE COMMISSION RULES, REGULATIONS, STATEMENTS AND INTERPRETATIONS UNDER THE HART-SCOTT-RODINO ANTITRUST IMPROVEMENTS ACT OF...

  5. 16 CFR 803.21 - Additional information shall be supplied within reasonable time.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 16 Commercial Practices 1 2012-01-01 2012-01-01 false Additional information shall be supplied within reasonable time. 803.21 Section 803.21 Commercial Practices FEDERAL TRADE COMMISSION RULES, REGULATIONS, STATEMENTS AND INTERPRETATIONS UNDER THE HART-SCOTT-RODINO ANTITRUST IMPROVEMENTS ACT OF...

  6. 16 CFR 803.21 - Additional information shall be supplied within reasonable time.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 16 Commercial Practices 1 2014-01-01 2014-01-01 false Additional information shall be supplied within reasonable time. 803.21 Section 803.21 Commercial Practices FEDERAL TRADE COMMISSION RULES, REGULATIONS, STATEMENTS AND INTERPRETATIONS UNDER THE HART-SCOTT-RODINO ANTITRUST IMPROVEMENTS ACT OF...

  7. 16 CFR 803.20 - Requests for additional information or documentary material.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 16 Commercial Practices 1 2012-01-01 2012-01-01 false Requests for additional information or documentary material. 803.20 Section 803.20 Commercial Practices FEDERAL TRADE COMMISSION RULES, REGULATIONS, STATEMENTS AND INTERPRETATIONS UNDER THE HART-SCOTT-RODINO ANTITRUST IMPROVEMENTS ACT OF 1976...

  8. 18 CFR 33.3 - Additional information requirements for applications involving horizontal competitive impacts.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 18 Conservation of Power and Water Resources 1 2014-04-01 2014-04-01 false Additional information... and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT OF ENERGY REGULATIONS UNDER THE... reserve existing transmission capacity needed for native load growth and network transmission...

  9. 18 CFR 33.3 - Additional information requirements for applications involving horizontal competitive impacts.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 18 Conservation of Power and Water Resources 1 2013-04-01 2013-04-01 false Additional information... and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT OF ENERGY REGULATIONS UNDER THE... reserve existing transmission capacity needed for native load growth and network transmission...

  10. 18 CFR 33.3 - Additional information requirements for applications involving horizontal competitive impacts.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 18 Conservation of Power and Water Resources 1 2012-04-01 2012-04-01 false Additional information... and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT OF ENERGY REGULATIONS UNDER THE... reserve existing transmission capacity needed for native load growth and network transmission...

  11. 40 CFR Table 42 to Subpart Uuu of... - Additional Information for Initial Notification of Compliance Status

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 13 2012-07-01 2012-07-01 false Additional Information for Initial Notification of Compliance Status 42 Table 42 to Subpart UUU of Part 63 Protection of Environment ENVIRONMENTAL... applicable emission limit and the continuous opacity or that the emission monitoring system meets...

  12. 17 CFR 229.1118 - (Item 1118) Reports and additional information.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 17 Commodity and Securities Exchanges 2 2010-04-01 2010-04-01 false (Item 1118) Reports and additional information. 229.1118 Section 229.1118 Commodity and Securities Exchanges SECURITIES AND EXCHANGE COMMISSION STANDARD INSTRUCTIONS FOR FILING FORMS UNDER SECURITIES ACT OF 1933, SECURITIES EXCHANGE ACT...

  13. 17 CFR 229.1118 - (Item 1118) Reports and additional information.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 17 Commodity and Securities Exchanges 2 2013-04-01 2013-04-01 false (Item 1118) Reports and additional information. 229.1118 Section 229.1118 Commodity and Securities Exchanges SECURITIES AND EXCHANGE COMMISSION STANDARD INSTRUCTIONS FOR FILING FORMS UNDER SECURITIES ACT OF 1933, SECURITIES EXCHANGE ACT...

  14. 38 CFR 39.4 - Decision makers, notifications, and additional information.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2011-07-01 2011-07-01 false Decision makers, notifications, and additional information. 39.4 Section 39.4 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS (CONTINUED) AID TO STATES FOR ESTABLISHMENT, EXPANSION, AND IMPROVEMENT,...

  15. 38 CFR 39.4 - Decision makers, notifications, and additional information.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2012-07-01 2012-07-01 false Decision makers, notifications, and additional information. 39.4 Section 39.4 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS (CONTINUED) AID FOR THE ESTABLISHMENT, EXPANSION, AND IMPROVEMENT, OR...

  16. 38 CFR 39.4 - Decision makers, notifications, and additional information.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2013-07-01 2013-07-01 false Decision makers, notifications, and additional information. 39.4 Section 39.4 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS (CONTINUED) AID FOR THE ESTABLISHMENT, EXPANSION, AND IMPROVEMENT, OR...

  17. 38 CFR 39.4 - Decision makers, notifications, and additional information.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2014-07-01 2014-07-01 false Decision makers, notifications, and additional information. 39.4 Section 39.4 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS (CONTINUED) AID FOR THE ESTABLISHMENT, EXPANSION, AND IMPROVEMENT, OR...

  18. 30 CFR 250.418 - What additional information must I submit with my APD?

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ..., DEPARTMENT OF THE INTERIOR OFFSHORE OIL AND GAS AND SULPHUR OPERATIONS IN THE OUTER CONTINENTAL SHELF Oil and Gas Drilling Operations Applying for A Permit to Drill § 250.418 What additional information must I submit with my APD? You must include the following with the APD: (a) Rated capacities of the drilling...

  19. 30 CFR 250.418 - What additional information must I submit with my APD?

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ..., DEPARTMENT OF THE INTERIOR OFFSHORE OIL AND GAS AND SULPHUR OPERATIONS IN THE OUTER CONTINENTAL SHELF Oil and Gas Drilling Operations Applying for A Permit to Drill § 250.418 What additional information must I submit with my APD? You must include the following with the APD: (a) Rated capacities of the drilling...

  20. 30 CFR 250.418 - What additional information must I submit with my APD?

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ..., DEPARTMENT OF THE INTERIOR OFFSHORE OIL AND GAS AND SULPHUR OPERATIONS IN THE OUTER CONTINENTAL SHELF Oil and Gas Drilling Operations Applying for A Permit to Drill § 250.418 What additional information must I submit with my APD? You must include the following with the APD: (a) Rated capacities of the drilling...

  1. 30 CFR 250.418 - What additional information must I submit with my APD?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... INTERIOR OFFSHORE OIL AND GAS AND SULPHUR OPERATIONS IN THE OUTER CONTINENTAL SHELF Oil and Gas Drilling Operations Applying for A Permit to Drill § 250.418 What additional information must I submit with my APD? You must include the following with the APD: (a) Rated capacities of the drilling rig and...

  2. 38 CFR 61.15 - Capital grants-obtaining additional information and awarding capital grants.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2013-07-01 2013-07-01 false Capital grants-obtaining additional information and awarding capital grants. 61.15 Section 61.15 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS (CONTINUED) VA HOMELESS PROVIDERS GRANT AND PER DIEM...

  3. 38 CFR 61.15 - Obtaining additional information and awarding capital grants.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2012-07-01 2012-07-01 false Obtaining additional information and awarding capital grants. 61.15 Section 61.15 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS (CONTINUED) VA HOMELESS PROVIDERS GRANT AND PER DIEM PROGRAM § 61.15...

  4. 38 CFR 61.15 - Obtaining additional information and awarding capital grants.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2011-07-01 2011-07-01 false Obtaining additional information and awarding capital grants. 61.15 Section 61.15 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS (CONTINUED) VA HOMELESS PROVIDERS GRANT AND PER DIEM PROGRAM § 61.15...

  5. 38 CFR 61.15 - Capital grants-obtaining additional information and awarding capital grants.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2014-07-01 2014-07-01 false Capital grants-obtaining additional information and awarding capital grants. 61.15 Section 61.15 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS (CONTINUED) VA HOMELESS PROVIDERS GRANT AND PER DIEM...

  6. 18 CFR 33.4 - Additional information requirements for applications involving vertical competitive impacts.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 18 Conservation of Power and Water Resources 1 2010-04-01 2010-04-01 false Additional information... and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT OF ENERGY REGULATIONS UNDER THE... entities that provides inputs to electricity products and one or more merging entities that...

  7. 18 CFR 33.4 - Additional information requirements for applications involving vertical competitive impacts.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 18 Conservation of Power and Water Resources 1 2011-04-01 2011-04-01 false Additional information... and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT OF ENERGY REGULATIONS UNDER THE... entities that provides inputs to electricity products and one or more merging entities that...

  8. 18 CFR 33.4 - Additional information requirements for applications involving vertical competitive impacts.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 18 Conservation of Power and Water Resources 1 2014-04-01 2014-04-01 false Additional information... and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT OF ENERGY REGULATIONS UNDER THE... entities that provides inputs to electricity products and one or more merging entities that...

  9. The physics of complex systems in information and biology

    NASA Astrophysics Data System (ADS)

    Walker, Dylan

    study the interaction between popularity and quality, we introduce simple stochastic models of user behavior that approximate differing user quality and susceptibility to the common notion of popularity. We define a metric to quantify user reputation in a manner that is self-consistent, adaptable and content-blind and shows good correlation with the probability that a user behaves in an optimal fashion. We further construct a mechanism for ranking documents that take into account user reputation and provides substantial improvement in the time-critical performance of the system. The structure of complex systems have been well studied in the context of both information and biological systems. More recently, dynamics in complex systems that occur over the background of the underlying network has received a great deal of attention. In particular, the study of fluctuations in complex systems has emerged as an issue central to understanding dynamical behavior. We approach the problem of collective effects of the underlying network on dynamical fluctuations by considering the protein-protein interaction networks for the system of the living cell. We consider two types of fluctuations in the mass-action equilibrium in protein binding networks. The first type is driven by relatively slow changes in total concentrations (copy numbers) of interacting proteins. The second type, to which we refer to as spontaneous, is caused by quickly decaying thermodynamic deviations away from the mass-action equilibrium of the system. As such they are amenable to methods of equilibrium statistical mechanics used in our study. We investigate the effects of network connectivity on these fluctuations by comparing them to different scenarios in which the interacting pair is isolated form the rest of the network. Such comparison allows us to analytically derive upper and lower bounds on network fluctuations. The collective effects are shown to sometimes lead to relatively large amplification of

  10. Stochastic resonance in biology. How noise can enhance detection of weak signals and help improve biological information processing.

    PubMed

    Hänggi, Peter

    2002-03-12

    Noise is usually thought of as the enemy of order rather than as a constructive influence. In nonlinear systems that possess some sort of threshold, random noise plays a beneficial role in enhancing the detection of weak information-carrying signals. This phenomenon, termed stochastic resonance, does find useful applications in physical, biological, and biomedical contexts. Certain biological systems may even use this effect for optimizing function and behavior.

  11. Time optimal control of an additional food provided predator-prey system with applications to pest management and biological conservation.

    PubMed

    Srinivasu, P D N; Prasad, B S R V

    2010-04-01

    Use of additional food has been widely recognized by experimental scientists as one of the important tools for biological control such as species conservation and pest management. The quality and quantity of additional food supplied to the predators is known to play a vital role in the controllability of the system. The present study is continuation of a previous work that highlights the importance of quality and quantity of the additional food in the dynamics of a predator-prey system in the context of biological control. In this article the controllability of the predator-prey system is analyzed by considering inverse of quality of the additional food as the control variable. Control strategies are offered to steer the system from a given initial state to a required terminal state in a minimum time by formulating Mayer problem of optimal control. It is observed that an optimal strategy is a combination of bang-bang controls and could involve multiple switches. Properties of optimal paths are derived using necessary conditions for Mayer problem. In the light of the results evolved in this work it is possible to eradicate the prey from the eco-system in the minimum time by providing the predator with high quality additional food, which is relevant in the pest management. In the perspective of biological conservation this study highlights the possibilities to drive the state to an admissible interior equilibrium (irrespective of its stability nature) of the system in a minimum time.

  12. CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources

    PubMed Central

    Bleda, Marta; Tarraga, Joaquin; de Maria, Alejandro; Salavert, Francisco; Garcia-Alonso, Luz; Celma, Matilde; Martin, Ainoha; Dopazo, Joaquin; Medina, Ignacio

    2012-01-01

    During the past years, the advances in high-throughput technologies have produced an unprecedented growth in the number and size of repositories and databases storing relevant biological data. Today, there is more biological information than ever but, unfortunately, the current status of many of these repositories is far from being optimal. Some of the most common problems are that the information is spread out in many small databases; frequently there are different standards among repositories and some databases are no longer supported or they contain too specific and unconnected information. In addition, data size is increasingly becoming an obstacle when accessing or storing biological data. All these issues make very difficult to extract and integrate information from different sources, to analyze experiments or to access and query this information in a programmatic way. CellBase provides a solution to the growing necessity of integration by easing the access to biological data. CellBase implements a set of RESTful web services that query a centralized database containing the most relevant biological data sources. The database is hosted in our servers and is regularly updated. CellBase documentation can be found at http://docs.bioinfo.cipf.es/projects/cellbase. PMID:22693220

  13. CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources.

    PubMed

    Bleda, Marta; Tarraga, Joaquin; de Maria, Alejandro; Salavert, Francisco; Garcia-Alonso, Luz; Celma, Matilde; Martin, Ainoha; Dopazo, Joaquin; Medina, Ignacio

    2012-07-01

    During the past years, the advances in high-throughput technologies have produced an unprecedented growth in the number and size of repositories and databases storing relevant biological data. Today, there is more biological information than ever but, unfortunately, the current status of many of these repositories is far from being optimal. Some of the most common problems are that the information is spread out in many small databases; frequently there are different standards among repositories and some databases are no longer supported or they contain too specific and unconnected information. In addition, data size is increasingly becoming an obstacle when accessing or storing biological data. All these issues make very difficult to extract and integrate information from different sources, to analyze experiments or to access and query this information in a programmatic way. CellBase provides a solution to the growing necessity of integration by easing the access to biological data. CellBase implements a set of RESTful web services that query a centralized database containing the most relevant biological data sources. The database is hosted in our servers and is regularly updated. CellBase documentation can be found at http://docs.bioinfo.cipf.es/projects/cellbase.

  14. Guidance manual for the input of biological information to water-intake-structure design

    SciTech Connect

    Neitzel, D.A.; Simmons, M.A.; McKenzie, D.H.

    1981-12-01

    This manual is intended to provide guidance to the biologist who is asked to provide biological input during the construction or subsequent alteration of a water intake structure. Examples of the types of biological information that might be included in intake design are presented. Procedures for quantifying biological information and defining specific tasks that will generate quantifiable data are discussed. Procedures described apply both to new and modified water intake structures.

  15. Chemical and biological consequences of using carbon dioxide versus acid additions in ocean acidification experiments

    USGS Publications Warehouse

    Yates, Kimberly K.; DuFore, Christopher M.; Robbins, Lisa L.

    2013-01-01

    Use of different approaches for manipulating seawater chemistry during ocean acidification experiments has confounded comparison of results from various experimental studies. Some of these discrepancies have been attributed to whether addition of acid (such as hydrochloric acid, HCl) or carbon dioxide (CO2) gas has been used to adjust carbonate system parameters. Experimental simulations of carbonate system parameter scenarios for the years 1766, 2007, and 2100 were performed using the carbonate speciation program CO2SYS to demonstrate the variation in seawater chemistry that can result from use of these approaches. Results showed that carbonate system parameters were 3 percent and 8 percent lower than target values in closed-system acid additions, and 1 percent and 5 percent higher in closed-system CO2 additions for the 2007 and 2100 simulations, respectively. Open-system simulations showed that carbonate system parameters can deviate by up to 52 percent to 70 percent from target values in both acid addition and CO2 addition experiments. Results from simulations for the year 2100 were applied to empirically derived equations that relate biogenic calcification to carbonate system parameters for calcifying marine organisms including coccolithophores, corals, and foraminifera. Calculated calcification rates for coccolithophores, corals, and foraminifera differed from rates at target conditions by 0.5 percent to 2.5 percent in closed-system CO2 gas additions, from 0.8 percent to 15 percent in the closed-system acid additions, from 4.8 percent to 94 percent in open-system acid additions, and from 7 percent to 142 percent in open-system CO2 additions.

  16. Didactics of Biology. A Selected Bibliography for 1985. Information Bulletin.

    ERIC Educational Resources Information Center

    Altmann, Antonin, Ed.; Lipertova, Pavla, Ed.

    Selected articles on various aspects of biology teaching published in 1985 have been annotated in this bibliography. Entries from 25 journals representing nine countries are presented according to a topic area classification scheme listed at the beginning of the volume. Countries represented include: Bulgaria; Czechoslovakia; Federal Republic of…

  17. Conservation characteristics of wilted perennial ryegrass silage made using biological or chemical additives.

    PubMed

    Conaghan, P; O'Kiely, P; O'Mara, F P

    2010-02-01

    The effects of 7 additive treatments on the fermentation and aerobic stability characteristics of wilted grass silage were studied under laboratory conditions. Treatments included no additive applied (untreated control), ammonium tetraformate at 3 and 6 L/t, homofermentative lactic acid bacteria alone ((ho)LAB), a mixture of Lactobacillus buchneri plus homofermentative lactic acid bacteria ((he+ho)LAB), and an antimicrobial mixture of sodium benzoate, sodium propionate, sodium nitrite, and hexamethylenetetramine at 2.5 and 5 L/t. Additives were compared across 3 consecutive harvests of 2 perennial ryegrass cultivars (AberDart and Fennema) following a 24-h wilt. Silos were opened after at least 100 d of ensilage and aerobic stability was assessed. Season of harvest had a large effect on grass composition at ensiling, producing herbages of relatively low (approximately 145g/kg), medium (approximately 250g/kg), and high (approximately 365g/kg) dry matter (DM) concentrations. Within harvests there were lesser differences between cultivars. The untreated control and (ho)LAB additive produced badly fermented silage from the low-DM herbages and well-fermented silage from the medium- and high-DM herbages. The ammonium tetraformate treatments produced both well-fermented and badly fermented silage from the low-DM herbages depending on cultivar, and consistently well-fermented silage from the medium- and high-DM herbages. The (he+ho)LAB silages had similar or slightly lower standard of fermentation than the untreated and (ho)LAB silages. The antimicrobial mixture produced more silages of lower standard of fermentation than the untreated control and ammonium tetraformate and (ho)LAB additives. All additive treatments, including the untreated control, failed to consistently increase residual water-soluble carbohydrate concentrations at silo opening. Ammonium tetraformate at 6 L/t was the most successful and (he+ho)LAB the least successful additive at increasing residual WSC

  18. Fates of chlorinated volatile organic compounds in aerobic biological treatment processes: the effects of aeration and sludge addition.

    PubMed

    Chen, Wei-Hsiang; Yang, Wen-Ben; Yuan, Chung-Shin; Yang, Jun-Chen; Zhao, Qing-Liang

    2014-05-01

    The emission of volatile organic compounds (VOCs) from wastewater treatment plants (WWTPs) is becoming an environmental issue of increasing concern. As biological treatment has been considered as one important approach for VOC removal, lab-scale batch experiments were conducted in this study to investigate the fates of four chlorinated hydrocarbons, including chloroform, carbon tetrachloride, trichloroethylene (TCE), and tetrachloroethylene (PERC), in the biological treatment processes with respect to the effects of aeration and sludge addition. The VOC concentrations in the phases of air, water, and sludge under four simulated treatment stages (the first sedimentation, the forepart and rear part of aerobic biological treatment, and the second sedimentation) were analyzed. The results were used to understand the three-phase partitioning of these compounds and to estimate their potentials for volatilization and biological sorption and degradation in these technologies with the concept of fugacity. It was observed that the VOCs were mainly present in the water phase through the experiments. The effects of aeration or sludge addition on the fates of these VOCs occurred but appeared to be relatively limited. The concentration distributions of the VOCs were well below the reported partitioning coefficients. It was suggested that these compounds were unsaturated in the air and sludge phases, enhancing their potentials for volatilization and biological sorption/degradation through the processes. However, the properties of these chlorinated VOCs such as the volatility, polarity, or even biodegradability caused by their structural characteristics (e.g., the number of chlorine, saturated or unsaturated) may represent more significant factors for their fates in the aerobic biological treatment processes. These findings prove the complication behind the current knowledge of VOC pollutions in WWTPs and are of help to manage the adverse impacts on the environment and public

  19. Method for imaging informational biological molecules on a semiconductor substrate

    NASA Technical Reports Server (NTRS)

    Coles, L. Stephen (Inventor)

    1994-01-01

    Imaging biological molecules such as DNA at rates several times faster than conventional imaging techniques is carried out using a patterned silicon wafer having nano-machined grooves which hold individual molecular strands and periodically spaced unique bar codes permitting repeatably locating all images. The strands are coaxed into the grooves preferably using gravity and pulsed electric fields which induce electric charge attraction to the molecular strands in the bottom surfaces of the grooves. Differential imaging removes substrate artifacts.

  20. Information Fluency for Undergraduate Biology Majors: Applications of Inquiry-based Learning in a Developmental Biology Course

    PubMed Central

    Gehring, Kathleen M.

    2008-01-01

    Many initiatives for the improvement of undergraduate science education call for inquiry-based learning that emphasizes investigative projects and reading of the primary literature. These approaches give students an understanding of science as a process and help them integrate content presented in courses. At the same time, general initiatives to promote information fluency are being promoted on many college and university campuses. Information fluency refers to discipline-specific processing of information, and it involves integration of gathered information with specific ideas to form logical conclusions. We have implemented the use of inquiry-based learning to enhance and study discipline-specific information fluency skills in an upper-level undergraduate Developmental Biology course. In this study, an information literacy tutorial and a set of linked assignments using primary literature analysis were integrated with two inquiry-based laboratory research projects. Quantitaitve analysis of student responses suggests that the abilities of students to identify and apply valid sources of information were enhanced. Qualitative assessment revealed a set of patterns by which students gather and apply information. Self-assessment responses indicated that students recognized the impact of the assignments on their abilities to gather and apply information and that they were more confident about these abilities for future biology courses and beyond. PMID:18316808

  1. Thiopeptin, a New Feed-Additive Antibiotic: Biological Studies and Field Trials

    PubMed Central

    Mine, K.; Miyairi, N.; Takano, N.; Mori, S.; Watanabe, N.

    1972-01-01

    Thiopeptin is a new antibiotic, produced by Streptomyces tateyamensis and developed solely for animal use as a feed additive. The antibiotic content in animal tissue and feed was assayed in terms of the antimicrobial activity against Mycoplasma laidlawii A. This antibiotic was found to be relatively nontoxic in rats and mice. In chickens, this antibiotic is excreted into feces within 48 hr of administration and is not absorbed in tissue. It is well tolerated in both broilers and swine and is highly stable in animal feed. Thiopeptin-supplemented feed contributes to the improvement of weight gain, feed efficiency in chickens and swine, and the egg performance in layers. Thus, thiopeptin, when used as a feed additive, is quite suitable for supplementing animal nutrition. PMID:4680812

  2. Integrating paleobiology, archeology, and history to inform biological conservation.

    PubMed

    Rick, Torben C; Lockwood, Rowan

    2013-02-01

    The search for novel approaches to establishing ecological baselines (reference conditions) is constrained by the fact that most ecological studies span the past few decades, at most, and investigate ecosystems that have been substantially altered by human activities for decades, centuries, or more. Paleobiology, archeology, and history provide historical ecological context for biological conservation, remediation, and restoration. We argue that linking historical ecology explicitly with conservation can help unify related disciplines of conservation paleobiology, conservation archeobiology, and environmental history. Differences in the spatial and temporal resolution and extent (scale) of prehistoric, historic, and modern ecological data remain obstacles to integrating historical ecology and conservation biology, but the prolonged temporal extents of historical ecological data can help establish more complete baselines for restoration, document a historical range of ecological variability, and assist in determining desired future conditions. We used the eastern oyster (Crassostrea virginica) fishery of the Chesapeake Bay (U.S.A.) to demonstrate the utility of historical ecological data for elucidating oyster conservation and the need for an approach to conservation that transcends disciplinary boundaries. Historical ecological studies from the Chesapeake have documented dramatic declines (as much as 99%) in oyster abundance since the early to mid-1800 s, changes in oyster size in response to different nutrient levels from the sixteenth to nineteenth centuries, and substantial reductions in oyster accretion rates (from 10 mm/year to effectively 0 mm/year) from the Late Holocene to modern times. Better integration of different historical ecological data sets and increased collaboration between paleobiologists, geologists, archeologists, environmental historians, and ecologists to create standardized research designs and methodologies will help unify prehistoric

  3. Social insect colony as a biological regulatory system: modelling information flow in dominance networks

    PubMed Central

    Nandi, Anjan K.; Sumana, Annagiri; Bhattacharya, Kunal

    2014-01-01

    Social insects provide an excellent platform to investigate flow of information in regulatory systems since their successful social organization is essentially achieved by effective information transfer through complex connectivity patterns among the colony members. Network representation of such behavioural interactions offers a powerful tool for structural as well as dynamical analysis of the underlying regulatory systems. In this paper, we focus on the dominance interaction networks in the tropical social wasp Ropalidia marginata—a species where behavioural observations indicate that such interactions are principally responsible for the transfer of information between individuals about their colony needs, resulting in a regulation of their own activities. Our research reveals that the dominance networks of R. marginata are structurally similar to a class of naturally evolved information processing networks, a fact confirmed also by the predominance of a specific substructure—the ‘feed-forward loop’—a key functional component in many other information transfer networks. The dynamical analysis through Boolean modelling confirms that the networks are sufficiently stable under small fluctuations and yet capable of more efficient information transfer compared to their randomized counterparts. Our results suggest the involvement of a common structural design principle in different biological regulatory systems and a possible similarity with respect to the effect of selection on the organization levels of such systems. The findings are also consistent with the hypothesis that dominance behaviour has been shaped by natural selection to co-opt the information transfer process in such social insect species, in addition to its primal function of mediation of reproductive competition in the colony. PMID:25320069

  4. Social insect colony as a biological regulatory system: modelling information flow in dominance networks.

    PubMed

    Nandi, Anjan K; Sumana, Annagiri; Bhattacharya, Kunal

    2014-12-06

    Social insects provide an excellent platform to investigate flow of information in regulatory systems since their successful social organization is essentially achieved by effective information transfer through complex connectivity patterns among the colony members. Network representation of such behavioural interactions offers a powerful tool for structural as well as dynamical analysis of the underlying regulatory systems. In this paper, we focus on the dominance interaction networks in the tropical social wasp Ropalidia marginata-a species where behavioural observations indicate that such interactions are principally responsible for the transfer of information between individuals about their colony needs, resulting in a regulation of their own activities. Our research reveals that the dominance networks of R. marginata are structurally similar to a class of naturally evolved information processing networks, a fact confirmed also by the predominance of a specific substructure-the 'feed-forward loop'-a key functional component in many other information transfer networks. The dynamical analysis through Boolean modelling confirms that the networks are sufficiently stable under small fluctuations and yet capable of more efficient information transfer compared to their randomized counterparts. Our results suggest the involvement of a common structural design principle in different biological regulatory systems and a possible similarity with respect to the effect of selection on the organization levels of such systems. The findings are also consistent with the hypothesis that dominance behaviour has been shaped by natural selection to co-opt the information transfer process in such social insect species, in addition to its primal function of mediation of reproductive competition in the colony.

  5. Ground-Level Ozone Following Astrophysical Ionizing Radiation Events: An Additional Biological Hazard?

    PubMed

    Thomas, Brian C; Goracke, Byron D

    2016-01-01

    Astrophysical ionizing radiation events such as supernovae, gamma-ray bursts, and solar proton events have been recognized as a potential threat to life on Earth, primarily through depletion of stratospheric ozone and subsequent increase in solar UV radiation at Earth's surface and in the upper levels of the ocean. Other work has also considered the potential impact of nitric acid rainout, concluding that no significant threat is likely. Not yet studied to date is the potential impact of ozone produced in the lower atmosphere following an ionizing radiation event. Ozone is a known irritant to organisms on land and in water and therefore may be a significant additional hazard. Using previously completed atmospheric chemistry modeling, we examined the amount of ozone produced in the lower atmosphere for the case of a gamma-ray burst and found that the values are too small to pose a significant additional threat to the biosphere. These results may be extended to other ionizing radiation events, including supernovae and extreme solar proton events.

  6. 21 CFR 601.51 - Confidentiality of data and information in applications for biologics licenses.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 7 2011-04-01 2010-04-01 true Confidentiality of data and information in applications for biologics licenses. 601.51 Section 601.51 Food and Drugs FOOD AND DRUG ADMINISTRATION... information shall submit a request under the Freedom of Information Act. (e) After a license has been...

  7. Understanding the Information Needs of Academic Scholars in Agricultural and Biological Sciences

    ERIC Educational Resources Information Center

    Kuruppu, Pali U.; Gruber, Anne Marie

    2006-01-01

    This study investigates the information needs of faculty and graduate students in agricultural and biological sciences. Qualitative research methods, interviews and focus groups, were used to examine what types of information these scholars need for their research, teaching and learning, how they seek that information, and perceptions. The…

  8. Sender–receiver systems and applying information theory for quantitative synthetic biology

    PubMed Central

    Barcena Menendez, Diego; Senthivel, Vivek Raj; Isalan, Mark

    2015-01-01

    Sender–receiver (S–R) systems abound in biology, with communication systems sending information in various forms. Information theory provides a quantitative basis for analysing these processes and is being applied to study natural genetic, enzymatic and neural networks. Recent advances in synthetic biology are providing us with a wealth of artificial S–R systems, giving us quantitative control over networks with a finite number of well-characterised components. Combining the two approaches can help to predict how to maximise signalling robustness, and will allow us to make increasingly complex biological computers. Ultimately, pushing the boundaries of synthetic biology will require moving beyond engineering the flow of information and towards building more sophisticated circuits that interpret biological meaning. PMID:25282688

  9. Sender-receiver systems and applying information theory for quantitative synthetic biology.

    PubMed

    Barcena Menendez, Diego; Senthivel, Vivek Raj; Isalan, Mark

    2015-02-01

    Sender-receiver (S-R) systems abound in biology, with communication systems sending information in various forms. Information theory provides a quantitative basis for analysing these processes and is being applied to study natural genetic, enzymatic and neural networks. Recent advances in synthetic biology are providing us with a wealth of artificial S-R systems, giving us quantitative control over networks with a finite number of well-characterised components. Combining the two approaches can help to predict how to maximise signalling robustness, and will allow us to make increasingly complex biological computers. Ultimately, pushing the boundaries of synthetic biology will require moving beyond engineering the flow of information and towards building more sophisticated circuits that interpret biological meaning.

  10. An engineer's view on genetic information and biological evolution.

    PubMed

    Battail, Gérard

    2004-01-01

    We develop ideas on genome replication introduced in Battail [Europhys. Lett. 40 (1997) 343]. Starting with the hypothesis that the genome replication process uses error-correcting means, and the auxiliary one that nested codes are used to this end, we first review the concepts of redundancy and error-correcting codes. Then we show that these hypotheses imply that: distinct species exist with a hierarchical taxonomy, there is a trend of evolution towards complexity, and evolution proceeds by discrete jumps. At least the first two features above may be considered as biological facts so, in the absence of direct evidence, they provide an indirect proof in favour of the hypothesized error-correction system. The very high redundancy of genomes makes it possible. In order to explain how it is implemented, we suggest that soft codes and replication decoding, to be briefly described, are plausible candidates. Experimentally proven properties of long-range correlation of the DNA message substantiate this claim.

  11. PAT-1 safety analysis report addendum author responses to request for additional information.

    SciTech Connect

    Weiner, Ruth F.; Schmale, David T.; Kalan, Robert J.; Akin, Lili A.; Miller, David Russell; Knorovsky, Gerald Albert; Yoshimura, Richard Hiroyuki; Lopez, Carlos; Harding, David Cameron; Jones, Perry L.; Morrow, Charles W.

    2010-09-01

    The Plutonium Air Transportable Package, Model PAT-1, is certified under Title 10, Code of Federal Regulations Part 71 by the U.S. Nuclear Regulatory Commission (NRC) per Certificate of Compliance (CoC) USA/0361B(U)F-96 (currently Revision 9). The National Nuclear Security Administration (NNSA) submitted SAND Report SAND2009-5822 to NRC that documented the incorporation of plutonium (Pu) metal as a new payload for the PAT-1 package. NRC responded with a Request for Additional Information (RAI), identifying information needed in connection with its review of the application. The purpose of this SAND report is to provide the authors responses to each RAI. SAND Report SAND2010-6106 containing the proposed changes to the Addendum is provided separately.

  12. 30 CFR 550.216 - What biological, physical, and socioeconomic information must accompany the EP?

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 30 Mineral Resources 2 2012-07-01 2012-07-01 false What biological, physical, and socioeconomic... and Information Contents of Exploration Plans (ep) § 550.216 What biological, physical, and.... (b) Physical environment reports. Site-specific meteorological, physical oceanographic,...

  13. 30 CFR 550.216 - What biological, physical, and socioeconomic information must accompany the EP?

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 30 Mineral Resources 2 2014-07-01 2014-07-01 false What biological, physical, and socioeconomic... and Information Contents of Exploration Plans (ep) § 550.216 What biological, physical, and.... (b) Physical environment reports. Site-specific meteorological, physical oceanographic,...

  14. 30 CFR 550.216 - What biological, physical, and socioeconomic information must accompany the EP?

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 30 Mineral Resources 2 2013-07-01 2013-07-01 false What biological, physical, and socioeconomic... and Information Contents of Exploration Plans (ep) § 550.216 What biological, physical, and.... (b) Physical environment reports. Site-specific meteorological, physical oceanographic,...

  15. Information Use by PhD Students in Agriculture and Biology: A Dissertation Citation Analysis

    ERIC Educational Resources Information Center

    Kuruppu, Pali U.; Moore, Debra C.

    2008-01-01

    This article reports the findings of a study conducted to examine the types of information used by graduate students in the fields of biological and agricultural sciences at Iowa State University (ISU). The citations of doctoral dissertations submitted in nine agriculture and biological science subject fields (crop production and physiology;…

  16. Science Seeker: A New Model for Teaching Information Literacy to Entry-Level Biology Undergraduates

    ERIC Educational Resources Information Center

    Petzold, Jacquelyn; Winterman, Brian; Montooth, Kristi

    2010-01-01

    In order to integrate library instruction seamlessly into an introductory biology course, two librarians collaborated with a biology faculty member to create a three-part series of instruction sessions known as the Science Seeker. The Science Seeker taught students about the structure of scientific information by tracing the path that discoveries…

  17. 77 FR 40090 - Proposed Collection of Information; Comment Request: Biological Sciences Proposal Classification...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-07-06

    ... From the Federal Register Online via the Government Publishing Office NATIONAL SCIENCE FOUNDATION Proposed Collection of Information; Comment Request: Biological Sciences Proposal Classification Form AGENCY: National Science Foundation. ACTION: Notice. SUMMARY: The National Science Foundation (NSF)...

  18. Information resources and the correlation of response patterns between biological end points

    SciTech Connect

    Malling, H.V.; Wassom, J.S.

    1990-12-31

    This paper focuses on the analysis of information for mutagenesis, a biological end point that is important in the overall process of assessing possible adverse health effects from chemical exposure. 17 refs.

  19. The effect of sterilization on biological, organic geochemical and morphological information in natural samples

    NASA Technical Reports Server (NTRS)

    Hochstein, L. I.; Kvenvolden, K. A.; Philpott, D. E.

    1974-01-01

    The loss of biological, organic geochemical, and morphological science information that may occur should a Mars surface sample be sterilized prior to return to earth is examined. Results of experimental studies are summarized.

  20. Information theory in systems biology. Part I: Gene regulatory and metabolic networks.

    PubMed

    Mousavian, Zaynab; Kavousi, Kaveh; Masoudi-Nejad, Ali

    2016-03-01

    "A Mathematical Theory of Communication", was published in 1948 by Claude Shannon to establish a framework that is now known as information theory. In recent decades, information theory has gained much attention in the area of systems biology. The aim of this paper is to provide a systematic review of those contributions that have applied information theory in inferring or understanding of biological systems. Based on the type of system components and the interactions between them, we classify the biological systems into 4 main classes: gene regulatory, metabolic, protein-protein interaction and signaling networks. In the first part of this review, we attempt to introduce most of the existing studies on two types of biological networks, including gene regulatory and metabolic networks, which are founded on the concepts of information theory.

  1. 30 CFR 250.216 - What biological, physical, and socioeconomic information must accompany the EP?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... information on chemosynthetic communities, federally listed threatened or endangered species, marine mammals protected under the Marine Mammal Protection Act (MMPA), sensitive underwater features, marine sanctuaries, critical habitat designated under the Endangered Species Act (ESA), or other areas of biological...

  2. Biological effect of food additive titanium dioxide nanoparticles on intestine: an in vitro study.

    PubMed

    Song, Zheng-Mei; Chen, Ni; Liu, Jia-Hui; Tang, Huan; Deng, Xiaoyong; Xi, Wen-Song; Han, Kai; Cao, Aoneng; Liu, Yuanfang; Wang, Haifang

    2015-10-01

    Titanium dioxide nanoparticles (TiO2 NPs) are widely found in food-related consumer products. Understanding the effect of TiO2 NPs on the intestinal barrier and absorption is essential and vital for the safety assessment of orally administrated TiO2 NPs. In this study, the cytotoxicity and translocation of two native TiO2 NPs, and these two TiO2 NPs pretreated with the digestion simulation fluid or bovine serum albumin were investigated in undifferentiated Caco-2 cells, differentiated Caco-2 cells and Caco-2 monolayer. TiO2 NPs with a concentration less than 200 µg ml(-1) did not induce any toxicity in differentiated cells and Caco-2 monolayer after 24 h exposure. However, TiO2 NPs pretreated with digestion simulation fluids at 200 µg ml(-1) inhibited the growth of undifferentiated Caco-2 cells. Undifferentiated Caco-2 cells swallowed native TiO2 NPs easily, but not pretreated NPs, implying the protein coating on NPs impeded the cellular uptake. Compared with undifferentiated cells, differentiated ones possessed much lower uptake ability of these TiO2 NPs. Similarly, the traverse of TiO2 NPs through the Caco-2 monolayer was also negligible. Therefore, we infer the possibility of TiO2 NPs traversing through the intestine of animal or human after oral intake is quite low. This study provides valuable information for the risk assessment of TiO2 NPs in food.

  3. 41 CFR 102-79.111 - Where may Executive agencies find additional information on Integrated Workplace concepts?

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... agencies find additional information on Integrated Workplace concepts? 102-79.111 Section 102-79.111 Public... Space Integrated Workplace § 102-79.111 Where may Executive agencies find additional information on Integrated Workplace concepts? The GSA Office of Governmentwide Policy provides additional guidance in...

  4. 41 CFR 102-79.111 - Where may Executive agencies find additional information on Integrated Workplace concepts?

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... agencies find additional information on Integrated Workplace concepts? 102-79.111 Section 102-79.111 Public... Space Integrated Workplace § 102-79.111 Where may Executive agencies find additional information on Integrated Workplace concepts? The GSA Office of Governmentwide Policy provides additional guidance in...

  5. 41 CFR 102-79.111 - Where may Executive agencies find additional information on Integrated Workplace concepts?

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... agencies find additional information on Integrated Workplace concepts? 102-79.111 Section 102-79.111 Public... Space Integrated Workplace § 102-79.111 Where may Executive agencies find additional information on Integrated Workplace concepts? The GSA Office of Governmentwide Policy provides additional guidance in...

  6. 41 CFR 102-79.111 - Where may Executive agencies find additional information on Integrated Workplace concepts?

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... agencies find additional information on Integrated Workplace concepts? 102-79.111 Section 102-79.111 Public... Space Integrated Workplace § 102-79.111 Where may Executive agencies find additional information on Integrated Workplace concepts? The GSA Office of Governmentwide Policy provides additional guidance in...

  7. An optimized workflow for the integration of biological information into radiotherapy planning: experiences with T1w DCE-MRI

    NASA Astrophysics Data System (ADS)

    Neff, T.; Kiessling, F.; Brix, G.; Baudendistel, K.; Zechmann, C.; Giesel, F. L.; Bendl, R.

    2005-09-01

    Planning of radiotherapy is often difficult due to restrictions on morphological images. New imaging techniques enable the integration of biological information into treatment planning and help to improve the detection of vital and aggressive tumour areas. This might improve clinical outcome. However, nowadays morphological data sets are still the gold standard in the planning of radiotherapy. In this paper, we introduce an in-house software platform enabling us to combine images from different imaging modalities yielding biological and morphological information in a workflow driven approach. This is demonstrated for the combination of morphological CT, MRI, functional DCE-MRI and PET data. Data of patients with a tumour of the prostate and with a meningioma were examined with DCE-MRI by applying pharmacokinetic two-compartment models for post-processing. The results were compared with the clinical plans for radiation therapy. Generated parameter maps give additional information about tumour spread, which can be incorporated in the definition of safety margins.

  8. Filtering genetic variants and placing informative priors based on putative biological function.

    PubMed

    Friedrichs, Stefanie; Malzahn, Dörthe; Pugh, Elizabeth W; Almeida, Marcio; Liu, Xiao Qing; Bailey, Julia N

    2016-02-03

    High-density genetic marker data, especially sequence data, imply an immense multiple testing burden. This can be ameliorated by filtering genetic variants, exploiting or accounting for correlations between variants, jointly testing variants, and by incorporating informative priors. Priors can be based on biological knowledge or predicted variant function, or even be used to integrate gene expression or other omics data. Based on Genetic Analysis Workshop (GAW) 19 data, this article discusses diversity and usefulness of functional variant scores provided, for example, by PolyPhen2, SIFT, or RegulomeDB annotations. Incorporating functional scores into variant filters or weights and adjusting the significance level for correlations between variants yielded significant associations with blood pressure traits in a large family study of Mexican Americans (GAW19 data set). Marker rs218966 in gene PHF14 and rs9836027 in MAP4 significantly associated with hypertension; additionally, rare variants in SNUPN significantly associated with systolic blood pressure. Variant weights strongly influenced the power of kernel methods and burden tests. Apart from variant weights in test statistics, prior weights may also be used when combining test statistics or to informatively weight p values while controlling false discovery rate (FDR). Indeed, power improved when gene expression data for FDR-controlled informative weighting of association test p values of genes was used. Finally, approaches exploiting variant correlations included identity-by-descent mapping and the optimal strategy for joint testing rare and common variants, which was observed to depend on linkage disequilibrium structure.

  9. Biologically inspired information theory: Adaptation through construction of external reality models by living systems.

    PubMed

    Nakajima, Toshiyuki

    2015-12-01

    Higher animals act in the world using their external reality models to cope with the uncertain environment. Organisms that have not developed such information-processing organs may also have external reality models built in the form of their biochemical, physiological, and behavioral structures, acquired by natural selection through successful models constructed internally. Organisms subject to illusions would fail to survive in the material universe. How can organisms, or living systems in general, determine the external reality from within? This paper starts with a phenomenological model, in which the self constitutes a reality model developed through the mental processing of phenomena. Then, the it-from-bit concept is formalized using a simple mathematical model. For this formalization, my previous work on an algorithmic process is employed to constitute symbols referring to the external reality, called the inverse causality, with additional improvements to the previous work. Finally, as an extension of this model, the cognizers system model is employed to describe the self as one of many material entities in a world, each of which acts as a subject by responding to the surrounding entities. This model is used to propose a conceptual framework of information theory that can deal with both the qualitative (semantic) and quantitative aspects of the information involved in biological processes.

  10. What Information Is Hidden in Chaotic Signals of Biological Systems?

    NASA Astrophysics Data System (ADS)

    Timashev, S. F.; Vstovsky, G. V.; Kaplan, A. Ya.; Solovieva, A. B.

    2005-08-01

    Applications of the Flicker-Noise Spectroscopy (FNS) to analysis of electroencephalograms (EEG) are demonstrated. We present the double correlation function for the EEG measured in the C4 and O2 points for two patients — a healthy ("normal") child and a sick Schizophrenia child. The drastic differences in the behavior of the two-correlators manifest the information meaning of the similar dependences. We conclude that the FNS approach could be considered as a new instrument to early diagnostics of various brain diseases.

  11. BioMedia: multimedia information systems for biology research, education, and collaboration

    NASA Astrophysics Data System (ADS)

    Lank, E.; Petkovic, Dragutin; Ramirez-Weber, F. A.; Hafernik, J.; Hsieh, J.; Maag, J.; Pathuri, S.; Pekiner, C.; Raghavendra, S.

    2003-12-01

    The long-term goals of the recently started Biomedia project at SFSU are to provide multimedia information systems and applications for the research and education needs of several projects in the SFSU Biology Department. These applications involve a considerable amount of images and image sequence data, in addition to traditional text, genomic, and experimental measurement data. Our systems will allow biology researchers and students to store, index, annotate, search, visualize, analyze, collaborate, and share a large amount of heterogeneous biomedical data. Our initial focus in BioMedia is the creation of collaborative WWW site for the Hedgehog gene pathway. The Hedgehog (Hh) protein super family constitutes a group of closely related secreted proteins that control many crucial processes during the embryogenesis of tissues. The overall goals of the Hh WWW Site project are as follows: a) to provide a WWW site to be used by researchers and students studying the Hedgehog gene pathway and made available to broad community, and b) to provide advanced and innovative functionality enabling easy usage and management, community based content submission and updates, and asynchronous collaboration between researchers and students. In this paper we present the status and first results in building and researching technologies necessary for this WWW site.

  12. Emerging Technologies in the Built Environment: Geographic Information Science (GIS), 3D Printing, and Additive Manufacturing

    SciTech Connect

    New, Joshua Ryan

    2014-01-01

    Abstract 1: Geographic information systems emerged as a computer application in the late 1960s, led in part by projects at ORNL. The concept of a GIS has shifted through time in response to new applications and new technologies, and is now part of a much larger world of geospatial technology. This presentation discusses the relationship of GIS and estimating hourly and seasonal energy consumption profiles in the building sector at spatial scales down to the individual parcel. The method combines annual building energy simulations for city-specific prototypical buildings and commonly available geospatial data in a GIS framework. Abstract 2: This presentation focuses on 3D printing technologies and how they have rapidly evolved over the past couple of years. At a basic level, 3D printing produces physical models quickly and easily from 3D CAD, BIM (Building Information Models), and other digital data. Many AEC firms have adopted 3D printing as part of commercial building design development and project delivery. This presentation includes an overview of 3D printing, discusses its current use in building design, and talks about its future in relation to the HVAC industry. Abstract 3: This presentation discusses additive manufacturing and how it is revolutionizing the design of commercial and residential facilities. Additive manufacturing utilizes a broad range of direct manufacturing technologies, including electron beam melting, ultrasonic, extrusion, and laser metal deposition for rapid prototyping. While there is some overlap with the 3D printing talk, this presentation focuses on the materials aspect of additive manufacturing and also some of the more advanced technologies involved with rapid prototyping. These technologies include design of carbon fiber composites, lightweight metals processing, transient field processing, and more.

  13. Prepositioned Stocks: Additional Information and a Consistent Definition Would Make DOD’s Annual Report More Useful

    DTIC Science & Technology

    2015-06-01

    PREPOSITIONED STOCKS Additional Information and a Consistent Definition Would Make DOD’s Annual Report More Useful...COVERED 00-00-2015 to 00-00-2015 4. TITLE AND SUBTITLE Prepositioned Stocks: Additional Information and a Consistent Definition Would Make DOD’s...STOCKS Additional Information and a Consistent Definition Would Make DOD’s Annual Report More Useful Why GAO Did This Study DOD prepositions stocks

  14. Causal information quantification of prominent dynamical features of biological neurons.

    PubMed

    Montani, Fernando; Baravalle, Roman; Montangie, Lisandro; Rosso, Osvaldo A

    2015-12-13

    Neurons tend to fire a spike when they are near a bifurcation from the resting state to spiking activity. It is a delicate balance between noise, dynamic currents and initial condition that determines the phase diagram of neural activity. Many possible ionic mechanisms can be accounted for as the source of spike generation. Moreover, the biophysics and the dynamics behind it can usually be described through a phase diagram that involves membrane voltage versus the activation variable of the ionic channel. In this paper, we present a novel methodology to characterize the dynamics of this system, which takes into account the fine temporal 'structures' of the complex neuronal signals. This allows us to accurately distinguish the most fundamental properties of neurophysiological neurons that were previously described by Izhikevich considering the phase-space trajectory, using a time causal space: statistical complexity versus Fisher information versus Shannon entropy.

  15. Sonochemical degradation of the pharmaceutical fluoxetine: Effect of parameters, organic and inorganic additives and combination with a biological system.

    PubMed

    Serna-Galvis, Efraím A; Silva-Agredo, Javier; Giraldo-Aguirre, Ana L; Torres-Palma, Ricardo A

    2015-08-15

    Fluoxetine (FLX), one of the most widely used antidepressants in the world, is an emergent pollutant found in natural waters that causes disrupting effects on the endocrine systems of some aquatic species. This work explores the total elimination of FLX by sonochemical treatment coupled to a biological system. The biological process acting alone was shown to be unable to remove the pollutant, even under favourable conditions of pH and temperature. However, sonochemical treatment (600 kHz) was shown to be able to remove the pharmaceutical. Several parameters were evaluated for the ultrasound application: the applied power (20-60 W), dissolved gas (air, Ar and He), pH (3-11) and initial concentration of fluoxetine (2.9-162.0 μmol L(-1)). Additionally, the presence of organic (1-hexanol and 2-propanol) and inorganic (Fe(2+)) compounds in the water matrix and the degradation of FLX in a natural mineral water were evaluated. The sonochemical treatment readily eliminates FLX following a kinetic Langmuir. After 360 min of ultrasonic irradiation, 15% mineralization was achieved. Analysis of the biodegradability provided evidence that the sonochemical process transforms the pollutant into biodegradable substances, which can then be mineralized in a subsequent biological treatment.

  16. A novel approach for phosphorus recovery and no wasted sludge in enhanced biological phosphorus removal process with external COD addition.

    PubMed

    Xia, Cheng-Wang; Ma, Yun-Jie; Zhang, Fang; Lu, Yong-Ze; Zeng, Raymond J

    2014-01-01

    In enhanced biological phosphorus removal (EBPR) process, phosphorus (P) in wastewater is removed via wasted sludge without actual recovery. A novel approach to realize phosphorus recovery with special external chemical oxygen demand (COD) addition in EBPR process was proposed. During the new operating approach period, it was found that (1) no phosphorus was detected in the effluent; (2) with an external addition of 10 % of influent COD amount, 79 % phosphorus in the wastewater influent was recovered; (3) without wasted sludge, the MLVSS concentration in the system increased from 2,010 to 3,400 mg/L and kept stable after day 11 during 24-day operating period. This demonstrates that the novel approach is feasible to realize phosphorus recovery with no wasted sludge discharge in EBPR process. Furthermore, this approach decouples P removal and sludge age, which may enhance the application of membrane bioreactor for P removal.

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

    PubMed

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

    2016-03-01

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

  18. Satellite Tracking of Sympatric Marine Megafauna Can Inform the Biological Basis for Species Co-Management

    PubMed Central

    Gredzens, Christian; Marsh, Helene; Fuentes, Mariana M. P. B.; Limpus, Colin J.; Shimada, Takahiro; Hamann, Mark

    2014-01-01

    Context Systematic conservation planning is increasingly used to identify priority areas for protection in marine systems. However, ecosystem-based approaches typically use density estimates as surrogates for animal presence and spatial modeling to identify areas for protection and may not take into account daily or seasonal movements of animals. Additionally, sympatric and inter-related species are often managed separately, which may not be cost-effective. This study aims to demonstrate an evidence-based method to inform the biological basis for co-management of two sympatric species, dugongs and green sea turtles. This approach can then be used in conservation planning to delineate areas to maximize species protection. Methodology/Results Fast-acquisition satellite telemetry was used to track eleven dugongs and ten green turtles at two geographically distinct foraging locations in Queensland, Australia to evaluate the inter- and intra-species spatial relationships and assess the efficacy of existing protection zones. Home-range analysis and bathymetric modeling were used to determine spatial use and compared with existing protection areas using GIS. Dugong and green turtle home-ranges significantly overlapped in both locations. However, both species used different core areas and differences existed between regions in depth zone use and home-range size, especially for dugongs. Both species used existing protection areas in Shoalwater Bay, but only a single tracked dugong used the existing protection area in Torres Strait. Conclusions/Significance: Fast-acquisition satellite telemetry can provide evidence-based information on individual animal movements to delineate relationships between dugongs and green turtles in regions where they co-occur. This information can be used to increase the efficacy of conservation planning and complement more broadly based survey information. These species also use similar habitats, making complimentary co-management possible, but

  19. NLP-based information extraction for managing the molecular biology literature.

    PubMed Central

    Libbus, Bisharah; Rindflesch, Thomas C.

    2002-01-01

    We present research aimed at devising a tool for using natural language processing to identify and extract biomedical information from text for the purpose of assisting researchers in molecular biology manage large amounts of information. A pilot project based on the molecular genetics of diabetes demonstrates our ability to explore the interaction of genomic phenomena and clinical findings. We suggest the cooperation of this extracted information with systems for clustering text and constructing labeled networks of data. PMID:12463863

  20. 77 FR 31068 - Additional Identifying Information Associated With Persons Whose Property and Interests in...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-24

    ... Information Technology AGENCY: Office of Foreign Assets Control, Treasury. ACTION: Notice. SUMMARY: The... Technology,'' whose property and interests in property are blocked. FOR FURTHER INFORMATION CONTACT... Information Technology,'' (the ``Order'') pursuant to, inter alia, the International Emergency Economic...

  1. Bayesian spatiotemporal analysis of zero-inflated biological population density data by a delta-normal spatiotemporal additive model.

    PubMed

    Arcuti, Simona; Pollice, Alessio; Ribecco, Nunziata; D'Onghia, Gianfranco

    2016-03-01

    We evaluate the spatiotemporal changes in the density of a particular species of crustacean known as deep-water rose shrimp, Parapenaeus longirostris, based on biological sample data collected during trawl surveys carried out from 1995 to 2006 as part of the international project MEDITS (MEDiterranean International Trawl Surveys). As is the case for many biological variables, density data are continuous and characterized by unusually large amounts of zeros, accompanied by a skewed distribution of the remaining values. Here we analyze the normalized density data by a Bayesian delta-normal semiparametric additive model including the effects of covariates, using penalized regression with low-rank thin-plate splines for nonlinear spatial and temporal effects. Modeling the zero and nonzero values by two joint processes, as we propose in this work, allows to obtain great flexibility and easily handling of complex likelihood functions, avoiding inaccurate statistical inferences due to misclassification of the high proportion of exact zeros in the model. Bayesian model estimation is obtained by Markov chain Monte Carlo simulations, suitably specifying the complex likelihood function of the zero-inflated density data. The study highlights relevant nonlinear spatial and temporal effects and the influence of the annual Mediterranean oscillations index and of the sea surface temperature on the distribution of the deep-water rose shrimp density.

  2. 77 FR 67655 - Agency Information Collection Activities; Proposed Collection; Comment Request; Food Additive...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-11-13

    ...) Moderate Category: For a food additive petition without complex chemistry, manufacturing, efficacy, or...) Complex Category: For a food additive petition with complex chemistry, manufacturing, efficacy, and/or... investigational food additive file without complex chemistry, manufacturing, efficacy, or safety issues,...

  3. Systematics of the family Plectopylidae in Vietnam with additional information on Chinese taxa (Gastropoda, Pulmonata, Stylommatophora)

    PubMed Central

    Páll-Gergely, Barna; Hunyadi, András; Ablett, Jonathan; Lương, Hào Văn; Fred Naggs; Asami, Takahiro

    2015-01-01

    Abstract Vietnamese species from the family Plectopylidae are revised based on the type specimens of all known taxa, more than 600 historical non-type museum lots, and almost 200 newly-collected samples. Altogether more than 7000 specimens were investigated. The revision has revealed that species diversity of the Vietnamese Plectopylidae was previously overestimated. Overall, thirteen species names (anterides Gude, 1909, bavayi Gude, 1901, congesta Gude, 1898, fallax Gude, 1909, gouldingi Gude, 1909, hirsuta Möllendorff, 1901, jovia Mabille, 1887, moellendorffi Gude, 1901, persimilis Gude, 1901, pilsbryana Gude, 1901, soror Gude, 1908, tenuis Gude, 1901, verecunda Gude, 1909) were synonymised with other species. In addition to these, Gudeodiscus hemmeni sp. n. and Gudeodiscus messageri raheemi ssp. n. are described from north-western Vietnam. Sixteen species and two subspecies are recognized from Vietnam. The reproductive anatomy of eight taxa is described. Based on anatomical information, Halongella gen. n. is erected to include Plectopylis schlumbergeri and Plectopylis fruhstorferi. Additionally, the genus Gudeodiscus is subdivided into two subgenera (Gudeodiscus and Veludiscus subgen. n.) on the basis of the morphology of the reproductive anatomy and the radula. The Chinese Gudeodiscus phlyarius werneri Páll-Gergely, 2013 is moved to synonymy of Gudeodiscus phlyarius. A spermatophore was found in the organ situated next to the gametolytic sac in one specimen. This suggests that this organ in the Plectopylidae is a diverticulum. Statistically significant evidence is presented for the presence of calcareous hook-like granules inside the penis being associated with the absence of embryos in the uterus in four genera. This suggests that these probably play a role in mating periods before disappearing when embryos develop. Sicradiscus mansuyi is reported from China for the first time. PMID:25632253

  4. Positional information and reaction-diffusion: two big ideas in developmental biology combine.

    PubMed

    Green, Jeremy B A; Sharpe, James

    2015-04-01

    One of the most fundamental questions in biology is that of biological pattern: how do the structures and shapes of organisms arise? Undoubtedly, the two most influential ideas in this area are those of Alan Turing's 'reaction-diffusion' and Lewis Wolpert's 'positional information'. Much has been written about these two concepts but some confusion still remains, in particular about the relationship between them. Here, we address this relationship and propose a scheme of three distinct ways in which these two ideas work together to shape biological form.

  5. 75 FR 78950 - Availability of Additional Information for the Proposed Rulemaking for Colorado's Attainment...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-17

    ... provided, unless the comment includes information claimed to be Confidential Business Information (CBI) or... contact information unless you provide it in the body of your comment. If you send an e-mail comment... information in the body of your comment and with any disk or CD-ROM you submit. If EPA cannot read...

  6. Landauer in the Age of Synthetic Biology: Energy Consumption and Information Processing in Biochemical Networks

    NASA Astrophysics Data System (ADS)

    Mehta, Pankaj; Lang, Alex H.; Schwab, David J.

    2016-03-01

    A central goal of synthetic biology is to design sophisticated synthetic cellular circuits that can perform complex computations and information processing tasks in response to specific inputs. The tremendous advances in our ability to understand and manipulate cellular information processing networks raises several fundamental physics questions: How do the molecular components of cellular circuits exploit energy consumption to improve information processing? Can one utilize ideas from thermodynamics to improve the design of synthetic cellular circuits and modules? Here, we summarize recent theoretical work addressing these questions. Energy consumption in cellular circuits serves five basic purposes: (1) increasing specificity, (2) manipulating dynamics, (3) reducing variability, (4) amplifying signal, and (5) erasing memory. We demonstrate these ideas using several simple examples and discuss the implications of these theoretical ideas for the emerging field of synthetic biology. We conclude by discussing how it may be possible to overcome these limitations using "post-translational" synthetic biology that exploits reversible protein modification.

  7. Describing the complexity of systems: multivariable "set complexity" and the information basis of systems biology.

    PubMed

    Galas, David J; Sakhanenko, Nikita A; Skupin, Alexander; Ignac, Tomasz

    2014-02-01

    Context dependence is central to the description of complexity. Keying on the pairwise definition of "set complexity," we use an information theory approach to formulate general measures of systems complexity. We examine the properties of multivariable dependency starting with the concept of interaction information. We then present a new measure for unbiased detection of multivariable dependency, "differential interaction information." This quantity for two variables reduces to the pairwise "set complexity" previously proposed as a context-dependent measure of information in biological systems. We generalize it here to an arbitrary number of variables. Critical limiting properties of the "differential interaction information" are key to the generalization. This measure extends previous ideas about biological information and provides a more sophisticated basis for the study of complexity. The properties of "differential interaction information" also suggest new approaches to data analysis. Given a data set of system measurements, differential interaction information can provide a measure of collective dependence, which can be represented in hypergraphs describing complex system interaction patterns. We investigate this kind of analysis using simulated data sets. The conjoining of a generalized set complexity measure, multivariable dependency analysis, and hypergraphs is our central result. While our focus is on complex biological systems, our results are applicable to any complex system.

  8. Additional information is not ignored: New evidence for information integration and inhibition in take-the-best decisions.

    PubMed

    Dummel, Sebastian; Rummel, Jan; Voss, Andreas

    2016-01-01

    Ignoring information when making a decision is at the heart of the take-the-best (TTB) strategy, according to which decision makers only consider information about the most valid cue (TTB-relevant) and ignore less valid cues (TTB-irrelevant). Results of four experiments, however, show that participants do not ignore information when cues are easily available (Experiments 1a, 1b, and 3) or when task instructions emphasize decision accuracy (Experiment 2). In all four experiments we found that the consistency between the TTB-relevant cue and a supposedly TTB-irrelevant cue systematically affected decision times and confidence ratings of even those participants whose choices were consistently driven by only the TTB-relevant cue. In Experiments 1a and 1b, we also found that these participants were more likely to ignore information when cues had to be acquired sequentially, suggesting that whether or not participants ignore information depends on information availability. Experiment 2 further showed that different task instructions (emphasizing decision accuracy vs. speed) affect whether or not participants ignore information. Finally, Experiment 3 addressed the question of how participants process information that, according to TTB, is considered irrelevant for their choices. We find first evidence that participants who consistently make choices in line with TTB inhibit information about a TTB-irrelevant cue when this information conflicts with their decisions. Findings are considered and discussed in relation to current models of decision making.

  9. The biological effects of subacute inhalation of diesel exhaust following addition of cerium oxide nanoparticles in atherosclerosis-prone mice☆

    PubMed Central

    Cassee, Flemming R.; Campbell, Arezoo; Boere, A. John F.; McLean, Steven G.; Duffin, Rodger; Krystek, Petra; Gosens, Ilse; Miller, Mark R.

    2012-01-01

    Background Cerium oxide (CeO2) nanoparticles improve the burning efficiency of fuel, however, little is known about health impacts of altered emissions from the vehicles. Methods Atherosclerosis-prone apolipoprotein E knockout (ApoE−/−) mice were exposed by inhalation to diluted exhaust (1.7 mg/m3, 20, 60 or 180 min, 5 day/week, for 4 weeks), from an engine using standard diesel fuel (DE) or the same diesel fuel containing 9 ppm cerium oxide nanoparticles (DCeE). Changes in hematological indices, clinical chemistry, atherosclerotic burden, tissue levels of inflammatory cytokines and pathology of the major organs were assessed. Results Addition of CeO2 to fuel resulted in a reduction of the number (30%) and surface area (10%) of the particles in the exhaust, whereas the gaseous co-pollutants were increased (6–8%). There was, however, a trend towards an increased size and complexity of the atherosclerotic plaques following DE exposure, which was not evident in the DCeE group. There were no clear signs of altered hematological or pathological changes induced by either treatment. However, levels of proinflammatory cytokines were modulated in a brain region and liver following DCeE exposure. Conclusions These results imply that addition of CeO2 nanoparticles to fuel decreases the number of particles in exhaust and may reduce atherosclerotic burden associated with exposure to standard diesel fuel. From the extensive assessment of biological parameters performed, the only concerning effect of cerium addition was a slightly raised level of cytokines in a region of the central nervous system. Overall, the use of cerium as a fuel additive may be a potentially useful way to limit the health effects of vehicle exhaust. However, further testing is required to ensure that such an approach is not associated with a chronic inflammatory response which may eventually cause long-term health effects. PMID:22507957

  10. The biological effects of subacute inhalation of diesel exhaust following addition of cerium oxide nanoparticles in atherosclerosis-prone mice

    SciTech Connect

    Cassee, Flemming R.; Campbell, Arezoo; Boere, A. John F.; McLean, Steven G.; Krystek, Petra; Gosens, Ilse; Miller, Mark R.

    2012-05-15

    Background: Cerium oxide (CeO{sub 2}) nanoparticles improve the burning efficiency of fuel, however, little is known about health impacts of altered emissions from the vehicles. Methods: Atherosclerosis-prone apolipoprotein E knockout (ApoE{sup -/-}) mice were exposed by inhalation to diluted exhaust (1.7 mg/m{sup 3}, 20, 60 or 180 min, 5 day/week, for 4 weeks), from an engine using standard diesel fuel (DE) or the same diesel fuel containing 9 ppm cerium oxide nanoparticles (DCeE). Changes in hematological indices, clinical chemistry, atherosclerotic burden, tissue levels of inflammatory cytokines and pathology of the major organs were assessed. Results: Addition of CeO{sub 2} to fuel resulted in a reduction of the number (30%) and surface area (10%) of the particles in the exhaust, whereas the gaseous co-pollutants were increased (6-8%). There was, however, a trend towards an increased size and complexity of the atherosclerotic plaques following DE exposure, which was not evident in the DCeE group. There were no clear signs of altered hematological or pathological changes induced by either treatment. However, levels of proinflammatory cytokines were modulated in a brain region and liver following DCeE exposure. Conclusions: These results imply that addition of CeO{sub 2} nanoparticles to fuel decreases the number of particles in exhaust and may reduce atherosclerotic burden associated with exposure to standard diesel fuel. From the extensive assessment of biological parameters performed, the only concerning effect of cerium addition was a slightly raised level of cytokines in a region of the central nervous system. Overall, the use of cerium as a fuel additive may be a potentially useful way to limit the health effects of vehicle exhaust. However, further testing is required to ensure that such an approach is not associated with a chronic inflammatory response which may eventually cause long-term health effects.

  11. 40 CFR 79.21 - Information and assurances to be provided by the additive manufacturer.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) REGISTRATION OF FUELS AND FUEL ADDITIVES Additive... application for registration submitted by the manufacturer of a designated fuel additive shall include the..., percentage by weight, and method of analysis of each element in the additive are required provided,...

  12. Development and investigation of MOEMS type displacement-pressure sensor for biological information monitoring

    NASA Astrophysics Data System (ADS)

    Ostasevicius, Vytautas; Malinauskas, Karolis; Janusas, Giedrius; Palevicius, Arvydas; Cekas, Elingas

    2016-04-01

    The aim of this paper is to develop and investigate MOEMS displacement-pressure sensor for biological information monitoring. Developing computational periodical microstructure models using COMSOL Multiphysics modeling software for modal and shape analysis and implementation of these results for design MOEMS displacement-pressure sensor for biological information monitoring was performed. The micro manufacturing technology of periodical microstructure having good diffraction efficiency was proposed. Experimental setup for characterisation of optical properties of periodical microstructure used for design of displacement-pressure sensor was created. Pulsating human artery dynamic characteristics in this paper were analysed.

  13. Assessing the influence of methanol-containing additive on biological characteristics of diesel exhaust emissions using microtox and mutatox assays.

    PubMed

    Lin, Ta-Chang; Chao, Mu-Rong

    2002-02-04

    Here we investigate the effect of the methanol-containing additive (MCA) on the biological characteristics of diesel exhaust emissions. Microtox and Mutatox assays, respectively, were used to evaluate the acute toxicity and genotoxicity of crude extracts from diesel engine exhaust. The engine was tested on a series of diesel fuels blended with five additive levels (0, 5, 8, 10 and 15% of MCA by volume). Emission tests were performed over the hot start portion of the transient Heavy-Duty-Federal Test Procedure (HD-FTP) and two selected steady-state modes. Microtox results show that MCA additive moderately lowers the toxicity levels of particle-associated (SOF) samples, but generally increase the vapor-phase (XOC) associated toxicity. A strong correlation was found between XOC-associated toxicity and total hydrocarbon (THC) concentrations, while only a slight link was found between SOF-associated toxicity and particulate matter (PM) concentrations. For Mutatox test results, when either 5 or 8% MCA used, XOC and SOF-associated genotoxicity in both steady-state and hot-start transient cycle tests were relatively lower compared to those of the base diesel. The genotoxic potential of XOC samples was significantly increased after treatment with an exogenous metabolic activation system (S9). On the contrary, the genotoxic potential of SOF samples without S9 metabolic activation was generally higher than those with S9. It is noteworthy that the total particle-associated (SOF) PAHs emissions showed trends quite similar to that of the genotoxic potential. As expected, the total particle-associated (SOF) PAHs correlated moderately with direct mutagenicity, and fairly well with indirect mutagenicity. Finally, the genotoxicity data did not parallel the Microtox results in this study, indicating that potentially long-term genotoxic agents may not be revealed by short-term toxicity assays.

  14. 40 CFR 79.21 - Information and assurances to be provided by the additive manufacturer.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... fuel additive will be sold, offered for sale, or introduced into commerce, and the fuel additive manufacturer's recommended range of concentration and purpose-in-use for each such type of fuel. (e) Such other... (e) of this section as provided in § 79.5(b). (g) Assurances that the additive manufacturer will...

  15. Quantum formalism as an optimisation procedure of information flows for physical and biological systems.

    PubMed

    Baladrón, Carlos; Khrennikov, Andrei

    2016-12-01

    The similarities between biological and physical systems as respectively defined in quantum information biology (QIB) and in a Darwinian approach to quantum mechanics (DAQM) have been analysed. In both theories the processing of information is a central feature characterising the systems. The analysis highlights a mutual support on the thesis contended by each theory. On the one hand, DAQM provides a physical basis that might explain the key role played by quantum information at the macroscopic level for bio-systems in QIB. On the other hand, QIB offers the possibility, acting as a macroscopic testing ground, to analyse the emergence of quantumness from classicality in the terms held by DAQM. As an added result of the comparison, a tentative definition of quantum information in terms of classical information flows has been proposed. The quantum formalism would appear from this comparative analysis between QIB and DAQM as an optimal information scheme that would maximise the stability of biological and physical systems at any scale.

  16. User's Guide to Biome Information from the United States International Biological Program (IBP). First Edition.

    ERIC Educational Resources Information Center

    Hinckley, A. Dexter; Haug, Peter T.

    This publication is a guide to the biome research conducted under the International Biological Program. The guide lists biome researchers by interest and by biome as well as a central list. A site list, map, information sources section reporting abstracts, bibliographies, journals, books, evaluations, and data books are also included. Three…

  17. Modeling external carbon addition in biological nutrient removal processes with an extension of the international water association activated sludge model.

    PubMed

    Swinarski, M; Makinia, J; Stensel, H D; Czerwionka, K; Drewnowski, J

    2012-08-01

    The aim of this study was to expand the International Water Association Activated Sludge Model No. 2d (ASM2d) to account for a newly defined readily biodegradable substrate that can be consumed by polyphosphate-accumulating organisms (PAOs) under anoxic and aerobic conditions, but not under anaerobic conditions. The model change was to add a new substrate component and process terms for its use by PAOs and other heterotrophic bacteria under anoxic and aerobic conditions. The Gdansk (Poland) wastewater treatment plant (WWTP), which has a modified University of Cape Town (MUCT) process for nutrient removal, provided field data and mixed liquor for batch tests for model evaluation. The original ASM2d was first calibrated under dynamic conditions with the results of batch tests with settled wastewater and mixed liquor, in which nitrate-uptake rates, phosphorus-release rates, and anoxic phosphorus uptake rates were followed. Model validation was conducted with data from a 96-hour measurement campaign in the full-scale WWTP. The results of similar batch tests with ethanol and fusel oil as the external carbon sources were used to adjust kinetic and stoichiometric coefficients in the expanded ASM2d. Both models were compared based on their predictions of the effect of adding supplemental carbon to the anoxic zone of an MUCT process. In comparison with the ASM2d, the new model better predicted the anoxic behaviors of carbonaceous oxygen demand, nitrate-nitrogen (NO3-N), and phosphorous (PO4-P) in batch experiments with ethanol and fusel oil. However, when simulating ethanol addition to the anoxic zone of a full-scale biological nutrient removal facility, both models predicted similar effluent NO3-N concentrations (6.6 to 6.9 g N/m3). For the particular application, effective enhanced biological phosphorus removal was predicted by both models with external carbon addition but, for the new model, the effluent PO4-P concentration was approximately one-half of that found from

  18. 36 CFR 1290.2 - Scope of additional records and information.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... describe the agency's: (1) Records policies and schedules; (2) Filing systems and organization; (3) Storage... Act; and (6) Reclassification to a higher level, transfer, destruction, or other information...

  19. 41 CFR 102-75.140 - In addition to the title report, and all necessary environmental information and certifications...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 102-75.140 Public Contracts and Property Management Federal Property Management Regulations System... 41 Public Contracts and Property Management 3 2010-07-01 2010-07-01 false In addition to the title report, and all necessary environmental information and certifications, what information must...

  20. Global change and biological soil crusts: Effects of ultraviolet augmentation under altered precipitation regimes and nitrogen additions

    USGS Publications Warehouse

    Belnap, J.; Phillips, S.L.; Flint, S.; Money, J.; Caldwell, M.

    2008-01-01

    Biological soil crusts (BSCs), a consortium of cyanobacteria, lichens, and mosses, are essential in most dryland ecosystems. As these organisms are relatively immobile and occur on the soil surface, they are exposed to high levels of ultraviolet (UV) radiation and atmospheric nitrogen (N) deposition, rising temperatures, and alterations in precipitation patterns. In this study, we applied treatments to three types of BSCs (early, medium, and late successional) over three time periods (spring, summer, and spring-fall). In the first year, we augmented UV and altered precipitation patterns, and in the second year, we augmented UV and N. In the first year, with average air temperatures, we saw little response to our treatments except quantum yield, which was reduced in dark BSCs during one of three sample times and in Collema BSCs two of three sample times. There was more response to UV augmentation the second year when air temperatures were above average. Declines were seen in 21% of the measured variables, including quantum yield, chlorophyll a, UV-protective pigments, nitrogenase activity, and extracellular polysaccharides. N additions had some negative effects on light and dark BSCs, including the reduction of quantum yield, ??-carotene, nitrogenase activity, scytonemin, and xanthophylls. N addition had no effects on the Collema BSCs. When N was added to samples that had received augmented UV, there were only limited effects relative to samples that received UV without N. These results indicate that the negative effect of UV and altered precipitation on BSCs will be heightened as global temperatures increase, and that as their ability to produce UV-protective pigments is compromised, physiological functioning will be impaired. N deposition will only ameliorate UV impacts in a limited number of cases. Overall, increases in UV will likely lead to lowered productivity and increased mortality in BSCs through time, which, in turn, will reduce their ability to contribute

  1. 14 CFR 121.317 - Passenger information requirements, smoking prohibitions, and additional seat belt requirements.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 14 Aeronautics and Space 3 2013-01-01 2013-01-01 false Passenger information requirements, smoking... OPERATIONS Instrument and Equipment Requirements § 121.317 Passenger information requirements, smoking... command. (c) No person may operate an airplane on a flight on which smoking is prohibited by part 252...

  2. 14 CFR 121.317 - Passenger information requirements, smoking prohibitions, and additional seat belt requirements.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 14 Aeronautics and Space 3 2012-01-01 2012-01-01 false Passenger information requirements, smoking... OPERATIONS Instrument and Equipment Requirements § 121.317 Passenger information requirements, smoking... command. (c) No person may operate an airplane on a flight on which smoking is prohibited by part 252...

  3. Facile preparation and biological imaging of luminescent polymeric nanoprobes with aggregation-induced emission characteristics through Michael addition reaction.

    PubMed

    Lv, Qiulan; Wang, Ke; Xu, Dazhuang; Liu, Meiying; Wan, Qing; Huang, Hongye; Liang, Shangdong; Zhang, Xiaoyong; Wei, Yen

    2016-09-01

    Water dispersion aggregation-induced emission (AIE) dyes based nanomaterials have recently attracted increasing attention in the biomedical fields because of their unique optical properties, outstanding performance as imaging and therapeutic agents. The methods to conjugate hydrophilic polymers with AIE dyes to solve the hydrophobic nature of AIE dyes and makeS them widely used in biomedicine, which have been extensively explored and paid great effort previously. Although great advance has been made in the fabrication and biomedical applications of AIE-active polymeric nanoprobes, facile and efficient strategies for fabrication of biodegradable AIE-active nanoprobes are still high desirable. In this work, amphiphilic biodegradable fluorescent organic nanoparticles (PLL-TPE-O-E FONs) have been fabricated for the first time by conjugation of AIE dye tetraphenylethene acrylate (TPE-O-E) with Poly-l-Lysine (PLL) through a facile one-step Michael addition reaction, which was carried out under rather mild conditions, included air atmosphere, near room temperature and absent of metal catalysts or hazardous reagents. Due to the unique AIE properties, these amphiphilic copolymers tend to self-assemble into high luminescent water dispersible nanoparticles with size range from 400 to 600nm. Laser scanning microscope and cytotoxicity results revealed that PLL-TPE-O-E FONs can be internalized into cytoplasm with negative cytotoxicity, which implied that PLL-TPE-O-E FONs are promising for biological applications.

  4. Modeling the Effect of External Carbon Source Addition under Different Electron Acceptor Conditions in Biological Nutrient Removal Activated Sludge Systems.

    PubMed

    Hu, Xiang; Wisniewski, Kamil; Czerwionka, Krzysztof; Zhou, Qi; Xie, Li; Makinia, Jacek

    2016-02-16

    The aim of this study was to expand the International Water Association Activated Sludge Model No. 2d (ASM2d) to predict the aerobic/anoxic behavior of polyphosphate accumulating organisms (PAOs) and "ordinary" heterotrophs in the presence of different external carbon sources and electron acceptors. The following new aspects were considered: (1) a new type of the readily biodegradable substrate, not available for the anaerobic activity of PAOs, (2) nitrite as an electron acceptor, and (3) acclimation of "ordinary" heterotrophs to the new external substrate via enzyme synthesis. The expanded model incorporated 30 new or modified process rate equations. The model was evaluated against data from several, especially designed laboratory experiments which focused on the combined effects of different types of external carbon sources (acetate, ethanol and fusel oil) and electron acceptors (dissolved oxygen, nitrate and nitrite) on the behavior of PAOs and "ordinary" heterotrophs. With the proposed expansions, it was possible to improve some deficiencies of the ASM2d in predicting the behavior of biological nutrient removal (BNR) systems with the addition of external carbon sources, including the effect of acclimation to the new carbon source.

  5. Subjectivity: A Case of Biological Individuation and an Adaptive Response to Informational Overflow

    PubMed Central

    Jonkisz, Jakub

    2016-01-01

    The article presents a perspective on the scientific explanation of the subjectivity of conscious experience. It proposes plausible answers for two empirically valid questions: the ‘how’ question concerning the developmental mechanisms of subjectivity, and the ‘why’ question concerning its function. Biological individuation, which is acquired in several different stages, serves as a provisional description of how subjective perspectives may have evolved. To the extent that an individuated informational space seems the most efficient way for a given organism to select biologically valuable information, subjectivity is deemed to constitute an adaptive response to informational overflow. One of the possible consequences of this view is that subjectivity might be (at least functionally) dissociated from consciousness, insofar as the former primarily facilitates selection, the latter action. PMID:27555835

  6. 14 CFR 121.317 - Passenger information requirements, smoking prohibitions, and additional seat belt requirements.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... prohibitions, and additional seat belt requirements. 121.317 Section 121.317 Aeronautics and Space FEDERAL... prohibitions, and additional seat belt requirements. (a) Except as provided in paragraph (l) of this section... paragraph (l) of this section, the “Fasten Seat Belt” sign shall be turned on during any movement on...

  7. 14 CFR 121.317 - Passenger information requirements, smoking prohibitions, and additional seat belt requirements.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... prohibitions, and additional seat belt requirements. 121.317 Section 121.317 Aeronautics and Space FEDERAL... prohibitions, and additional seat belt requirements. (a) Except as provided in paragraph (l) of this section... paragraph (l) of this section, the “Fasten Seat Belt” sign shall be turned on during any movement on...

  8. Input-output relations in biological systems: measurement, information and the Hill equation

    PubMed Central

    2013-01-01

    Biological systems produce outputs in response to variable inputs. Input-output relations tend to follow a few regular patterns. For example, many chemical processes follow the S-shaped Hill equation relation between input concentrations and output concentrations. That Hill equation pattern contradicts the fundamental Michaelis-Menten theory of enzyme kinetics. I use the discrepancy between the expected Michaelis-Menten process of enzyme kinetics and the widely observed Hill equation pattern of biological systems to explore the general properties of biological input-output relations. I start with the various processes that could explain the discrepancy between basic chemistry and biological pattern. I then expand the analysis to consider broader aspects that shape biological input-output relations. Key aspects include the input-output processing by component subsystems and how those components combine to determine the system’s overall input-output relations. That aggregate structure often imposes strong regularity on underlying disorder. Aggregation imposes order by dissipating information as it flows through the components of a system. The dissipation of information may be evaluated by the analysis of measurement and precision, explaining why certain common scaling patterns arise so frequently in input-output relations. I discuss how aggregation, measurement and scale provide a framework for understanding the relations between pattern and process. The regularity imposed by those broader structural aspects sets the contours of variation in biology. Thus, biological design will also tend to follow those contours. Natural selection may act primarily to modulate system properties within those broad constraints. Reviewers This article was reviewed by Eugene Koonin, Georg Luebeck and Sergei Maslov. PMID:24308849

  9. Integrating clinical and biological information in a shanghai biobank: an introduction to the sample repository and information sharing platform project.

    PubMed

    Cui, Wenbin; Zheng, Peiyong; Yang, Jiahong; Zhao, Rong; Gao, Jiechun; Yu, Guangjun

    2015-02-01

    Biobanks are important resources and central tools for translational medicine, which brings scientific research outcomes to clinical practice. The key purpose of biobanking in translational medicine and other medical research is to provide biological samples that are integrated with clinical information. In 2008, the Shanghai Municipal Government launched the "Shanghai Tissue Bank" in an effort to promote research in translational medicine. Now a sharing service platform has been constructed to integrate clinical practice and biological information that can be used in diverse medical and pharmaceutical research studies. The platform collects two kinds of data: sample data and clinical data. The sample data are obtained from the hospital biobank management system, and mainly include the donors' age, gender, marital status, sample source, sample type, collection time, deposit time, and storage method. The clinical data are collected from the "Hospital-Link" system (a medical information sharing system that connects 23 tertiary hospitals in Shanghai). The main contents include donors' corresponding medication information, test reports, inspection reports, and hospital information. As of the end of September 2014, the project has a collection of 16,020 donors and 148,282 samples, which were obtained from 12 medical institutions, and automatically acquired donors' corresponding clinical data from the "Hospital-Link" system for 6830 occurrences. This project will contribute to scientific research at medical institutions in Shanghai, and will also support the development of the biopharmaceutical industry. In this article, we will describe the significance, the construction phases, the application prospects, and benefits of the sample repository and information sharing service platform.

  10. Script, code, information: how to differentiate analogies in the "prehistory" of molecular biology.

    PubMed

    Kogge, Werner

    2012-01-01

    The remarkable fact that twentieth-century molecular biology developed its conceptual system on the basis of sign-like terms has been the object of numerous studies and debates. Throughout these, the assumption is made that this vocabulary's emergence should be seen in the historical context of mathematical communication theory and cybernetics. This paper, in contrast, sets out the need for a more differentiated view: whereas the success of the terms "code" and "information" would probably be unthinkable outside that historical context, general semiotic and especially scriptural concepts arose far earlier in the "prehistory" of molecular biology, and in close association with biological research and phenomena. This distinction, established through a reconstruction of conceptual developments between 1870 and 1950, makes it possible to separate off a critique of the reductive implications of particular information-based concepts from the use of semiotic and scriptural concepts, which is fundamental to molecular biology. Gene-centrism and determinism are not implications of semiotic and scriptural analogies, but arose only when the vocabulary of information was superimposed upon them.

  11. Towards BioDBcore: a community-defined information specification for biological databases

    PubMed Central

    Gaudet, Pascale; Bairoch, Amos; Field, Dawn; Sansone, Susanna-Assunta; Taylor, Chris; Attwood, Teresa K.; Bateman, Alex; Blake, Judith A.; Bult, Carol J.; Cherry, J. Michael; Chisholm, Rex L.; Cochrane, Guy; Cook, Charles E.; Eppig, Janan T.; Galperin, Michael Y.; Gentleman, Robert; Goble, Carole A.; Gojobori, Takashi; Hancock, John M.; Howe, Douglas G.; Imanishi, Tadashi; Kelso, Janet; Landsman, David; Lewis, Suzanna E.; Mizrachi, Ilene Karsch; Orchard, Sandra; Ouellette, B. F. Francis; Ranganathan, Shoba; Richardson, Lorna; Rocca-Serra, Philippe; Schofield, Paul N.; Smedley, Damian; Southan, Christopher; Tan, Tin Wee; Tatusova, Tatiana; Whetzel, Patricia L.; White, Owen; Yamasaki, Chisato

    2011-01-01

    The present article proposes the adoption of a community-defined, uniform, generic description of the core attributes of biological databases, BioDBCore. The goals of these attributes are to provide a general overview of the database landscape, to encourage consistency and interoperability between resources and to promote the use of semantic and syntactic standards. BioDBCore will make it easier for users to evaluate the scope and relevance of available resources. This new resource will increase the collective impact of the information present in biological databases. PMID:21097465

  12. Towards BioDBcore: a community-defined information specification for biological databases.

    PubMed

    Gaudet, Pascale; Bairoch, Amos; Field, Dawn; Sansone, Susanna-Assunta; Taylor, Chris; Attwood, Teresa K; Bateman, Alex; Blake, Judith A; Bult, Carol J; Cherry, J Michael; Chisholm, Rex L; Cochrane, Guy; Cook, Charles E; Eppig, Janan T; Galperin, Michael Y; Gentleman, Robert; Goble, Carole A; Gojobori, Takashi; Hancock, John M; Howe, Douglas G; Imanishi, Tadashi; Kelso, Janet; Landsman, David; Lewis, Suzanna E; Mizrachi, Ilene Karsch; Orchard, Sandra; Ouellette, B F Francis; Ranganathan, Shoba; Richardson, Lorna; Rocca-Serra, Philippe; Schofield, Paul N; Smedley, Damian; Southan, Christopher; Tan, Tin Wee; Tatusova, Tatiana; Whetzel, Patricia L; White, Owen; Yamasaki, Chisato

    2011-01-01

    The present article proposes the adoption of a community-defined, uniform, generic description of the core attributes of biological databases, BioDBCore. The goals of these attributes are to provide a general overview of the database landscape, to encourage consistency and interoperability between resources and to promote the use of semantic and syntactic standards. BioDBCore will make it easier for users to evaluate the scope and relevance of available resources. This new resource will increase the collective impact of the information present in biological databases.

  13. 36 CFR 1290.2 - Scope of additional records and information.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... PRESIDENT JOHN F. KENNEDY ASSASSINATION RECORDS COLLECTION ACT OF 1992 (JFK ACT) § 1290.2 Scope of... Act; and (6) Reclassification to a higher level, transfer, destruction, or other information...

  14. 21 CFR 803.12 - Where and how do I submit reports and additional information?

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... SERVICES (CONTINUED) MEDICAL DEVICES MEDICAL DEVICE REPORTING General Provisions § 803.12 Where and how do... information required under this part to FDA, CDRH, Medical Device Reporting, P.O. Box 3002, Rockville,...

  15. 21 CFR 803.12 - Where and how do I submit reports and additional information?

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... SERVICES (CONTINUED) MEDICAL DEVICES MEDICAL DEVICE REPORTING General Provisions § 803.12 Where and how do... information required under this part to FDA, CDRH, Medical Device Reporting, P.O. Box 3002, Rockville,...

  16. 21 CFR 71.15 - Confidentiality of data and information in color additive petitions.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... has been abandoned and they no longer represent a trade secret or confidential commercial or financial... studies and tests of a color additive on animals and humans and all studies and tests on a color...

  17. 21 CFR 71.15 - Confidentiality of data and information in color additive petitions.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... has been abandoned and they no longer represent a trade secret or confidential commercial or financial... studies and tests of a color additive on animals and humans and all studies and tests on a color...

  18. 21 CFR 71.15 - Confidentiality of data and information in color additive petitions.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... established in § 20.61 of this chapter. (6) All records showing the Food and Drug Administration's testing of... studies and tests of a color additive on animals and humans and all studies and tests on a color...

  19. Role of quantity of additional food to predators as a control in predator-prey systems with relevance to pest management and biological conservation.

    PubMed

    Srinivasu, P D N; Prasad, B S R V

    2011-10-01

    Necessity to understand the role of additional food as a tool in biological control programs is being increasingly felt, particularly due to its eco-friendly nature. A thorough mathematical analysis in this direction revealed the vital role of quality and quantity of the additional food in the controllability of the predator-prey systems. In this article controllability of the additional food--provided predator-prey system is studied from perspectives of pest eradication and biological conservation. Time optimal paths have been constructed to drive the state of the system to a desired terminal state by choosing quantity of the additional food as control variable. The theory developed in this article has been illustrated by solving problems related to pest eradication and biological conservation.

  20. 30 CFR 550.247 - What biological, physical, and socioeconomic information must accompany the DPP or DOCD?

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 30 Mineral Resources 2 2013-07-01 2013-07-01 false What biological, physical, and socioeconomic... Operations Coordination Documents (docd) § 550.247 What biological, physical, and socioeconomic information... under the ESA, or other areas of biological concern. (b) Physical environment reports....

  1. 30 CFR 550.247 - What biological, physical, and socioeconomic information must accompany the DPP or DOCD?

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 30 Mineral Resources 2 2014-07-01 2014-07-01 false What biological, physical, and socioeconomic... Operations Coordination Documents (docd) § 550.247 What biological, physical, and socioeconomic information... under the ESA, or other areas of biological concern. (b) Physical environment reports....

  2. 30 CFR 550.247 - What biological, physical, and socioeconomic information must accompany the DPP or DOCD?

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 30 Mineral Resources 2 2012-07-01 2012-07-01 false What biological, physical, and socioeconomic... Operations Coordination Documents (docd) § 550.247 What biological, physical, and socioeconomic information... under the ESA, or other areas of biological concern. (b) Physical environment reports....

  3. The definitions of information and meaning two possible boundaries between physics and biology.

    PubMed

    Barbieri, Marcello

    2004-01-01

    The standard approach to the definition of the physical quantities has not produced satisfactory results with the concepts of information and meaning. In the case of information we have at least two unrelated definitions, while in the case of meaning we have no definition at all. Here it is shown that both information and meaning can be defined by operative procedures, but it is also pointed out that we need to recognize them as a new type of natural entities. They are not quantities (neither fundamental nor derived) because they cannot be measured, and they are not qualities because are not subjective features. Here it is proposed to call them nominable entities, i.e., entities which can be specified only by naming their components in their natural order. If the genetic code is not a linguistic metaphor but a reality, we must conclude that information and meaning are real natural entities, and now we must also conclude that they are not equivalent to the quantities and qualities of our present theoretical framework. This gives us two options. One is to extend the definition of physics and say that the list of its fundamental entities must include information and meaning. The other is to say that physics is the science of quantities only, and in this case information and meaning become the exclusive province of biology. The boundary between physics and biology, in short, is a matter of convention, but the existence of information and meaning is not. We can decide to study them in the framework of an extended physics or in a purely biological framework, but we cannot avoid studying them for what they are, i.e., as fundamental components of the fabric of Nature.

  4. Organising multi-dimensional biological image information: the BioImage Database.

    PubMed

    Carazo, J M; Stelzer, E H; Engel, A; Fita, I; Henn, C; Machtynger, J; McNeil, P; Shotton, D M; Chagoyen, M; de Alarcón, P A; Fritsch, R; Heymann, J B; Kalko, S; Pittet, J J; Rodriguez-Tomé, P; Boudier, T

    1999-01-01

    Nowadays it is possible to unravel complex information at all levels of cellular organization by obtaining multi-dimensional image information. At the macromolecular level, three-dimensional (3D) electron microscopy, together with other techniques, is able to reach resolutions at the nanometer or subnanometer level. The information is delivered in the form of 3D volumes containing samples of a given function, for example, the electron density distribution within a given macromolecule. The same situation happens at the cellular level with the new forms of light microscopy, particularly confocal microscopy, all of which produce biological 3D volume information. Furthermore, it is possible to record sequences of images over time (videos), as well as sequences of volumes, bringing key information on the dynamics of living biological systems. It is in this context that work on BioImage started two years ago, and that its first version is now presented here. In essence, BioImage is a database specifically designed to contain multi-dimensional images, perform queries and interactively work with the resulting multi-dimensional information on the World Wide Web, as well as accomplish the required cross-database links. Two sister home pages of BioImage can be accessed at http://www. bioimage.org and http://www-embl.bioimage.org

  5. Synergistic and Additive Effect of Oregano Essential Oil and Biological Silver Nanoparticles against Multidrug-Resistant Bacterial Strains

    PubMed Central

    Scandorieiro, Sara; de Camargo, Larissa C.; Lancheros, Cesar A. C.; Yamada-Ogatta, Sueli F.; Nakamura, Celso V.; de Oliveira, Admilton G.; Andrade, Célia G. T. J.; Duran, Nelson; Nakazato, Gerson; Kobayashi, Renata K. T.

    2016-01-01

    Bacterial resistance to conventional antibiotics has become a clinical and public health problem, making therapeutic decisions more challenging. Plant compounds and nanodrugs have been proposed as potential antimicrobial alternatives. Studies have shown that oregano (Origanum vulgare) essential oil (OEO) and silver nanoparticles have potent antibacterial activity, also against multidrug-resistant strains; however, the strong organoleptic characteristics of OEO and the development of resistance to these metal nanoparticles can limit their use. This study evaluated the antibacterial effect of a two-drug combination of biologically synthesized silver nanoparticles (bio-AgNP), produced by Fusarium oxysporum, and OEO against Gram-positive and Gram-negative bacteria, including multidrug-resistant strains. OEO and bio-AgNP showed bactericidal effects against all 17 strains tested, with minimal inhibitory concentrations (MIC) ranging from 0.298 to 1.193 mg/mL and 62.5 to 250 μM, respectively. Time-kill curves indicated that OEO acted rapidly (within 10 min), while the metallic nanoparticles took 4 h to kill Gram-negative bacteria and 24 h to kill Gram-positive bacteria. The combination of the two compounds resulted in a synergistic or additive effect, reducing their MIC values and reducing the time of action compared to bio-AgNP used alone, i.e., 20 min for Gram-negative bacteria and 7 h for Gram-positive bacteria. Scanning electron microscopy (SEM) revealed similar morphological alterations in Staphylococcus aureus (non-methicillin-resistant S. aureus, non-MRSA) cells exposed to three different treatments (OEO, bio-AgNP and combination of the two), which appeared cell surface blebbing. Individual and combined treatments showed reduction in cell density and decrease in exopolysaccharide matrix compared to untreated bacterial cells. It indicated that this composition have an antimicrobial activity against S. aureus by disrupting cells. Both compounds showed very low

  6. Twenty-five additional cases of trisomy 9 mosaic: Birth information, medical conditions, and developmental status.

    PubMed

    Bruns, Deborah A; Campbell, Emily

    2015-05-01

    Limited literature exists on children and adults diagnosed with the mosaic form of trisomy 9. Data from the Tracking Rare Incidence Syndromes (TRIS) project has provided physical characteristics and medical conditions for 14 individuals. This article provides TRIS Survey results of 25 additional cases at two data points (birth and survey completion) as well as developmental status. Results confirmed a number of phenotypic features and medical conditions. In addition, a number of cardiac anomalies were reported along with feeding and respiratory difficulties in the immediate postnatal period. In addition, developmental status data indicated a range in functioning level up to skills in the 36 and 48-month range. Strengths were also noted across the sample in language and communication, fine motor and social-emotional development. Implications for professionals caring for children with this genetic condition are offered.

  7. 21 CFR 803.12 - Where and how do I submit reports and additional information?

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... information? 803.12 Section 803.12 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN... health emergency, this can be brought to FDA's attention by contacting the FDA Office of Emergency Operations (HFA-615), Office of Crisis Management, Office of the Commissioner, at 301-443-1240, followed...

  8. 14 CFR 121.317 - Passenger information requirements, smoking prohibitions, and additional seat belt requirements.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... lavatory a sign or placard that reads: “Federal law provides for a penalty of up to $2,000 for tampering..., no person may operate an airplane unless it is equipped with passenger information signs that meet... signs must be constructed so that the crewmembers can turn them on and off. (b) Except as provided...

  9. 49 CFR 40.331 - To what additional parties must employers and service agents release information?

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... Transportation PROCEDURES FOR TRANSPORTATION WORKPLACE DRUG AND ALCOHOL TESTING PROGRAMS Confidentiality and... information about that employee's drug or alcohol tests to an identified person, you must provide the... for this part and DOT agency drug and alcohol program functions. (2) All written, printed,...

  10. Software for Information Storage and Retrieval Tested, Evaluated and Compared: Part VI--Various Additional Programs.

    ERIC Educational Resources Information Center

    Sieverts, Eric G.; And Others

    1993-01-01

    Reports on tests evaluating nine microcomputer software packages designed for information storage and retrieval: BRS-Search, dtSearch, InfoBank, Micro-OPC, Q&A, STN-PFS, Strix, TINman, and ZYindex. Tables and narrative evaluations detail results related to security, hardware, user features, search capability, indexing, input, maintenance of files,…

  11. 13 CFR 126.403 - May SBA require additional information from a HUBZone SBC?

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... information from a HUBZone SBC? 126.403 Section 126.403 Business Credit and Assistance SMALL BUSINESS... HUBZone SBC? (a) At the discretion of the D/HUB, SBA has the right to require that a HUBZone SBC submit... adverse inference from the failure of a HUBZone SBC to cooperate with a program examination or...

  12. 29 CFR 2590.702-1 - Additional requirements prohibiting discrimination based on genetic information.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... diabetes. A begins to experience excessive sweating, thirst, and fatigue. A's physician examines A and... adult onset diabetes mellitus (Type 2 diabetes). (ii) Conclusion. In this Example 1, A has been... involved. The diagnosis is not based principally on genetic information. Thus, Type 2 diabetes...

  13. 45 CFR 146.122 - Additional requirements prohibiting discrimination based on genetic information.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... diabetes. A begins to experience excessive sweating, thirst, and fatigue. A's physician examines A and... adult onset diabetes mellitus (Type 2 diabetes). (ii) Conclusion. In this Example 1, A has been... involved. The diagnosis is not based principally on genetic information. Thus, Type 2 diabetes...

  14. Information recovery in molecular biology: causal modelling of regulated promoter switching experiments.

    PubMed

    Anderssen, Robert S; Helliwell, Christopher A

    2013-07-01

    The recovery of information from indirect measurements takes different forms depending on the sophistication with which the process being researched can be modelled mathematically. The forms range from (1) the historical and classical inverse problems regularization situation where explicit models which guaranteed existence and uniqueness have been formulated, through (2) situations where model formulation is performed implicitly as a calibration-and-prediction ansatz, to (3) the exploratory (biology) situation where the underlying mechanism is unknown and constraining information about its dynamics is being sought through appropriate experimentation. Each represents a different aspect of the solution of inverse problems. It is the nature of the exploratory form that is discussed in this paper. The focus is the causal modelling of regulated promoter switching experiments performed to understand the dynamics of the genetic control of various biological developmental processes such as vernalization in plants; in particular, regulated promoter switching experiments used to examine the relationship between FLC transcription activity and the associated histone H3 lysine 27 trimethylation at a vernalization-responsive gene in plants. Using a causal representation with Kohlrausch function fading memory, it is shown how such modelling can be used to quantitatively assess the closeness of the linking of one biological process with another, and, in particular, to conclude that the dynamics of FLC transcription and associated H3K27me3 activity are closely linked biologically.

  15. The National Biological Information Infrastructure as an E-Government tool

    USGS Publications Warehouse

    Sepic, R.; Kase, K.

    2002-01-01

    Coordinated by the U.S. Geological Survey (USGS), the National Biological Information Infrastructure (NBII) is a Web-based system that provides access to data and information on the nation's biological resources. Although it was begun in 1993, predating any formal E-Government initiative, the NBII typifies the E-Government concepts outlined in the President's Management Agenda, as well as in the proposed E-Government Act of 2002. This article-an individual case study and not a broad survey with extensive references to the literature-explores the structure and operation of the NBII in relation to several emerging trends in E-Government: end-user focus, defined and scalable milestones, public-private partnerships, alliances with stakeholders, and interagency cooperation. ?? 2002 Elsevier Science Inc. All rights reserved.

  16. 10 CFR 52.80 - Contents of applications; additional technical information.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    .... 52.80 Section 52.80 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) LICENSES, CERTIFICATIONS, AND APPROVALS FOR NUCLEAR POWER PLANTS Combined Licenses § 52.80 Contents of applications; additional technical... the circumstances associated with the loss of large areas of the plant due to explosions or fire...

  17. 10 CFR 52.80 - Contents of applications; additional technical information.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    .... 52.80 Section 52.80 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) LICENSES, CERTIFICATIONS, AND APPROVALS FOR NUCLEAR POWER PLANTS Combined Licenses § 52.80 Contents of applications; additional technical... the circumstances associated with the loss of large areas of the plant due to explosions or fire...

  18. 10 CFR 52.80 - Contents of applications; additional technical information.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    .... 52.80 Section 52.80 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) LICENSES, CERTIFICATIONS, AND APPROVALS FOR NUCLEAR POWER PLANTS Combined Licenses § 52.80 Contents of applications; additional technical... the circumstances associated with the loss of large areas of the plant due to explosions or fire...

  19. 10 CFR 52.80 - Contents of applications; additional technical information.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    .... 52.80 Section 52.80 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) LICENSES, CERTIFICATIONS, AND APPROVALS FOR NUCLEAR POWER PLANTS Combined Licenses § 52.80 Contents of applications; additional technical... the circumstances associated with the loss of large areas of the plant due to explosions or fire...

  20. 10 CFR 52.80 - Contents of applications; additional technical information.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    .... 52.80 Section 52.80 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) LICENSES, CERTIFICATIONS, AND APPROVALS FOR NUCLEAR POWER PLANTS Combined Licenses § 52.80 Contents of applications; additional technical... the circumstances associated with the loss of large areas of the plant due to explosions or fire...

  1. Facing Facts: Can the Face-Name Mnemonic Strategy Accommodate Additional Factual Information?

    ERIC Educational Resources Information Center

    Carney, Russell N.; Levin, Joel R.

    2012-01-01

    In 3 experiments, undergraduates used their own best method (control) or an "imposed" face-name mnemonic strategy to associate 18 caricatured faces, names, and additional facts. On all immediate tests (prompted by the faces), and on the delayed tests of Experiments 2a and 2b combined, mnemonic students statistically outperformed control students…

  2. 40 CFR 79.21 - Information and assurances to be provided by the additive manufacturer.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... will be accepted in lieu thereof; (2) In the case of an additive for engine oil, only the name..., that a percentage figure combining the percentages of carbon, hydrogen, and/or oxygen may be provided... any 1975 or subsequent model year vehicle or engine, or that the manufacturer has obtained a...

  3. 40 CFR 79.21 - Information and assurances to be provided by the additive manufacturer.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... will be accepted in lieu thereof; (2) In the case of an additive for engine oil, only the name..., that a percentage figure combining the percentages of carbon, hydrogen, and/or oxygen may be provided... any 1975 or subsequent model year vehicle or engine, or that the manufacturer has obtained a...

  4. 40 CFR 79.21 - Information and assurances to be provided by the additive manufacturer.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... will be accepted in lieu thereof; (2) In the case of an additive for engine oil, only the name..., that a percentage figure combining the percentages of carbon, hydrogen, and/or oxygen may be provided... any 1975 or subsequent model year vehicle or engine, or that the manufacturer has obtained a...

  5. 77 FR 58911 - Additional Identifying Information for One (1) Individual Designated Pursuant to Executive Order...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-09-24

    ... Threaten to Disrupt the Middle East Peace Process'' (the ``Order''). DATES: The addition by the Director of... sanctions on persons who threaten to disrupt the Middle East peace process. The President identified in the... Middle East peace ] process; or (2) assist in, sponsor, or provide financial, material, or...

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

    PubMed

    Humphreys, K; Demetriou, G; Gaizauskas, R

    2000-01-01

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

  7. Quantifying control effort of biological and technical movements: an information-entropy-based approach.

    PubMed

    Haeufle, D F B; Günther, M; Wunner, G; Schmitt, S

    2014-01-01

    In biomechanics and biorobotics, muscles are often associated with reduced movement control effort and simplified control compared to technical actuators. This is based on evidence that the nonlinear muscle properties positively influence movement control. It is, however, open how to quantify the simplicity aspect of control effort and compare it between systems. Physical measures, such as energy consumption, stability, or jerk, have already been applied to compare biological and technical systems. Here a physical measure of control effort based on information entropy is presented. The idea is that control is simpler if a specific movement is generated with less processed sensor information, depending on the control scheme and the physical properties of the systems being compared. By calculating the Shannon information entropy of all sensor signals required for control, an information cost function can be formulated allowing the comparison of models of biological and technical control systems. Exemplarily applied to (bio-)mechanical models of hopping, the method reveals that the required information for generating hopping with a muscle driven by a simple reflex control scheme is only I=32 bits versus I=660 bits with a DC motor and a proportional differential controller. This approach to quantifying control effort captures the simplicity of a control scheme and can be used to compare completely different actuators and control approaches.

  8. Quantifying control effort of biological and technical movements: An information-entropy-based approach

    NASA Astrophysics Data System (ADS)

    Haeufle, D. F. B.; Günther, M.; Wunner, G.; Schmitt, S.

    2014-01-01

    In biomechanics and biorobotics, muscles are often associated with reduced movement control effort and simplified control compared to technical actuators. This is based on evidence that the nonlinear muscle properties positively influence movement control. It is, however, open how to quantify the simplicity aspect of control effort and compare it between systems. Physical measures, such as energy consumption, stability, or jerk, have already been applied to compare biological and technical systems. Here a physical measure of control effort based on information entropy is presented. The idea is that control is simpler if a specific movement is generated with less processed sensor information, depending on the control scheme and the physical properties of the systems being compared. By calculating the Shannon information entropy of all sensor signals required for control, an information cost function can be formulated allowing the comparison of models of biological and technical control systems. Exemplarily applied to (bio-)mechanical models of hopping, the method reveals that the required information for generating hopping with a muscle driven by a simple reflex control scheme is only I =32bits versus I =660bits with a DC motor and a proportional differential controller. This approach to quantifying control effort captures the simplicity of a control scheme and can be used to compare completely different actuators and control approaches.

  9. 24 CFR 903.9 - May HUD request additional information in the Annual Plan of a troubled PHA?

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 24 Housing and Urban Development 4 2013-04-01 2013-04-01 false May HUD request additional information in the Annual Plan of a troubled PHA? 903.9 Section 903.9 Housing and Urban Development REGULATIONS RELATING TO HOUSING AND URBAN DEVELOPMENT (CONTINUED) OFFICE OF ASSISTANT SECRETARY FOR PUBLIC...

  10. 12 CFR 516.220 - If OTS requests additional information to complete my application, how will it process my...

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... complete my application, how will it process my application? 516.220 Section 516.220 Banks and Banking... Standard Treatment § 516.220 If OTS requests additional information to complete my application, how will it... your response. OTS will notify you that it has extended the period before the end of the initial...

  11. 12 CFR 390.128 - If the FDIC requests additional information to complete my application, how will it process my...

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... complete my application, how will it process my application? 390.128 Section 390.128 Banks and Banking... additional information to complete my application, how will it process my application? (a) You may use the... will notify you that it has extended the period before the end of the initial 15-day period and...

  12. 12 CFR 116.220 - If the OCC requests additional information to complete my application, how will it process my...

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... complete my application, how will it process my application? 116.220 Section 116.220 Banks and Banking... Treatment § 116.220 If the OCC requests additional information to complete my application, how will it... that it has extended the period before the end of the initial 15-day period and will briefly...

  13. 12 CFR 516.220 - If OTS requests additional information to complete my application, how will it process my...

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... complete my application, how will it process my application? 516.220 Section 516.220 Banks and Banking... Standard Treatment § 516.220 If OTS requests additional information to complete my application, how will it... your response. OTS will notify you that it has extended the period before the end of the initial...

  14. 41 CFR 102-79.111 - Where may Executive agencies find additional information on Integrated Workplace concepts?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 41 Public Contracts and Property Management 3 2010-07-01 2010-07-01 false Where may Executive agencies find additional information on Integrated Workplace concepts? 102-79.111 Section 102-79.111 Public Contracts and Property Management Federal Property Management Regulations System (Continued)...

  15. A new species of Neparholaspis (Acari: Parholaspididae) from Russia, with additional information on Neparholaspis evansi Krantz, 1960.

    PubMed

    Marchenko, Irina I

    2016-08-23

    Neparholaspis dubatolovi sp. nov. is described and illustrated from adult females and males collected from litter and moss in montane forest in north-eastern Sikhote-Alin Ridge in the Far East of Russia. Additional morphological information and illustrations of Neparholaspis evansi Krantz, 1960 are provided, based on examination of a paratype. A key to the world species of Neparholaspis is provided.

  16. 76 FR 80377 - Notice of Submission of Proposed Information Collection to OMB Additional On-Site Data Collection...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-12-23

    ... of Submission of Proposed Information Collection to OMB Additional On-Site Data Collection for the... HCV programs. The proposed data collection will take place through site visits to up to 30 PHAs and... the PHA. The results of the site visits will be used to identify PHAs to participate in a...

  17. Tautomers of a Fluorescent G Surrogate and Their Distinct Photophysics Provide Additional Information Channels.

    PubMed

    Sholokh, Marianna; Improta, Roberto; Mori, Mattia; Sharma, Rajhans; Kenfack, Cyril; Shin, Dongwon; Voltz, Karine; Stote, Roland H; Zaporozhets, Olga A; Botta, Maurizio; Tor, Yitzhak; Mély, Yves

    2016-07-04

    Thienoguanosine ((th) G) is an isomorphic nucleoside analogue acting as a faithful fluorescent substitute of G, with respectable quantum yield in oligonucleotides. Photophysical analysis of (th) G reveals the existence of two ground-state tautomers with significantly shifted absorption and emission wavelengths, and high quantum yield in buffer. Using (TD)-DFT calculations, the tautomers were identified as the H1 and H3 keto-amino tautomers. When incorporated into the loop of (-)PBS, the (-)DNA copy of the HIV-1 primer binding site, both tautomers are observed and show differential sensitivity to protein binding. The red-shifted H1 tautomer is strongly favored in matched (-)/(+)PBS duplexes, while the relative emission of the H3 tautomer can be used to detect single nucleotide polymorphisms. These tautomers and their distinct environmental sensitivity provide unprecedented information channels for analyzing G residues in oligonucleotides and their complexes.

  18. Tautomers of a Fluorescent G Surrogate and Their Distinct Photophysics Provide Additional Information Channels

    PubMed Central

    Sharma, Rajhans; Kenfack, Cyril; Shin, Dongwon; Voltz, Karine; Stote, Roland H.; Zaporozhets, Olga A.; Botta, Maurizio; Tor, Yitzhak; Mély, Yves

    2016-01-01

    Thienoguanosine (thG) is an isomorphic nucleoside analogue acting as a faithful fluorescent substitute of G, with respectable quantum yield in oligonucleotides. Photophysical analysis of thG reveals the existence of two ground-state tautomers with significantly shifted absorption and emission wavelengths, and high quantum yield in buffer. Using (TD)-DFT calculations, the tautomers were identified as the H1 and H3 keto-amino tautomers. When incorporated into the loop of (−)PBS, the (−)DNA copy of the HIV-1 primer binding site, both tautomers are observed and show differential sensitivity to protein binding. The red-shifted H1 tautomer is strongly favored in matched (−)/(+)PBS duplexes, while the relative emission of the H3 tautomer can be used to detect single nucleotide polymorphisms. These tautomers and their distinct environmental sensitivity provide unprecedented information channels for analyzing G residues in oligonucleotides and their complexes. PMID:27273741

  19. Measuring information flow in cellular networks by the systems biology method through microarray data.

    PubMed

    Chen, Bor-Sen; Li, Cheng-Wei

    2015-01-01

    In general, it is very difficult to measure the information flow in a cellular network directly. In this study, based on an information flow model and microarray data, we measured the information flow in cellular networks indirectly by using a systems biology method. First, we used a recursive least square parameter estimation algorithm to identify the system parameters of coupling signal transduction pathways and the cellular gene regulatory network (GRN). Then, based on the identified parameters and systems theory, we estimated the signal transductivities of the coupling signal transduction pathways from the extracellular signals to each downstream protein and the information transductivities of the GRN between transcription factors in response to environmental events. According to the proposed method, the information flow, which is characterized by signal transductivity in coupling signaling pathways and information transductivity in the GRN, can be estimated by microarray temporal data or microarray sample data. It can also be estimated by other high-throughput data such as next-generation sequencing or proteomic data. Finally, the information flows of the signal transduction pathways and the GRN in leukemia cancer cells and non-leukemia normal cells were also measured to analyze the systematic dysfunction in this cancer from microarray sample data. The results show that the signal transductivities of signal transduction pathways change substantially from normal cells to leukemia cancer cells.

  20. Measuring information flow in cellular networks by the systems biology method through microarray data

    PubMed Central

    Chen, Bor-Sen; Li, Cheng-Wei

    2015-01-01

    In general, it is very difficult to measure the information flow in a cellular network directly. In this study, based on an information flow model and microarray data, we measured the information flow in cellular networks indirectly by using a systems biology method. First, we used a recursive least square parameter estimation algorithm to identify the system parameters of coupling signal transduction pathways and the cellular gene regulatory network (GRN). Then, based on the identified parameters and systems theory, we estimated the signal transductivities of the coupling signal transduction pathways from the extracellular signals to each downstream protein and the information transductivities of the GRN between transcription factors in response to environmental events. According to the proposed method, the information flow, which is characterized by signal transductivity in coupling signaling pathways and information transductivity in the GRN, can be estimated by microarray temporal data or microarray sample data. It can also be estimated by other high-throughput data such as next-generation sequencing or proteomic data. Finally, the information flows of the signal transduction pathways and the GRN in leukemia cancer cells and non-leukemia normal cells were also measured to analyze the systematic dysfunction in this cancer from microarray sample data. The results show that the signal transductivities of signal transduction pathways change substantially from normal cells to leukemia cancer cells. PMID:26082788

  1. Inclusion of Additional Plant Species and Trait Information in Dynamic Vegetation Modeling of Arctic Tundra and Boreal Forest Ecosystem

    NASA Astrophysics Data System (ADS)

    Euskirchen, E. S.; Patil, V.; Roach, J.; Griffith, B.; McGuire, A. D.

    2015-12-01

    Dynamic vegetation models (DVMs) have been developed to model the ecophysiological characteristics of plant functional types in terrestrial ecosystems. They have frequently been used to answer questions pertaining to processes such as disturbance, plant succession, and community composition under historical and future climate scenarios. While DVMs have proved useful in these types of applications, it has often been questioned if additional detail, such as including plant dynamics at the species-level and/or including species-specific traits would make these models more accurate and/or broadly applicable. A sub-question associated with this issue is, 'How many species, or what degree of functional diversity, should we incorporate to sustain ecosystem function in modeled ecosystems?' Here, we focus on how the inclusion of additional plant species and trait information may strengthen dynamic vegetation modeling in applications pertaining to: (1) forage for caribou in northern Alaska, (2) above- and belowground carbon storage in the boreal forest and lake margin wetlands of interior Alaska, and (3) arctic tundra and boreal forest leaf phenology. While the inclusion of additional information generally proved valuable in these three applications, this additional detail depends on field data that may not always be available and may also result in increased computational complexity. Therefore, it is important to assess these possible limitations against the perceived need for additional plant species and trait information in the development and application of dynamic vegetation models.

  2. Theoretical approaches for the dynamics of complex biological systems from information of networks

    PubMed Central

    MOCHIZUKI, Atsushi

    2016-01-01

    Modern biology has provided many examples of large networks describing the interactions between multiple species of bio-molecules. It is believed that the dynamics of molecular activities based on such networks are the origin of biological functions. On the other hand, we have a limited understanding for dynamics of molecular activity based on networks. To overcome this problem, we have developed two structural theories, by which the important aspects of the dynamical properties of the system are determined only from information on the network structure, without assuming other quantitative details. The first theory, named Linkage Logic, determines a subset of molecules in regulatory networks, by which any long-term dynamical behavior of the whole system can be identified/controlled. The second theory, named Structural Sensitivity Analysis, determines the sensitivity responses of the steady state of chemical reaction networks to perturbations of the reaction rate. The first and second theories investigate the dynamical properties of regulatory and reaction networks, respectively. The first theory targets the attractors of the regulatory network systems, whereas the second theory applies only to the steady states of the reaction network systems, but predicts their detailed behavior. To demonstrate the utility of our methods several biological network systems, and show they are practically useful to analyze behaviors of biological systems. PMID:27725468

  3. An Internet compendium of analytical methods and spectroscopic information for monomers and additives used in food packaging plastics.

    PubMed

    Gilbert, J; Simoneau, C; Cote, D; Boenke, A

    2000-10-01

    An internet website (http:¿cpf.jrc.it/smt/) has been produced as a means of dissemination of methods of analysis and supporting spectroscopic information on monomers and additives used for food contact materials (principally packaging). The site which is aimed primarily at assisting food control laboratories in the European Union contains analytical information on monomers, starting substances and additives used in the manufacture of plastics materials. A searchable index is provided giving PM and CAS numbers for each of 255 substances. For each substance a data sheet gives regulatory information, chemical structures, physico-chemical information and background information on the use of the substance in particular plastics, and the food packaging applications. For monomers and starting substances (155 compounds) the infra-red and mass spectra are provided, and for additives (100 compounds); additionally proton NMR are available for about 50% of the entries. Where analytical methods have been developed for determining these substances as residual amounts in plastics or as trace amounts in food simulants these methods are also on the website. All information is provided in portable document file (PDF) format which means that high quality copies can be readily printed, using freely available Adobe Acrobat Reader software. The website will in future be maintained and up-dated by the European Commission's Joint Research Centre (JRC) as new substances are authorized for use by the European Commission (DG-ENTR formerly DGIII). Where analytical laboratories (food control or other) require reference substances these can be obtained free-of-charge from a reference collection housed at the JRC and maintained in conjunction with this website compendium.

  4. Information on black-footed ferret biology collected within the framework of ferret conservation

    USGS Publications Warehouse

    Biggins, Dean E.

    2012-01-01

    Once feared to be extinct, black-footed ferrets (Mustela nigripes) were rediscovered near Meeteetse, Wyoming, in 1981, resulting in renewed conservation and research efforts for this highly endangered species. A need for information directly useful to recovery has motivated much monitoring of ferrets since that time, but field activities have enabled collection of data relevant to broader biological themes. This special feature is placed in a context of similar books and proceedings devoted to ferret biology and conservation. Articles include general observations on ferrets, modeling of potential impacts of ferrets on prairie dogs (Cynomys spp.), discussions on relationships of ferrets to prairie dog habitats at several spatial scales (from individual burrows to patches of burrow systems) and a general treatise on the status of black-footed ferret recovery.

  5. Biological versus electronic adaptive coloration: how can one inform the other?

    PubMed

    Kreit, Eric; Mäthger, Lydia M; Hanlon, Roger T; Dennis, Patrick B; Naik, Rajesh R; Forsythe, Eric; Heikenfeld, Jason

    2013-01-06

    Adaptive reflective surfaces have been a challenge for both electronic paper (e-paper) and biological organisms. Multiple colours, contrast, polarization, reflectance, diffusivity and texture must all be controlled simultaneously without optical losses in order to fully replicate the appearance of natural surfaces and vividly communicate information. This review merges the frontiers of knowledge for both biological adaptive coloration, with a focus on cephalopods, and synthetic reflective e-paper within a consistent framework of scientific metrics. Currently, the highest performance approach for both nature and technology uses colourant transposition. Three outcomes are envisioned from this review: reflective display engineers may gain new insights from millions of years of natural selection and evolution; biologists will benefit from understanding the types of mechanisms, characterization and metrics used in synthetic reflective e-paper; all scientists will gain a clearer picture of the long-term prospects for capabilities such as adaptive concealment and signaling.

  6. Biological versus electronic adaptive coloration: how can one inform the other?

    PubMed Central

    Kreit, Eric; Mäthger, Lydia M.; Hanlon, Roger T.; Dennis, Patrick B.; Naik, Rajesh R.; Forsythe, Eric; Heikenfeld, Jason

    2013-01-01

    Adaptive reflective surfaces have been a challenge for both electronic paper (e-paper) and biological organisms. Multiple colours, contrast, polarization, reflectance, diffusivity and texture must all be controlled simultaneously without optical losses in order to fully replicate the appearance of natural surfaces and vividly communicate information. This review merges the frontiers of knowledge for both biological adaptive coloration, with a focus on cephalopods, and synthetic reflective e-paper within a consistent framework of scientific metrics. Currently, the highest performance approach for both nature and technology uses colourant transposition. Three outcomes are envisioned from this review: reflective display engineers may gain new insights from millions of years of natural selection and evolution; biologists will benefit from understanding the types of mechanisms, characterization and metrics used in synthetic reflective e-paper; all scientists will gain a clearer picture of the long-term prospects for capabilities such as adaptive concealment and signalling. PMID:23015522

  7. Stationary distribution of self-organized states and biological information generation

    NASA Astrophysics Data System (ADS)

    Woo, Hyung Jun

    2013-11-01

    Self-organization, where spontaneous orderings occur under driven conditions, is one of the hallmarks of biological systems. We consider a statistical mechanical treatment of the biased distribution of such organized states, which become favored as a result of their catalytic activity under chemical driving forces. A generalization of the equilibrium canonical distribution describes the stationary state, which can be used to model shifts in conformational ensembles sampled by an enzyme in working conditions. The basic idea is applied to the process of biological information generation from random sequences of heteropolymers, where unfavorable Shannon entropy is overcome by the catalytic activities of selected genes. The ordering process is demonstrated with the genetic distance to a genotype with high catalytic activity as an order parameter. The resulting free energy can have multiple minima, corresponding to disordered and organized phases with first-order transitions between them.

  8. The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web.

    PubMed

    Hastings, Janna; Chepelev, Leonid; Willighagen, Egon; Adams, Nico; Steinbeck, Christoph; Dumontier, Michel

    2011-01-01

    Cheminformatics is the application of informatics techniques to solve chemical problems in silico. There are many areas in biology where cheminformatics plays an important role in computational research, including metabolism, proteomics, and systems biology. One critical aspect in the application of cheminformatics in these fields is the accurate exchange of data, which is increasingly accomplished through the use of ontologies. Ontologies are formal representations of objects and their properties using a logic-based ontology language. Many such ontologies are currently being developed to represent objects across all the domains of science. Ontologies enable the definition, classification, and support for querying objects in a particular domain, enabling intelligent computer applications to be built which support the work of scientists both within the domain of interest and across interrelated neighbouring domains. Modern chemical research relies on computational techniques to filter and organise data to maximise research productivity. The objects which are manipulated in these algorithms and procedures, as well as the algorithms and procedures themselves, enjoy a kind of virtual life within computers. We will call these information entities. Here, we describe our work in developing an ontology of chemical information entities, with a primary focus on data-driven research and the integration of calculated properties (descriptors) of chemical entities within a semantic web context. Our ontology distinguishes algorithmic, or procedural information from declarative, or factual information, and renders of particular importance the annotation of provenance to calculated data. The Chemical Information Ontology is being developed as an open collaborative project. More details, together with a downloadable OWL file, are available at http://code.google.com/p/semanticchemistry/ (license: CC-BY-SA).

  9. The Importance of Spatiotemporal Information in Biological Motion Perception: White Noise Presented with a Step-like Motion Activates the Biological Motion Area.

    PubMed

    Callan, Akiko; Callan, Daniel; Ando, Hiroshi

    2017-02-01

    Humans can easily recognize the motion of living creatures using only a handful of point-lights that describe the motion of the main joints (biological motion perception). This special ability to perceive the motion of animate objects signifies the importance of the spatiotemporal information in perceiving biological motion. The posterior STS (pSTS) and posterior middle temporal gyrus (pMTG) region have been established by many functional neuroimaging studies as a locus for biological motion perception. Because listening to a walking human also activates the pSTS/pMTG region, the region has been proposed to be supramodal in nature. In this study, we investigated whether the spatiotemporal information from simple auditory stimuli is sufficient to activate this biological motion area. We compared spatially moving white noise, having a running-like tempo that was consistent with biological motion, with stationary white noise. The moving-minus-stationary contrast showed significant differences in activation of the pSTS/pMTG region. Our results suggest that the spatiotemporal information of the auditory stimuli is sufficient to activate the biological motion area.

  10. Students' perceptions of motivation in high school biology class: Informing current theories

    NASA Astrophysics Data System (ADS)

    McManic, Janet A.

    The purpose of this study was to investigate students' perceptions of motivation to achieve while participating in general level high school biology classes. In a national poll of teacher's attitudes, student's motivation was a top concern of teachers (Elam, 1989). The student's perceptions of motivation are important to understand if improvements and advancements in motivation are to be implemented in the science classroom. This qualitative study was conducted in an urban high school that is located in a major metropolitan area in the southeast of the United States. The student body of 1100 is composed of Caucasian, African-American, Hispanic, and Asian students. The focus question of the study was: What are students' perceptions of their motivation in biology class? From general level biology classes, purposeful sampling narrowed the participants to fifteen students. Semi-structured interviews were conducted with the participants having varying measurements of motivation on the Scale of Intrinsic versus Extrinsic Orientation in the Classroom (Harter, 1980). The interviews were recorded and transcribed. After transcription, the interviews were coded by the constant comparative method (Glaser & Strauss, 1967). The coded data of students' responses were analyzed and compared to current theories of motivation. The current theories are the social-cognitive model (Bandura, 1977), attribution theory (Weiner, 1979), basic needs theory (Maslow, 1954) and choice theory (Glasser, 1986). The results of this study support the social cognitive model of motivation (Bandura, 1977) through the description of family structure and its relationship to motivation (Gonzalez, 2002). The study upheld previous research in that extrinsic orientation was shown to be prevalent in older students (Harter, 1981; Anderman & Maehr, 1994). In addition, the students' responses disclosed the difficulties encountered in studying biology. Students expressed the opinion that biology terms are

  11. 21 CFR 601.50 - Confidentiality of data and information in an investigational new drug notice for a biological...

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 7 2010-04-01 2010-04-01 false Confidentiality of data and information in an investigational new drug notice for a biological product. 601.50 Section 601.50 Food and Drugs FOOD AND DRUG... Information § 601.50 Confidentiality of data and information in an investigational new drug notice for...

  12. Membrane stiffness is modified by integral membrane proteins† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c6sm01186a Click here for additional data file. Click here for additional data file. Click here for additional data file. Click here for additional data file. Click here for additional data file. Click here for additional data file. Click here for additional data file. Click here for additional data file. Click here for additional data file. Click here for additional data file. Click here for additional data file. Click here for additional data file. Click here for additional data file.

    PubMed Central

    Fowler, Philip W.; Hélie, Jean; Duncan, Anna; Chavent, Matthieu; Koldsø, Heidi

    2016-01-01

    The ease with which a cell membrane can bend and deform is important for a wide range of biological functions. Peripheral proteins that induce curvature in membranes (e.g. BAR domains) have been studied for a number of years. Little is known, however, about the effect of integral membrane proteins on the stiffness of a membrane (characterised by the bending rigidity, K c). We demonstrate by computer simulation that adding integral membrane proteins at physiological densities alters the stiffness of the membrane. First we establish that the coarse-grained MARTINI forcefield is able to accurately reproduce the bending rigidity of a small patch of 1500 phosphatidyl choline lipids by comparing the calculated value to both experiment and an atomistic simulation of the same system. This enables us to simulate the dynamics of large (ca. 50 000 lipids) patches of membrane using the MARTINI coarse-grained description. We find that altering the lipid composition changes the bending rigidity. Adding integral membrane proteins to lipid bilayers also changes the bending rigidity, whilst adding a simple peripheral membrane protein has no effect. Our results suggest that integral membrane proteins can have different effects, and in the case of the bacterial outer membrane protein, BtuB, the greater the density of protein, the larger the reduction in stiffness. PMID:27722554

  13. DNA as information: at the crossroads between biology, mathematics, physics and chemistry.

    PubMed

    Cartwright, Julyan H E; Giannerini, Simone; González, Diego L

    2016-03-13

    On the one hand, biology, chemistry and also physics tell us how the process of translating the genetic information into life could possibly work, but we are still very far from a complete understanding of this process. On the other hand, mathematics and statistics give us methods to describe such natural systems-or parts of them-within a theoretical framework. Also, they provide us with hints and predictions that can be tested at the experimental level. Furthermore, there are peculiar aspects of the management of genetic information that are intimately related to information theory and communication theory. This theme issue is aimed at fostering the discussion on the problem of genetic coding and information through the presentation of different innovative points of view. The aim of the editors is to stimulate discussions and scientific exchange that will lead to new research on why and how life can exist from the point of view of the coding and decoding of genetic information. The present introduction represents the point of view of the editors on the main aspects that could be the subject of future scientific debate.

  14. DNA as information: at the crossroads between biology, mathematics, physics and chemistry

    PubMed Central

    2016-01-01

    On the one hand, biology, chemistry and also physics tell us how the process of translating the genetic information into life could possibly work, but we are still very far from a complete understanding of this process. On the other hand, mathematics and statistics give us methods to describe such natural systems—or parts of them—within a theoretical framework. Also, they provide us with hints and predictions that can be tested at the experimental level. Furthermore, there are peculiar aspects of the management of genetic information that are intimately related to information theory and communication theory. This theme issue is aimed at fostering the discussion on the problem of genetic coding and information through the presentation of different innovative points of view. The aim of the editors is to stimulate discussions and scientific exchange that will lead to new research on why and how life can exist from the point of view of the coding and decoding of genetic information. The present introduction represents the point of view of the editors on the main aspects that could be the subject of future scientific debate. PMID:26857674

  15. Supra-additive contribution of shape and surface information to individual face discrimination as revealed by fast periodic visual stimulation.

    PubMed

    Dzhelyova, Milena; Rossion, Bruno

    2014-12-24

    Face perception depends on two main sources of information--shape and surface cues. Behavioral studies suggest that both of them contribute roughly equally to discrimination of individual faces, with only a small advantage provided by their combination. However, it is difficult to quantify the respective contribution of each source of information to the visual representation of individual faces with explicit behavioral measures. To address this issue, facial morphs were created that varied in shape only, surface only, or both. Electrocephalogram (EEG) were recorded from 10 participants during visual stimulation at a fast periodic rate, in which the same face was presented four times consecutively and the fifth face (the oddball) varied along one of the morphed dimensions. Individual face discrimination was indexed by the periodic EEG response at the oddball rate (e.g., 5.88 Hz/5 = 1.18 Hz). While shape information was discriminated mainly at right occipitotemporal electrode sites, surface information was coded more bilaterally and provided a larger response overall. Most importantly, shape and surface changes alone were associated with much weaker responses than when both sources of information were combined in the stimulus, revealing a supra-additive effect. These observations suggest that the two kinds of information combine nonlinearly to provide a full individual face representation, face identity being more than the sum of the contribution of shape and surface cues.

  16. Using Information and Communication Technology (ICT) to the Maximum: Learning and Teaching Biology with Limited Digital Technologies

    ERIC Educational Resources Information Center

    Van Rooy, Wilhelmina S.

    2012-01-01

    Background: The ubiquity, availability and exponential growth of digital information and communication technology (ICT) creates unique opportunities for learning and teaching in the senior secondary school biology curriculum. Digital technologies make it possible for emerging disciplinary knowledge and understanding of biological processes…

  17. How Can Biologically-Based Modeling of Arsenic Kinetics and Dynamics Inform the Risk Assessment Process? -- ETD

    EPA Science Inventory

    Quantitative biologically-based models describing key events in the continuum from arsenic exposure to the development of adverse health effects provide a framework to integrate information obtained across diverse research areas. For example, genetic polymorphisms in arsenic me...

  18. Clarification of the Use of Biological Data and Information in the 2002 Integrated Water Quality Monitoring and Assessment Report Guidance

    EPA Pesticide Factsheets

    The memorandum modifies the 2002 Integrated Water Quality Monitoring and Assessment Report Guidance to provide clarity and promote consistency in the manner in which states use biological data and information in developing their 2002 submissions.

  19. BEAUTY: an enhanced BLAST-based search tool that integrates multiple biological information resources into sequence similarity search results.

    PubMed

    Worley, K C; Wiese, B A; Smith, R F

    1995-09-01

    BEAUTY (BLAST enhanced alignment utility) is an enhanced version of the NCBI's BLAST data base search tool that facilitates identification of the functions of matched sequences. We have created new data bases of conserved regions and functional domains for protein sequences in NCBI's Entrez data base, and BEAUTY allows this information to be incorporated directly into BLAST search results. A Conserved Regions Data Base, containing the locations of conserved regions within Entrez protein sequences, was constructed by (1) clustering the entire data base into families, (2) aligning each family using our PIMA multiple sequence alignment program, and (3) scanning the multiple alignments to locate the conserved regions within each aligned sequence. A separate Annotated Domains Data Base was constructed by extracting the locations of all annotated domains and sites from sequences represented in the Entrez, PROSITE, BLOCKS, and PRINTS data bases. BEAUTY performs a BLAST search of those Entrez sequences with conserved regions and/or annotated domains. BEAUTY then uses the information from the Conserved Regions and Annotated Domains data bases to generate, for each matched sequence, a schematic display that allows one to directly compare the relative locations of (1) the conserved regions, (2) annotated domains and sites, and (3) the locally aligned regions matched in the BLAST search. In addition, BEAUTY search results include World-Wide Web hypertext links to a number of external data bases that provide a variety of additional types of information on the function of matched sequences. This convenient integration of protein families, conserved regions, annotated domains, alignment displays, and World-Wide Web resources greatly enhances the biological informativeness of sequence similarity searches. BEAUTY searches can be performed remotely on our system using the "BCM Search Launcher" World-Wide Web pages (URL is < http:/ /gc.bcm.tmc.edu:8088/ search-launcher/launcher.html > ).

  20. Website Use and Effects of Online Information About Tobacco Additives Among the Dutch General Population: A Randomized Controlled Trial

    PubMed Central

    Crutzen, Rik; Kienhuis, Anne S; Talhout, Reinskje; de Vries, Hein

    2017-01-01

    Background As a legal obligation, the Dutch government publishes online information about tobacco additives to make sure that it is publicly available. Little is known about the influence this website (”tabakinfo”) has on visitors and how the website is evaluated by them. Objective This study assesses how visitors use the website and its effect on their knowledge, risk perception, attitude, and smoking behavior. The study will also assess how the website is evaluated by visitors using a sample of the Dutch general population, including smokers and nonsmokers. Methods A randomized controlled trial was conducted, recruiting participants from an online panel. At baseline, participants (N=672) were asked to fill out an online questionnaire about tobacco additives. Next, participants were randomly allocated to either one of two experimental groups and invited to visit the website providing information about tobacco additives (either with or without a database containing product-specific information) or to a control group that had no access to the website. After 3 months, follow-up measurements took place. Results At follow-up (n=492), no statistically significant differences were found for knowledge, risk perception, attitude, or smoking behavior between the intervention and control groups. Website visits were positively related to younger participants (B=–0.07, 95% CI –0.12 to –0.01; t11=–2.43, P=.02) and having a low risk perception toward tobacco additives (B=–0.32, 95% CI –0.63 to –0.02; t11=–2.07, P=.04). In comparison, having a lower education (B=–0.67, 95% CI –1.14 to –0.17; t11=–2.65, P=.01) was a significant predictor for making less use of the website. Furthermore, the website was evaluated less positively by smokers compared to nonsmokers (t324=–3.55, P<.001), and males compared to females (t324=–2.21, P=.02). Conclusions The website did not change perceptions of tobacco additives or smoking behavior. Further research is

  1. Utilization of Bacillus sp. strain TAT105 as a biological additive to reduce ammonia emissions during composting of swine feces.

    PubMed

    Kuroda, Kazutaka; Waki, Miyoko; Yasuda, Tomoko; Fukumoto, Yasuyuki; Tanaka, Akihiro; Nakasaki, Kiyohiko

    2015-01-01

    Bacillus sp. strain TAT105 is a thermophilic, ammonium-tolerant bacterium that grows assimilating ammonium nitrogen and reduces ammonia emission during composting of swine feces. To develop a practical use of TAT105, a dried solid culture of TAT105 (5.3 × 10(9) CFU/g of dry matter) was prepared as an additive. It could be stored for one year without significant reduction of TAT105. Laboratory-scale composting of swine feces was conducted by mixing the additive. When the additive, mixed with an equal weight of water one day before use, was added to obtain a TAT105 concentration of above 10(7) CFU/g of dry matter in the initial material, the ammonia concentration emitted was lower and nitrogen loss was approximately 22% lower in the treatment with the additive than in the control treatment without the additive. The colony formation on an agar medium containing high ammonium could be used for enumeration of TAT105 in the composted materials.

  2. [Rad-Esito: new informational additions in the integration of content of hospital discharge cards for acute patients].

    PubMed

    Rini, F; Piscioneri, C; Consolante, C; Fara, G M

    2009-01-01

    Since the January 2008 the tracking of additional information about hospital discharge card's content has been activated in Latium. The new data, noticed by RAD-Esito card, regard the hospitalizations for acute myocardial infarction, femoral neck fracture and coronary artery bypass surgery. This study's objective has been to evaluate the quality of the data collected with the new card, at the end of the 1st semester of experimentation, concerning two institutes of care of Latium, the Casilino Polyclinic (ASL Rome B) and the Anzio-Nettuno hospital (Assembled Hospitals, ASL Rome H). Furthermore, any significant correlation's existence between a few variables for acute myocardial infarction and femoral fracture with the mortality rate and the average hospitalization period has been statistically verified. This study's preliminary results show how the integration of the hospital informative flow with the new clinical variables will be able to allow the promotion of the quality in the coding of the diagnosis and procedures, according to the current international innovations. This additional information will also be able to support the regional appropriateness and outcome of the treatments evaluation programs.

  3. Individuals with post-stroke hemiparesis are able to use additional sensory information to reduce postural sway.

    PubMed

    Cunha, B P; Alouche, S R; Araujo, I M G; Freitas, S M S F

    2012-03-28

    The present study aimed to investigate whether stroke survivals are able to use the additional somatosensory information provided by the light touch to reduce their postural sway during the upright stance. Eight individuals, naturally right-handed pre-stroke, and eight healthy age-matched adults stood as quiet as possible on a force plate during 35s. Participants performed two trials for each visual condition (eyes open and closed) and somatosensory condition (with and without the right or left index fingertip touching an instrumented rigid and fixed bar). When participants touched the bar, they were asked to apply less than 1N of vertical force. The postural sway was assessed by the center of pressure (COP) displacement area, mean amplitude and velocity. In addition, the mean and standard deviation of the force vertically applied on the bar during the trials with touch were assessed. The averaged values of COP area, amplitude and velocity were greater for stroke individuals compared to healthy adults during all visual and somatosensory conditions. For both groups, the values of all variables increased when participants stood with eyes closed and reduced when they touched the bar regardless of the side of the touch. Overall, the results suggested that, as healthy individuals, persons with post-stroke hemiparesis are able to use the additional somatosensory information provided by the light touch to reduce the postural sway.

  4. Improvement of mechanical and biological properties of TiNi alloys by addition of Cu and Co to orthodontic archwires.

    PubMed

    Phukaoluan, Aphinan; Khantachawana, Anak; Kaewtatip, Pongpan; Dechkunakorn, Surachai; Kajornchaiyakul, Julathep

    2016-09-01

    The purpose of this study was to investigate improved performances of TiNi in order to promote tooth movement. Special attention was paid to the effect on the clinical properties of TiNi of adding Cu and Co to this alloy. Ti49.4Ni50.6, Ti49Ni46Cu5 and Ti50Ni47Co3 (at %) alloys were prepared. Specimens were cold-rolled at 30% reduction and heat-treated at 400°C for 60min. Then, the test results were compared with two types of commercial archwires. The findings showed that superelasticity properties were confirmed in the manufactured commercial alloys at mouth temperature. The difference of stress plateau in TiNi, TiNiCo and commercial wires B at 25°C changed significantly at various testing temperatures due to the combination of martensite and austenite phases. At certain temperatures the alloys exhibited zero recovery stress at 2% strain and consequently produced zero activation force for moving teeth. The corrosion test showed that the addition of Cu and Co to TiNi alloys generates an increase in corrosion potential (Ecorr) and corrosion current densities (Icorr). Finally, we observed that addition of Cu and Co improved cell viability. We conclude that addition of an appropriate amount of a third alloying element can help enhance the performances of TiNi orthodontic archwires.

  5. Biological activities of thermo-tolerant microbes from fermented rice bran as an alternative microbial feed additive.

    PubMed

    Koh, J H; Suh, H J

    2009-06-01

    To evaluate the commercial potential of new microbial feed additive, Issatchenkia orientalis Y266 and Bacillus subtilis B266 from commercial fermented rice bran were tested for their tolerance or resistance to pH, bile, oxgall, and temperature. It was found that the strains grew very well up to pH 3.0 and resistant to relatively high concentrations of bile salt and oxgall. I. orientalis and B. subtilis are extremely tolerant in range of 70-90 degrees C in solid medium. B. subtilis B266 also has excellent tolerant property up to 90 degrees C in liquid medium. The health indexes (the microflora in the small intestines and the antibody titer to Newcastle disease virus) of chicks were significantly improved in the fermented rice bran with these strains (0.25% addition to diet) in comparison with the Avilamycin (20 mg/kg diet)-fed group (p < 0.05). The fermented rice bran-fed group showed a better microbial flora in the small intestines. Accordingly, it would appear that the fermented rice bran with these strains may be a potential candidate for an alternative microbial feed additive.

  6. An integrated data-warehouse-concept for clinical and biological information.

    PubMed

    Brammen, Dominik; Katzer, Christian; Röhrig, Rainer; Weismüller, Katja; Maier, Michael; Hossain, Hamid; Menges, Thilo; Hempelmann, Gunter; Chakraborty, Trinad

    2005-01-01

    The development of medical research networks within the framework of translational research has fostered interest in the integration of clinical and biological research data in a common database. The building of one single database integrating clinical data and biological research data requires a concept which enables scientists to retrieve information and to connect known facts to new findings. Clinical parameters are collected by a Patient Data Management System and viewed in a database which also includes genomic data. This database is designed as an Entity Attribute Value model, which implicates the development of a data warehouse concept. For the realization of this project, various requirements have to be taken into account which has to be fulfilled sufficiently in order to align with international standards. Data security and protection of data privacy are most important parts of the data warehouse concept. It has to be clear how patient pseudonymization has to be carried out in order to be within the scope of data security law. To be able to evaluate the data stored in a database consisting of clinical data collected by a Patient Data Management System and genomic research data easily, a data warehouse concept based on an Entity Attribute Value datamodel has been developed.

  7. Bringing together an ocean of information: An extensible data integration framework for biological oceanography

    NASA Astrophysics Data System (ADS)

    Stocks, Karen I.; Condit, Chris; Qian, Xufei; Brewin, Paul E.; Gupta, Amarnath

    2009-09-01

    As increasing volumes and varieties of data are becoming available online, the challenges of accessing and using heterogeneous data resources are growing. We have developed a mediator-based data integration system called Cartel for biological oceanography data. A mediation approach is appropriate in cases where a single central warehouse is not desirable, such as when the needed data sources change frequently through time, or when there are advantages for holding heterogeneous data in their native formats. Through Cartel, data sources of a variety of types can be registered to the system, and users can query against simplified virtual schemas, without needing to know the underlying schema and computational capabilities of each data source. The system can operate on a variety of relational and geospatial data formats, and can perform joins between formats. We tested the performance of the Cartel mediator in two biological oceanography application areas, and found that the system was able to support the variety of data types needed in a typical ecology study, but that the response times were unacceptably slow when very large databases (i.e. Ocean Biogeographic Information System and the World Ocean Atlas) were used. Indexing and caching are currently being added to the system to improve response times. The mediator is an open-source product, and was developed to be a generic, extensible component available to projects developing oceanography data systems.

  8. a Simple Probabilistic, Biologically Informed Model of the Population Dynamics of Desert Shrubs

    NASA Astrophysics Data System (ADS)

    Worman, S.; Furbish, D. J.; Clarke, J. H.; Roberts, A. S.

    2010-12-01

    In arid environments, spatiotemporal variations in the processes of erosion and deposition are strongly coupled with the structure and dynamics of plant communities as well as the specific life behavior of individual plants. Understanding how physical transport processes affect the evolution of the land surface on geomorphic time-scales therefore requires considering how long-term changes in plant dynamics may in turn impact such processes. The development of this desert shrub population dynamics model is therefore motivated by the need to link rain-splash induced mound building at the shrub-scale with the unfolding ‘biological play’ occurring on a hillslope. Using the Master Equation to conserve shrub age, probabilistic and biologically informed statements for recruitment and mortality are formulated to function as source and sink terms respectively. This simple accounting framework, by tracking the number of individuals entering and leaving a population, captures the changes in shrub count that can be expected in time as the key variables driving the dynamics of these plant communities (i.e. precipitation) also change in time. The result is a tool through which it is possible to statistically describe the aggregate spatiotemporal behavior of different shrub populations, with their own characteristic life-cycles and physical dimensions, under different external forcing scenarios. This model features inputs that have a solid biophysical basis and insofar as it has the capacity to mimic key features of real processes, leads to outputs which appear consistent with findings reported in the literature.

  9. Synthetic biology with artificially expanded genetic information systems. From personalized medicine to extraterrestrial life.

    PubMed

    Benner, Steven A; Hutter, Daniel; Sismour, A Michael

    2003-01-01

    Over 15 years ago, the Benner group noticed that the DNA alphabet need not be limited to the four standard nucleotides known in natural DNA. Rather, twelve nucleobases forming six base pairs joined by mutually exclusive hydrogen bonding patterns are possible within the geometry of the Watson-Crick pair (Fig. 1). Synthesis and studies on these compounds have brought us to the threshold of a synthetic biology, an artificial chemical system that does basic processes needed for life (in particular, Darwinian evolution), but with unnatural chemical structures. At the same time, the artificial genetic information systems (AEGIS) that we have developed have been used in FDA-approved commercial tests for managing HIV and hepatitis C infections in individual patients, and in a tool that seeks the virus for severe acute respiratory syndrome (SARS). AEGIS also supports the next generation of robotic probes to search for genetic molecules on Mars, Europa, and elsewhere where NASA probes will travel.

  10. 30 CFR 250.247 - What biological, physical, and socioeconomic information must accompany the DPP or DOCD?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 30 Mineral Resources 2 2010-07-01 2010-07-01 false What biological, physical, and socioeconomic information must accompany the DPP or DOCD? 250.247 Section 250.247 Mineral Resources MINERALS MANAGEMENT... SHELF Plans and Information Contents of Development and Production Plans (dpp) and...

  11. Using circulating tumor cells to inform on prostate cancer biology and clinical utility

    PubMed Central

    Li, Jing; Gregory, Simon G.; Garcia-Blanco, Mariano A.; Armstrong, Andrew J.

    2016-01-01

    Substantial advances in the molecular biology of prostate cancer have led to the approval of multiple new systemic agents to treat men with metastatic castration-resistant prostate cancer (mCRPC). These treatments encompass androgen receptor directed therapies, immunotherapies, bone targeting radiopharmaceuticals and cytotoxic chemotherapies. There is, however, great heterogeneity in the degree of patient benefit with these agents, thus fueling the need to develop predictive biomarkers that are able to rationally guide therapy. Circulating tumor cells (CTCs) have the potential to provide an assessment of tumor-specific biomarkers through a non-invasive, repeatable “liquid biopsy” of a patient’s cancer at a given point in time. CTCs have been extensively studied in men with mCRPC, where CTC enumeration using the Cellsearch® method has been validated and FDA approved to be used in conjunction with other clinical parameters as a prognostic biomarker in metastatic prostate cancer. In addition to enumeration, more sophisticated molecular profiling of CTCs is now feasible and may provide more clinical utility as it may reflect tumor evolution within an individual particularly under the pressure of systemic therapies. Here, we review technologies used to detect and characterize CTCs, and the potential biological and clinical utility of CTC molecular profiling in men with metastatic prostate cancer. PMID:26079252

  12. Separate information required for nuclear and subnuclear localization: additional complexity in localizing an enzyme shared by mitochondria and nuclei.

    PubMed Central

    Rose, A M; Joyce, P B; Hopper, A K; Martin, N C

    1992-01-01

    The TRM1 gene of Saccharomyces cerevisiae codes for a tRNA modification enzyme, N2,N2-dimethylguanosine-specific tRNA methyltransferase (m2(2)Gtase), shared by mitochondria and nuclei. Immunofluorescent staining at the nuclear periphery demonstrates that m2(2)Gtase localizes at or near the nuclear membrane. In determining sequences necessary for targeting the enzyme to nuclei and mitochondria, we found that information required to deliver the enzyme to the nucleus is not sufficient for its correct subnuclear localization. We also determined that mislocalizing the enzyme from the nucleus to the cytoplasm does not destroy its biological function. This change in location was caused by altering a sequence similar to other known nuclear targeting signals (KKSKKKRC), suggesting that shared enzymes are likely to use the same import pathway as proteins that localize only to the nucleus. As with other well-characterized mitochondrial proteins, the mitochondrial import of the shared methyltransferase depends on amino-terminal amino acids, and removal of the first 48 amino acids prevents its import into mitochondria. While this truncated protein is still imported into nuclei, the immunofluorescent staining is uniform throughout rather than at the nuclear periphery, a staining pattern identical to that described for a fusion protein consisting of the first 213 amino acids of m2(2)Gtase in frame with beta-galactosidase. As both of these proteins together contain the entire m2(2)Gtase coding region, the information necessary for association with the nuclear periphery must be more complex than the short linear sequence necessary for nuclear localization. Images PMID:1448094

  13. The most informative spacing test effectively discovers biologically relevant outliers or multiple modes in expression

    PubMed Central

    Wu, Gang; Edmonson, Michael; Liu, Zhifa; Gruber, Tanja; Zhang, Jinghui; Pounds, Stan

    2014-01-01

    Summary: Several outlier and subgroup identification statistics (OASIS) have been proposed to discover transcriptomic features with outliers or multiple modes in expression that are indicative of distinct biological processes or subgroups. Here, we borrow ideas from the OASIS methods in the bioinformatics and statistics literature to develop the ‘most informative spacing test’ (MIST) for unsupervised detection of such transcriptomic features. In an example application involving 14 cases of pediatric acute megakaryoblastic leukemia, MIST more robustly identified features that perfectly discriminate subjects according to gender or the presence of a prognostically relevant fusion-gene than did seven other OASIS methods in the analysis of RNA-seq exon expression, RNA-seq exon junction expression and micorarray exon expression data. MIST was also effective at identifying features related to gender or molecular subtype in an example application involving 157 adult cases of acute myeloid leukemia. Availability: MIST will be freely available in the OASIS R package at http://www.stjuderesearch.org/site/depts/biostats Contact: stanley.pounds@stjude.org Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24458951

  14. Exploiting Publicly Available Biological and Biochemical Information for the Discovery of Novel Short Linear Motifs

    PubMed Central

    Sayadi, Ahmed; Briganti, Leonardo; Tramontano, Anna; Via, Allegra

    2011-01-01

    The function of proteins is often mediated by short linear segments of their amino acid sequence, called Short Linear Motifs or SLiMs, the identification of which can provide important information about a protein function. However, the short length of the motifs and their variable degree of conservation makes their identification hard since it is difficult to correctly estimate the statistical significance of their occurrence. Consequently, only a small fraction of them have been discovered so far. We describe here an approach for the discovery of SLiMs based on their occurrence in evolutionarily unrelated proteins belonging to the same biological, signalling or metabolic pathway and give specific examples of its effectiveness in both rediscovering known motifs and in discovering novel ones. An automatic implementation of the procedure, available for download, allows significant motifs to be identified, automatically annotated with functional, evolutionary and structural information and organized in a database that can be inspected and queried. An instance of the database populated with pre-computed data on seven organisms is accessible through a publicly available server and we believe it constitutes by itself a useful resource for the life sciences (http://www.biocomputing.it/modipath). PMID:21799808

  15. Inframolecular acid–base and coordination properties towards Na+ and Mg2+ of myo-inositol 1,3,4,5,6-pentakisphosphate: a structural approach to biologically relevant species† †Electronic supplementary information (ESI) available: Application of the Cluster Expansion Method (Table S1); 31P NMR spectra (Fig. S1); Structural details of Ins(1,3,4,5,6)P 5–Mg2+ interaction (Fig. S2); Comparative fit of alternative chemical models for the Ins(1,3,4,5,6)P 5–Na+ system (Fig. S3). See DOI: 10.1039/c2dt31807e Click here for additional data file.

    PubMed Central

    Torres, Julia; Macho, Israel; Gómez, Kerman; Godage, Himali Y.; Riley, Andrew M.; Potter, Barry V. L.; González, Gabriel; Kremer, Carlos

    2013-01-01

    The myo-inositol phosphates (InsPs) are specific signalling metabolites ubiquitous in eukaryotic cells. Although Ins(1,3,4,5,6)P 5 is the second most abundant member of the InsPs family, its certain biological roles are far from being elucidated, in part due to the large number of species formed by Ins(1,3,4,5,6)P 5 in the presence of metal ions. In light of this, we have strived in the past to make a complete and at the same time “biological-user-friendly” description of the Ins(1,3,4,5,6)P 5 chemistry with mono and multivalent cations. In this work we expand these studies focusing on the inframolecular aspects of its protonation equilibria and the microscopic details of its coordination behaviour towards biologically relevant metal ions. We present here a systematic study of the Ins(1,3,4,5,6)P 5 intrinsic acid–base processes, in a non-interacting medium, and over a wide pH range, analyzing the 31P NMR curves by means of a model based on the Cluster Expansion Method. In addition, we have used a computational approach to analyse the energetic and structural features of the protonation and conformational changes of Ins(1,3,4,5,6)P 5, and how they are influenced by the presence of two physiologically relevant cations, Na+ and Mg2+. PMID:23183928

  16. Healthy older observers cannot use biological-motion point-light information efficiently within 4 m of themselves

    PubMed Central

    Legault, Isabelle; Troje, Nikolaus F; Faubert, Jocelyn

    2012-01-01

    Healthy aging is associated with a number of perceptual changes, but measures of biological-motion perception have yielded conflicting results. Biological motion provides information about a walker, from gender and identity to speed, direction, and distance. In our natural environment, as someone approaches us (closer distances), the walker spans larger areas of our field of view, the extent of which can be underutilized with age. Yet, the effect of age on biological-motion perception in such real-world scenarios remains unknown. We assessed the effect of age on discriminating walking direction in upright and inverted biological-motion patterns, positioned at various distances in virtual space. Findings indicate that discrimination is worse at closer distances, an effect exacerbated by age. Older adults’ performance decreases at distances as far away as 4 m, whereas younger adults maintain their performance as close as 1 m (worse at 0.5 m). This suggests that older observers are limited in their capacity to integrate information over larger areas of the visual field and supports the notion that age-related effects are more apparent when larger neural networks are required to process simultaneous information. This has further implications for social contexts where information from biological motion is critical. PMID:23145271

  17. Are Aquatic Viruses a Biological Archive of Genetic Information from Universe?

    NASA Astrophysics Data System (ADS)

    Toparceanu, F.; Negoita, Gh. T.; Nita, I. I.; Sava, D.

    2009-04-01

    After 1990, when the viruses were admited as the most abundant lifeforms from aquatic environments, it became obvious that viral lysis had an essential role on release and recycling of nutrients. Studies on cellular cultures and modeling suggest that this is an important quantitative process. The viruses from oceans represent the widest source of genetic diversity on the Earth, uncharacterized yet. The ancient lifeforms records stretching back a million years are locked in ice caps. The trend of glaciers melting as effect of actual climate change will promote the release of ancient viruses from ice caps. The increasing of the freshwater layer led to the replace of some algae species by others. Law-Racovitza Station (69o23'S 76o23'E) from East Antarctica (Larsemann Hills Oasis) offers opportunities to study the Antarctic marine ecosystem, as well as archaic aquatic ecosystems from this area ( 150 lakes and waterways resulted from ice and snow melting during the austral summer). According to Law-Racovitza Station Scientific Program, we are performing studies regarding the effect of climate changes on virus-algae host relationship in these aquatic ecosystems. Phycodnaviruses, that infect the eukaryote algae, are comprised of ancient genes and they are considered a "peek" of genetic diversity useful in biological studies and exobiology regarding the evolution of genetic sequencing. The latest discoveries of the giant aquatic viruses open the unexpected perspectives for understanding the role of viral infection in global ecosystem; beyond the old concept which considered that the viruses were only etiological agents of human, animals and plants illnesses. The aquatic viruses which infect microalgae contain similar genes of other viruses, bacteria, arhebacteria and eukaryotes, all of them being on the same genome. Which is the signification of enormous abundance of viruses and excessive diversity of genetic information encoded by viruses? There is the possibility that

  18. Information theoretic approach to complex biological network reconstruction: application to cytokine release in RAW 264.7 macrophages

    PubMed Central

    2014-01-01

    Background High-throughput methods for biological measurements generate vast amounts of quantitative data, which necessitate the development of advanced approaches to data analysis to help understand the underlying mechanisms and networks. Reconstruction of biological networks from measured data of different components is a significant challenge in systems biology. Results We use an information theoretic approach to reconstruct phosphoprotein-cytokine networks in RAW 264.7 macrophage cells. Cytokines are secreted upon activation of a wide range of regulatory signals transduced by the phosphoprotein network. Identifying these components can help identify regulatory modules responsible for the inflammatory phenotype. The information theoretic approach is based on estimation of mutual information of interactions by using kernel density estimators. Mutual information provides a measure of statistical dependencies between interacting components. Using the topology of the network derived, we develop a data-driven parsimonious input–output model of the phosphoprotein-cytokine network. Conclusions We demonstrate the applicability of our information theoretic approach to reconstruction of biological networks. For the phosphoprotein-cytokine network, this approach not only captures most of the known signaling components involved in cytokine release but also predicts new signaling components involved in the release of cytokines. The results of this study are important for gaining a clear understanding of macrophage activation during the inflammation process. PMID:24964861

  19. 43 CFR 3276.13 - What additional information must I give BLM in the monthly report for flash and dry steam...

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... BLM in the monthly report for flash and dry steam facilities? 3276.13 Section 3276.13 Public Lands... What additional information must I give BLM in the monthly report for flash and dry steam facilities? In addition to the regular monthly report information required by § 3276.12, send to BLM: (a)...

  20. 43 CFR 3276.13 - What additional information must I give BLM in the monthly report for flash and dry steam...

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... BLM in the monthly report for flash and dry steam facilities? 3276.13 Section 3276.13 Public Lands... What additional information must I give BLM in the monthly report for flash and dry steam facilities? In addition to the regular monthly report information required by § 3276.12, send to BLM: (a)...

  1. 43 CFR 3276.13 - What additional information must I give BLM in the monthly report for flash and dry steam...

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... BLM in the monthly report for flash and dry steam facilities? 3276.13 Section 3276.13 Public Lands... What additional information must I give BLM in the monthly report for flash and dry steam facilities? In addition to the regular monthly report information required by § 3276.12, send to BLM: (a)...

  2. 43 CFR 3276.13 - What additional information must I give BLM in the monthly report for flash and dry steam...

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... BLM in the monthly report for flash and dry steam facilities? 3276.13 Section 3276.13 Public Lands... What additional information must I give BLM in the monthly report for flash and dry steam facilities? In addition to the regular monthly report information required by § 3276.12, send to BLM: (a)...

  3. Use of basic biological information for rapid prediction of the response of species to habitat loss.

    PubMed

    Hockey, Philip A R; Curtis, Odette E

    2009-02-01

    Much research has focused on identifying traits that can act as useful indicators of how habitat loss affects the extinction risk of species, and the results are mixed. We developed 2 simple, rapid-assessment models of the susceptibility of species to habitat loss. We based both on an index of range size, but one also incorporated an index of body mass and the other an index combining habitat and dietary specialization. We applied the models to samples of birds (Accipitridae and Bucerotidae) and to the lemurs of Madagascar and compared the models' classifications of risk with the IUCN's global threat status of each species. The model derived from ecological attributes was much more robust than the one derived from body mass. Ecological attributes identified threatened birds and lemurs with an average of 80% accuracy and endangered and critically endangered species with 100% accuracy and identified some species not currently listed as threatened that almost certainly warrant conservation consideration. Appropriate analysis of even fairly crude biological information can help raise early-warning flags to the relative susceptibilities of species to habitat loss and thus provide a useful and rapid technique for highlighting potential species-level conservation issues. Advantages of this approach to classifying risk include flexibility in the specialization parameters used as well as its applicability at a range of spatial scales.

  4. Bioie: retargetable information extraction and ontological annotation of biological interactions from the literature.

    PubMed

    Kim, Jung-Jae; Park, Jong C

    2004-09-01

    The need for extracting general biological interactions of arbitrary types from the rapidly growing volume of the biomedical literature is drawing increased attention, while the need for this much diversity also requires both a robust treatment of complex linguistic phenomena and a method to consistently characterize the results. We present a biomedical information extraction system, BioIE, to address both of these needs by utilizing a full-fledged English grammar formalism, or a combinatory categorial grammar, and by annotating the results with the terms of Gene Ontology, which provides a common and controlled vocabulary. BioIE deals with complex linguistic phenomena such as coordination, relative structures, acronyms, appositive structures, and anaphoric expressions. In order to deal with real-world syntactic variations of ontological terms, BioIE utilizes the syntactic dependencies between words in sentences as well, based on the observation that the component words in an ontological term usually appear in a sentence with known patterns of syntactic dependencies.

  5. Microbial ecology and performance of ammonia oxidizing bacteria (AOB) in biological processes treating petrochemical wastewater with high strength of ammonia: effect of Na(2)CO(3) addition.

    PubMed

    Whang, L M; Yang, K H; Yang, Y F; Han, Y L; Chen, Y J; Cheng, S S

    2009-01-01

    This study evaluated nitrification performance and microbial ecology of AOB in a full-scale biological process, powder activated carbon treatment (PACT), and a pilot-scale biological process, moving bed biofilm reactor (MBBR), treating wastewater collected from a petrochemical industry park. The petrochemical influent wastewater characteristics showed a relative low carbon to nitrogen ratio around 1 with average COD and ammonia concentrations of 310 mg/L and 325 mg-N/L, respectively. The average nitrification efficiency of the full-scale PACT process was around 11% during this study. For the pilot-scale MBBR, the average nitrification efficiency was 24% during the Run I operation mode, which provided a slightly better performance in nitrification than that of the PACT process. During the Run II operation, the pH control mode was switched from addition of NaOH to Na(2)CO(3), leading to a significant improvement in nitrification efficiency of 51%. In addition to a dramatic change in nitrification performance, the microbial ecology of AOB, monitored with the terminal restriction fragment length polymorphism (T-RFLP) molecular methodology, was found to be different between Runs I and II. The amoA-based TRFLP results indicated that Nitrosomonas europaea lineage was the dominant AOB population during Run I operation, while Nitrosospira-like AOB was dominant during Run II operation. To confirm the effects of Na(2)CO(3) addition on the nitrification performance and AOB microbial ecology observed in the MBBR process, batch experiments were conducted. The results suggest that addition of Na(2)CO(3) as a pH control strategy can improve nitrification performance and also influence AOB microbial ecology as well. Although the exact mechanisms are not clear at this time, the results showing the effects of adding different buffering chemicals such as NaOH or Na(2)CO(3) on AOB populations have never been demonstrated until this study.

  6. Dose Addition Models Based on Biologically Relevant Reductions in Fetal Testosterone Accurately Predict Postnatal Reproductive Tract Alterations by a Phthalate Mixture in Rats

    PubMed Central

    Howdeshell, Kembra L.; Rider, Cynthia V.; Wilson, Vickie S.; Furr, Johnathan R.; Lambright, Christy R.; Gray, L. Earl

    2015-01-01

    Challenges in cumulative risk assessment of anti-androgenic phthalate mixtures include a lack of data on all the individual phthalates and difficulty determining the biological relevance of reduction in fetal testosterone (T) on postnatal development. The objectives of the current study were 2-fold: (1) to test whether a mixture model of dose addition based on the fetal T production data of individual phthalates would predict the effects of a 5 phthalate mixture on androgen-sensitive postnatal male reproductive tract development, and (2) to determine the biological relevance of the reductions in fetal T to induce abnormal postnatal reproductive tract development using data from the mixture study. We administered a dose range of the mixture (60, 40, 20, 10, and 5% of the top dose used in the previous fetal T production study consisting of 300 mg/kg per chemical of benzyl butyl (BBP), di(n)butyl (DBP), diethyl hexyl phthalate (DEHP), di-isobutyl phthalate (DiBP), and 100 mg dipentyl (DPP) phthalate/kg; the individual phthalates were present in equipotent doses based on their ability to reduce fetal T production) via gavage to Sprague Dawley rat dams on GD8-postnatal day 3. We compared observed mixture responses to predictions of dose addition based on the previously published potencies of the individual phthalates to reduce fetal T production relative to a reference chemical and published postnatal data for the reference chemical (called DAref). In addition, we predicted DA (called DAall) and response addition (RA) based on logistic regression analysis of all 5 individual phthalates when complete data were available. DA ref and DA all accurately predicted the observed mixture effect for 11 of 14 endpoints. Furthermore, reproductive tract malformations were seen in 17–100% of F1 males when fetal T production was reduced by about 25–72%, respectively. PMID:26350170

  7. Additives in plastics.

    PubMed Central

    Deanin, R D

    1975-01-01

    The polymers used in plastics are generally harmless. However, they are rarely used in pure form. In almost all commercial plastics, they are "compounded" with monomeric ingredients to improve their processing and end-use performance. In order of total volume used, these monomeric additives may be classified as follows: reinforcing fibers, fillers, and coupling agents; plasticizers; colorants; stabilizers (halogen stabilizers, antioxidants, ultraviolet absorbers, and biological preservatives); processing aids (lubricants, others, and flow controls); flame retardants, peroxides; and antistats. Some information is already available, and much more is needed, on potential toxicity and safe handling of these additives during processing and manufacture of plastics products. PMID:1175566

  8. Additives in plastics.

    PubMed

    Deanin, R D

    1975-06-01

    The polymers used in plastics are generally harmless. However, they are rarely used in pure form. In almost all commercial plastics, they are "compounded" with monomeric ingredients to improve their processing and end-use performance. In order of total volume used, these monomeric additives may be classified as follows: reinforcing fibers, fillers, and coupling agents; plasticizers; colorants; stabilizers (halogen stabilizers, antioxidants, ultraviolet absorbers, and biological preservatives); processing aids (lubricants, others, and flow controls); flame retardants, peroxides; and antistats. Some information is already available, and much more is needed, on potential toxicity and safe handling of these additives during processing and manufacture of plastics products.

  9. Regulatory and information support for evaluation of biological productivity of Ukrainian forests and climate change

    NASA Astrophysics Data System (ADS)

    Lakyda, Petro; Vasylyshyn, Roman; Lakyda, Ivan

    2013-04-01

    Stabilization and preservation of the planet's climate system today is regarded as one of the most important global political-economic, environmental and social problems of mankind. Rising concentration of carbon dioxide in the planet's atmosphere due to anthropogenic impact is the main reason leading to global climate change. Due to the above mentioned, social demands on forests are changing their biosphere role and function of natural sink of greenhouse gases becomes top priority. It is known that one of the most essential components of biological productivity of forests is their live biomass. Absorption, long-term sequestration of carbon and generation of oxygen are secured by its components. System research of its parametric structure and development of regulatory and reference information for assessment of aboveground live biomass components of trees and stands of the main forest-forming tree species in Ukraine began over twenty-five years ago at the department of forest mensuration and forest inventory of National University of Life and Environmental Sciences of Ukraine, involving staff from other research institutions. Today, regulatory and reference materials for evaluation of parametric structure of live biomass are developed for trees of the following major forest-forming tree species of Ukraine: Scots pine of natural and artificial origin, Crimean pine, Norway spruce, silver fir, pedunculate oak, European beech, hornbeam, ash, common birch, aspen and black alder (P.I. Lakyda et al., 2011). An ongoing process on development of similar regulatory and reference materials for forest stands of the abovementioned forest-forming tree species of Ukraine is secured by scientists of departments of forest management, and forest mensuration and forest inventory. The total experimental research base is 609 temporary sample plots, where 4880 model trees were processed, including 3195 model trees with estimates of live biomass components. Laboratory studies conducted

  10. On the additional information content of hyperspectral remote sensing data for estimating ecosystem carbon dioxde and energy exchange

    NASA Astrophysics Data System (ADS)

    Wohlfahrt, Georg; Hammerle, Albin; Tomelleri, Enrico

    2015-04-01

    Radiation reflected back from an ecosystem carries a spectral signature resulting from the interaction of radiation with the vegetation canopy and the underlying soil and thus allows drawing conclusions about the structure and functioning of an ecosystem. When this information is linked to a model of the leaf CO2 exchange, the ecosystem-scale CO2 exchange can be simulated. A well-known and very simplistic example for this approach is the light-use efficiency (LUE) model proposed by Monteith which links the flux of absorbed photosynthetically active radiation times a LUE parameter, both of which may be estimated based on remote sensing data, to predict the ecosystem gross photosynthesis. Here we explore the ability of a more elaborate approach by using near-surface remote sensing of hyperspectral reflected radiation, eddy covariance CO2 and energy flux measurements and a coupled radiative transfer and soil-vegetation-atmosphere-transfer (SVAT) model. Our main objective is to understand to what degree the joint assimilation of hyperspectral reflected radiation and eddy covariance flux measurements into the model helps to better constrain model parameters. To this end we use the SCOPE model, a combination of the well-known PROSAIL model and a SVAT model, and the Bayesian inversion algorithm DREAM. In order to explicitly link reflectance in the visible light and the leaf CO2 exchange, a novel parameterisation of the maximum carboxylation capacity parameter (Vcmax) on the leaf a+b chlorophyll content parameter of PROSAIL is introduced. Results are discussed with respect to the additional information content the hyperspectral data yield for simulating canopy photosynthesis.

  11. Adiponectin Provides Additional Information to Conventional Cardiovascular Risk Factors for Assessing the Risk of Atherosclerosis in Both Genders

    PubMed Central

    Yoon, Jin-Ha; Kim, Sung-Kyung; Choi, Ho-June; Choi, Soo-In; Cha, So-Youn; Koh, Sang-Baek

    2013-01-01

    Background This study evaluated the relation between adiponectin and atherosclerosis in both genders, and investigated whether adiponectin provides useful additional information for assessing the risk of atherosclerosis. Methods We measured serum adiponectin levels and other cardiovascular risk factors in 1033 subjects (454 men, 579 women) from the Korean Genomic Rural Cohort study. Carotid intima–media-thickness (CIMT) was used as measure of atherosclerosis. Odds ratios (ORs) with 95% confidence intervals (95% CI) were calculated using multiple logistic regression, and receiver operating characteristic curves (ROC), the category-free net reclassification improvement (NRI) and integrated discrimination improvement (IDI) were calculated. Results After adjustment for conventional cardiovascular risk factors, such as age, waist circumference, smoking history, low-density and high-density lipoprotein cholesterol, triglycerides, systolic blood pressure and insulin resistance, the ORs (95%CI) of the third tertile adiponectin group were 0.42 (0.25–0.72) in men and 0.47 (0.29–0.75) in women. The area under the curve (AUC) on the ROC analysis increased significantly by 0.025 in men and 0.022 in women when adiponectin was added to the logistic model of conventional cardiovascular risk factors (AUC in men: 0.655 to 0.680, p = 0.038; AUC in women: 0.654 to 0.676, p = 0.041). The NRI was 0.32 (95%CI: 0.13–0.50, p<0.001), and the IDI was 0.03 (95%CI: 0.01–0.04, p<0.001) for men. For women, the category-free NRI was 0.18 (95%CI: 0.02–0.34, p = 0.031) and the IDI was 0.003 (95%CI: −0.002–0.008, p = 0.189). Conclusion Adiponectin and atherosclerosis were significantly related in both genders, and these relationships were independent of conventional cardiovascular risk factors. Furthermore, adiponectin provided additional information to conventional cardiovascular risk factors regarding the risk of atherosclerosis. PMID:24116054

  12. A Short, Informal History of the Biological Sciences at Yale University

    PubMed Central

    Moore, Peter B.

    2012-01-01

    In May 2012, Yale University’s Graduate School of Arts and Sciences held a reunion for all who have received doctorates from Yale in the biological sciences. The proceedings began with two presentations on the history of biological research at Yale: one focused on the Medical School, and the other centered on the rest of the University. This essay is a lightly edited version of my account of the history of the biological sciences outside the Medical School. PMID:23239954

  13. Information Interactions between Members of Science-Profession Dyads as Reflected by Journal Use: Ichthyology and Fisheries Biology.

    ERIC Educational Resources Information Center

    Martin, F. Douglas

    1992-01-01

    This study examined the science-profession dyad of ichthyology and fisheries biology through citation analysis of the journal literature. It found that the fields overlap in the journals cited, and, although differences in citation behavior were identified, some exchange of information within the dyad was indicated. (38 references) (Author/MES)

  14. Influence of powdered activated carbon addition on water quality, sludge properties, and microbial characteristics in the biological treatment of commingled industrial wastewater.

    PubMed

    Hu, Qing-Yuan; Li, Meng; Wang, Can; Ji, Min

    2015-09-15

    A powdered activated carbon-activated sludge (PAC-AS) system, a traditional activated sludge (AS) system, and a powdered activated carbon (PAC) system were operated to examine the insights into the influence of PAC addition on biological treatment. The average COD removal efficiencies of the PAC-AS system (39%) were nearly double that of the AS system (20%). Compared with the average efficiencies of the PAC system (7%), COD removal by biodegradation in the PAC-AS system was remarkably higher than that in the AS system. The analysis of the influence of PAC on water quality and sludge properties showed that PAC facilitated the removal of hydrophobic matter and metabolic acidic products, and also enhanced the biomass accumulation, sludge settleability, and specific oxygen uptake rate inside the biological system. The microbial community structures in the PAC-AS and AS systems were monitored. The results showed that the average well color development in the PAC-AS system was higher than that in the AS system. The utilization of various substrates by microorganisms in the two systems did not differ. The dissimilarity index was far less than one; thus, showing that the microbial community structures of the two systems were the same.

  15. Information content-based Gene Ontology functional similarity measures: which one to use for a given biological data type?

    PubMed

    Mazandu, Gaston K; Mulder, Nicola J

    2014-01-01

    The current increase in Gene Ontology (GO) annotations of proteins in the existing genome databases and their use in different analyses have fostered the improvement of several biomedical and biological applications. To integrate this functional data into different analyses, several protein functional similarity measures based on GO term information content (IC) have been proposed and evaluated, especially in the context of annotation-based measures. In the case of topology-based measures, each approach was set with a specific functional similarity measure depending on its conception and applications for which it was designed. However, it is not clear whether a specific functional similarity measure associated with a given approach is the most appropriate, given a biological data set or an application, i.e., achieving the best performance compared to other functional similarity measures for the biological application under consideration. We show that, in general, a specific functional similarity measure often used with a given term IC or term semantic similarity approach is not always the best for different biological data and applications. We have conducted a performance evaluation of a number of different functional similarity measures using different types of biological data in order to infer the best functional similarity measure for each different term IC and semantic similarity approach. The comparisons of different protein functional similarity measures should help researchers choose the most appropriate measure for the biological application under consideration.

  16. Hofmeister effects in biology: effect of choline addition on the salt-induced super activity of horseradish peroxidase and its implication for salt resistance of plants.

    PubMed

    Pinna, M C; Bauduin, P; Touraud, D; Monduzzi, M; Ninham, B W; Kunz, W

    2005-09-01

    The effect of choline addition on the salt-induced super activity of horseradish peroxidase (HRP) is investigated. HRP is presented in the literature as an efficient H(2)O(2) scavenger, and choline is the precursor of glycine betaine, a strong osmoprotectant molecule. Both the regulations of H(2)O(2) and of osmoprotectant concentrations are implicated in plants in order to counteract salt-induced cell damage. For the oxidation of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt (ABTS), sulfate anions were found to play a crucial role in the increase of HRP activity. This induced super activity can be strongly reduced by adding choline chloride. The phenomena provide an example of physicochemical Hofmeister effects playing a central regulatory role in an important biological system.

  17. The Value of Mechanistic Biophysical Information for Systems-Level Understanding of Complex Biological Processes Such as Cytokinesis

    PubMed Central

    Pollard, Thomas D.

    2014-01-01

    This review illustrates the value of quantitative information including concentrations, kinetic constants and equilibrium constants in modeling and simulating complex biological processes. Although much has been learned about some biological systems without these parameter values, they greatly strengthen mechanistic accounts of dynamical systems. The analysis of muscle contraction is a classic example of the value of combining an inventory of the molecules, atomic structures of the molecules, kinetic constants for the reactions, reconstitutions with purified proteins and theoretical modeling to account for the contraction of whole muscles. A similar strategy is now being used to understand the mechanism of cytokinesis using fission yeast as a favorable model system. PMID:25468329

  18. Biological Data Analysis as an Information Theory Problem: Multivariable Dependence Measures and the Shadows Algorithm

    PubMed Central

    Sakhanenko, Nikita A.

    2015-01-01

    Abstract Information theory is valuable in multiple-variable analysis for being model-free and nonparametric, and for the modest sensitivity to undersampling. We previously introduced a general approach to finding multiple dependencies that provides accurate measures of levels of dependency for subsets of variables in a data set, which is significantly nonzero only if the subset of variables is collectively dependent. This is useful, however, only if we can avoid a combinatorial explosion of calculations for increasing numbers of variables.  The proposed dependence measure for a subset of variables, τ, differential interaction information, Δ(τ), has the property that for subsets of τ some of the factors of Δ(τ) are significantly nonzero, when the full dependence includes more variables. We use this property to suppress the combinatorial explosion by following the “shadows” of multivariable dependency on smaller subsets. Rather than calculating the marginal entropies of all subsets at each degree level, we need to consider only calculations for subsets of variables with appropriate “shadows.” The number of calculations for n variables at a degree level of d grows therefore, at a much smaller rate than the binomial coefficient (n, d), but depends on the parameters of the “shadows” calculation. This approach, avoiding a combinatorial explosion, enables the use of our multivariable measures on very large data sets. We demonstrate this method on simulated data sets, and characterize the effects of noise and sample numbers. In addition, we analyze a data set of a few thousand mutant yeast strains interacting with a few thousand chemical compounds. PMID:26335709

  19. Biological data analysis as an information theory problem: multivariable dependence measures and the shadows algorithm.

    PubMed

    Sakhanenko, Nikita A; Galas, David J

    2015-11-01

    Information theory is valuable in multiple-variable analysis for being model-free and nonparametric, and for the modest sensitivity to undersampling. We previously introduced a general approach to finding multiple dependencies that provides accurate measures of levels of dependency for subsets of variables in a data set, which is significantly nonzero only if the subset of variables is collectively dependent. This is useful, however, only if we can avoid a combinatorial explosion of calculations for increasing numbers of variables.  The proposed dependence measure for a subset of variables, τ, differential interaction information, Δ(τ), has the property that for subsets of τ some of the factors of Δ(τ) are significantly nonzero, when the full dependence includes more variables. We use this property to suppress the combinatorial explosion by following the "shadows" of multivariable dependency on smaller subsets. Rather than calculating the marginal entropies of all subsets at each degree level, we need to consider only calculations for subsets of variables with appropriate "shadows." The number of calculations for n variables at a degree level of d grows therefore, at a much smaller rate than the binomial coefficient (n, d), but depends on the parameters of the "shadows" calculation. This approach, avoiding a combinatorial explosion, enables the use of our multivariable measures on very large data sets. We demonstrate this method on simulated data sets, and characterize the effects of noise and sample numbers. In addition, we analyze a data set of a few thousand mutant yeast strains interacting with a few thousand chemical compounds.

  20. The Diamond Light Source and the challenges ahead for structural biology: some informal remarks

    PubMed Central

    Ramakrishnan, V.

    2015-01-01

    The remarkable advances in structural biology in the past three decades have led to the determination of increasingly complex structures that lie at the heart of many important biological processes. Many of these advances have been made possible by the use of X-ray crystallography using synchrotron radiation. In this short article, some of the challenges and prospects that lie ahead will be summarized. PMID:25624524

  1. The Diamond Light Source and the challenges ahead for structural biology: some informal remarks.

    PubMed

    Ramakrishnan, V

    2015-03-06

    The remarkable advances in structural biology in the past three decades have led to the determination of increasingly complex structures that lie at the heart of many important biological processes. Many of these advances have been made possible by the use of X-ray crystallography using synchrotron radiation. In this short article, some of the challenges and prospects that lie ahead will be summarized.

  2. Using Course Syllabi to Assess Research Expectations of Biology Majors: Implications for Further Development of Information Literacy Skills in the Curriculum

    ERIC Educational Resources Information Center

    Dinkelman, Andrea L.

    2010-01-01

    This article describes an analysis of course syllabi from selected courses in the biology curriculum at Iowa State University. The purpose of this research was to learn about the numbers and types of information literacy assignments given to students majoring in biology. Overall, the most common assignment type for biology majors was a lab report…

  3. Additive effects of predator cues and dimethoate on different levels of biological organisation in the non-biting midge Chironomus riparius.

    PubMed

    Van Praet, Nander; De Jonge, Maarten; Stoks, Robby; Bervoets, Lieven

    2014-10-01

    The combined effects of a pesticide and predation risk on sublethal endpoints in the midge Chironomus riparius were investigated using a combination of predator-release kairomones from common carp (Cyprinus carpio) and alarm substances from conspecifics together with the pesticide dimethoate. Midge larvae were exposed for 30 days to three sublethal dimethoate concentrations (0.01, 0.1 and 0.25 mg L(-1)) in the presence or absence of predator cues. Sublethal endpoints were analysed at different levels of biological organisation. Available energy reserves, enzyme biomarkers, feeding rate and life history endpoints were investigated. Three endpoints were significantly affected by the two highest dimethoate concentrations, i.e. AChE activity, age at emergence and emergence success, with a significant decrease in response after exposure to 0.25, 0.1 and 0.01 mg L(-1) dimethoate, respectively. Four sublethal endpoints were significantly affected by predator stress: Total protein content, GST activity and biomass decreased only in the presence of the predation risk, while AChE activity further decreased significantly in the presence of predation cues and effects on AChE of combined exposure were additive. From this study we can conclude that sublethal life history characteristics should be included in ecotoxicity testing as well as natural environmental stressors such as predator stress, which might act additively with pollutants on fitness related endpoints.

  4. Evolution of natural history information in the 21st century – developing an integrated framework for biological and geographical data

    USGS Publications Warehouse

    Reusser, Deborah A.; Lee, Henry

    2011-01-01

    Threats to marine and estuarine species operate over many spatial scales, from nutrient enrichment at the watershed/estuarine scale to invasive species and climate change at regional and global scales. To help address research questions across these scales, we provide here a standardized framework for a biogeographical information system containing queriable biological data that allows extraction of information on multiple species, across a variety of spatial scales based on species distributions, natural history attributes and habitat requirements. As scientists shift from research on localized impacts on individual species to regional and global scale threats, macroecological approaches of studying multiple species over broad geographical areas are becoming increasingly important. The standardized framework described here for capturing and integrating biological and geographical data is a critical first step towards addressing these macroecological questions and we urge organizations capturing biogeoinformatics data to consider adopting this framework.

  5. 36 CFR 1281.12 - What information must be provided to NARA for its report to Congress on a change or addition to a...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... provided to NARA for its report to Congress on a change or addition to a Presidential library facility... ADMINISTRATION NARA FACILITIES PRESIDENTIAL LIBRARY FACILITIES § 1281.12 What information must be provided to NARA for its report to Congress on a change or addition to a Presidential library facility? (a)...

  6. 36 CFR 1281.12 - What information must be provided to NARA for its report to Congress on a change or addition to a...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... provided to NARA for its report to Congress on a change or addition to a Presidential library facility... ADMINISTRATION NARA FACILITIES PRESIDENTIAL LIBRARY FACILITIES § 1281.12 What information must be provided to NARA for its report to Congress on a change or addition to a Presidential library facility? (a)...

  7. 36 CFR 1281.12 - What information must be provided to NARA for its report to Congress on a change or addition to a...

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... provided to NARA for its report to Congress on a change or addition to a Presidential library facility... ADMINISTRATION NARA FACILITIES PRESIDENTIAL LIBRARY FACILITIES § 1281.12 What information must be provided to NARA for its report to Congress on a change or addition to a Presidential library facility? (a)...

  8. 36 CFR 1281.12 - What information must be provided to NARA for its report to Congress on a change or addition to a...

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... provided to NARA for its report to Congress on a change or addition to a Presidential library facility... ADMINISTRATION NARA FACILITIES PRESIDENTIAL LIBRARY FACILITIES § 1281.12 What information must be provided to NARA for its report to Congress on a change or addition to a Presidential library facility? (a)...

  9. 36 CFR 1281.12 - What information must be provided to NARA for its report to Congress on a change or addition to a...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... provided to NARA for its report to Congress on a change or addition to a Presidential library facility... ADMINISTRATION NARA FACILITIES PRESIDENTIAL LIBRARY FACILITIES § 1281.12 What information must be provided to NARA for its report to Congress on a change or addition to a Presidential library facility? (a)...

  10. Using information and communication technology (ICT) to the maximum: learning and teaching biology with limited digital technologies

    NASA Astrophysics Data System (ADS)

    Van Rooy, Wilhelmina S.

    2012-04-01

    Background: The ubiquity, availability and exponential growth of digital information and communication technology (ICT) creates unique opportunities for learning and teaching in the senior secondary school biology curriculum. Digital technologies make it possible for emerging disciplinary knowledge and understanding of biological processes previously too small, large, slow or fast to be taught. Indeed, much of bioscience can now be effectively taught via digital technology, since its representational and symbolic forms are in digital formats. Purpose: This paper is part of a larger Australian study dealing with the technologies and modalities of learning biology in secondary schools. Sample: The classroom practices of three experienced biology teachers, working in a range of NSW secondary schools, are compared and contrasted to illustrate how the challenges of limited technologies are confronted to seamlessly integrate what is available into a number of molecular genetics lessons to enhance student learning. Design and method: The data are qualitative and the analysis is based on video classroom observations and semi-structured teacher interviews. Results: Findings indicate that if professional development opportunities are provided where the pedagogy of learning and teaching of both the relevant biology and its digital representations are available, then teachers see the immediate pedagogic benefit to student learning. In particular, teachers use ICT for challenging genetic concepts despite limited computer hardware and software availability. Conclusion: Experienced teachers incorporate ICT, however limited, in order to improve the quality of student learning.

  11. Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative

    PubMed Central

    Hucka, Michael; Nickerson, David P.; Bader, Gary D.; Bergmann, Frank T.; Cooper, Jonathan; Demir, Emek; Garny, Alan; Golebiewski, Martin; Myers, Chris J.; Schreiber, Falk; Waltemath, Dagmar; Le Novère, Nicolas

    2015-01-01

    The Computational Modeling in Biology Network (COMBINE) is a consortium of groups involved in the development of open community standards and formats used in computational modeling in biology. COMBINE’s aim is to act as a coordinator, facilitator, and resource for different standardization efforts whose domains of use cover related areas of the computational biology space. In this perspective article, we summarize COMBINE, its general organization, and the community standards and other efforts involved in it. Our goals are to help guide readers toward standards that may be suitable for their research activities, as well as to direct interested readers to relevant communities where they can best expect to receive assistance in how to develop interoperable computational models. PMID:25759811

  12. Alternatives of informed consent for storage and use of human biological material for research purposes: Brazilian regulation.

    PubMed

    Marodin, Gabriela; França, Paulo Henrique Condeixa de; Salgueiro, Jennifer Braathen; Motta, Marcia Luz da; Tannous, Gysélle Saddi; Lopes, Anibal Gil

    2014-12-01

    Informed consent is recognized as a primary ethical requirement to conduct research involving humans. In the investigations with the use of human biological material, informed consent (IC) assumes a differentiated condition on account of the many future possibilities. This work presents suitable alternatives for IC regarding the storage and use of human biological material in research, according to new Brazilian regulations. Both norms - Resolution 441/11 of the National Health Council, approved on 12 May 2011, and Ordinance 2.201 (NATIONAL GUIDELINES FOR BIOREPOSITORIES AND BIOBANKS OF HUMAN BIOLOGICAL MATERIAL FOR RESEARCH PURPOSE) of the Brazil Ministry of Health, approved on 14 September 2011 - state that the consent of subjects for the collection, storage and use of samples stored in Biobanks is necessarily established by means of a Free and Informed Consent Form (ICF). In order to obtain individual and formal statements, this form should contain the following two mutually exclusive options: an explanation about the use of the stored material in each research study, and the need for new consent or the waiver thereof when the material is used for a new study. On the other hand, ICF suitable for Biorepositories must be exclusive and related to specific research. Although Brazilian and international regulations identify the main aspects to be included in the IC, efforts are still necessary to improve the consent process, so that the document will become a bond of trust between subject and researcher.

  13. Motion as a source of environmental information: a fresh view on biological motion computation by insect brains.

    PubMed

    Egelhaaf, Martin; Kern, Roland; Lindemann, Jens Peter

    2014-01-01

    Despite their miniature brains insects, such as flies, bees and wasps, are able to navigate by highly erobatic flight maneuvers in cluttered environments. They rely on spatial information that is contained in the retinal motion patterns induced on the eyes while moving around ("optic flow") to accomplish their extraordinary performance. Thereby, they employ an active flight and gaze strategy that separates rapid saccade-like turns from translatory flight phases where the gaze direction is kept largely constant. This behavioral strategy facilitates the processing of environmental information, because information about the distance of the animal to objects in the environment is only contained in the optic flow generated by translatory motion. However, motion detectors as are widespread in biological systems do not represent veridically the velocity of the optic flow vectors, but also reflect textural information about the environment. This characteristic has often been regarded as a limitation of a biological motion detection mechanism. In contrast, we conclude from analyses challenging insect movement detectors with image flow as generated during translatory locomotion through cluttered natural environments that this mechanism represents the contours of nearby objects. Contrast borders are a main carrier of functionally relevant object information in artificial and natural sceneries. The motion detection system thus segregates in a computationally parsimonious way the environment into behaviorally relevant nearby objects and-in many behavioral contexts-less relevant distant structures. Hence, by making use of an active flight and gaze strategy, insects are capable of performing extraordinarily well even with a computationally simple motion detection mechanism.

  14. Fact Sheets and Additional information Regarding the 2012 Particulate Matter (PM) National Ambient Air Quality Standards (NAAQS)

    EPA Pesticide Factsheets

    Find tools for particulate matter, maps of nonattainment areas, an overview of the proposal, and information on designations, monitoring and permitting requirements and a presentation on the 2012 PM NAAQS revision.

  15. 78 FR 33846 - Agency Information Collection Activities; Proposed Collection; Comment Request; Biological...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-06-05

    ..., including Source Plasma, unlicensed registered blood establishments, and transfusion services, who had... Public Health Service Act (PHS Act) (42 U.S.C. 262), all biological products, including human blood and blood components, offered for sale in interstate commerce must be licensed and meet standards,...

  16. Demographic matrix model for informing swallow-wort (Vincetoxicum spp.) biological control

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Demographic matrix modeling of plant populations can be a powerful tool to identify key life stage transitions that contribute the most to population growth of an invasive plant and hence should be targeted for disruption (weak links) by biological control and/or other control tactics. Therefore, t...

  17. Employing spatial information technologies to monitor biological control of saltcedar in West Texas

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The saltcedar leaf beetle (Diorhadha spp.) has shown promise as a biocontrol agent for saltcedar (Tamarix spp.) invasions in the United States. In Texas, natural resource managers need assistance in monitoring biological control of invasive saltcedars. This study describes application of a medium fo...

  18. Information Literacy in the Lab: Graduate Teaching Experiences in First-Year Biology

    ERIC Educational Resources Information Center

    Lantz, Catherine

    2016-01-01

    The author interviewed 10 graduate teaching assistants leading lab sessions for first-year biology about how they introduce students to scientific literature. Qualitative data analysis of the interview transcripts revealed that both first-year students and graduate teaching assistants (many of whom are first-year teachers) struggle with…

  19. Construction of biological networks from unstructured information based on a semi-automated curation workflow.

    PubMed

    Szostak, Justyna; Ansari, Sam; Madan, Sumit; Fluck, Juliane; Talikka, Marja; Iskandar, Anita; De Leon, Hector; Hofmann-Apitius, Martin; Peitsch, Manuel C; Hoeng, Julia

    2015-06-17

    Capture and representation of scientific knowledge in a structured format are essential to improve the understanding of biological mechanisms involved in complex diseases. Biological knowledge and knowledge about standardized terminologies are difficult to capture from literature in a usable form. A semi-automated knowledge extraction workflow is presented that was developed to allow users to extract causal and correlative relationships from scientific literature and to transcribe them into the computable and human readable Biological Expression Language (BEL). The workflow combines state-of-the-art linguistic tools for recognition of various entities and extraction of knowledge from literature sources. Unlike most other approaches, the workflow outputs the results to a curation interface for manual curation and converts them into BEL documents that can be compiled to form biological networks. We developed a new semi-automated knowledge extraction workflow that was designed to capture and organize scientific knowledge and reduce the required curation skills and effort for this task. The workflow was used to build a network that represents the cellular and molecular mechanisms implicated in atherosclerotic plaque destabilization in an apolipoprotein-E-deficient (ApoE(-/-)) mouse model. The network was generated using knowledge extracted from the primary literature. The resultant atherosclerotic plaque destabilization network contains 304 nodes and 743 edges supported by 33 PubMed referenced articles. A comparison between the semi-automated and conventional curation processes showed similar results, but significantly reduced curation effort for the semi-automated process. Creating structured knowledge from unstructured text is an important step for the mechanistic interpretation and reusability of knowledge. Our new semi-automated knowledge extraction workflow reduced the curation skills and effort required to capture and organize scientific knowledge. The

  20. Effects of spawn, supplement and phase II compost additions and time of re-casing second break compost on mushroom (Agaricus bisporus) yield and biological efficiency.

    PubMed

    Royse, Daniel J; Chalupa, William

    2009-11-01

    Three cropping experiments (0710, 0803 and 0805) were conducted to determine the effect of adding spawn, various levels of delayed release nutrient, and phase II compost to 2nd break mushroom compost (2BkC) on mushroom yield and biological efficiency (BE). We also investigated the effect of delaying time of re-casing non-supplemented and supplemented 2BkC on mushroom yields and BEs. The addition of 14.6% spawn to nutrient-supplemented 2BkC (w.w./d.w) increased yield by 11.1% over the control (no spawn) but did not affect BE. The addition of delayed release supplements to 2BkC increased maximum yields by 29-54%, depending on the treatment. Substitution of 15% phase II compost in 2BkC (15/85) did not significantly affect mushroom yields. However, use of 15% phase II compost in 2BkC increased the response of the mixture to delayed release supplement. Yield response to increasing levels of supplement was greater in the 15/85 mixture compared to 100% 2BkC. Yields also increased as time of re-casing was delayed up to 10 days. Mushroom yields increased approximately 2.1% for each day re-casing was delayed. Overall yields were generally higher from commercial 2BkC compared to 2BkC originating from the Penn State Mushroom Research Center (MRC) probably due to nitrogen (N) content of the 2BkC. Nitrogen content in commercial 2BkC (Crop 0805) was 3% while N content in 2BkC from Crops 0710 and 0803 was 2.2% and 2.1%, respectively. By optimizing supplement levels and adding 15% phase II compost to commercial 2BkC, or by delaying casing by 5-10 days, it was possible to obtain BEs that were equivalent to supplemented phase II compost.

  1. 76 FR 16612 - Proposed Information Collection; Comment Request; Perceptions About the Biological and Socio...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-24

    .... Abstract The National Marine Fisheries Service (NMFS) proposes to collect demographic, socio-economic, and... using ethnographic methods--for example, participant observation, group and key informant interviews,...

  2. Effect of the addition of zero valent iron (Fe(0)) on the batch biological sulphate reduction using grass cellulose as carbon source.

    PubMed

    Mulopo, Jean; Schaefer, L

    2013-12-01

    Mineral mining generates acidic, saline, metal-rich mine waters, often referred to as acid mine drainage (AMD). Treatment of AMD and recovering saleable products during the treatment process are a necessity since water is, especially in South Africa, a scarce commodity. The aim of the study presented here was to investigate the effect of zero valent iron (Fe(0)) on the biological removal of sulphate from AMD in batch reactors. The performance of the reactors was assessed by means of sulphate reduction, chemical oxygen demand (COD), volatile fatty acid (VFA) utilisation and volatile suspended solids (VSS) concentration. To this end, three batch reactors, A, B and C (volume 2.5 L), were operated similarly with the exception of the addition of grass cuttings and iron filings. Reactors A and B received twice as much grass (100 g) as C (50 g). Reactor A received no iron filings to act as a control, while reactors B and C received 50-g iron filings for the experimental duration. The results showed that Fe(0) appears to provide sustained sulphate removal when sufficient grass substrate is available. In reactors A and C, sulphate removal efficiency was higher when the COD concentration was lower due to utilisation. In reactor B, sulphate removal efficiency was accompanied by an accumulation of COD as hydrogen (H2) provided by the Fe(0) was utilised for sulphate reduction. Furthermore, these results showed the potential of Fe(0) to enhance the participation of microorganisms in sulphate reduction.

  3. First report of Tequus schrottkyi (Konow) (Hymenoptera: Pergidae) in Uruguay, and information about its host plant and biology

    PubMed Central

    González, Andrés; Schmidt, Stefan

    2016-01-01

    Abstract Background The sawfly family Pergidae is best represented in South America, and it is the third largest family in the suborder Symphyta. Tequus is a Neotropical genus that has been reported in association with host plants of the genus Solanum (Solanaceae), with little information about the life history of its members. Tequus schrottkyi (Konow, 1906) was described from Paraguay, without any information about its biology and host plant. New information We report the first record of T. schrottkyi from Uruguay, with information on its host plant and details of its biology. The identification was based on morphology, DNA barcode is provided to allow identification using molecular characters. This sawfly species is associated with Solanum commersonii, a native plant common in Uruguay. Tequus schrottkyi presents several generations between March and July. The larvae feed on leaves and spin a silk cocoon in the soil in which they pupate. The adults exhibit sexual dimorphism, the female being larger than the male and with a different color pattern. The eggs are laid individually in the leaf margins into the leaf tissue. The larvae are unpalatable to a generalist predator, possibly due to defensive compounds sequestered from their host plant, known to contain toxic compounds. PMID:26929717

  4. Biological markers in animals can provide information on exposure and bioavailability of environmental contaminants

    SciTech Connect

    Shugart, L.R.; Adams, S.M.; Jimenez, B.D.; Talmage, S.S.; McCarthy, J.F.

    1987-01-01

    Epidemiologic studies of agents present in the environment seek to identify the extent to which they contribute to the causation of a specific toxic, clinical, or pathological endpoint. The multifactorial nature of disease etiology, long latency periods and the complexity of exposure, all contribute to the difficulty of establishing associations and casual relationships between a specific exposure and an adverse outcome. These barriers to studies of exposures and subsequent risk assessment cannot generally be changed. However, the appropriate use of biological markers in animal species living in a contaminated habitat can provide a measure of potential damage from that exposure and, in some instances, act as a surrogate for human environmental exposures. Quantitative predictivity of the effect of exposure to environmental pollutants is being approached by employing an appropriate array of biological end points. 34 refs., 1 fig., 6 tabs.

  5. Processing Biological Gender and Number Information during Chinese Pronoun Resolution: ERP Evidence for Functional Differentiation

    ERIC Educational Resources Information Center

    Xu, Xiaodong; Jiang, Xiaoming; Zhou, Xiaolin

    2013-01-01

    There have been a number of behavioral and neural studies on the processing of syntactic gender and number agreement information, marked by different morpho-syntactic features during sentence comprehension. By using the event-related potential (ERP) technique, the present study investigated whether the processing of semantic gender information and…

  6. Processing time of addition or withdrawal of single or combined balance-stabilizing haptic and visual information

    PubMed Central

    Honeine, Jean-Louis; Crisafulli, Oscar; Sozzi, Stefania

    2015-01-01

    We investigated the integration time of haptic and visual input and their interaction during stance stabilization. Eleven subjects performed four tandem-stance conditions (60 trials each). Vision, touch, and both vision and touch were added and withdrawn. Furthermore, vision was replaced with touch and vice versa. Body sway, tibialis anterior, and peroneus longus activity were measured. Following addition or withdrawal of vision or touch, an integration time period elapsed before the earliest changes in sway were observed. Thereafter, sway varied exponentially to a new steady-state while reweighting occurred. Latencies of sway changes on sensory addition ranged from 0.6 to 1.5 s across subjects, consistently longer for touch than vision, and were regularly preceded by changes in muscle activity. Addition of vision and touch simultaneously shortened the latencies with respect to vision or touch separately, suggesting cooperation between sensory modalities. Latencies following withdrawal of vision or touch or both simultaneously were shorter than following addition. When vision was replaced with touch or vice versa, adding one modality did not interfere with the effect of withdrawal of the other, suggesting that integration of withdrawal and addition were performed in parallel. The time course of the reweighting process to reach the new steady-state was also shorter on withdrawal than addition. The effects of different sensory inputs on posture stabilization illustrate the operation of a time-consuming, possibly supraspinal process that integrates and fuses modalities for accurate balance control. This study also shows the facilitatory interaction of visual and haptic inputs in integration and reweighting of stance-stabilizing inputs. PMID:26334013

  7. 33 CFR 148.108 - What if a Federal or State agency or other interested party requests additional information?

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... must state briefly why the information is needed. (c) The Commandant (CG-5) must receive the request... decision on whether or not to approve the license application. (d) The Commandant (CG-5) will consider... the application process. (e) The Commandant (CG-5) may discuss the recommendation with...

  8. 33 CFR 148.108 - What if a Federal or State agency or other interested party requests additional information?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... must state briefly why the information is needed. (c) The Commandant (CG-5) must receive the request... decision on whether or not to approve the license application. (d) The Commandant (CG-5) will consider... the application process. (e) The Commandant (CG-5) may discuss the recommendation with...

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

    PubMed

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

    2011-04-01

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

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

    PubMed Central

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

    2011-01-01

    The techniques used in protein production and structural biology have been developing rapidly, but techniques for recording the laboratory information produced have not kept pace. One approach is the development of laboratory information-management systems (LIMS), which typically use a relational database schema to model and store results from a laboratory workflow. The underlying philosophy and implementation of the Protein Information Management System (PiMS), a LIMS development specifically targeted at the flexible and unpredictable workflows of protein-production research laboratories of all scales, is described. PiMS is a web-based Java application that uses either Postgres or Oracle as the underlying relational database-management system. PiMS is available under a free licence to all academic laboratories either for local installation or for use as a managed service. PMID:21460443

  11. Space Takes Time: Concentration Dependent Output Codes from Primary Olfactory Networks Rapidly Provide Additional Information at Defined Discrimination Thresholds

    PubMed Central

    Daly, Kevin C.; Bradley, Samual; Chapman, Phillip D.; Staudacher, Erich M.; Tiede, Regina; Schachtner, Joachim

    2016-01-01

    As odor concentration increases, primary olfactory network representations expand in spatial distribution, temporal complexity and duration. However, the direct relationship between concentration dependent odor representations and the psychophysical thresholds of detection and discrimination is poorly understood. This relationship is absolutely critical as thresholds signify transition points whereby representations become meaningful to the organism. Here, we matched stimulus protocols for psychophysical assays and intracellular recordings of antennal lobe (AL) projection neurons (PNs) in the moth Manduca sexta to directly compare psychophysical thresholds and the output representations they elicit. We first behaviorally identified odor detection and discrimination thresholds across an odor dilution series for a panel of structurally similar odors. We then characterized spatiotemporal spiking patterns across a population of individually filled and identified AL PNs in response to those odors at concentrations below, at, and above identified thresholds. Using spatial and spatiotemporal based analyses we observed that each stimulus produced unique representations, even at sub-threshold concentrations. Mean response latency did not decrease and the percent glomerular activation did not increase with concentration until undiluted odor. Furthermore, correlations between spatial patterns for odor decreased, but only significantly with undiluted odor. Using time-integrated Euclidean distance (ED) measures, we determined that added spatiotemporal information was present at the discrimination but not detection threshold. This added information was evidenced by an increase in integrated distance between the sub-detection and discrimination threshold concentrations (of the same odor) that was not present in comparison of the sub-detection and detection threshold. After consideration of delays for information to reach the AL we find that it takes ~120–140 ms for the AL to

  12. 30 CFR 250.216 - What biological, physical, and socioeconomic information must accompany the EP?

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    .... Site-specific information on chemosynthetic communities, federally listed threatened or endangered species, marine mammals protected under the Marine Mammal Protection Act (MMPA), sensitive underwater features, marine sanctuaries, critical habitat designated under the Endangered Species Act (ESA), or...

  13. An information-based approach to change-point analysis with applications to biophysics and cell biology.

    PubMed

    Wiggins, Paul A

    2015-07-21

    This article describes the application of a change-point algorithm to the analysis of stochastic signals in biological systems whose underlying state dynamics consist of transitions between discrete states. Applications of this analysis include molecular-motor stepping, fluorophore bleaching, electrophysiology, particle and cell tracking, detection of copy number variation by sequencing, tethered-particle motion, etc. We present a unified approach to the analysis of processes whose noise can be modeled by Gaussian, Wiener, or Ornstein-Uhlenbeck processes. To fit the model, we exploit explicit, closed-form algebraic expressions for maximum-likelihood estimators of model parameters and estimated information loss of the generalized noise model, which can be computed extremely efficiently. We implement change-point detection using the frequentist information criterion (which, to our knowledge, is a new information criterion). The frequentist information criterion specifies a single, information-based statistical test that is free from ad hoc parameters and requires no prior probability distribution. We demonstrate this information-based approach in the analysis of simulated and experimental tethered-particle-motion data.

  14. Correlating Multimodal Physical Sensor Information with Biological Analysis in Ultra Endurance Cycling

    PubMed Central

    May, Gregory C.; Doherty, Aiden R.; Smeaton, Alan F.; Warrington, Giles D.

    2010-01-01

    The sporting domain has traditionally been used as a testing ground for new technologies which subsequently make their way into the public domain. This includes sensors. In this article a range of physical and biological sensors deployed in a 64 hour ultra-endurance non-stop cycling race are described. A novel algorithm to estimate the energy expenditure while cycling and resting during the event are outlined. Initial analysis in this noisy domain of “sensors in the field” are very encouraging and represent a first with respect to cycling. PMID:22163600

  15. Generic Information Can Retrieve Known Biological Associations: Implications for Biomedical Knowledge Discovery

    PubMed Central

    van Haagen, Herman H. H. B. M.; 't Hoen, Peter A. C.; Mons, Barend; Schultes, Erik A.

    2013-01-01

    Motivation Weighted semantic networks built from text-mined literature can be used to retrieve known protein-protein or gene-disease associations, and have been shown to anticipate associations years before they are explicitly stated in the literature. Our text-mining system recognizes over 640,000 biomedical concepts: some are specific (i.e., names of genes or proteins) others generic (e.g., ‘Homo sapiens’). Generic concepts may play important roles in automated information retrieval, extraction, and inference but may also result in concept overload and confound retrieval and reasoning with low-relevance or even spurious links. Here, we attempted to optimize the retrieval performance for protein-protein interactions (PPI) by filtering generic concepts (node filtering) or links to generic concepts (edge filtering) from a weighted semantic network. First, we defined metrics based on network properties that quantify the specificity of concepts. Then using these metrics, we systematically filtered generic information from the network while monitoring retrieval performance of known protein-protein interactions. We also systematically filtered specific information from the network (inverse filtering), and assessed the retrieval performance of networks composed of generic information alone. Results Filtering generic or specific information induced a two-phase response in retrieval performance: initially the effects of filtering were minimal but beyond a critical threshold network performance suddenly drops. Contrary to expectations, networks composed exclusively of generic information demonstrated retrieval performance comparable to unfiltered networks that also contain specific concepts. Furthermore, an analysis using individual generic concepts demonstrated that they can effectively support the retrieval of known protein-protein interactions. For instance the concept “binding” is indicative for PPI retrieval and the concept “mutation abnormality” is

  16. Motion as a source of environmental information: a fresh view on biological motion computation by insect brains

    PubMed Central

    Egelhaaf, Martin; Kern, Roland; Lindemann, Jens Peter

    2014-01-01

    Despite their miniature brains insects, such as flies, bees and wasps, are able to navigate by highly erobatic flight maneuvers in cluttered environments. They rely on spatial information that is contained in the retinal motion patterns induced on the eyes while moving around (“optic flow”) to accomplish their extraordinary performance. Thereby, they employ an active flight and gaze strategy that separates rapid saccade-like turns from translatory flight phases where the gaze direction is kept largely constant. This behavioral strategy facilitates the processing of environmental information, because information about the distance of the animal to objects in the environment is only contained in the optic flow generated by translatory motion. However, motion detectors as are widespread in biological systems do not represent veridically the velocity of the optic flow vectors, but also reflect textural information about the environment. This characteristic has often been regarded as a limitation of a biological motion detection mechanism. In contrast, we conclude from analyses challenging insect movement detectors with image flow as generated during translatory locomotion through cluttered natural environments that this mechanism represents the contours of nearby objects. Contrast borders are a main carrier of functionally relevant object information in artificial and natural sceneries. The motion detection system thus segregates in a computationally parsimonious way the environment into behaviorally relevant nearby objects and—in many behavioral contexts—less relevant distant structures. Hence, by making use of an active flight and gaze strategy, insects are capable of performing extraordinarily well even with a computationally simple motion detection mechanism. PMID:25389392

  17. Providing additional information about the benefits of statins in a leaflet for patients with coronary heart disease: a qualitative study of the impact on attitudes and beliefs

    PubMed Central

    Dickinson, Rebecca; Raynor, David K; MacDonald, Jan

    2016-01-01

    Objective To explore the impact of providing additional information about the potential benefits of simvastatin in a patient leaflet on attitudes and beliefs. Design Interview-based study using a generic qualitative approach and framework analysis. Participants 21 participants receiving a prescription for simvastatin were recruited from a general practitioner practice (from a total of 120). 8 participants were women; the age range was 55–92. Intervention Participants were provided with leaflets showing one of 3 types of additional benefit information: (1) textual statement, (2) number needed to treat (NNT) or (3) natural frequency. Semistructured interviews explored patient's attitudes and beliefs. Results A descriptive narrative of preferences for format suggested patients prefer textual as opposed to numerical benefit information. Significant barriers to the acceptance of numerical benefit information included difficulty in understanding the numbers. Patients overestimated the benefits of statins and expressed surprise at the numerical information. Conclusions Textual information was preferred but numerical information, in particular in the form of a natural frequency, may help patients make judgements about their medicines. NNTs were found to be very difficult to understand. This raises the prospect that some patients might reject medicines because of disappointment with the perceived low benefits of their medicines. The self-reported impact on behaviour appeared minimal with reports of intentions to ‘do what the doctor tells me’. Further research is needed to explore the impact of such statements on people who are yet to be prescribed a statin. PMID:27913558

  18. Information Learned from Generic Language Becomes Central to Children's Biological Concepts: Evidence from Their Open-Ended Explanations

    ERIC Educational Resources Information Center

    Cimpian, Andrei; Markman, Ellen M.

    2009-01-01

    Generic sentences (e.g., "Snakes have holes in their teeth") convey that a property (e.g., having holes in one's teeth) is true of a category (e.g., snakes). We test the hypothesis that, in addition to this basic aspect of their meaning, generic sentences also imply that the information they express is more conceptually central than the…

  19. Equilibrating errors: reliable estimation of information transmission rates in biological systems with spectral analysis-based methods.

    PubMed

    Ignatova, Irina; French, Andrew S; Immonen, Esa-Ville; Frolov, Roman; Weckström, Matti

    2014-06-01

    Shannon's seminal approach to estimating information capacity is widely used to quantify information processing by biological systems. However, the Shannon information theory, which is based on power spectrum estimation, necessarily contains two sources of error: time delay bias error and random error. These errors are particularly important for systems with relatively large time delay values and for responses of limited duration, as is often the case in experimental work. The window function type and size chosen, as well as the values of inherent delays cause changes in both the delay bias and random errors, with possibly strong effect on the estimates of system properties. Here, we investigated the properties of these errors using white-noise simulations and analysis of experimental photoreceptor responses to naturalistic and white-noise light contrasts. Photoreceptors were used from several insect species, each characterized by different visual performance, behavior, and ecology. We show that the effect of random error on the spectral estimates of photoreceptor performance (gain, coherence, signal-to-noise ratio, Shannon information rate) is opposite to that of the time delay bias error: the former overestimates information rate, while the latter underestimates it. We propose a new algorithm for reducing the impact of time delay bias error and random error, based on discovering, and then using that size of window, at which the absolute values of these errors are equal and opposite, thus cancelling each other, allowing minimally biased measurement of neural coding.

  20. EPA evaluation of the SYNERGY-1 fuel additive under Section 511 of the Motor Vehicle Information and Cost Savings Act. Technical report

    SciTech Connect

    Syria, S.L.

    1981-06-01

    This document announces the conclusions of the EPA evaluation of the 'SYNERGY-1' device under provisions of Section 511 of the Motor Vehicle Information and Cost Savings Act. This additive is intended to improve fuel economy and exhaust emission levels of two and four cycle gasoline fueled engines.

  1. Improve Quality of Life - additional criteria for health and social care information technology acceptance in an ageing world.

    PubMed

    Monteiro, Jorge

    2012-01-01

    Reversing the rising cost of health and social systems is needed in ageing developed and developing countries. A new model of ageing is advocated by the World Health Organization. This new model asks for more personal health accountability and a more integrated approach on care and preventive cure. Information systems and technologies can play an important role in supporting the changes needed in order to have better and more sustainable health and social care systems. Using value and results for patients as criteria by which systems are accepted by users and by organizations can contribute to a value based competition in health and social care systems. The unified theory of acceptance and use of technology is presented, and the pertinence of adding an extension to the theory in order capture Quality of Life improvements expectations is explored.

  2. Morphology of juvenile stages of Kuschelina bergi (Harold) with biological information (Coleoptera, Chrysomelidae, Alticini)

    PubMed Central

    Cabrera, Nora; Sosa, Alejandro; Telesnicki, Marta; Julien, Mic

    2016-01-01

    Abstract Kuschelina bergi (Harold, 1881) is being studied to be evaluated as a natural enemy of Phyla nodiflora var. minor (Hook.) N. O’Leary & Múlgura (Verbenaceae), an invasive weed in Australia. Eggs, and 1st and 3rd instar larvae are described and illustrated for the first time. The following characters distinguish Kuschelina bergi: presence of two medial setae in prosternum, mesosternum and metasternum, absence of tubercle on sternum I and eight setae in abdominal segment IX. The 3rd instar larvae of Kuschelina bergi resemble Kuschelina gibbitarsa (Say) larvae: the body shape and details of mouthparts are similar, but the morphology of the mandible is different, as is the tarsungulus which has a single seta. Differences between Kuschelina bergi and other known larvae of Oedionychina are discussed. New biological data based on laboratory rearing and field observation are also presented and discussed. PMID:27006616

  3. An Information Storage and Retrieval System for Biological and Geological Data. Interim Report.

    ERIC Educational Resources Information Center

    Squires, Donald F.

    A project is being conducted to test the feasibility of an information storage and retrieval system for museum specimen data, particularly for natural history museums. A pilot data processing system has been developed, with the specimen records from the national collections of birds, marine crustaceans, and rocks used as sample data. The research…

  4. BioTCM-SE: a semantic search engine for the information retrieval of modern biology and traditional Chinese medicine.

    PubMed

    Chen, Xi; Chen, Huajun; Bi, Xuan; Gu, Peiqin; Chen, Jiaoyan; Wu, Zhaohui

    2014-01-01

    Understanding the functional mechanisms of the complex biological system as a whole is drawing more and more attention in global health care management. Traditional Chinese Medicine (TCM), essentially different from Western Medicine (WM), is gaining increasing attention due to its emphasis on individual wellness and natural herbal medicine, which satisfies the goal of integrative medicine. However, with the explosive growth of biomedical data on the Web, biomedical researchers are now confronted with the problem of large-scale data analysis and data query. Besides that, biomedical data also has a wide coverage which usually comes from multiple heterogeneous data sources and has different taxonomies, making it hard to integrate and query the big biomedical data. Embedded with domain knowledge from different disciplines all regarding human biological systems, the heterogeneous data repositories are implicitly connected by human expert knowledge. Traditional search engines cannot provide accurate and comprehensive search results for the semantically associated knowledge since they only support keywords-based searches. In this paper, we present BioTCM-SE, a semantic search engine for the information retrieval of modern biology and TCM, which provides biologists with a comprehensive and accurate associated knowledge query platform to greatly facilitate the implicit knowledge discovery between WM and TCM.

  5. From linked open data to molecular interaction: studying selectivity trends for ligands of the human serotonin and dopamine transporter† †The authors declare no competing interests. ‡ ‡Electronic supplementary information (ESI) available. See DOI: 10.1039/c6md00207b Click here for additional data file. Click here for additional data file. Click here for additional data file. Click here for additional data file. Click here for additional data file. Click here for additional data file. Click here for additional data file. Click here for additional data file.

    PubMed Central

    Hellsberg, Eva; Viereck, Michael; Ecker, Gerhard F.

    2016-01-01

    Retrieval of congeneric and consistent SAR data sets for protein targets of interest is still a laborious task to do if no appropriate in-house data set is available. However, combining integrated open data sources (such as the Open PHACTS Discovery Platform) with workflow tools now offers the possibility of querying across multiple domains and tailoring the search to the given research question. Starting from two phylogenetically related protein targets of interest (the human serotonin and dopamine transporters), the whole chemical compound space was explored by implementing a scaffold-based clustering of compounds possessing biological measurements for both targets. In addition, potential hERG blocking liabilities were included. The workflow allowed studying the selectivity trends of scaffold series, identifying potentially harmful compound series, and performing SAR, docking studies and molecular dynamics (MD) simulations for a consistent data set of 56 cathinones. This delivered useful insights into driving determinants for hDAT selectivity over hSERT. With respect to the scaffold-based analyses it should be noted that the cathinone data set could be retrieved only when Murcko scaffold analyses were combined with similarity searches such as a common substructure search. PMID:27891211

  6. Comparing the information content of coral reef geomorphological and biological habitat maps, Amirantes Archipelago (Seychelles), Western Indian Ocean

    NASA Astrophysics Data System (ADS)

    Hamylton, S.; Andréfouët, S.; Spencer, T.

    2012-10-01

    Increasing the use of geomorphological map products in marine spatial planning has the potential to greatly enhance return on mapping investment as they are commonly two orders of magnitude cheaper to produce than biologically-focussed maps of benthic communities and shallow substrates. The efficacy of geomorphological maps derived from remotely sensed imagery as surrogates for habitat diversity is explored by comparing two map sets of the platform reefs and atolls of the Amirantes Archipelago (Seychelles), Western Indian Ocean. One mapping campaign utilised Compact Airborne Spectrographic Imagery (19 wavebands, 1 m spatial resolution) to classify 11 islands and associated reefs into 25 biological habitat classes while the other campaign used Landsat 7 + ETM imagery (7 bands, 30 m spatial resolution) to generate maps of 14 geomorphic classes. The maps were compared across a range of characteristics, including habitat richness (number of classes mapped), diversity (Shannon-Weiner statistic) and thematic content (Cramer's V statistic). Between maps, a strong relationship was revealed for habitat richness (R2 = 0.76), a moderate relationship for class diversity and evenness (R2 = 0.63) and a variable relationship for thematic content, dependent on site complexity (V range 0.43-0.93). Geomorphic maps emerged as robust predictors of the habitat richness in the Amirantes. Such maps therefore demonstrate high potential value for informing coastal management activities and conservation planning by drawing on information beyond their own thematic content and thus maximizing the return on mapping investment.

  7. Are head-to-head trials of biologics needed? The role of value of information methods in arthritis research.

    PubMed

    Welton, Nicky J; Madan, Jason; Ades, Anthony E

    2011-09-01

    Reimbursement decisions are typically based on cost-effectiveness analyses. While a cost-effectiveness analysis can identify the optimum strategy, there is usually some degree of uncertainty around this decision. Sources of uncertainty include statistical sampling error in treatment efficacy measures, underlying baseline risk, utility measures and costs, as well as uncertainty in the structure of the model. The optimal strategy is therefore only optimal on average, and a decision to adopt this strategy might still be the wrong decision if all uncertainty could be eliminated. This means that there is a quantifiable expected (average) loss attaching to decisions made under uncertainty, and hence a value in collecting information to reduce that uncertainty. Value of information (VOI) analyses can be used to provide guidance on whether more research would be cost-effective, which particular model inputs (parameters) have the most bearing on decision uncertainty, and can also help with the design and sample size of further research. Here, we introduce the key concepts in VOI analyses, and highlight the inputs required to calculate it. The adoption of the new biologic treatments for RA and PsA tends to be based on placebo-controlled trials. We discuss the possible role of VOI analyses in deciding whether head-to-head comparisons of the biologic therapies should be carried out, illustrating with examples from other fields. We emphasize the need for a model of the natural history of RA and PsA, which reflects a consensus view.

  8. Sensitivity analysis of biological Boolean networks using information fusion based on nonadditive set functions

    PubMed Central

    2014-01-01

    Background An algebraic method for information fusion based on nonadditive set functions is used to assess the joint contribution of Boolean network attributes to the sensitivity of the network to individual node mutations. The node attributes or characteristics under consideration are: in-degree, out-degree, minimum and average path lengths, bias, average sensitivity of Boolean functions, and canalizing degrees. The impact of node mutations is assessed using as target measure the average Hamming distance between a non-mutated/wild-type network and a mutated network. Results We find that for a biochemical signal transduction network consisting of several main signaling pathways whose nodes represent signaling molecules (mainly proteins), the algebraic method provides a robust classification of attribute contributions. This method indicates that for the biochemical network, the most significant impact is generated mainly by the combined effects of two attributes: out-degree, and average sensitivity of nodes. Conclusions The results support the idea that both topological and dynamical properties of the nodes need to be under consideration. The algebraic method is robust against the choice of initial conditions and partition of data sets in training and testing sets for estimation of the nonadditive set functions of the information fusion procedure. PMID:25189194

  9. Quantum One Go Computation and the Physical Computation Level of Biological Information Processing

    NASA Astrophysics Data System (ADS)

    Castagnoli, Giuseppe

    2010-02-01

    By extending the representation of quantum algorithms to problem-solution interdependence, the unitary evolution part of the algorithm entangles the register containing the problem with the register containing the solution. Entanglement becomes correlation, or mutual causality, between the two measurement outcomes: the string of bits encoding the problem and that encoding the solution. In former work, we showed that this is equivalent to the algorithm knowing in advance 50% of the bits of the solution it will find in the future, which explains the quantum speed up. Mutual causality between bits of information is also equivalent to seeing quantum measurement as a many body interaction between the parts of a perfect classical machine whose normalized coordinates represent the qubit populations. This “hidden machine” represents the problem to be solved. The many body interaction (measurement) satisfies all the constraints of a nonlinear Boolean network “together and at the same time”—in one go—thus producing the solution. Quantum one go computation can formalize the physical computation level of the theories that place consciousness in quantum measurement. In fact, in visual perception, we see, thus recognize, thus process, a significant amount of information “together and at the same time”. Identifying the fundamental mechanism of consciousness with that of the quantum speed up gives quantum consciousness, with respect to classical consciousness, a potentially enormous evolutionary advantage.

  10. Designing mental health interventions informed by child development and human biology theory: a social ecology intervention for child soldiers in Nepal.

    PubMed

    Kohrt, Brandon A; Jordans, Mark J D; Koirala, Suraj; Worthman, Carol M

    2015-01-01

    The anthropological study of human biology, health, and child development provides a model with potential to address the gap in population-wide mental health interventions. Four key concepts from human biology can inform public mental health interventions: life history theory and tradeoffs, redundancy and plurality of pathways, cascades and multiplier effects in biological systems, and proximate feedback systems. A public mental health intervention for former child soldiers in Nepal is used to illustrate the role of these concepts in intervention design and evaluation. Future directions and recommendations for applying human biology theory in pursuit of public mental health interventions are discussed.

  11. Habitat characteristics for different freshwater snail species as determined biologically through macroinvertebrate information.

    PubMed

    El-Khayat, Hanaa M M; Mahmoud, Kadria M A; Mostafa, Bayomy B; Tantawy, Ahmad A; El-Deeb, Fatma A; Ragb, Fawzy M; Ismail, Nahed M; El-Said, Kalil M; Taleb, Hoda M Abu

    2011-12-01

    Macro-invertebrates including freshwater snails collected from 643 sites over 8 successive seasons among the River Nile, branches, main canals and certain drains in eight Egyptian Governorates. Thirteen snail species and one bivalve species were identified. The most distributed were Lanistus carinatus and Physa acuta while the most abundant were Cleopatra bulimoides and Physa acuta during the whole study. The sites that harbored each snail species in all the examined water-courses were grouped seasonally and their biological assessment was determined by their minimum and maximum total point similarity percentage to that of the corresponded reference site and mean of the total points. Habitats for most snail species attained minimum total point's similarity percentage less than 21% (very poor habitat) during autumn and winter then spring while during summer very poor habitat was harbored by only few snail species. P. acuta was the only survived snails in habitat which attained 0 as a minimum total point's similarity percentage during two seasons and L. carinatus and Succinea cleopatra during one season. With respect to medically important snails very poor sites constituted 23% of Biomphalaria alexandrina sites, 14% of Lymnaea natalensis and 9.4% of Bulinus truncatus sites. The studied macroinvertebrate matrices, total number of organisms, taxa richness, the Ephemeroptera, Plecoptera, and Trichoptera (EPT) index, ratio of EPT index to chironomidae, ratio of scraper to filtering collector, contribution of dominant macroinvertebrate major group, comparison revealed descending tolerances from B. alexanrina followed by L. natalensis then B. truncates, but Hilsenhoff Biotic Index (HBI) showed the same tolerance to organic pollution.

  12. Dose addition models based on biologically-relevant reductions in fetal testosterone accurately predict postnatal reproductive tract alterations by a phthalate mixture in rats

    EPA Science Inventory

    Challenges in cumulative risk assessment of anti-androgenic phthalate mixtures include a lack of data on all the individual phthalates and difficulty determining the biological relevance of reduction in fetal testosterone (T) on postnatal development. The objectives of the curren...

  13. Information learned from generic language becomes central to children's biological concepts: evidence from their open-ended explanations.

    PubMed

    Cimpian, Andrei; Markman, Ellen M

    2009-10-01

    Generic sentences (e.g., "Snakes have holes in their teeth") convey that a property (e.g., having holes in one's teeth) is true of a category (e.g., snakes). We test the hypothesis that, in addition to this basic aspect of their meaning, generic sentences also imply that the information they express is more conceptually central than the information conveyed in similar non-generic sentences (e.g., "This snake has holes in his teeth"). To test this hypothesis, we elicited 4- and 5-year-old children's open-ended explanations for generic and non-generic versions of the same novel properties. Based on arguments in the categorization literature, we assumed that, relative to more peripheral properties, properties that are understood as conceptually central would be explained more often as causes and less often as effects of other features, behaviors, or processes. Two experiments confirmed the prediction that preschool-age children construe novel information learned from generics as more conceptually central than the same information learned from non-generics. Additionally, Experiment 2 suggested that the conceptual status of novel properties learned from generic sentences becomes similar to that of familiar properties that are already at the category core. These findings illustrate the power of generic language to shape children's concepts.

  14. Exploring the Factors Related to Acceptance of Evolutionary Theory among Turkish Preservice Biology Teachers: Toward a More Informative Conceptual Ecology for Biological Evolution

    ERIC Educational Resources Information Center

    Deniz, Hasan; Donnelly, Lisa A.; Yilmaz, Irfan

    2008-01-01

    In this study, using multiple regression analysis, we aimed to explore the factors related to acceptance of evolutionary theory among preservice Turkish biology teachers using conceptual ecology for biological evolution as a theoretical lens. We aimed to determine the extent to which we can account for the variance in acceptance of evolutionary…

  15. TOLKIN – Tree of Life Knowledge and Information Network: Filling a Gap for Collaborative Research in Biological Systematics

    PubMed Central

    Beaman, Reed S.; Traub, Greg H.; Dell, Christopher A.; Santiago, Nestor; Koh, Jin; Cellinese, Nico

    2012-01-01

    The development of biological informatics infrastructure capable of supporting growing data management and analysis environments is an increasing need within the systematics biology community. Although significant progress has been made in recent years on developing new algorithms and tools for analyzing and visualizing large phylogenetic data and trees, implementation of these resources is often carried out by bioinformatics experts, using one-off scripts. Therefore, a gap exists in providing data management support for a large set of non-technical users. The TOLKIN project (Tree of Life Knowledge and Information Network) addresses this need by supporting capabilities to manage, integrate, and provide public access to molecular, morphological, and biocollections data and research outcomes through a collaborative, web application. This data management framework allows aggregation and import of sequences, underlying documentation about their source, including vouchers, tissues, and DNA extraction. It combines features of LIMS and workflow environments by supporting management at the level of individual observations, sequences, and specimens, as well as assembly and versioning of data sets used in phylogenetic inference. As a web application, the system provides multi-user support that obviates current practices of sharing data sets as files or spreadsheets via email. PMID:22724002

  16. Evaluating AE Reporting of Two Off-Patent Biologics to Inform Future Biosimilar Naming and Reporting Practices.

    PubMed

    Stergiopoulos, Stella; Getz, Kenneth

    2015-08-01

    Historical studies of voluntary, spontaneous drug reports show poor attribution of adverse events to generic versions of commonly prescribed medications. As biosimilars enter the market place, it may be similarly difficult to accurately attribute adverse events to their respective reference products. At this time, lack of global consensus with regard to biosimilar naming conventions may result in drug reporting confusion, misattribution of adverse events and insufficient active monitoring of safety signals. Now, with the first biosimilar approval in the USA and many biosimilars expected to be launched globally in the near future, US Food and Drug Administration (FDA) guidance on biosimilar naming conventions will be essential. To inform the FDA and the global drug development community, the Tufts Center for the Study of Drug Development (Tufts CSDD) examined primary suspect reports sent to the FDA's Adverse Event Reporting System (FAERS) from US reporters for two biologics that have lost patent exclusivity--somatropin and human insulin--and extracted 4703 insulin reports and 6487 somatropin reports from FAERS. The results show that reporting practices are inconsistent between the two biologics that were evaluated and that manufacturer identifiability and traceability are lacking. Ways to improve biosimilar naming conventions and improve reporting practices are suggested.

  17. Insights on the Application of the Retro Michael-Type Addition on Maleimide-Functionalized Gold Nanoparticles in Biology and Nanomedicine.

    PubMed

    Weissman, Max R; Winger, Kathleen T; Ghiassian, Sara; Gobbo, Pierangelo; Workentin, Mark S

    2016-03-16

    The glutathione-mediated retro Michael-type addition reaction is demonstrated to take place at the interface of small water-soluble maleimide-functionalized gold nanoparticles (Maleimide-AuNP). The retro Michael-type addition reaction can be blocked by hydrolyzing the Michael addition thioether adduct at the nanoparticle's interface under reaction conditions that do not cause AuNP decomposition. This procedure "locks" the molecule of interest onto the Maleimide-AuNP template for potential uses in medical imaging and bioconjugation, ensuring no loss of the molecular cargo from the nanocarrier. On the other hand, the glutathione-mediated retro Michael-type addition reaction can be exploited for delivering a molecular payload. As a proof of concept, a fluorogenic molecular cargo was incorporated onto a Maleimide-AuNP and delivered via the glutathione-mediated retro Michael-type addition reaction.

  18. Time-resolved diffuse optical tomographic imaging for the provision of both anatomical and functional information about biological tissue

    NASA Astrophysics Data System (ADS)

    Zhao, Huijuan; Gao, Feng; Tanikawa, Yukari; Homma, Kazuhiro; Yamada, Yukio

    2005-04-01

    We present in vivo images of near-infrared (NIR) diffuse optical tomography (DOT) of human lower legs and forearm to validate the dual functions of a time-resolved (TR) NIR DOT in clinical diagnosis, i.e., to provide anatomical and functional information simultaneously. The NIR DOT system is composed of time-correlated single-photon-counting channels, and the image reconstruction algorithm is based on the modified generalized pulsed spectral technique, which effectively incorporates the TR data with reasonable computation time. The reconstructed scattering images of both the lower legs and the forearm revealed their anatomies, in which the bones were clearly distinguished from the muscles. In the absorption images, some of the blood vessels were observable. In the functional imaging, a subject was requested to do handgripping exercise to stimulate physiological changes in the forearm tissue. The images of oxyhemoglobin, deoxyhemoglobin, and total hemoglobin concentration changes in the forearm were obtained from the differential images of the absorption at three wavelengths between the exercise and the rest states, which were reconstructed with a differential imaging scheme. These images showed increases in both blood volume and oxyhemoglobin concentration in the arteries and simultaneously showed hypoxia in the corresponding muscles. All the results have demonstrated the capability of TR NIR DOT by reconstruction of the absolute images of the scattering and the absorption with a high spatial resolution that finally provided both the anatomical and functional information inside bulky biological tissues.

  19. How can biologically-based modeling of arsenic kinetics and dynamics inform the risk assessment process? - A workshop review.

    PubMed

    Kenyon, Elaina M; Klimecki, Walter T; El-Masri, Hisham; Conolly, Rory B; Clewell, Harvey J; Beck, Barbara D

    2008-11-01

    Quantitative biologically-based models describing key events in the continuum from arsenic exposure to the development of adverse health effects provide a framework to integrate information obtained across diverse research areas. For example, genetic polymorphisms in arsenic metabolizing enzymes can lead to differences in target tissue dosimetry for key metabolites causative in toxic and carcinogenic response. This type of variation can be quantitatively incorporated into pharmacokinetic (PK) models and used together with population-based modeling approaches to evaluate the impact of genetic variation in methylation capacity on dose of key metabolites to target tissue. The PK model is an essential bridge to the pharmacodynamic (PD) models. A particular benefit of PD modeling for arsenic is that alternative models can be constructed for multiple proposed modes of action for arsenicals. Genomics data will prove useful for identifying the key pathways involved in particular responses and aid in determining other types of data needed for quantitative modeling. These models, when linked with PK models, can be used to better understand and explain dose- and time-response behaviors. This in turn assists in prioritizing modes of action with respect to their risk assessment relevance and future research. This type of integrated modeling approach can form the basis for a highly informative mode-of-action directed risk assessment for inorganic arsenic (iAs). This paper will address both practical and theoretical aspects of integrating PK and PD data in a modeling framework, including practical barriers to its application.

  20. Differential cortical processing of local and global motion information in biological motion: an event-related potential study.

    PubMed

    Hirai, Masahiro; Kakigi, Ryusuke

    2008-12-15

    To reveal the neural dynamics underlying biological motion processing, we introduced a novel golf-swing point-light motion (PLM) stimulus with an adaptation paradigm and measured event-related potentials (ERPs). In the adaptation phase, PLM and scrambled PLM (sPLM) stimuli were presented; a static point-lights stimulus was also presented as a control condition. In the subsequent test phase, PLM or sPLM stimuli were presented. We measured ERPs from the onset of the test phase. Two negative components were observed and modulated differently: the amplitude of the N1 component was significantly attenuated by PLM and sPLM adaptation stimuli compared with the static point-light adaptation stimulus, whereas the amplitude of the N2 component in response to the PLM test stimulus was significantly attenuated only by the PLM adaptation stimulus. The amplitude of the N2 component in response to the PLM test stimulus was significantly larger than that in response to the sPLM test stimulus when a sPLM or static adaptation stimulus was used. These findings indicate that the N1 component is sensitive to local motion information while the N2 component is sensitive to the presence of a coherent form conveyed by global motion.

  1. Improving data analysis in herpetology: Using Akaike's information criterion (AIC) to assess the strength of biological hypotheses

    USGS Publications Warehouse

    Mazerolle, M.J.

    2006-01-01

    In ecology, researchers frequently use observational studies to explain a given pattern, such as the number of individuals in a habitat patch, with a large number of explanatory (i.e., independent) variables. To elucidate such relationships, ecologists have long relied on hypothesis testing to include or exclude variables in regression models, although the conclusions often depend on the approach used (e.g., forward, backward, stepwise selection). Though better tools have surfaced in the mid 1970's, they are still underutilized in certain fields, particularly in herpetology. This is the case of the Akaike information criterion (AIC) which is remarkably superior in model selection (i.e., variable selection) than hypothesis-based approaches. It is simple to compute and easy to understand, but more importantly, for a given data set, it provides a measure of the strength of evidence for each model that represents a plausible biological hypothesis relative to the entire set of models considered. Using this approach, one can then compute a weighted average of the estimate and standard error for any given variable of interest across all the models considered. This procedure, termed model-averaging or multimodel inference, yields precise and robust estimates. In this paper, I illustrate the use of the AIC in model selection and inference, as well as the interpretation of results analysed in this framework with two real herpetological data sets. The AIC and measures derived from it is should be routinely adopted by herpetologists. ?? Koninklijke Brill NV 2006.

  2. Biological Risks to Public Health: Lessons from an International Conference to Inform the Development of National Risk Communication Strategies

    PubMed Central

    Bhatiasevi, Aphaluck; Chaib, Fadela; Baggio, Ombretta; Banluta, Christina; Hollenweger, Lilian; Maaroufi, Abderrahmane

    2016-01-01

    Biological risk management in public health focuses on the impact of outbreaks on health, the economy, and other systems and on ensuring biosafety and biosecurity. To address this broad range of risks, the International Health Regulations (IHR, 2005) request that all member states build defined core capacities, risk communication being one of them. While there is existing guidance on the communication process and on what health authorities need to consider to design risk communication strategies that meet the requirements on a governance level, little has been done on implementation because of a number of factors, including lack of resources (human, financial, and others) and systems to support effective and consistent capacity for risk communication. The international conference on “Risk communication strategies before, during and after public health emergencies” provided a platform to present current strategies, facilitate learning from recent outbreaks of infectious diseases, and discuss recommendations to inform risk communication strategy development. The discussion concluded with 4 key areas for improvement in risk communication: consider communication as a multidimensional process in risk communication, broaden the biomedical paradigm by integrating social science intelligence into epidemiologic risk assessments, strengthen multisectoral collaboration including with local organizations, and spearhead changes in organizations for better risk communication governance. National strategies should design risk communication to be proactive, participatory, and multisectoral, facilitating the connection between sectors and strengthening collaboration. PMID:27875654

  3. Biological Risks to Public Health: Lessons from an International Conference to Inform the Development of National Risk Communication Strategies.

    PubMed

    Dickmann, Petra; Bhatiasevi, Aphaluck; Chaib, Fadela; Baggio, Ombretta; Banluta, Christina; Hollenweger, Lilian; Maaroufi, Abderrahmane

    Biological risk management in public health focuses on the impact of outbreaks on health, the economy, and other systems and on ensuring biosafety and biosecurity. To address this broad range of risks, the International Health Regulations (IHR, 2005) request that all member states build defined core capacities, risk communication being one of them. While there is existing guidance on the communication process and on what health authorities need to consider to design risk communication strategies that meet the requirements on a governance level, little has been done on implementation because of a number of factors, including lack of resources (human, financial, and others) and systems to support effective and consistent capacity for risk communication. The international conference on "Risk communication strategies before, during and after public health emergencies" provided a platform to present current strategies, facilitate learning from recent outbreaks of infectious diseases, and discuss recommendations to inform risk communication strategy development. The discussion concluded with 4 key areas for improvement in risk communication: consider communication as a multidimensional process in risk communication, broaden the biomedical paradigm by integrating social science intelligence into epidemiologic risk assessments, strengthen multisectoral collaboration including with local organizations, and spearhead changes in organizations for better risk communication governance. National strategies should design risk communication to be proactive, participatory, and multisectoral, facilitating the connection between sectors and strengthening collaboration.

  4. [Underreporting of tuberculosis in the Information System on Notifiable Diseases (SINAN): primary default and case detection from additional data sources using probabilistic record linkage].

    PubMed

    Pinheiro, Rejane Sobrino; Andrade, Vanusa de Lemos; Oliveira, Gisele Pinto de

    2012-08-01

    This study aimed to analyze underreporting of tuberculosis (TB) cases in the Information System on Notifiable Diseases (SINAN), based on the following data sources: Mortality Information System (SIM), Registry and Follow-up Book for TB Case Treatment (LPATB), and Laboratory Registry Book (LRLAB). Probabilistic record linkage was used between the SIM (2007-2008) and SINAN (2002-2008). A search was conducted in LPATB and LRLAB (2007-2008) for cases not recorded in SINAN. There were 125 deaths, of which 44.8% were not recorded in SINAN. In LPATB, 58 cases (5.1%) were in treatment and were not reported in SINAN. LRLAB showed 32 smear-positive cases not reported to SINAN and without treatment, representing primary default. Addition of the retrieved cases, led to a 14.6% increase in the incidence rate in 2007 and 11.6% in 2008. Underreporting of deaths from or with TB in the Mortality Information System and primary default revealed difficulties in access to adequate and timely treatment, calling for rethinking of strategies to detect cases for timely treatment.

  5. Preparation of layered double hydroxides and their applications as additives in polymers, as precursors to magnetic materials and in biology and medicine.

    PubMed

    Evans, David G; Duan, Xue

    2006-02-07

    In recent years layered double hydroxides (LDHs), also known as hydrotalcite-like materials, have attracted considerable interest from both industry and academia. In this article, we discuss methods of preparing LDHs with an emphasis on the way in which particle size and morphology can be controlled with regard to specific target applications; scale-up of one such preparation procedure is also described. In addition, we review selected applications of LDHs developed by our own and other laboratories.

  6. Biological membranes

    PubMed Central

    Watson, Helen

    2015-01-01

    Biological membranes allow life as we know it to exist. They form cells and enable separation between the inside and outside of an organism, controlling by means of their selective permeability which substances enter and leave. By allowing gradients of ions to be created across them, membranes also enable living organisms to generate energy. In addition, they control the flow of messages between cells by sending, receiving and processing information in the form of chemical and electrical signals. This essay summarizes the structure and function of membranes and the proteins within them, and describes their role in trafficking and transport, and their involvement in health and disease. Techniques for studying membranes are also discussed. PMID:26504250

  7. Three-year summary report of biological monitoring at the Southwest Ocean dredged-material disposal site and additional locations off Grays Harbor, Washington, 1990--1992

    SciTech Connect

    Antrim, L.D.; Shreffler, D.K.; Pearson, W.H.; Cullinan, V.I. )

    1992-12-01

    The Grays Harbor Navigation Improvement Project was initiated to improve navigation by widening and deepening the federal channel at Grays Harbor. Dredged-material disposal sites were selected after an extensive review process that included inter-agency agreements, biological surveys, other laboratory and field studies, and preparation of environmental impact statements The Southwest Site, was designated to receive materials dredged during annual maintenance dredging as well as the initial construction phase of the project. The Southwest Site was located, and the disposal operations designed, primarily to avoid impacts to Dungeness crab. The Final Environmental Impact Statement Supplement for the project incorporated a Site Monitoring Plan in which a tiered approach to disposal site monitoring was recommended. Under Tier I of the Site Monitoring Plan, Dungeness crab densities are monitored to confirm that large aggregations of newly settled Dungeness crab have not moved onto the Southwest Site. Tier 2 entails an increased sampling effort to determine whether a change in disposal operations is needed. Four epibenthic surveys using beam trawls were conducted in 1990, 1991, and 1992 at the Southwest Site and North Reference area, where high crab concentrations were found in the spring of 1985. Survey results during these three years prompted no Tier 2 activities. Epibenthic surveys were also conducted at two nearshore sites where construction of sediment berms has been proposed. This work is summarized in an appendix to this report.

  8. Integrated Bio-Search: challenges and trends for the integration, search and comprehensive processing of biological information.

    PubMed

    Masseroli, Marco; Mons, Barend; Bongcam-Rudloff, Erik; Ceri, Stefano; Kel, Alexander; Rechenmann, François; Lisacek, Frederique; Romano, Paolo

    2014-01-01

    Many efforts exist to design and implement approaches and tools for data capture, integration and analysis in the life sciences. Challenges are not only the heterogeneity, size and distribution of information sources, but also the danger of producing too many solutions for the same problem. Methodological, technological, infrastructural and social aspects appear to be essential for the development of a new generation of best practices and tools. In this paper, we analyse and discuss these aspects from different perspectives, by extending some of the ideas that arose during the NETTAB 2012 Workshop, making reference especially to the European context. First, relevance of using data and software models for the management and analysis of biological data is stressed. Second, some of the most relevant community achievements of the recent years, which should be taken as a starting point for future efforts in this research domain, are presented. Third, some of the main outstanding issues, challenges and trends are analysed. The challenges related to the tendency to fund and create large scale international research infrastructures and public-private partnerships in order to address the complex challenges of data intensive science are especially discussed. The needs and opportunities of Genomic Computing (the integration, search and display of genomic information at a very specific level, e.g. at the level of a single DNA region) are then considered. In the current data and network-driven era, social aspects can become crucial bottlenecks. How these may best be tackled to unleash the technical abilities for effective data integration and validation efforts is then discussed. Especially the apparent lack of incentives for already overwhelmed researchers appears to be a limitation for sharing information and knowledge with other scientists. We point out as well how the bioinformatics market is growing at an unprecedented speed due to the impact that new powerful in silico

  9. Integrated Bio-Search: challenges and trends for the integration, search and comprehensive processing of biological information

    PubMed Central

    2014-01-01

    Many efforts exist to design and implement approaches and tools for data capture, integration and analysis in the life sciences. Challenges are not only the heterogeneity, size and distribution of information sources, but also the danger of producing too many solutions for the same problem. Methodological, technological, infrastructural and social aspects appear to be essential for the development of a new generation of best practices and tools. In this paper, we analyse and discuss these aspects from different perspectives, by extending some of the ideas that arose during the NETTAB 2012 Workshop, making reference especially to the European context. First, relevance of using data and software models for the management and analysis of biological data is stressed. Second, some of the most relevant community achievements of the recent years, which should be taken as a starting point for future efforts in this research domain, are presented. Third, some of the main outstanding issues, challenges and trends are analysed. The challenges related to the tendency to fund and create large scale international research infrastructures and public-private partnerships in order to address the complex challenges of data intensive science are especially discussed. The needs and opportunities of Genomic Computing (the integration, search and display of genomic information at a very specific level, e.g. at the level of a single DNA region) are then considered. In the current data and network-driven era, social aspects can become crucial bottlenecks. How these may best be tackled to unleash the technical abilities for effective data integration and validation efforts is then discussed. Especially the apparent lack of incentives for already overwhelmed researchers appears to be a limitation for sharing information and knowledge with other scientists. We point out as well how the bioinformatics market is growing at an unprecedented speed due to the impact that new powerful in silico

  10. Effects of chemical, biological, and physical aging as well as soil addition on the sorption of pyrene to activated carbon and biochar.

    PubMed

    Hale, Sarah E; Hanley, Kelly; Lehmann, Johannes; Zimmerman, Andrewr; Cornelissen, Gerard

    2011-12-15

    In this study, the suitability of biochar and activated carbon (AC) for contaminated soil remediation is investigated by determining the sorption of pyrene to both materials in the presence and absence of soil and before as well as after aging. Biochar and AC were aged either alone or mixed with soil via exposure to (a) nutrients and microorganisms (biological), (b) 60 and 110 °C (chemical), and (c) freeze-thaw cycles (physical). Before and after aging, the pH, elemental composition, cation exchange capacity (CEC), microporous SA, and sorption isotherms of pyrene were quantified. Aging at 110 °C altered the physicochemical properties of all materials to the greatest extent (for example, pH increased by up to three units and CEC by up to 50% for biochar). Logarithmic K(Fr) values ranged from 7.80 to 8.21 (ng kg(-1))(ng L(-1))(-nF) for AC and 5.22 to 6.21 (ng kg(-1))(ng L(-1))(-nF) for biochar after the various aging regimes. Grinding biochar to a smaller particle size did not significantly affect the sorption of d(10) pyrene, implying that sorption processes operate on the subparticle scale. Chemical aging decreased the sorption of pyrene to the greatest extent (up to 1.8 log unit for the biochar+soil). The sorption to AC was affected more by the presence of soil than the sorption to biochar was. Our results suggest that AC and biochar have a high sorption capacity for pyrene that is maintained both in the presence of soil and during harsh aging. Both materials could therefore be considered in contaminated land remediation.

  11. Biology Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1982

    1982-01-01

    Presents procedures, exercises, demonstrations, and information on a variety of biology topics including labeling systems, biological indicators of stream pollution, growth of lichens, reproductive capacity of bulbous buttercups, a straw balance to measure transpiration, interaction of fungi, osmosis, and nitrogen fixation and crop production. (DC)

  12. [Effect of the addition of tropical fruits--pineapple (Ananas comosus) and papaya (Carica papaya)--on the production of biological silage from fish].

    PubMed

    Bello, R; Cardillo, E; Martínez, R

    1993-09-01

    Microbial Fish Silage was produced from under-utilized fish mixed with juice and waste fruits (pineapple and papaya) at 35 degrees C. Six different products were elaborated as following: A: fish muscle with pineapple juice; B: fish muscle with fruit wastes; C: gutted fish with pineapple juice; D: gutted fish with fruit wastes; E: whole fish with pineapple juice; F: whole fish with fruit wastes. Process development was evaluated by measuring: pH, acidity, non-protein nitrogen, consistency and exudate liquid. Results indicated a slow decrease in pH value and production of acidity during 20 storage days. The addition of fruits to silage did not have any effect on these values. Silage liquefaction or hydrolysis was related to the following parameters: consistency, non-protein nitrogen and exudate liquid. The addition of fruits was related to silage liquefaction or hydrolysis, and it was measured by the consistency. Exudate liquid and non-protein nitrogen increased during storage time. However silage made from whole fish showed highest values in those parameters than other processing conditions. This results suggested that hydrolysis involve first enzymes from guts and second enzymes from muscle and head. Pineapple juice did not contribute to hydrolysis process. Mainly sensory changes in the silage occurs during first 24 hours and they were related to chemical changes. Proximal analysis did not change during silage process and microbial counts indicated the freshness of raw material used i this study.

  13. Monitoring Subsurface Microbial Biomass, Community Composition and Physiological Status during Biological Uranium Reduction with Acetate Addition using Lipid Analysis, DNA Arrays and q-PCR

    NASA Astrophysics Data System (ADS)

    Peacock, A. D.; Long, P. E.; N'Guessan, L.; Williams, K. H.; Chandler, D.

    2011-12-01

    Our objectives for this effort were to investigate microbial community dynamics during each of the distinct terminal electron accepting phases that occur during long-term acetate addition for the immobilization of Uranium. Groundwater was collected from four wells (one up gradient and three down gradient) at three different depths and at four different times (pre-acetate injection, peak iron reduction, iron/sulfate reduction transition and during heavy sulfate reduction). Phospholipid fatty acid analysis (PLFA) results from ground water showed that microbial biomass was highest during Iron reduction and then lower during the transition from Iron reduction to Sulfate reduction and lowest during Sulfate reduction. Microbial community composition parameters as measured by PLFA showed distinct differences with terminal electron accepting status. Monounsaturated PLFA that have been shown to correspond with Gram-negative bacteria and Geobacteracea increased markedly with Iron reduction and then decreased with the onset of sulfate reduction. Bacterial physiological stress levels as measured by PLFA fluctuated with terminal electron acceptor status. Low bacterial stress levels coincided with pre-donor addition and Iron reduction but were much higher during Iron to Sulfate transition and during Sulfate reduction. Microarray results showed the expected progression of microbial signatures from Iron to Sulfate -reducers with changes in acetate amendment and in situ field conditions. The microarray response for Geobacter was highly correlated with qPCR for the same target gene (R2 = 0.84). Probes targeting Desulfobacter and Desulfitobacterium were the most reactive during the Iron to Sulfate transition and into Sulfate reduction, with a consistent Desulfotomaculum signature throughout the field experiment and a general decrease in Geobacter signal to noise ratios during the onset of Sulfate reducing conditions. Nitrate reducers represented by Dechloromonas and Dechlorosoma

  14. Fuel characteristics pertinent to the design of aircraft fuel systems, Supplement I : additional information on MIL-F-7914(AER) grade JP-5 fuel and several fuel oils

    NASA Technical Reports Server (NTRS)

    Barnett, Henry C; Hibbard, Robert R

    1953-01-01

    Since the release of the first NACA publication on fuel characteristics pertinent to the design of aircraft fuel systems (NACA-RM-E53A21), additional information has become available on MIL-F7914(AER) grade JP-5 fuel and several of the current grades of fuel oils. In order to make this information available to fuel-system designers as quickly as possible, the present report has been prepared as a supplement to NACA-RM-E53A21. Although JP-5 fuel is of greater interest in current fuel-system problems than the fuel oils, the available data are not as extensive. It is believed, however, that the limited data on JP-5 are sufficient to indicate the variations in stocks that the designer must consider under a given fuel specification. The methods used in the preparation and extrapolation of data presented in the tables and figures of this supplement are the same as those used in NACA-RM-E53A21.

  15. Seismic Absorption and Modulus Measurements in Porous Rocks in Lab and Field: Physical, Chemical, and Biological Effects of Fluids (Detecting a Biosurfactant Additive in a Field Irrigation Experiment)

    SciTech Connect

    Spetzler, Hartmut

    2006-05-01

    We have been exploring a new technology that is based on using low-frequency seismic attenuation data to monitor changes in fluid saturation conditions in two-fluid phase porous materials. The seismic attenuation mechanism is related to the loss of energy due to the hysteresis of resistance to meniscus movement (changes in surface tension, wettability) when a pore containing two fluids is stressed at very low frequencies (< 10 Hz). This technology has potential applications to monitoring changes in (1) leakage at buried waste sites, (2) contaminant remediation, and (3) flooding during enhanced petroleum recovery. We have concluded a three year field study at the Maricopa Agricultural Center site of the University of Arizona. Three sets of instruments were installed along an East-West line perpendicular to the 50m by 50m inigation site. Each set of instruments consisted of one three component seismometer and one tiltmeter. Microseisms and solid Earth-tides served as strain sources. The former have a power peak at a period of about 6 seconds and the tides have about two cycles per day. Installation of instruments commenced in late summer of 2002. The instruments operated nearly continuously until April 2005. During the fall of 2003 the site was irrigated with water and one year later with water containing 150 ppm of a biosurfactant additive. This biodegradable additive served to mimic a class of contaminants that change the surface tension of the inigation fluid. Tilt data clearly show tidal tilts superimposed on local tilts due to agricultural irrigation and field work. When the observed signals were correlated with site specific theoretical tilt signals we saw no anomalies for the water irrigation in 2003, but large anomalies on two stations for the surfactant irrigation in 2004. Occasional failures of seismometers as well as data acquisition systems contributed to less than continuous coverage. These data are noisier than the tilt data, but do also show possible

  16. Kinetic spectrophotometric H-point standard addition method for the simultaneous determination of diloxanide furoate and metronidazole in binary mixtures and biological fluids.

    PubMed

    Issa, Mahmoud Mohamed; Nejem, R'afat Mahmoud; Abu Shanab, Alaa Mohamed; Shaat, Nahed Talab

    2013-10-01

    Simple, reliable, and sensitive kinetic spectrophotometric method has been developed for the simultaneous determination of diloxanide furoate and metronidazole using H-point standard addition method (HPSAM). The method is based on the oxidation rate difference of diloxanide and metronidazole by potassium permanganate in basic medium. A green color has been developed and measured at 610 nm. Different experimental parameters were carefully optimized. The limiting logarithmic and the initial-rate methods were adopted for the construction of the calibration curve of each individual reaction with potassium permanganate. Under the optimum conditions, Beer's law was obeyed in the range of 1.0-20.0 and 5.0-25.0 μg ml(-1) for diloxanide furoate and metronidazole, respectively. The detection limits were 0.22 μg ml(-1) for diloxanide furoate and 0.83 μg ml(-1) for metronidazole. Correlation coefficients of the regression equations were greater than 0.9970 in all cases. The precision of the method was satisfactory; the maximum value of relative standard deviation did not exceed 1.06% (n=5). The accuracy, expressed as recovery was between 99.4% and 101.4% with relative error of 0.12 and 0.14 for diloxanide furoate and metronidazole, respectively. The proposed method was successfully applied for the simultaneous determination of both drugs in pharmaceutical dosage forms and human urine samples and compared with alternative HPLC method.

  17. Kinetic spectrophotometric H-point standard addition method for the simultaneous determination of diloxanide furoate and metronidazole in binary mixtures and biological fluids

    NASA Astrophysics Data System (ADS)

    Issa, Mahmoud Mohamed; Nejem, R.'afat Mahmoud; Shanab, Alaa Mohamed Abu; Shaat, Nahed Talab

    2013-10-01

    Simple, reliable, and sensitive kinetic spectrophotometric method has been developed for the simultaneous determination of diloxanide furoate and metronidazole using H-point standard addition method (HPSAM). The method is based on the oxidation rate difference of diloxanide and metronidazole by potassium permanganate in basic medium. A green color has been developed and measured at 610 nm. Different experimental parameters were carefully optimized. The limiting logarithmic and the initial-rate methods were adopted for the construction of the calibration curve of each individual reaction with potassium permanganate. Under the optimum conditions, Beer's law was obeyed in the range of 1.0-20.0 and 5.0-25.0 μg ml-1 for diloxanide furoate and metronidazole, respectively. The detection limits were 0.22 μg ml-1 for diloxanide furoate and 0.83 μg ml-1 for metronidazole. Correlation coefficients of the regression equations were greater than 0.9970 in all cases. The precision of the method was satisfactory; the maximum value of relative standard deviation did not exceed 1.06% (n = 5). The accuracy, expressed as recovery was between 99.4% and 101.4% with relative error of 0.12 and 0.14 for diloxanide furoate and metronidazole, respectively. The proposed method was successfully applied for the simultaneous determination of both drugs in pharmaceutical dosage forms and human urine samples and compared with alternative HPLC method.

  18. BioCreative V track 4: a shared task for the extraction of causal network information using the Biological Expression Language

    PubMed Central

    Rinaldi, Fabio; Ellendorff, Tilia Renate; Madan, Sumit; Clematide, Simon; van der Lek, Adrian; Mevissen, Theo; Fluck, Juliane

    2016-01-01

    Automatic extraction of biological network information is one of the most desired and most complex tasks in biological and medical text mining. Track 4 at BioCreative V attempts to approach this complexity using fragments of large-scale manually curated biological networks, represented in Biological Expression Language (BEL), as training and test data. BEL is an advanced knowledge representation format which has been designed to be both human readable and machine processable. The specific goal of track 4 was to evaluate text mining systems capable of automatically constructing BEL statements from given evidence text, and of retrieving evidence text for given BEL statements. Given the complexity of the task, we designed an evaluation methodology which gives credit to partially correct statements. We identified various levels of information expressed by BEL statements, such as entities, functions, relations, and introduced an evaluation framework which rewards systems capable of delivering useful BEL fragments at each of these levels. The aim of this evaluation method is to help identify the characteristics of the systems which, if combined, would be most useful for achieving the overall goal of automatically constructing causal biological networks from text. PMID:27402677

  19. Windows to the soul: vision science as a tool for studying biological mechanisms of information processing deficits in schizophrenia.

    PubMed

    Yoon, Jong H; Sheremata, Summer L; Rokem, Ariel; Silver, Michael A

    2013-10-31

    Cognitive and information processing deficits are core features and important sources of disability in schizophrenia. Our understanding of the neural substrates of these deficits remains incomplete, in large part because the complexity of impairments in schizophrenia makes the identification of specific deficits very challenging. Vision science presents unique opportunities in this regard: many years of basic research have led to detailed characterization of relationships between structure and function in the early visual system and have produced sophisticated methods to quantify visual perception and characterize its neural substrates. We present a selective review of research that illustrates the opportunities for discovery provided by visual studies in schizophrenia. We highlight work that has been particularly effective in applying vision science methods to identify specific neural abnormalities underlying information processing deficits in schizophrenia. In addition, we describe studies that have utilized psychophysical experimental designs that mitigate generalized deficit confounds, thereby revealing specific visual impairments in schizophrenia. These studies contribute to accumulating evidence that early visual cortex is a useful experimental system for the study of local cortical circuit abnormalities in schizophrenia. The high degree of similarity across neocortical areas of neuronal subtypes and their patterns of connectivity suggests that insights obtained from the study of early visual cortex may be applicable to other brain regions. We conclude with a discussion of future studies that combine vision science and neuroimaging methods. These studies have the potential to address pressing questions in schizophrenia, including the dissociation of local circuit deficits vs. impairments in feedback modulation by cognitive processes such as spatial attention and working memory, and the relative contributions of glutamatergic and GABAergic deficits.

  20. Windows to the soul: vision science as a tool for studying biological mechanisms of information processing deficits in schizophrenia

    PubMed Central

    Yoon, Jong H.; Sheremata, Summer L.; Rokem, Ariel; Silver, Michael A.

    2013-01-01

    Cognitive and information processing deficits are core features and important sources of disability in schizophrenia. Our understanding of the neural substrates of these deficits remains incomplete, in large part because the complexity of impairments in schizophrenia makes the identification of specific deficits very challenging. Vision science presents unique opportunities in this regard: many years of basic research have led to detailed characterization of relationships between structure and function in the early visual system and have produced sophisticated methods to quantify visual perception and characterize its neural substrates. We present a selective review of research that illustrates the opportunities for discovery provided by visual studies in schizophrenia. We highlight work that has been particularly effective in applying vision science methods to identify specific neural abnormalities underlying information processing deficits in schizophrenia. In addition, we describe studies that have utilized psychophysical experimental designs that mitigate generalized deficit confounds, thereby revealing specific visual impairments in schizophrenia. These studies contribute to accumulating evidence that early visual cortex is a useful experimental system for the study of local cortical circuit abnormalities in schizophrenia. The high degree of similarity across neocortical areas of neuronal subtypes and their patterns of connectivity suggests that insights obtained from the study of early visual cortex may be applicable to other brain regions. We conclude with a discussion of future studies that combine vision science and neuroimaging methods. These studies have the potential to address pressing questions in schizophrenia, including the dissociation of local circuit deficits vs. impairments in feedback modulation by cognitive processes such as spatial attention and working memory, and the relative contributions of glutamatergic and GABAergic deficits. PMID

  1. Food additives

    PubMed Central

    Spencer, Michael

    1974-01-01

    Food additives are discussed from the food technology point of view. The reasons for their use are summarized: (1) to protect food from chemical and microbiological attack; (2) to even out seasonal supplies; (3) to improve their eating quality; (4) to improve their nutritional value. The various types of food additives are considered, e.g. colours, flavours, emulsifiers, bread and flour additives, preservatives, and nutritional additives. The paper concludes with consideration of those circumstances in which the use of additives is (a) justified and (b) unjustified. PMID:4467857

  2. Biology Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1984

    1984-01-01

    Presents information on the teaching of nutrition (including new information relating to many current O-level syllabi) and part 16 of a reading list for A- and S-level biology. Also includes a note on using earthworms as a source of material for teaching meiosis. (JN)

  3. BPI-ANCA Provides Additional Clinical Information to Anti-Pseudomonas Serology: Results from a Cohort of 117 Swedish Cystic Fibrosis Patients.

    PubMed

    Lindberg, Ulrika; Carlsson, Malin; Hellmark, Thomas; Segelmark, Mårten

    2015-01-01

    Patients with cystic fibrosis (CF) colonized with Pseudomonas aeruginosa (P. aeruginosa) have worse prognosis compared with patients who are not. BPI-ANCA is an anti-neutrophil cytoplasmic antibody against BPI (bactericidal/permeability increasing protein) correlating with P. aeruginosa colonization and adverse long time prognosis. Whether it provides additional information as compared to standard anti-P. aeruginosa serology tests is not known. 117 nontransplanted CF patients at the CF centre in Lund, Sweden, were followed prospectively for ten years. Bacterial colonisation was classified according to the Leeds criteria. IgA BPI-ANCA was compared with assays for antibodies against alkaline protease (AP), Elastase (ELA), and Exotoxin A (ExoA). Lung function and patient outcome, alive, lung transplanted, or dead, were registered. BPI-ANCA showed the highest correlation with lung function impairment with an r-value of 0.44. Forty-eight of the 117 patients were chronically colonized with P. aeruginosa. Twenty of these patients experienced an adverse outcome. Receiver operator curve (ROC) analysis revealed that this could be predicted by BPI-ANCA (AUC = 0.77), (p = 0.002) to a better degree compared with serology tests. BPI-ANCA correlates better with lung function impairment and long time prognosis than anti-P. aeruginosa serology and has similar ability to identify patients with chronic P. aeruginosa.

  4. Biological Oxidation of DCE through Manganese Addition

    DTIC Science & Technology

    2008-08-01

    grams/L NaHCO3 2.5 CaCl2 · 2H2O 0.1 KCl 0.1 NH4Cl 1.5 NaH2PO4 · H2O 0.6 NaCH3COO 6.8 Yeast extract 0.2 Trace Minerals (0.1X) grams/L...Nitrolotriacetic acid 1.5 Na2MoO4 0.025 NiCl2 · 6H2O 0.024 MgSO4 7H2O 3 MnSO4 · 2H2O 0.5 NaCl 1 FeSO4 · 7H2O 0.1 CoSO4 or CoCl2 0.1 CaCl2 · 2H2O 0.1...ZnSO4 0.1 CuSO4 · 5H2O 0.01 ALK(SO4)2 0.01 H3BO3 0.01 APPENDIX C MICROCOSM DATA APPENDIX C1 cDCE Analyses in Microcosms Established

  5. Biological warfare agents.

    PubMed

    Thavaselvam, Duraipandian; Vijayaraghavan, Rajagopalan

    2010-07-01

    The recent bioterrorist attacks using anthrax spores have emphasized the need to detect and decontaminate critical facilities in the shortest possible time. There has been a remarkable progress in the detection, protection and decontamination of biological warfare agents as many instrumentation platforms and detection methodologies are developed and commissioned. Even then the threat of biological warfare agents and their use in bioterrorist attacks still remain a leading cause of global concern. Furthermore in the past decade there have been threats due to the emerging new diseases and also the re-emergence of old diseases and development of antimicrobial resistance and spread to new geographical regions. The preparedness against these agents need complete knowledge about the disease, better research and training facilities, diagnostic facilities and improved public health system. This review on the biological warfare agents will provide information on the biological warfare agents, their mode of transmission and spread and also the detection systems available to detect them. In addition the current information on the availability of commercially available and developing technologies against biological warfare agents has also been discussed. The risk that arise due to the use of these agents in warfare or bioterrorism related scenario can be mitigated with the availability of improved detection technologies.

  6. Evolutionary Design in Biology

    NASA Astrophysics Data System (ADS)

    Wiese, Kay C.

    Much progress has been achieved in recent years in molecular biology and genetics. The sheer volume of data in the form of biological sequences has been enormous and efficient methods for dealing with these huge amounts of data are needed. In addition, the data alone does not provide information on the workings of biological systems; hence much research effort has focused on designing mathematical and computational models to address problems from molecular biology. Often, the terms bioinformatics and computational biology are used to refer to the research fields concerning themselves with designing solutions to molecular problems in biology. However, there is a slight distinction between bioinformatics and computational biology: the former is concerned with managing the enormous amounts of biological data and extracting information from it, while the latter is more concerned with the design and development of new algorithms to address problems such as protein or RNA folding. However, the boundary is blurry, and there is no consistent usage of the terms. We will use the term bioinformatics to encompass both fields. To cover all areas of research in bioinformatics is beyond the scope of this section and we refer the interested reader to [2] for a general introduction. A large part of what bioinformatics is concerned about is evolution and function of biological systems on a molecular level. Evolutionary computation and evolutionary design are concerned with developing computational systems that "mimic" certain aspects of natural evolution (mutation, crossover, selection, fitness). Much of the inner workings of natural evolutionary systems have been copied, sometimes in modified format into evolutionary computation systems. Artificial neural networks mimic the functioning of simple brain cell clusters. Fuzzy systems are concerned with the "fuzzyness" in decision making, similar to a human expert. These three computational paradigms fall into the category of

  7. Food additives

    MedlinePlus

    ... or natural. Natural food additives include: Herbs or spices to add flavor to foods Vinegar for pickling ... Certain colors improve the appearance of foods. Many spices, as well as natural and man-made flavors, ...

  8. Quantum biology of the retina.

    PubMed

    Sia, Paul Ikgan; Luiten, André N; Stace, Thomas M; Wood, John Pm; Casson, Robert J

    2014-08-01

    The emerging field of quantum biology has led to a greater understanding of biological processes at the microscopic level. There is recent evidence to suggest that non-trivial quantum features such as entanglement, tunnelling and coherence have evolved in living systems. These quantum features are particularly evident in supersensitive light-harvesting systems such as in photosynthesis and photoreceptors. A biomimetic strategy utilizing biological quantum phenomena might allow new advances in the field of quantum engineering, particularly in quantum information systems. In addition, a better understanding of quantum biological features may lead to novel medical diagnostic and therapeutic developments. In the present review, we discuss the role of quantum physics in biological systems with an emphasis on the retina.

  9. BIOLOGICAL WARFARE

    PubMed Central

    Beeston, John

    1953-01-01

    The use of biological agents as controlled weapons of war is practical although uncertain. Three types of agents are feasible, including pathogenic organisms and biological pests, toxins, and synthetic hormones regulating plant growth. These agents may be chosen for selective effects varying from prolonged incipient illness to death of plants, man and domestic animals. For specific preventive and control measures required to combat these situations, there must be careful and detailed planning. The nucleus of such a program is available within the existing framework of public health activities. Additional research and expansion of established activities in time of attack are necessary parts of biological warfare defense. PMID:13059641

  10. Bats in the Classroom: A Conceptual Guide for Biology Teachers.

    ERIC Educational Resources Information Center

    Rankin, W. T.; Lewis, Norma G.

    2002-01-01

    Explains how to use bats to introduce different biological concepts such as classification and phylogeny, altruistic behavior, flight, coevolution, or physiological adaptations. Discusses common myths regarding bats and provides information on additional classroom materials. (YDS)

  11. Creating biological nanomaterials using synthetic biology

    NASA Astrophysics Data System (ADS)

    Rice, MaryJoe K.; Ruder, Warren C.

    2014-02-01

    Synthetic biology is a new discipline that combines science and engineering approaches to precisely control biological networks. These signaling networks are especially important in fields such as biomedicine and biochemical engineering. Additionally, biological networks can also be critical to the production of naturally occurring biological nanomaterials, and as a result, synthetic biology holds tremendous potential in creating new materials. This review introduces the field of synthetic biology, discusses how biological systems naturally produce materials, and then presents examples and strategies for incorporating synthetic biology approaches in the development of new materials. In particular, strategies for using synthetic biology to produce both organic and inorganic nanomaterials are discussed. Ultimately, synthetic biology holds the potential to dramatically impact biological materials science with significant potential applications in medical systems.

  12. Creating biological nanomaterials using synthetic biology.

    PubMed

    Rice, MaryJoe K; Ruder, Warren C

    2014-02-01

    Synthetic biology is a new discipline that combines science and engineering approaches to precisely control biological networks. These signaling networks are especially important in fields such as biomedicine and biochemical engineering. Additionally, biological networks can also be critical to the production of naturally occurring biological nanomaterials, and as a result, synthetic biology holds tremendous potential in creating new materials. This review introduces the field of synthetic biology, discusses how biological systems naturally produce materials, and then presents examples and strategies for incorporating synthetic biology approaches in the development of new materials. In particular, strategies for using synthetic biology to produce both organic and inorganic nanomaterials are discussed. Ultimately, synthetic biology holds the potential to dramatically impact biological materials science with significant potential applications in medical systems.

  13. Potlining Additives

    SciTech Connect

    Rudolf Keller

    2004-08-10

    In this project, a concept to improve the performance of aluminum production cells by introducing potlining additives was examined and tested. Boron oxide was added to cathode blocks, and titanium was dissolved in the metal pool; this resulted in the formation of titanium diboride and caused the molten aluminum to wet the carbonaceous cathode surface. Such wetting reportedly leads to operational improvements and extended cell life. In addition, boron oxide suppresses cyanide formation. This final report presents and discusses the results of this project. Substantial economic benefits for the practical implementation of the technology are projected, especially for modern cells with graphitized blocks. For example, with an energy savings of about 5% and an increase in pot life from 1500 to 2500 days, a cost savings of $ 0.023 per pound of aluminum produced is projected for a 200 kA pot.

  14. Phosphazene additives

    DOEpatents

    Harrup, Mason K; Rollins, Harry W

    2013-11-26

    An additive comprising a phosphazene compound that has at least two reactive functional groups and at least one capping functional group bonded to phosphorus atoms of the phosphazene compound. One of the at least two reactive functional groups is configured to react with cellulose and the other of the at least two reactive functional groups is configured to react with a resin, such as an amine resin of a polycarboxylic acid resin. The at least one capping functional group is selected from the group consisting of a short chain ether group, an alkoxy group, or an aryloxy group. Also disclosed are an additive-resin admixture, a method of treating a wood product, and a wood product.

  15. The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community.

    PubMed

    Rhee, Seung Yon; Beavis, William; Berardini, Tanya Z; Chen, Guanghong; Dixon, David; Doyle, Aisling; Garcia-Hernandez, Margarita; Huala, Eva; Lander, Gabriel; Montoya, Mary; Miller, Neil; Mueller, Lukas A; Mundodi, Suparna; Reiser, Leonore; Tacklind, Julie; Weems, Dan C; Wu, Yihe; Xu, Iris; Yoo, Daniel; Yoon, Jungwon; Zhang, Peifen

    2003-01-01

    Arabidopsis thaliana is the most widely-studied plant today. The concerted efforts of over 11 000 researchers and 4000 organizations around the world are generating a rich diversity and quantity of information and materials. This information is made available through a comprehensive on-line resource called the Arabidopsis Information Resource (TAIR) (http://arabidopsis.org), which is accessible via commonly used web browsers and can be searched and downloaded in a number of ways. In the last two years, efforts have been focused on increasing data content and diversity, functionally annotating genes and gene products with controlled vocabularies, and improving data retrieval, analysis and visualization tools. New information include sequence polymorphisms including alleles, germplasms and phenotypes, Gene Ontology annotations, gene families, protein information, metabolic pathways, gene expression data from microarray experiments and seed and DNA stocks. New data visualization and analysis tools include SeqViewer, which interactively displays the genome from the whole chromosome down to 10 kb of nucleotide sequence and AraCyc, a metabolic pathway database and map tool that allows overlaying expression data onto the pathway diagrams. Finally, we have recently incorporated seed and DNA stock information from the Arabidopsis Biological Resource Center (ABRC) and implemented a shopping-cart style on-line ordering system.

  16. A comparative approach for the investigation of biological information processing: An examination of the structure and function of computer hard drives and DNA

    PubMed Central

    2010-01-01

    Background The robust storage, updating and utilization of information are necessary for the maintenance and perpetuation of dynamic systems. These systems can exist as constructs of metal-oxide semiconductors and silicon, as in a digital computer, or in the "wetware" of organic compounds, proteins and nucleic acids that make up biological organisms. We propose that there are essential functional properties of centralized information-processing systems; for digital computers these properties reside in the computer's hard drive, and for eukaryotic cells they are manifest in the DNA and associated structures. Methods Presented herein is a descriptive framework that compares DNA and its associated proteins and sub-nuclear structure with the structure and function of the computer hard drive. We identify four essential properties of information for a centralized storage and processing system: (1) orthogonal uniqueness, (2) low level formatting, (3) high level formatting and (4) translation of stored to usable form. The corresponding aspects of the DNA complex and a computer hard drive are categorized using this classification. This is intended to demonstrate a functional equivalence between the components of the two systems, and thus the systems themselves. Results Both the DNA complex and the computer hard drive contain components that fulfill the essential properties of a centralized information storage and processing system. The functional equivalence of these components provides insight into both the design process of engineered systems and the evolved solutions addressing similar system requirements. However, there are points where the comparison breaks down, particularly when there are externally imposed information-organizing structures on the computer hard drive. A specific example of this is the imposition of the File Allocation Table (FAT) during high level formatting of the computer hard drive and the subsequent loading of an operating system (OS). Biological

  17. A Review and Synthesis of the Scientific Information Related to the Biology and Management of Species of Special Concern at Cape Hatteras National Seashore, North Carolina

    USGS Publications Warehouse

    Cohen, Jonathan B.; Erwin, R. Michael; French, John B.; Marion, Jeffrey L.; Meyers, J. Michael

    2009-01-01

    The U.S. Geological Survey's Patuxent Wildlife Research Center (PWRC) conducted a study for the National Park Service (NPS) Southeast Region, Atlanta, GA, and Cape Hatteras National Seashore (CAHA) in North Carolina to review, evaluate, and summarize the available scientific information for selected species of concern at CAHA (piping plovers, sea turtles, seabeach amaranth, American oystercatchers, and colonial waterbirds). This work consisted of reviewing the scientific literature and evaluating the results of studies that examined critical life history stages of each species, and focused on the scientific findings reported that are relevant to the management of these species and their habitats at CAHA. The chapters that follow provide the results of that review separately for each species and present scientifically based options for resource management at CAHA. Although no new original research or experimental work was conducted, this synthesis of the existing information was peer reviewed by over 15 experts with familiarity with these species. This report does not establish NPS management protocols but does highlight scientific information on the biology of these species to be considered by NPS managers who make resource management decisions at CAHA. To ensure that the best available information is considered when assessing each species of interest at CAHA, this review included published research as well as practical experience of scientists and wildlife managers who were consulted in 2005. PWRC scientists evaluated the literature, consulted wildlife managers, and produced an initial draft that was sent to experts for scientific review. Revisions based on those comments were incorporated into the document. The final draft of the document was reviewed by NPS personnel to ensure that the description of the recent status and management of these species at CAHA was accurately represented and that the report was consistent with our work agreement. The following

  18. Biology Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1981

    1981-01-01

    Presents content information and/or laboratory procedures and experiments on different biology topics including small-scale cultivation of watercress and its use in water-culture experiments, microbiology of the phylloplane, use of mouthbrooders in science class, and the gene. (DC)

  19. Marine Biology

    ERIC Educational Resources Information Center

    Dewees, Christopher M.; Hooper, Jon K.

    1976-01-01

    A variety of informational material for a course in marine biology or oceanology at the secondary level is presented. Among the topics discussed are: food webs and pyramids, planktonic blooms, marine life, plankton nets, food chains, phytoplankton, zooplankton, larval plankton and filter feeders. (BT)

  20. A Remote Sensing/Geographic Information Systems Approach in the Selection of Mars Sites of Biological Interest

    NASA Technical Reports Server (NTRS)

    Lobitz, B. M.; Wood, B. L.; Averner, M.; McKay, C.

    2000-01-01

    The search for extinct or extant life on Mars is the search for past or present liquid water, respectively. There are numerous signs of past liquid water on Mars in the form of dry river valleys, paleolakes, and their associated flow and sediment patterns. While some of these features are recent (Amazonian, 1.8 billion years ago to present), there is no evidence that any are currently flowing. Liquid water on the surface would only be possible at those sites with sufficiently high temperatures and pressure. The key to the selection of sites on Mars to search for evidence of life is the search for the presence of water. An approach to this problem is the use of remotely sensed data incorporated in a geographic information system (GIS). A GIS is a computer-based system capable of assembling, storing, manipulating, and displaying geographically referenced information, i.e., data identified according to their locations. In planetary studies these data are acquired from remote sensing (RS) platforms (orbiters). These data are co-registered layers and, through the use of GIS analysis functions, areas on these layers can be selected as a function of the information desired. Our work used existing data layers from the Viking and Mars Global Surveyor missions to determine where water could be possible in liquid form on the Martian surface, based on the phase diagram for water.

  1. Professional Development for Biology Teachers in the Knowledge Economy

    ERIC Educational Resources Information Center

    Eiser, Simone; Knight, Bruce Allen

    2008-01-01

    Increasingly, the general media cover new advancements and research in the field of biology. Stem cell research, emerging diseases and bioethics are some of the issues gaining public attention. The rate of increase of these new developments creates additional challenges to teachers of biology as they try to remain abreast of new information and…

  2. Environmental Assessment for the Construction of an Addition to USSOCOM Command and Control Facility, an Information Technology Facility, and a Permanent Parking Lot MacDill AFB, Florida

    DTIC Science & Technology

    2004-01-01

    In addition, since the site is larger than one acre in area, a National Pollutant Discharge Elimination System (NPDES) Phase II Storm water...Clean Air Act (CAA), as amended in 1977 and 1990, provides the basis for regulating air pollution to the atmosphere. The United States Environmental...Protection Agency (USEPA) set air quality standards for six “criteria” pollutants : carbon monoxide (CO), nitrogen dioxide (NO2), ozone (O3), sulfur

  3. Introduction to the analysis of the intracellular sorting information in protein sequences: from molecular biology to artificial neural networks.

    PubMed

    Aguilar, R Claudio

    2015-01-01

    A precise spatial-temporal organization of cell components is required for basic cellular activities such as proliferation and for complex multicellular processes such as embryo development. Particularly important is the maintenance and control of the cellular distribution of proteins, as these components fulfill crucial structural and catalytic functions. Membrane protein localization within the cell is determined and maintained by intracellular elements known as adaptors that interpret sorting information encoded in the amino acid sequence of cargoes. Understanding the sorting sequence code of cargo proteins would have a profound impact on many areas of the life sciences. For example, it would shed light onto the molecular mechanisms of several genetic diseases and would eventually allow us to control the fate of proteins. This chapter constitutes a primer on protein-sorting information analysis and localization/trafficking prediction. We provide the rationale for and a discussion of a simple basic protocol for protein sequence dissection looking for sorting signals, from simple sequence inspection techniques to more sophisticated artificial neural networks analysis of sorting signal recognition data.

  4. ENGINEERING BULLETIN: BIOLOGICAL TOXICITY TESTING

    EPA Science Inventory

    This Engineering Bulletin is intended to provide site managers with information on ecological assessment and biological toxicity testing, applicability of biological toxicity testing, planning effective biological toxicity assessments, descriptions of test methods, limitations, c...

  5. Two new endemic species of Ameiva (Squamata: Teiidae) from the dry forest of northwestern Peru and additional information on Ameiva concolor Ruthven, 1924.

    PubMed

    Koch, Claudia; Venegas, Pablo J; Rödder, Dennis; Flecks, Morris; Böhme, Wolfgang

    2013-12-04

    We describe two new species of Ameiva Meyer, 1795 from the dry forest of the Northern Peruvian Andes. The new species Ameiva nodam sp. nov. and Ameiva aggerecusans sp. nov. share a divided frontal plate and are differentiated from each other and from their congeners based on genetic (12S and 16S rRNA genes) and morphological characteristics. A. nodam sp. nov. has dilated postbrachials, a maximum known snout-vent length of 101 mm, 10 longitudinal rows of ventral plates, 86-113 midbody granules, 25-35 lamellae under the fourth toe, and a color pattern with 5 longitudinal yellow stripes on the dorsum. Ameiva aggerecusans sp. nov. has not or only hardly dilated postbrachials, a maximum known snout-vent length of 99.3 mm, 10-12 longitudinal rows of ventral plates, 73-92 midbody granules, 31-39 lamellae under the fourth toe, and the females and juveniles of the species normally exhibit a cream-colored vertebral stripe on a dark dorsum ground color. We provide information on the intraspecific variation and distribution of A. concolor. Furthermore, we provide information on the environmental niches of the taxa and test for niche conservatism. 

  6. Preservation of biological information in thermal spring deposits: developing a strategy for the search for fossil life on Mars.

    PubMed

    Walter, M R; Des Marais, D J

    1993-01-01

    Current interpretations of the early history of Mars suggest many similarities with the early Earth and therefore raise the possibility that the Archean and Proterozoic history of life on Earth could have a counterpart on Mars. Terrestrial experience suggests that, with techniques that can be employed remotely, ancient springs, including thermal springs, could well yield important information. By delivering water and various dissolved species to the sunlit surface of Mars, springs very likely created an environment suitable for life, which could have been difficult, if not impossible, to attain elsewhere. The chemical and temperature gradients associated with thermal springs sort organisms into sharply delineated, distinctive and different communities, and so diverse organisms are concentrated into relatively small areas in a predictable and informative fashion. A wide range of metabolic strategies are concentrated into small areas, thus furnishing a useful and representative sampling of the existing biota. Mineral-charged springwaters frequently deposit chemical precipitates of silica and/or carbonate which incorporate microorganisms and preserve them as fossils. The juxtaposition of stream valley headwaters with volcanoes and impact craters on Mars strongly implies that subsurface heating of groundwater created thermal springs. On Earth, thermal springs create distinctive geomorphic features and chemical signatures which can be detected by remote sensing. Spring deposits can be quite different chemically from adjacent rocks. Individual springs can be hundreds of meters wide, and complexes of springs occupy areas up to several kilometers wide. Benthic microbial mats and the resultant stromatolites occupy a large fraction of the available area. The relatively high densities of fossils and microbial mat fabrics within these deposits make them highly prospective in any search for morphological evidence of life, and there are examples of microbial fossils in spring

  7. Multiplex ligation-dependent probe amplification assay identifies additional copy number changes compared with R-band karyotype and provide more accuracy prognostic information in myelodysplastic syndromes

    PubMed Central

    Xu, Zefeng; Zhang, Yue; Liu, Jinqin; Li, Bing; Fang, Liwei; Zhang, Hongli; Pan, Lijuan; Hu, Naibo; Qu, Shiqiang; Cai, Wenyu; Ru, Kun; Jia, Yujiao; Huang, Gang; Xiao, Zhijian

    2017-01-01

    Cytogenetic analysis provides important diagnostic and prognostic information for patients with Myelodysplastic syndromes (MDS) and plays an essential role in the International Prognostic Scoring System (IPSS) and the revised International Prognostic Scoring System (IPSS-R). Multiplex ligation-dependent probe amplification (MLPA) assay is a recently developed technique to identify targeted cytogenetic aberrations in MDS patients. In the present study, we evaluated the results obtained using an MLPA assay in 437 patients with MDS to determine the efficacy of MLPA analysis. Using R-banding karyotyping, 45% (197/437) of MDS patients had chromosomal abnormalities, whereas MLPA analysis detected that 35% (153/437) of MDS cases contained at least one copy-number variations (CNVs) .2/5 individuals (40%) with R-band karyotype failures had trisomy 8 detected using only MLPA. Clonal cytogenetic abnormalities were detected in 20/235 (8.5%) MDS patients with a normal R-band karyotype, and 12/20 (60%) of those patients were reclassified into a higher-risk IPSS-R prognostic category. When sequencing and cytogenetics were combined, the fraction of patients with MDS-related oncogenic lesions increased to 87.3% (233/267 cases). MLPA analysis determined that the median OS of patients with a normal karyotype (n=218) was 65 months compared with 27 months in cases with an aberrant karyotype (P=0.002) in 240 patients with normal or failed karyotypes by R-banding karyotyping. The high-resolution MPLA assay is an efficient and reliable method that can be used in conjunction with R-band karyotyping to detect chromosomal abnormalities in patients with suspected MDS. MLPA may also provide more accurate prognostic information. PMID:27906673

  8. (Biological dosimetry)

    SciTech Connect

    Preston, R.J.

    1990-12-17

    The traveler attended the 1st International Conference on Biological Dosimetry in Madrid, Spain. This conference was organized to provide information to a general audience of biologists, physicists, radiotherapists, industrial hygiene personnel and individuals from related fields on the current ability of cytogenetic analysis to provide estimates of radiation dose in cases of occupational or environmental exposure. There is a growing interest in Spain in biological dosimetry because of the increased use of radiation sources for medical and occupational uses, and with this the anticipated and actual increase in numbers of overexposure. The traveler delivered the introductory lecture on Biological Dosimetry: Mechanistic Concepts'' that was intended to provide a framework by which the more applied lectures could be interpreted in a mechanistic way. A second component of the trip was to provide advice with regard to several recent cases of overexposure that had been or were being assessed by the Radiopathology and Radiotherapy Department of the Hospital General Gregorio Maranon'' in Madrid. The traveler had provided information on several of these, and had analyzed cells from some exposed or purportedly exposed individuals. The members of the biological dosimetry group were referred to individuals at REACTS at Oak Ridge Associated Universities for advice on follow-up treatment.

  9. The Viking biology results

    NASA Technical Reports Server (NTRS)

    Klein, Harold P.

    1989-01-01

    A brief review of the purposes and the results from the Viking Biology experiments is presented, in the expectation that the lessons learned from this mission will be useful in planning future approaches to the biological exploration of Mars. Since so little was then known about potential micro-environments on Mars, three different experiments were included in the Viking mission, each one based on different assumptions about what Martian organisms might be like. In addition to the Viking Biology Instrument (VBI), important corollary information was obtained from the Viking lander imaging system and from the molecular analysis experiments that were conducted using the gas chromatograph-mass spectrometer (GCMS) instrument. No biological objects were noted by the lander imaging instrument. The GCMS did not detect any organic compounds. A description of the tests conducted by the Gas Exchange Experiment, the Labeled Release experiment, and the Pyrolytic Release experiment is given. Results are discussed. Taken as a whole, the Viking data yielded no unequivocal evidence for a Martian biota at either landing site. The results also revealed the presence of one or more reactive oxidants in the surface material and these need to be further characterized, as does the range of micro-environments, before embarking upon future searches for extant life on Mars.

  10. The OncoPPi network of cancer-focused protein–protein interactions to inform biological insights and therapeutic strategies

    PubMed Central

    Li, Zenggang; Ivanov, Andrei A.; Su, Rina; Gonzalez-Pecchi, Valentina; Qi, Qi; Liu, Songlin; Webber, Philip; McMillan, Elizabeth; Rusnak, Lauren; Pham, Cau; Chen, Xiaoqian; Mo, Xiulei; Revennaugh, Brian; Zhou, Wei; Marcus, Adam; Harati, Sahar; Chen, Xiang; Johns, Margaret A.; White, Michael A.; Moreno, Carlos; Cooper, Lee A. D.; Du, Yuhong; Khuri, Fadlo R.; Fu, Haian

    2017-01-01

    As genomics advances reveal the cancer gene landscape, a daunting task is to understand how these genes contribute to dysregulated oncogenic pathways. Integration of cancer genes into networks offers opportunities to reveal protein–protein interactions (PPIs) with functional and therapeutic significance. Here, we report the generation of a cancer-focused PPI network, termed OncoPPi, and identification of >260 cancer-associated PPIs not in other large-scale interactomes. PPI hubs reveal new regulatory mechanisms for cancer genes like MYC, STK11, RASSF1 and CDK4. As example, the NSD3 (WHSC1L1)–MYC interaction suggests a new mechanism for NSD3/BRD4 chromatin complex regulation of MYC-driven tumours. Association of undruggable tumour suppressors with drug targets informs therapeutic options. Based on OncoPPi-derived STK11-CDK4 connectivity, we observe enhanced sensitivity of STK11-silenced lung cancer cells to the FDA-approved CDK4 inhibitor palbociclib. OncoPPi is a focused PPI resource that links cancer genes into a signalling network for discovery of PPI targets and network-implicated tumour vulnerabilities for therapeutic interrogation. PMID:28205554

  11. The OncoPPi network of cancer-focused protein-protein interactions to inform biological insights and therapeutic strategies.

    PubMed

    Li, Zenggang; Ivanov, Andrei A; Su, Rina; Gonzalez-Pecchi, Valentina; Qi, Qi; Liu, Songlin; Webber, Philip; McMillan, Elizabeth; Rusnak, Lauren; Pham, Cau; Chen, Xiaoqian; Mo, Xiulei; Revennaugh, Brian; Zhou, Wei; Marcus, Adam; Harati, Sahar; Chen, Xiang; Johns, Margaret A; White, Michael A; Moreno, Carlos; Cooper, Lee A D; Du, Yuhong; Khuri, Fadlo R; Fu, Haian

    2017-02-16

    As genomics advances reveal the cancer gene landscape, a daunting task is to understand how these genes contribute to dysregulated oncogenic pathways. Integration of cancer genes into networks offers opportunities to reveal protein-protein interactions (PPIs) with functional and therapeutic significance. Here, we report the generation of a cancer-focused PPI network, termed OncoPPi, and identification of >260 cancer-associated PPIs not in other large-scale interactomes. PPI hubs reveal new regulatory mechanisms for cancer genes like MYC, STK11, RASSF1 and CDK4. As example, the NSD3 (WHSC1L1)-MYC interaction suggests a new mechanism for NSD3/BRD4 chromatin complex regulation of MYC-driven tumours. Association of undruggable tumour suppressors with drug targets informs therapeutic options. Based on OncoPPi-derived STK11-CDK4 connectivity, we observe enhanced sensitivity of STK11-silenced lung cancer cells to the FDA-approved CDK4 inhibitor palbociclib. OncoPPi is a focused PPI resource that links cancer genes into a signalling network for discovery of PPI targets and network-implicated tumour vulnerabilities for therapeutic interrogation.

  12. Applicability of computational systems biology in toxicology.

    PubMed

    Kongsbak, Kristine; Hadrup, Niels; Audouze, Karine; Vinggaard, Anne Marie

    2014-07-01

    Systems biology as a research field has emerged within the last few decades. Systems biology, often defined as the antithesis of the reductionist approach, integrates information about individual components of a biological system. In integrative systems biology, large data sets from various sources and databases are used to model and predict effects of chemicals on, for instance, human health. In toxicology, computational systems biology enables identification of important pathways and molecules from large data sets; tasks that can be extremely laborious when performed by a classical literature search. However, computational systems biology offers more advantages than providing a high-throughput literature search; it may form the basis for establishment of hypotheses on potential links between environmental chemicals and human diseases, which would be very difficult to establish experimentally. This is possible due to the existence of comprehensive databases containing information on networks of human protein-protein interactions and protein-disease associations. Experimentally determined targets of the specific chemical of interest can be fed into these networks to obtain additional information that can be used to establish hypotheses on links between the chemical and human diseases. Such information can also be applied for designing more intelligent animal/cell experiments that can test the established hypotheses. Here, we describe how and why to apply an integrative systems biology method in the hypothesis-generating phase of toxicological research.

  13. Advanced in silico approaches for drug discovery: Mining information from multiple biological and chemical data through mtk-QSBER and pt-QSPR strategies.

    PubMed

    Speck-Planche, Alejandro; Cordeiro, Maria Natália Dias Soeiro

    2017-01-24

    The last decade has been seeing an increase of public-private partnerships in drug discovery, mostly driven by factors such as the decline in productivity, the high costs, time, and resources needed, along with the requirements of regulatory agencies. In this context, traditional computer-aided drug discovery techniques have been playing an important role, enabling the identification of new molecular entities at early stages. However, recent advances in chemoinformatics and systems pharmacology, alongside with a growing body of high quality, publicly accessible medicinal chemistry data, have led to the emergence of novel in silico approaches. These novel approaches are able to integrate a vast amount of multiple chemical and biological data into a single modeling equation. The present review analyzes two main kinds of such cutting-edge in silico approaches. In a first subsection, we discuss the updates on multitasking models for quantitative structure-biological effect relationships (mtk-QSBER), whose applications have been significantly increasing in the past years. In a second subsection, we provide detailed information regarding a novel approach that combines perturbation theory with quantitative structure-property relationships modeling tools (pt-QSPR). Finally, and most importantly, we show that the joint use of mtk-QSBER and pt-QSPR modeling tools are apt to guide drug discovery through its multiple stages: from in vitro assays to preclinical studies and clinical trials.

  14. Segmentation of biological target volumes on multi-tracer PET images based on information fusion for achieving dose painting in radiotherapy.

    PubMed

    Lelandais, Benoît; Gardin, Isabelle; Mouchard, Laurent; Vera, Pierre; Ruan, Su

    2012-01-01

    Medical imaging plays an important role in radiotherapy. Dose painting consists in the application of a nonuniform dose prescription on a tumoral region, and is based on an efficient segmentation of biological target volumes (BTV). It is derived from PET images, that highlight tumoral regions of enhanced glucose metabolism (FDG), cell proliferation (FLT) and hypoxia (FMiso). In this paper, a framework based on Belief Function Theory is proposed for BTV segmentation and for creating 3D parametric images for dose painting. We propose to take advantage of neighboring voxels for BTV segmentation, and also multi-tracer PET images using information fusion to create parametric images. The performances of BTV segmentation was evaluated on an anthropomorphic phantom and compared with two other methods. Quantitative results show the good performances of our method. It has been applied to data of five patients suffering from lung cancer. Parametric images show promising results by highlighting areas where a high frequency or dose escalation could be planned.

  15. A fast and precise method to identify indolic glucosinolates and camalexin in plants by combining mass spectrometric and biological information.

    PubMed

    Zandalinas, Sara Izquierdo; Vives-Peris, Vicente; Gómez-Cadenas, Aurelio; Arbona, Vicent

    2012-09-05

    In this manuscript, a fast and accurate identification and quantitation by mass spectrometry of indolic glucosinolates and camalexin involved in defense in Arabidopsis thaliana are described. Two elicitation systems, inoculation with Botrytis cinerea and treatment with AgNO(3), were used in Col-0 wild-type and mutant genotypes impaired in the biosynthesis of the selected metabolites. Identification of analytes was carried out by nontargeted LC/ESI-QTOF-MS profiling. Confirmation of indolic glucosinolates and camalexin was achieved by their absence in the cyp79B2/B3 and pad3 mutants as well as their respective fragmentation upon collision-induced dissociation. Camalexin accumulation was induced only after AgNO(3) treatment, whereas all indolic glucosinolates were constitutively present. Inoculation with Botrytis did not influence camalexin concentration but caused most aliphatic and indolic glucosinolates contents to decrease. Only the pen 3.1 mutant showed increased indolic glucosinolate levels after Botrytis or AgNO(3) treatments. In addition, profiles of secondary metabolite in nontreated Col-0 and mutant plants were analyzed by means of partial least squares coupled to discriminant analysis (PLS-DA), and differences in the basal levels of indolic glucosinolates and tryptophan between cyp79B2/B3 plants and the rest of genotypes, including Col-0, were found. This probably has to be taken into consideration when comparing stress responses of Col-0 and cyp79B2/B3. The use of mutants carrying alterations in biosynthetic pathways is proposed as a useful strategy to identify secondary metabolites.

  16. Controlled vocabularies and semantics in systems biology.

    PubMed

    Courtot, Mélanie; Juty, Nick; Knüpfer, Christian; Waltemath, Dagmar; Zhukova, Anna; Dräger, Andreas; Dumontier, Michel; Finney, Andrew; Golebiewski, Martin; Hastings, Janna; Hoops, Stefan; Keating, Sarah; Kell, Douglas B; Kerrien, Samuel; Lawson, James; Lister, Allyson; Lu, James; Machne, Rainer; Mendes, Pedro; Pocock, Matthew; Rodriguez, Nicolas; Villeger, Alice; Wilkinson, Darren J; Wimalaratne, Sarala; Laibe, Camille; Hucka, Michael; Le Novère, Nicolas

    2011-10-25

    The use of computational modeling to describe and analyze biological systems is at the heart of systems biology. Model structures, simulation descriptions and numerical results can be encoded in structured formats, but there is an increasing need to provide an additional semantic layer. Semantic information adds meaning to components of structured descriptions to help identify and interpret them unambiguously. Ontologies are one of the tools frequently used for this purpose. We describe here three ontologies created specifically to address the needs of the systems biology community. The Systems Biology Ontology (SBO) provides semantic information about the model components. The Kinetic Simulation Algorithm Ontology (KiSAO) supplies information about existing algorithms available for the simulation of systems biology models, their characterization and interrelationships. The Terminology for the Description of Dynamics (TEDDY) categorizes dynamical features of the simulation results and general systems behavior. The provision of semantic information extends a model's longevity and facilitates its reuse. It provides useful insight into the biology of modeled processes, and may be used to make informed decisions on subsequent simulation experiments.

  17. Using Stereoscopy to Teach Complex Biological Concepts

    ERIC Educational Resources Information Center

    Ferdig, Richard; Blank, James; Kratcoski, Annette; Clements, Robert

    2015-01-01

    Used effectively, stereoscopic three-dimensional (3D) technologies can engage students with complex disciplinary content as they are presented with informative representations of abstract concepts. In addition, preliminary evidence suggests that stereoscopy may enhance learning and retention in some educational settings. Biological concepts…

  18. A systematic review of the psychobiological burden of informal caregiving for patients with dementia: Focus on cognitive and biological markers of chronic stress.

    PubMed

    Allen, Andrew P; Curran, Eileen A; Duggan, Áine; Cryan, John F; Chorcoráin, Aoife Ní; Dinan, Timothy G; Molloy, D William; Kearney, Patricia M; Clarke, Gerard

    2017-02-01

    As the physiological impact of chronic stress is difficult to study in humans, naturalistic stressors are invaluable sources of information in this area. This review systematically evaluates the research literature examining biomarkers of chronic stress, including neurocognition, in informal dementia caregivers. We identified 151 papers for inclusion in the final review, including papers examining differences between caregivers and controls as well as interventions aimed at counteracting the biological burden of chronic caregiving stress. Results indicate that cortisol was increased in caregivers in a majority of studies examining this biomarker. There was mixed evidence for differences in epinephrine, norepinephrine and other cardiovascular markers. There was a high level of heterogeneity in immune system measures. Caregivers performed more poorly on attention and executive functioning tests. There was mixed evidence for memory performance. Interventions to reduce stress improved cognition but had mixed effects on cortisol. Risk of bias was generally low to moderate. Given the rising need for family caregivers worldwide, the implications of these findings can no longer be neglected.

  19. NGSI student activities in open source information analysis in support of the training program of the U.S. DOE laboratories for the entry into force of the additional protocol

    SciTech Connect

    Sandoval, M Analisa; Uribe, Eva C; Sandoval, Marisa N; Boyer, Brian D; Stevens, Rebecca S

    2009-01-01

    In 2008 a joint team from Los Alamos National Laboratory (LANL) and Brookhaven National Laboratory (BNL) consisting of specialists in training of IAEA inspectors in the use of complementary access activities formulated a training program to prepare the U.S. Doe laboratories for the entry into force of the Additional Protocol. As a major part of the support of the activity, LANL summer interns provided open source information analysis to the LANL-BNL mock inspection team. They were a part of the Next Generation Safeguards Initiative's (NGSI) summer intern program aimed at producing the next generation of safeguards specialists. This paper describes how they used open source information to 'backstop' the LANL-BNL team's effort to construct meaningful Additional Protocol Complementary Access training scenarios for each of the three DOE laboratories, Lawrence Livermore National Laboratory, Idaho National Laboratory, and Oak Ridge National Laboratory.

  20. Twenty-four new species of Aleiodes Wesmael from the eastern Andes of Ecuador with associated biological information (Hymenoptera, Braconidae, Rogadinae)

    PubMed Central

    Shimbori, Eduardo Mitio; Shaw, Scott Richard

    2014-01-01

    Abstract Aleiodes Wesmael is the most diverse rogadine genus worldwide, with specialized koinobiont endoparasitic development in Lepidoptera caterpillars resulting in mummification of the host remains. This paper focuses on describing new Aleiodes species from the Yanayacu Biological Station, with special interest in those with biological information. We describe 24 new species (Aleiodes albidactyl sp. n., Aleiodes albigena sp. n., Aleiodes albiviria sp. n., Aleiodes bimaculatus sp. n., Aleiodes cacuangoi sp. n., Aleiodes colberti sp. n., Aleiodes delicatus sp. n., Aleiodes dyeri sp. n., Aleiodes elleni sp. n., Aleiodes falloni sp. n., Aleiodes frosti sp. n., Aleiodes kingmani sp. n., Aleiodes longikeros sp. n., Aleiodes luteosicarius sp. n., Aleiodes marilynae sp. n., Aleiodes mirandae sp. n., Aleiodes napo sp. n., Aleiodes nubicola sp. n., Aleiodes onyx sp. n., Aleiodes shakirae sp. n., Aleiodes stewarti sp. n., Aleiodes townsendi sp. n., Aleiodes tzantza sp. n., and Aleiodes yanayacu sp. n.) from Napo Province in Ecuador, 16 of which were reared from host caterpillars. With these results 89 species of Neotropical Aleiodes are now known, with 41 of them having host records. The most commonly reared species were in the circumscriptus/gastritor species-group, and mostly associated with Geometridae hosts (six of ten species). Three species of seriatus species-group, in contrast, were each reared from a different family. One of these species (i.e. A. frosti sp. n.), reared from Notodontidae, cuts a posterior radial opening in the mummy for emergence, a unique behavior in Aleiodes, recorded here for the first time. A. luteosicarius sp. n. is the first described species from Ecuador in the pallidator species-group. Differing from previously described pallidator species, which attack only Lymantriinae larvae, A. luteosicarius sp. n. attacks several species of Arctiinae larvae, being both subfamilies within Erebidae with densely setose caterpillars. We also describe new