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, consistent...

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, consistent...

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.

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. © 2012 New York Academy of Sciences.

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... § 33.10 Additional information. The Director of the Office of Energy Market Regulation, or his designee...

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 authorized...

10 CFR 810.14 - Additional information.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 4 2012-01-01 2012-01-01 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 authorized...

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 authorized...

10 CFR 810.14 - Additional information.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 4 2014-01-01 2014-01-01 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 authorized...

Statistical approach for selection of biologically informative genes.

PubMed

Das, Samarendra; Rai, Anil; Mishra, D C; Rai, Shesh N

2018-05-20

Selection of informative genes from high dimensional gene expression data has emerged as an important research area in genomics. Many gene selection techniques have been proposed so far are either based on relevancy or redundancy measure. Further, the performance of these techniques has been adjudged through post selection classification accuracy computed through a classifier using the selected genes. This performance metric may be statistically sound but may not be biologically relevant. A statistical approach, i.e. Boot-MRMR, was proposed based on a composite measure of maximum relevance and minimum redundancy, which is both statistically sound and biologically relevant for informative gene selection. For comparative evaluation of the proposed approach, we developed two biological sufficient criteria, i.e. Gene Set Enrichment with QTL (GSEQ) and biological similarity score based on Gene Ontology (GO). Further, a systematic and rigorous evaluation of the proposed technique with 12 existing gene selection techniques was carried out using five gene expression datasets. This evaluation was based on a broad spectrum of statistically sound (e.g. subject classification) and biological relevant (based on QTL and GO) criteria under a multiple criteria decision-making framework. The performance analysis showed that the proposed technique selects informative genes which are more biologically relevant. The proposed technique is also found to be quite competitive with the existing techniques with respect to subject classification and computational time. Our results also showed that under the multiple criteria decision-making setup, the proposed technique is best for informative gene selection over the available alternatives. Based on the proposed approach, an R Package, i.e. BootMRMR has been developed and available at https://cran.r-project.org/web/packages/BootMRMR. This study will provide a practical guide to select statistical techniques for selecting informative genes

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)

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.

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.

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 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, consistent...

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.

43 CFR 3430.4-2 - Additional information.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 43 Public Lands: Interior 2 2014-10-01 2014-10-01 false Additional information. 3430.4-2 Section... Leases § 3430.4-2 Additional information. (a) If the applicant for a preference right lease has submitted timely, some, but not all of the information required in § 3430.4-1 of this title, the authorized officer...

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

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 the...

Saccharomyces genome database informs human biology

PubMed Central

Skrzypek, Marek S; Nash, Robert S; Wong, Edith D; MacPherson, Kevin A; Karra, Kalpana; Binkley, Gail; Simison, Matt; Miyasato, Stuart R

2018-01-01

Abstract The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is an expertly curated database of literature-derived functional information for the model organism budding yeast, Saccharomyces cerevisiae. SGD constantly strives to synergize new types of experimental data and bioinformatics predictions with existing data, and to organize them into a comprehensive and up-to-date information resource. The primary mission of SGD is to facilitate research into the biology of yeast and to provide this wealth of information to advance, in many ways, research on other organisms, even those as evolutionarily distant as humans. To build such a bridge between biological kingdoms, SGD is curating data regarding yeast-human complementation, in which a human gene can successfully replace the function of a yeast gene, and/or vice versa. These data are manually curated from published literature, made available for download, and incorporated into a variety of analysis tools provided by SGD. PMID:29140510

Saccharomyces genome database informs human biology.

PubMed

Skrzypek, Marek S; Nash, Robert S; Wong, Edith D; MacPherson, Kevin A; Hellerstedt, Sage T; Engel, Stacia R; Karra, Kalpana; Weng, Shuai; Sheppard, Travis K; Binkley, Gail; Simison, Matt; Miyasato, Stuart R; Cherry, J Michael

2018-01-04

The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is an expertly curated database of literature-derived functional information for the model organism budding yeast, Saccharomyces cerevisiae. SGD constantly strives to synergize new types of experimental data and bioinformatics predictions with existing data, and to organize them into a comprehensive and up-to-date information resource. The primary mission of SGD is to facilitate research into the biology of yeast and to provide this wealth of information to advance, in many ways, research on other organisms, even those as evolutionarily distant as humans. To build such a bridge between biological kingdoms, SGD is curating data regarding yeast-human complementation, in which a human gene can successfully replace the function of a yeast gene, and/or vice versa. These data are manually curated from published literature, made available for download, and incorporated into a variety of analysis tools provided by SGD. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

[Correction of schoolchildren's diets with biologically active additives].

PubMed

Diudiakov, A A; Rakhmanov, R S; Korotunov, Iu V; Gruzdeva, A E

2002-01-01

The actual nutrition of schoolchildren in the Nizni-Novgorod district is imbalanced due to the deficiency of protein and vitamins and to the high contents of fats and carbohydrates. The authors provide evidence for a combined preparation to correct the children's diets, which incorporates animal protein, biologically active plant additives, and egg-shell calcium. The use of the preparation in combination with liquid bifidumbacterin contributes to increases in morphofunctional parameters in adolescents.

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.

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. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

49 CFR Appendix A to Part 24 - Additional Information

Code of Federal Regulations, 2013 CFR

2013-10-01

... 49 Transportation 1 2013-10-01 2013-10-01 false Additional Information A Appendix A to Part 24... Information This appendix provides additional information to explain the intent of certain provisions of this... additional information is gathered. If a decision is later made to permanently relocate such persons, those...

10 CFR 1.3 - Sources of additional information.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Sources of additional information. 1.3 Section 1.3 Energy NUCLEAR REGULATORY COMMISSION STATEMENT OF ORGANIZATION AND GENERAL INFORMATION Introduction § 1.3 Sources of additional information. (a) A statement of the NRC's organization, policies, procedures...

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

Biological Information Document, Radioactive Liquid Waste Treatment Facility

DOE Office of Scientific and Technical Information (OSTI.GOV)

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 Proposedmore » 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.« less

Towards the understanding of network information processing in biology

NASA Astrophysics Data System (ADS)

Singh, Vijay

Living organisms perform incredibly well in detecting a signal present in the environment. This information processing is achieved near optimally and quite reliably, even though the sources of signals are highly variable and complex. The work in the last few decades has given us a fair understanding of how individual signal processing units like neurons and cell receptors process signals, but the principles of collective information processing on biological networks are far from clear. Information processing in biological networks, like the brain, metabolic circuits, cellular-signaling circuits, etc., involves complex interactions among a large number of units (neurons, receptors). The combinatorially large number of states such a system can exist in makes it impossible to study these systems from the first principles, starting from the interactions between the basic units. The principles of collective information processing on such complex networks can be identified using coarse graining approaches. This could provide insights into the organization and function of complex biological networks. Here I study models of biological networks using continuum dynamics, renormalization, maximum likelihood estimation and information theory. Such coarse graining approaches identify features that are essential for certain processes performed by underlying biological networks. We find that long-range connections in the brain allow for global scale feature detection in a signal. These also suppress the noise and remove any gaps present in the signal. Hierarchical organization with long-range connections leads to large-scale connectivity at low synapse numbers. Time delays can be utilized to separate a mixture of signals with temporal scales. Our observations indicate that the rules in multivariate signal processing are quite different from traditional single unit signal processing.

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…

40 CFR 141.154 - Required additional health information.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 24 2012-07-01 2012-07-01 false Required additional health information... Required additional health information. (a) All reports must prominently display the following language... from their health care providers. EPA/CDC guidelines on appropriate means to lessen the risk of...

40 CFR 141.154 - Required additional health information.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 23 2011-07-01 2011-07-01 false Required additional health information... Required additional health information. (a) All reports must prominently display the following language... from their health care providers. EPA/CDC guidelines on appropriate means to lessen the risk of...

40 CFR 141.154 - Required additional health information.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 22 2010-07-01 2010-07-01 false Required additional health information... Required additional health information. (a) All reports must prominently display the following language... from their health care providers. EPA/CDC guidelines on appropriate means to lessen the risk of...

40 CFR 141.154 - Required additional health information.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 24 2013-07-01 2013-07-01 false Required additional health information... Required additional health information. (a) All reports must prominently display the following language... from their health care providers. EPA/CDC guidelines on appropriate means to lessen the risk of...

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…

47 CFR 1.10017 - How can I submit additional information?

Code of Federal Regulations, 2010 CFR

2010-10-01

... 47 Telecommunication 1 2010-10-01 2010-10-01 false How can I submit additional information? 1... International Bureau Filing System § 1.10017 How can I submit additional information? In response to an official request for information from the International Bureau, you can submit additional information...

Leaf LIMS: A Flexible Laboratory Information Management System with a Synthetic Biology Focus.

PubMed

Craig, Thomas; Holland, Richard; D'Amore, Rosalinda; Johnson, James R; McCue, Hannah V; West, Anthony; Zulkower, Valentin; Tekotte, Hille; Cai, Yizhi; Swan, Daniel; Davey, Robert P; Hertz-Fowler, Christiane; Hall, Anthony; Caddick, Mark

2017-12-15

This paper presents Leaf LIMS, a flexible laboratory information management system (LIMS) designed to address the complexity of synthetic biology workflows. At the project's inception there was a lack of a LIMS designed specifically to address synthetic biology processes, with most systems focused on either next generation sequencing or biobanks and clinical sample handling. Leaf LIMS implements integrated project, item, and laboratory stock tracking, offering complete sample and construct genealogy, materials and lot tracking, and modular assay data capture. Hence, it enables highly configurable task-based workflows and supports data capture from project inception to completion. As such, in addition to it supporting synthetic biology it is ideal for many laboratory environments with multiple projects and users. The system is deployed as a web application through Docker and is provided under a permissive MIT license. It is freely available for download at https://leaflims.github.io .

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.

15 CFR 970.2601 - Additional information.

Code of Federal Regulations, 2010 CFR

2010-01-01

... ENVIRONMENTAL DATA SERVICE DEEP SEABED MINING REGULATIONS FOR EXPLORATION LICENSES Miscellaneous § 970.2601 Additional information. Any United States citizen filing notice under § 970.2402 or § 970.2501 of this part...

Information content and cross-talk in biological signal transduction: An information theory study

NASA Astrophysics Data System (ADS)

Prasad, Ashok; Lyons, Samanthe

2014-03-01

Biological cells respond to chemical cues provided by extra-cellular chemical signals, but many of these chemical signals and the pathways they activate interfere and overlap with one another. How well cells can distinguish between interfering extra-cellular signals is thus an important question in cellular signal transduction. Here we use information theory with stochastic simulations of networks to address the question of what happens to total information content when signals interfere. We find that both total information transmitted by the biological pathway, as well as its theoretical capacity to discriminate between overlapping signals, are relatively insensitive to cross-talk between the extracellular signals, until significantly high levels of cross-talk have been reached. This robustness of information content against cross-talk requires that the average amplitude of the signals are large. We predict that smaller systems, as exemplified by simple phosphorylation relays (two-component systems) in bacteria, should be significantly much less robust against cross-talk. Our results suggest that mammalian signal transduction can tolerate a high amount of cross-talk without degrading information content, while smaller bacterial systems cannot.

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 time additional information concerning any application, or any other submission or pleading regarding...

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. Copyright © 2015 Elsevier Ltd. All rights reserved.

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 Requirements...

24 CFR 1710.116 - Additional information.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 24 Housing and Urban Development 5 2011-04-01 2011-04-01 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 Requirements...

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... URBAN DEVELOPMENT (INTERSTATE LAND SALES REGISTRATION PROGRAM) LAND REGISTRATION Reporting Requirements...

24 CFR 1710.116 - Additional information.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 24 Housing and Urban Development 5 2012-04-01 2012-04-01 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 Requirements...

Traceability of Biologics in The Netherlands: An Analysis of Information-Recording Systems in Clinical Practice and Spontaneous ADR Reports.

PubMed

Klein, Kevin; Scholl, Joep H G; Vermeer, Niels S; Broekmans, André W; Van Puijenbroek, Eugène P; De Bruin, Marie L; Stolk, Pieter

2016-02-01

Pharmacovigilance requirements for biologics mandate that EU Member States shall ensure that any biologic that is the subject of a suspected adverse drug reaction (ADR) is identifiable by brand name and batch number. Recent studies showed that brand name identification is well established, whereas batch numbers are (still) poorly reported. We evaluated information-recording systems and practices in the Dutch hospital setting to identify determinants for brand name and batch number recording as well as success factors and bottlenecks for traceability. We surveyed Dutch hospital pharmacists with an online questionnaire on systems and practices in hospitals for recording brand names and batch numbers. Additionally, we performed an analysis of the traceability of recombinant biologics in spontaneous ADR reports (received between 2009 and 2014) from the Netherlands Pharmacovigilance Centre Lareb. The survey showed that brand names are not routinely recorded in the clinical practice of Dutch hospitals, whereas batch numbers are poorly recorded. Seventy-six percent of the 1523 ADR reports for recombinant biologics had a traceable brand name whereas 5% of these reports contained a batch number. The results suggest a possible relationship between the availability of brand and batch number information in clinical practice and the inclusion of this information in ADR reports for biologics. The limited traceability of brand names and batch numbers in ADR reports may be primarily caused by the shortcomings in the recording of information in clinical practice. We recommend efforts to improve information-recording systems as a first step to improve the traceability of biologics in ADR reporting.

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

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 § 5.21...

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 § 5.21...

Biological versus Electronic Adaptive Coloration: How Can One Inform the Other?

DTIC Science & Technology

2012-01-01

Hyperspectral imaging of cuttlefish camouflage indicates good color match in the eyes of fish predators. Proc. Natl Acad. Sci. USA 108, 9148–9153. (doi...Patrick B. Dennis, Rajesh R. Naik, Eric Forsythe and inform the other? Biological versus electronic adaptive coloration : how can one References...TYPE 3. DATES COVERED 00-00-2012 to 00-00-2012 4. TITLE AND SUBTITLE Biological versus electronic adaptive coloration : how can one inform the

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

PubMed

Li, Le; Yip, Kevin Y

2016-12-15

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. Source code of Unicorn is available at http://yiplab.cse.cuhk.edu.hk/unicorn/.

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

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

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-06

... NATIONAL SCIENCE FOUNDATION Proposed Collection of Information; Comment Request: Biological Sciences Proposal Classification Form AGENCY: National Science Foundation. ACTION: Notice. SUMMARY: The... Biological Sciences has a continuing commitment to monitor its information collection in order to preserve...

Information fluency for undergraduate biology majors: applications of inquiry-based learning in a developmental biology course.

PubMed

Gehring, Kathleen M; Eastman, Deborah A

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. Quantitative 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.

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

Advances in metabolome information retrieval: turning chemistry into biology. Part II: biological information recovery.

PubMed

Tebani, Abdellah; Afonso, Carlos; Bekri, Soumeya

2018-05-01

This work reports the second part of a review intending to give the state of the art of major metabolic phenotyping strategies. It particularly deals with inherent advantages and limits regarding data analysis issues and biological information retrieval tools along with translational challenges. This Part starts with introducing the main data preprocessing strategies of the different metabolomics data. Then, it describes the main data analysis techniques including univariate and multivariate aspects. It also addresses the challenges related to metabolite annotation and characterization. Finally, functional analysis including pathway and network strategies are discussed. The last section of this review is devoted to practical considerations and current challenges and pathways to bring metabolomics into clinical environments.

PubSearch and PubFetch: a simple management system for semiautomated retrieval and annotation of biological information from the literature.

PubMed

Yoo, Danny; Xu, Iris; Berardini, Tanya Z; Rhee, Seung Yon; Narayanasamy, Vijay; Twigger, Simon

2006-03-01

For most systems in biology, a large body of literature exists that describes the complexity of the system based on experimental results. Manual review of this literature to extract targeted information into biological databases is difficult and time consuming. To address this problem, we developed PubSearch and PubFetch, which store literature, keyword, and gene information in a relational database, index the literature with keywords and gene names, and provide a Web user interface for annotating the genes from experimental data found in the associated literature. A set of protocols is provided in this unit for installing, populating, running, and using PubSearch and PubFetch. In addition, we provide support protocols for performing controlled vocabulary annotations. Intended users of PubSearch and PubFetch are database curators and biology researchers interested in tracking the literature and capturing information about genes of interest in a more effective way than with conventional spreadsheets and lab notebooks.

Translational environmental biology: cell biology informing conservation.

PubMed

Traylor-Knowles, Nikki; Palumbi, Stephen R

2014-05-01

Typically, findings from cell biology have been beneficial for preventing human disease. However, translational applications from cell biology can also be applied to conservation efforts, such as protecting coral reefs. Recent efforts to understand the cell biological mechanisms maintaining coral health such as innate immunity and acclimatization have prompted new developments in conservation. Similar to biomedicine, we urge that future efforts should focus on better frameworks for biomarker development to protect coral reefs. Copyright © 2014 Elsevier Ltd. All rights reserved.

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. Copyright © 2014 Elsevier Ltd. All rights reserved.

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....51 Confidentiality of data and information in applications for biologics licenses. (a) For purposes of this section the biological product file includes all data and information submitted with or...

How to derive biological information from the value of the normalization constant in allometric equations.

PubMed

Kaitaniemi, Pekka

2008-04-09

Allometric equations are widely used in many branches of biological science. The potential information content of the normalization constant b in allometric equations of the form Y = bX(a) has, however, remained largely neglected. To demonstrate the potential for utilizing this information, I generated a large number of artificial datasets that resembled those that are frequently encountered in biological studies, i.e., relatively small samples including measurement error or uncontrolled variation. The value of X was allowed to vary randomly within the limits describing different data ranges, and a was set to a fixed theoretical value. The constant b was set to a range of values describing the effect of a continuous environmental variable. In addition, a normally distributed random error was added to the values of both X and Y. Two different approaches were then used to model the data. The traditional approach estimated both a and b using a regression model, whereas an alternative approach set the exponent a at its theoretical value and only estimated the value of b. Both approaches produced virtually the same model fit with less than 0.3% difference in the coefficient of determination. Only the alternative approach was able to precisely reproduce the effect of the environmental variable, which was largely lost among noise variation when using the traditional approach. The results show how the value of b can be used as a source of valuable biological information if an appropriate regression model is selected.

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... APPROVALS FOR NUCLEAR POWER PLANTS Manufacturing Licenses § 52.158 Contents of application; additional technical information. The application must contain: (a)(1) Inspections, tests, analyses, and acceptance...

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

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 2 2010-01-01 2010-01-01 false Contents of applications; additional technical information... APPROVALS FOR NUCLEAR POWER PLANTS Combined Licenses § 52.80 Contents of applications; additional technical information. The application must contain: (a) The proposed inspections, tests, and analyses, including those...

20 CFR 609.23 - Furnishing additional information.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 20 Employees' Benefits 3 2010-04-01 2010-04-01 false Furnishing additional information. 609.23 Section 609.23 Employees' Benefits EMPLOYMENT AND TRAINING ADMINISTRATION, DEPARTMENT OF LABOR UNEMPLOYMENT COMPENSATION FOR FEDERAL CIVILIAN EMPLOYEES Responsibilities of Federal Agencies § 609.23...

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. Copyright © 2015 Elsevier Ltd. All rights reserved.

Text-mining and information-retrieval services for molecular biology

PubMed Central

Krallinger, Martin; Valencia, Alfonso

2005-01-01

Text-mining in molecular biology - defined as the automatic extraction of information about genes, proteins and their functional relationships from text documents - has emerged as a hybrid discipline on the edges of the fields of information science, bioinformatics and computational linguistics. A range of text-mining applications have been developed recently that will improve access to knowledge for biologists and database annotators. PMID:15998455

Human development I: twenty fundamental problems of biology, medicine, and neuro-psychology related to biological information.

PubMed

Hermansen, Tyge Dahl; Ventegodt, Søren; Rald, Erik; Clausen, Birgitte; Nielsen, Maj Lyck; Merrick, Joav

2006-07-06

In a new series of papers, we address a number of unsolved problems in biology today. First of all, the unsolved enigma concerning how the differentiation from a single zygote to an adult individual happens has been object for severe research for decades. By uncovering a new holistic biological paradigm that introduces an energetic-informational interpretation of reality as a new way to experience biology, these papers will try to solve the problems connected with the events of biological ontogenesis involving a fractal hierarchy, from a single cell to the function of the human brain. The problems discussed are interpreted within the frames of a universe of roomy fractal structures containing energetic patterns that are able to deliver biological information. We think biological organization is guided by energetic changes on the level of quantum mechanics, interacting with the intention that again guides the energetic conformation of the fractal structures to gain disorders or healthiness. Furthermore, we introduce two new concepts: "metamorphous top down" evolution and "adult human metamorphosis". The first is a new evolutionary theory involving metamorphosis as a main concept of evolution. The last is tightly linked to the evolutionary principle and explains how human self-recovery is governed. Other subjects of special interest that we shall look deeper into are the immunological self-nonself discrimination, the structure and function of the human brain, the etiology and salutogenesis of mental and somatic diseases, and the structure of the consciousness of a human being. We shall criticize Szentagothai's model for the modulated structure of the human cerebral cortex and Jerne's theory of the immunological regulatory anti-idiotypic network.

Information Complexity and Biology

NASA Astrophysics Data System (ADS)

Bagnoli, Franco; Bignone, Franco A.; Cecconi, Fabio; Politi, Antonio

Kolmogorov contributed directly to Biology in essentially three problems: the analysis of population dynamics (Lotka-Volterra equations), the reaction-diffusion formulation of gene spreading (FKPP equation), and some discussions about Mendel's laws. However, the widely recognized importance of his contribution arises from his work on algorithmic complexity. In fact, the limited direct intervention in Biology reflects the generally slow growth of interest of mathematicians towards biological issues. From the early work of Vito Volterra on species competition, to the slow growth of dynamical systems theory, contributions to the study of matter and the physiology of the nervous system, the first 50-60 years have witnessed important contributions, but as scattered pieces apparently uncorrelated, and in branches often far away from Biology. Up to the 40' it is hard to see the initial loose build up of a convergence, for those theories that will become mainstream research by the end of the century, and connected by the study of biological systems per-se.

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. Copyright © 2015 Elsevier Ltd. All rights reserved.

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 Application...

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 Application...

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 Application...

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 Application...

Analysis of biological time-lapse microscopic experiment from the point of view of the information theory.

PubMed

Štys, Dalibor; Urban, Jan; Vaněk, Jan; Císař, Petr

2011-06-01

We report objective analysis of information in the microscopic image of the cell monolayer. The process of transfer of information about the cell by the microscope is analyzed in terms of the classical Shannon information transfer scheme. The information source is the biological object, the information transfer channel is the whole microscope including the camera chip. The destination is the model of biological system. The information contribution is analyzed as information carried by a point to overall information in the image. Subsequently we obtain information reflection of the biological object. This is transformed in the biological model which, in information terminology, is the destination. This, we propose, should be constructed as state transitions in individual cells modulated by information bonds between the cells. We show examples of detected cell states in multidimensional state space. This space is reflected as colour channel intensity phenomenological state space. We have also observed information bonds and show examples of them.

Analysis of biological time-lapse microscopic experiment from the point of view of the information theory.

PubMed

Stys, Dalibor; Urban, Jan; Vanek, Jan; Císar, Petr

2010-07-01

We report objective analysis of information in the microscopic image of the cell monolayer. The process of transfer of information about the cell by the microscope is analyzed in terms of the classical Shannon information transfer scheme. The information source is the biological object, the information transfer channel is the whole microscope including the camera chip. The destination is the model of biological system. The information contribution is analyzed as information carried by a point to overall information in the image. Subsequently we obtain information reflection of the biological object. This is transformed in the biological model which, in information terminology, is the destination. This, we propose, should be constructed as state transitions in individual cells modulated by information bonds between the cells. We show examples of detected cell states in multidimensional state space reflected in space an colour channel intensity phenomenological state space. We have also observed information bonds and show examples of them. Copyright 2010 Elsevier Ltd. All rights reserved.

UK–South Asian patients’ experiences of and satisfaction toward receiving information about biologics in rheumatoid arthritis

PubMed Central

Kumar, Kanta; Raizada, Sabrina R; Mallen, Christian D; Stack, Rebecca J

2018-01-01

Background Rheumatoid arthritis (RA) causes painful joint inflammation and is incurable, but treatments control RA. Drug regimens are complex, and patients often do not take their medication as expected. Poor medication adherence can lead to poorly controlled disease and worse patient outcomes. Biologics treatments are expensive and require full engagement from patients. We have previously shown that patients from Black ethnic minority backgrounds do not fully engage into treatment plan. This study explored the patients’ experiences in and satisfaction toward receiving information about biologics and future support preferences in South Asian patients with RA. Methods Twenty South Asian patients with RA from Royal Wolverhampton Hospitals NHS Trust and Central Manchester University Hospitals NHS Foundation Trust participated in individual semistructured interviews. Interviews were transcribed and data were analyzed by using thematic analysis approach. Results Four overarching themes describe the patients’ experience in and satisfaction toward receiving information on biologics: 1) current provision of information regarding the “biologics journey” and understanding of RA: in this theme, non-English-speaking patients expressed heightened anxiety about stepping up to biologics; 2) experience and perceptions of biologics: many patients were positive about the biologic experience; however, there were patient-perceived delays in getting on to the biologics; 3) factors influencing willingness to try biologics: in this theme, a number of factors were identified including seeking advice from doctors abroad; and 4) recommendations on the desired information to fully understand the use of biologics: some patients valued group discussions, while others suggested receiving RA and biologic information through a video interaction. Conclusion This novel study provides insight into South Asian RA patients’ experiences in and satisfaction toward receiving information about

25 CFR 215.17 - Additional information required.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 25 Indians 1 2011-04-01 2011-04-01 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... application, must file one certified copy of articles of incorporation and, if a foreign corporation, evidence...

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.

25 CFR 215.17 - Additional information required.

Code of Federal Regulations, 2010 CFR

2010-04-01

... interested in lead and zinc mining leases, or land under the jurisdiction of the Quapaw Indian Agency, and... 25 Indians 1 2010-04-01 2010-04-01 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...

Developing Information Fluency in Introductory Biology Students in the Context of an Investigative Laboratory

ERIC Educational Resources Information Center

Lindquester, Gary J.; Burks, Romi L.; Jaslow, Carolyn R.

2005-01-01

Students of biology must learn the scientific method for generating information in the field. Concurrently, they should learn how information is reported and accessed. We developed a progressive set of exercises for the undergraduate introductory biology laboratory that combine these objectives. Pre- and postassessments of approximately 100…

BioRAT: extracting biological information from full-length papers.

PubMed

Corney, David P A; Buxton, Bernard F; Langdon, William B; Jones, David T

2004-11-22

Converting the vast quantity of free-format text found in journals into a concise, structured format makes the researcher's quest for information easier. Recently, several information extraction systems have been developed that attempt to simplify the retrieval and analysis of biological and medical data. Most of this work has used the abstract alone, owing to the convenience of access and the quality of data. Abstracts are generally available through central collections with easy direct access (e.g. PubMed). The full-text papers contain more information, but are distributed across many locations (e.g. publishers' web sites, journal web sites and local repositories), making access more difficult. In this paper, we present BioRAT, a new information extraction (IE) tool, specifically designed to perform biomedical IE, and which is able to locate and analyse both abstracts and full-length papers. BioRAT is a Biological Research Assistant for Text mining, and incorporates a document search ability with domain-specific IE. We show first, that BioRAT performs as well as existing systems, when applied to abstracts; and second, that significantly more information is available to BioRAT through the full-length papers than via the abstracts alone. Typically, less than half of the available information is extracted from the abstract, with the majority coming from the body of each paper. Overall, BioRAT recalled 20.31% of the target facts from the abstracts with 55.07% precision, and achieved 43.6% recall with 51.25% precision on full-length papers.

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.

12 CFR 335.801 - Inapplicable SEC regulations; FDIC substituted regulations; additional information.

Code of Federal Regulations, 2010 CFR

2010-01-01

... For information and answers to technical questions or problems relating to the use of FDICconnect... regulations; additional information. 335.801 Section 335.801 Banks and Banking FEDERAL DEPOSIT INSURANCE... Inapplicable SEC regulations; FDIC substituted regulations; additional information. (a) Filing fees. Filing...

12 CFR 1272.7 - Examinations; requests for additional information.

Code of Federal Regulations, 2014 CFR

2014-01-01

... information. 1272.7 Section 1272.7 Banks and Banking FEDERAL HOUSING FINANCE AGENCY FEDERAL HOME LOAN BANKS NEW BUSINESS ACTIVITIES § 1272.7 Examinations; requests for additional information. (a) General... business activity, nothing in this part shall limit the right of the FHFA at any time to: (1) Request...

12 CFR 1272.7 - Examinations; requests for additional information.

Code of Federal Regulations, 2012 CFR

2012-01-01

... information. 1272.7 Section 1272.7 Banks and Banking FEDERAL HOUSING FINANCE AGENCY FEDERAL HOME LOAN BANKS NEW BUSINESS ACTIVITIES § 1272.7 Examinations; requests for additional information. (a) General... business activity, nothing in this part shall limit the right of the FHFA at any time to: (1) Request...

12 CFR 1272.7 - Examinations; requests for additional information.

Code of Federal Regulations, 2013 CFR

2013-01-01

... information. 1272.7 Section 1272.7 Banks and Banking FEDERAL HOUSING FINANCE AGENCY FEDERAL HOME LOAN BANKS NEW BUSINESS ACTIVITIES § 1272.7 Examinations; requests for additional information. (a) General... business activity, nothing in this part shall limit the right of the FHFA at any time to: (1) Request...

Conference: Statistical Physics and Biological Information

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gross, David J.; Hwa, Terence

OAK B188 In the spring of 2001, the Institute for Theoretical Physics ran a 6 month scientific program on Statistical Physics and Biological Information. This program was organized by Walter Fitch (UC Irvine), Terence Hwa (UC San Diego), Luca Peliti (University Federico II), Naples Gary Stormo (Washington University School of Medicine) and Chao Tang (NEC). Overall scientific supervision was provided by David Gross, Director, ITP. The ITP has an online conference/program proceeding which consists of audio and transparencies of almost all of the talks held during this program. Over 100 talks are available on the site at http://online.kitp.ucsb.edu/online/infobio01/.

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.

Mutual information estimation reveals global associations between stimuli and biological processes

PubMed Central

Suzuki, Taiji; Sugiyama, Masashi; Kanamori, Takafumi; Sese, Jun

2009-01-01

Background Although microarray gene expression analysis has become popular, it remains difficult to interpret the biological changes caused by stimuli or variation of conditions. Clustering of genes and associating each group with biological functions are often used methods. However, such methods only detect partial changes within cell processes. Herein, we propose a method for discovering global changes within a cell by associating observed conditions of gene expression with gene functions. Results To elucidate the association, we introduce a novel feature selection method called Least-Squares Mutual Information (LSMI), which computes mutual information without density estimaion, and therefore LSMI can detect nonlinear associations within a cell. We demonstrate the effectiveness of LSMI through comparison with existing methods. The results of the application to yeast microarray datasets reveal that non-natural stimuli affect various biological processes, whereas others are no significant relation to specific cell processes. Furthermore, we discover that biological processes can be categorized into four types according to the responses of various stimuli: DNA/RNA metabolism, gene expression, protein metabolism, and protein localization. Conclusion We proposed a novel feature selection method called LSMI, and applied LSMI to mining the association between conditions of yeast and biological processes through microarray datasets. In fact, LSMI allows us to elucidate the global organization of cellular process control. PMID:19208155

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…

Informing Biological Design by Integration of Systems and Synthetic Biology

PubMed Central

Smolke, Christina D.; Silver, Pamela A.

2011-01-01

Synthetic biology aims to make the engineering of biology faster and more predictable. In contrast, systems biology focuses on the interaction of myriad components and how these give rise to the dynamic and complex behavior of biological systems. Here, we examine the synergies between these two fields. PMID:21414477

Informing biological design by integration of systems and synthetic biology.

PubMed

Smolke, Christina D; Silver, Pamela A

2011-03-18

Synthetic biology aims to make the engineering of biology faster and more predictable. In contrast, systems biology focuses on the interaction of myriad components and how these give rise to the dynamic and complex behavior of biological systems. Here, we examine the synergies between these two fields. Copyright © 2011 Elsevier Inc. All rights reserved.

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. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

[Exposure to biological agents used in Polish enterprises: analysis of data derived from the National Register of Biological Agent].

PubMed

Kozajda, Anna; Szadkowska-Stańczyk, Irena

2011-01-01

The National Register of Biological Agents at Work and the National Information Centre for Biological Agents Present at Workplaces were established in the Nofer Institute of Occupational Medicine in 2005. The National Information Centre carries out consultation and education activities concerning occupational exposure and risk assessment, development and implementation of preventive programs and accurate registration of reliable information about the use of biological agents. Educational materials on biological exposure are published on the website. The National Register of Biological Agents (database) collects and periodically analyzes the information obtained from employers about the use of biological agents for research, diagnostic or industrial purposes. As of 10 December 2010 there were 240 notifications from companies, which use biological agents for the following purposes: research--69, industrial--30 and diagnostic--321. Near 75% of all notifications were obtained from different diagnostic laboratories (public and private). In total, 3226 workers, including 2967 (92%) women and 256 (8%) men were exposed to biological agents. In general, occupational exposure to 209 biological agents (186 of risk group 2 and 23 of risk group 3, of which 16 are additionally marked by 3**) were registered in the data base.

Incorporating biological information in sparse principal component analysis with application to genomic data.

PubMed

Li, Ziyi; Safo, Sandra E; Long, Qi

2017-07-11

Sparse principal component analysis (PCA) is a popular tool for dimensionality reduction, pattern recognition, and visualization of high dimensional data. It has been recognized that complex biological mechanisms occur through concerted relationships of multiple genes working in networks that are often represented by graphs. Recent work has shown that incorporating such biological information improves feature selection and prediction performance in regression analysis, but there has been limited work on extending this approach to PCA. In this article, we propose two new sparse PCA methods called Fused and Grouped sparse PCA that enable incorporation of prior biological information in variable selection. Our simulation studies suggest that, compared to existing sparse PCA methods, the proposed methods achieve higher sensitivity and specificity when the graph structure is correctly specified, and are fairly robust to misspecified graph structures. Application to a glioblastoma gene expression dataset identified pathways that are suggested in the literature to be related with glioblastoma. The proposed sparse PCA methods Fused and Grouped sparse PCA can effectively incorporate prior biological information in variable selection, leading to improved feature selection and more interpretable principal component loadings and potentially providing insights on molecular underpinnings of complex diseases.

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.

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

The Default Mode Network Differentiates Biological From Non-Biological Motion

PubMed Central

Dayan, Eran; Sella, Irit; Mukovskiy, Albert; Douek, Yehonatan; Giese, Martin A.; Malach, Rafael; Flash, Tamar

2016-01-01

The default mode network (DMN) has been implicated in an array of social-cognitive functions, including self-referential processing, theory of mind, and mentalizing. Yet, the properties of the external stimuli that elicit DMN activity in relation to these domains remain unknown. Previous studies suggested that motion kinematics is utilized by the brain for social-cognitive processing. Here, we used functional MRI to examine whether the DMN is sensitive to parametric manipulations of observed motion kinematics. Preferential responses within core DMN structures differentiating non-biological from biological kinematics were observed for the motion of a realistically looking, human-like avatar, but not for an abstract object devoid of human form. Differences in connectivity patterns during the observation of biological versus non-biological kinematics were additionally observed. Finally, the results additionally suggest that the DMN is coupled more strongly with key nodes in the action observation network, namely the STS and the SMA, when the observed motion depicts human rather than abstract form. These findings are the first to implicate the DMN in the perception of biological motion. They may reflect the type of information used by the DMN in social-cognitive processing. PMID:25217472

29 CFR 502.44 - Additional information, if required.

Code of Federal Regulations, 2010 CFR

2010-07-01

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29 CFR 501.44 - Additional information, if required.

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2010-07-01

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Understanding Pictorial Information in Biology: Students' Cognitive Activities and Visual Reading Strategies

ERIC Educational Resources Information Center

Brandstetter, Miriam; Sandmann, Angela; Florian, Christine

2017-01-01

In classroom, scientific contents are increasingly communicated through visual forms of representations. Students' learning outcomes rely on their ability to read and understand pictorial information. Understanding pictorial information in biology requires cognitive effort and can be challenging to students. Yet evidence-based knowledge about…

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 DISTRIBUTION...

21 CFR 207.31 - Additional drug listing information.

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2014-04-01

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21 CFR 207.31 - Additional drug listing information.

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2013-04-01

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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 DISTRIBUTION...

ICON: 3D reconstruction with 'missing-information' restoration in biological electron tomography.

PubMed

Deng, Yuchen; Chen, Yu; Zhang, Yan; Wang, Shengliu; Zhang, Fa; Sun, Fei

2016-07-01

Electron tomography (ET) plays an important role in revealing biological structures, ranging from macromolecular to subcellular scale. Due to limited tilt angles, ET reconstruction always suffers from the 'missing wedge' artifacts, thus severely weakens the further biological interpretation. In this work, we developed an algorithm called Iterative Compressed-sensing Optimized Non-uniform fast Fourier transform reconstruction (ICON) based on the theory of compressed-sensing and the assumption of sparsity of biological specimens. ICON can significantly restore the missing information in comparison with other reconstruction algorithms. More importantly, we used the leave-one-out method to verify the validity of restored information for both simulated and experimental data. The significant improvement in sub-tomogram averaging by ICON indicates its great potential in the future application of high-resolution structural determination of macromolecules in situ. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

25 CFR 227.7 - Additional information from applicant.

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2014-04-01

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Objects and processes: Two notions for understanding biological information.

PubMed

Mercado-Reyes, Agustín; Padilla-Longoria, Pablo; Arroyo-Santos, Alfonso

2015-09-07

In spite of being ubiquitous in life sciences, the concept of information is harshly criticized. Uses of the concept other than those derived from Shannon׳s theory are denounced as metaphoric. We perform a computational experiment to explore whether Shannon׳s information is adequate to describe the uses of said concept in commonplace scientific practice. Our results show that semantic sequences do not have unique complexity values different from the value of meaningless sequences. This result suggests that quantitative theoretical frameworks do not account fully for the complex phenomenon that the term "information" refers to. We propose a restructuring of the concept into two related, but independent notions, and conclude that a complete theory of biological information must account completely not only for both notions, but also for the relationship between them. Copyright © 2015 Elsevier Ltd. All rights reserved.

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.

SSGP: SNP-set based genomic prediction to incorporate biological information

USDA-ARS?s Scientific Manuscript database

Genomic prediction has emerged as an effective approach in plant and animal breeding and in precision medicine. Much research has been devoted to an improved accuracy in genomic prediction, and one of the potential ways is to incorporate biological information. Due to the statistical and computation...

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.

25 CFR 227.7 - Additional information from applicant.

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Set membership experimental design for biological systems.

PubMed

Marvel, Skylar W; Williams, Cranos M

2012-03-21

Experimental design approaches for biological systems are needed to help conserve the limited resources that are allocated for performing experiments. The assumptions used when assigning probability density functions to characterize uncertainty in biological systems are unwarranted when only a small number of measurements can be obtained. In these situations, the uncertainty in biological systems is more appropriately characterized in a bounded-error context. Additionally, effort must be made to improve the connection between modelers and experimentalists by relating design metrics to biologically relevant information. Bounded-error experimental design approaches that can assess the impact of additional measurements on model uncertainty are needed to identify the most appropriate balance between the collection of data and the availability of resources. In this work we develop a bounded-error experimental design framework for nonlinear continuous-time systems when few data measurements are available. This approach leverages many of the recent advances in bounded-error parameter and state estimation methods that use interval analysis to generate parameter sets and state bounds consistent with uncertain data measurements. We devise a novel approach using set-based uncertainty propagation to estimate measurement ranges at candidate time points. We then use these estimated measurements at the candidate time points to evaluate which candidate measurements furthest reduce model uncertainty. A method for quickly combining multiple candidate time points is presented and allows for determining the effect of adding multiple measurements. Biologically relevant metrics are developed and used to predict when new data measurements should be acquired, which system components should be measured and how many additional measurements should be obtained. The practicability of our approach is illustrated with a case study. This study shows that our approach is able to 1) identify

Set membership experimental design for biological systems

PubMed Central

2012-01-01

Background Experimental design approaches for biological systems are needed to help conserve the limited resources that are allocated for performing experiments. The assumptions used when assigning probability density functions to characterize uncertainty in biological systems are unwarranted when only a small number of measurements can be obtained. In these situations, the uncertainty in biological systems is more appropriately characterized in a bounded-error context. Additionally, effort must be made to improve the connection between modelers and experimentalists by relating design metrics to biologically relevant information. Bounded-error experimental design approaches that can assess the impact of additional measurements on model uncertainty are needed to identify the most appropriate balance between the collection of data and the availability of resources. Results In this work we develop a bounded-error experimental design framework for nonlinear continuous-time systems when few data measurements are available. This approach leverages many of the recent advances in bounded-error parameter and state estimation methods that use interval analysis to generate parameter sets and state bounds consistent with uncertain data measurements. We devise a novel approach using set-based uncertainty propagation to estimate measurement ranges at candidate time points. We then use these estimated measurements at the candidate time points to evaluate which candidate measurements furthest reduce model uncertainty. A method for quickly combining multiple candidate time points is presented and allows for determining the effect of adding multiple measurements. Biologically relevant metrics are developed and used to predict when new data measurements should be acquired, which system components should be measured and how many additional measurements should be obtained. Conclusions The practicability of our approach is illustrated with a case study. This study shows that our

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.

Value Addition in Information Technology and Literacy: An Empirical Investigation

ERIC Educational Resources Information Center

Sanghera, Kamaljeet K.

2009-01-01

The purpose of the research is to analyze the value addition in students' information communication and technology (ICT) literacy level and confidence in using technology after completing a general education information technology course at a four-year university. An online survey was created to examine students' perceptions. The findings revealed…

The Default Mode Network Differentiates Biological From Non-Biological Motion.

PubMed

Dayan, Eran; Sella, Irit; Mukovskiy, Albert; Douek, Yehonatan; Giese, Martin A; Malach, Rafael; Flash, Tamar

2016-01-01

The default mode network (DMN) has been implicated in an array of social-cognitive functions, including self-referential processing, theory of mind, and mentalizing. Yet, the properties of the external stimuli that elicit DMN activity in relation to these domains remain unknown. Previous studies suggested that motion kinematics is utilized by the brain for social-cognitive processing. Here, we used functional MRI to examine whether the DMN is sensitive to parametric manipulations of observed motion kinematics. Preferential responses within core DMN structures differentiating non-biological from biological kinematics were observed for the motion of a realistically looking, human-like avatar, but not for an abstract object devoid of human form. Differences in connectivity patterns during the observation of biological versus non-biological kinematics were additionally observed. Finally, the results additionally suggest that the DMN is coupled more strongly with key nodes in the action observation network, namely the STS and the SMA, when the observed motion depicts human rather than abstract form. These findings are the first to implicate the DMN in the perception of biological motion. They may reflect the type of information used by the DMN in social-cognitive processing. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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.

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

Improving phylogenetic analyses by incorporating additional information from genetic sequence databases.

PubMed

Liang, Li-Jung; Weiss, Robert E; Redelings, Benjamin; Suchard, Marc A

2009-10-01

Statistical analyses of phylogenetic data culminate in uncertain estimates of underlying model parameters. Lack of additional data hinders the ability to reduce this uncertainty, as the original phylogenetic dataset is often complete, containing the entire gene or genome information available for the given set of taxa. Informative priors in a Bayesian analysis can reduce posterior uncertainty; however, publicly available phylogenetic software specifies vague priors for model parameters by default. We build objective and informative priors using hierarchical random effect models that combine additional datasets whose parameters are not of direct interest but are similar to the analysis of interest. We propose principled statistical methods that permit more precise parameter estimates in phylogenetic analyses by creating informative priors for parameters of interest. Using additional sequence datasets from our lab or public databases, we construct a fully Bayesian semiparametric hierarchical model to combine datasets. A dynamic iteratively reweighted Markov chain Monte Carlo algorithm conveniently recycles posterior samples from the individual analyses. We demonstrate the value of our approach by examining the insertion-deletion (indel) process in the enolase gene across the Tree of Life using the phylogenetic software BALI-PHY; we incorporate prior information about indels from 82 curated alignments downloaded from the BAliBASE database.

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.

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

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.; Karsch Mizrachi, Ilene; Orchard, Sandra; Ouellette, B.F. Francis; Ranganathan, Shoba; Richardson, Lorna; Rocca-Serra, Philippe; Schofield, Paul N.; Smedley, Damian; Southan, Christopher; Tan, Tin W.; 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:21205783

Zone analysis in biology articles as a basis for information extraction.

PubMed

Mizuta, Yoko; Korhonen, Anna; Mullen, Tony; Collier, Nigel

2006-06-01

In the field of biomedicine, an overwhelming amount of experimental data has become available as a result of the high throughput of research in this domain. The amount of results reported has now grown beyond the limits of what can be managed by manual means. This makes it increasingly difficult for the researchers in this area to keep up with the latest developments. Information extraction (IE) in the biological domain aims to provide an effective automatic means to dynamically manage the information contained in archived journal articles and abstract collections and thus help researchers in their work. However, while considerable advances have been made in certain areas of IE, pinpointing and organizing factual information (such as experimental results) remains a challenge. In this paper we propose tackling this task by incorporating into IE information about rhetorical zones, i.e. classification of spans of text in terms of argumentation and intellectual attribution. As the first step towards this goal, we introduce a scheme for annotating biological texts for rhetorical zones and provide a qualitative and quantitative analysis of the data annotated according to this scheme. We also discuss our preliminary research on automatic zone analysis, and its incorporation into our IE framework.

A DIRECTORY OF INFORMATION RESOURCES IN THE UNITED STATES. PHYSICAL SCIENCES, BIOLOGICAL SCIENCES, ENGINEERING.

ERIC Educational Resources Information Center

Library of Congress, Washington, DC.

SOURCES OF INFORMATION FOR BIOLOGICAL AND PHYSICAL SCIENCE AND ENGINEERING ARE LISTED. THEY INCLUDE--(1) LIBRARIES, (2) CENTRALIZED INFORMATION CENTERS, (3) PROFESSIONAL SOCIETIES AND OTHER SPECIALIZING ORGANIZATIONS, (4) INDUSTRIAL FIRMS, (5) GOVERNMENTAL AGENCIES OR OFFICES, AND (6) OTHER INFORMATION SOURCES WHICH MAKE SCIENTIFIC AND…

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

... 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 a biological product. (a) The existence of an IND notice for a biological product will not be disclosed by the...

Biological warfare agents

PubMed Central

Thavaselvam, Duraipandian; Vijayaraghavan, Rajagopalan

2010-01-01

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. PMID:21829313

DETAIL OF PLAQUE WITH ADDITIONAL DESIGN AND CONSTRUCTION INFORMATION, SOUTHEAST ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

DETAIL OF PLAQUE WITH ADDITIONAL DESIGN AND CONSTRUCTION INFORMATION, SOUTHEAST ABUTMENT - Connecticut Avenue Bridge, Spans Rock Creek & Potomac Parkway at Connecticut Avenue, Washington, District of Columbia, DC

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;…

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…

36 CFR 1290.3 - Sources of assassination records and additional records and information.

Code of Federal Regulations, 2010 CFR

2010-07-01

... Sources of assassination records and additional records and information. Assassination records and... 36 Parks, Forests, and Public Property 3 2010-07-01 2010-07-01 false Sources of assassination records and additional records and information. 1290.3 Section 1290.3 Parks, Forests, and Public Property...

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.

Acoustic fine structure may encode biologically relevant information for zebra finches.

PubMed

Prior, Nora H; Smith, Edward; Lawson, Shelby; Ball, Gregory F; Dooling, Robert J

2018-04-18

The ability to discriminate changes in the fine structure of complex sounds is well developed in birds. However, the precise limit of this discrimination ability and how it is used in the context of natural communication remains unclear. Here we describe natural variability in acoustic fine structure of male and female zebra finch calls. Results from psychoacoustic experiments demonstrate that zebra finches are able to discriminate extremely small differences in fine structure, which are on the order of the variation in acoustic fine structure that is present in their vocal signals. Results from signal analysis methods also suggest that acoustic fine structure may carry information that distinguishes between biologically relevant categories including sex, call type and individual identity. Combined, our results are consistent with the hypothesis that zebra finches can encode biologically relevant information within the fine structure of their calls. This study provides a foundation for our understanding of how acoustic fine structure may be involved in animal communication.

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 1974 PROCEDURAL REGULATIONS UNDER THE...

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.

H-point standard additions method for simultaneous determination of sulfamethoxazole and trimethoprim in pharmaceutical formulations and biological fluids with simultaneous addition of two analytes

NASA Astrophysics Data System (ADS)

Givianrad, M. H.; Saber-Tehrani, M.; Aberoomand-Azar, P.; Mohagheghian, M.

2011-03-01

The applicability of H-point standard additions method (HPSAM) to the resolving of overlapping spectra corresponding to the sulfamethoxazole and trimethoprim is verified by UV-vis spectrophotometry. The results show that the H-point standard additions method with simultaneous addition of both analytes is suitable for the simultaneous determination of sulfamethoxazole and trimethoprim in aqueous media. The results of applying the H-point standard additions method showed that the two drugs could be determined simultaneously with the concentration ratios of sulfamethoxazole to trimethoprim varying from 1:18 to 16:1 in the mixed samples. Also, the limits of detections were 0.58 and 0.37 μmol L -1 for sulfamethoxazole and trimethoprim, respectively. In addition the means of the calculated RSD (%) were 1.63 and 2.01 for SMX and TMP, respectively in synthetic mixtures. The proposed method has been successfully applied to the simultaneous determination of sulfamethoxazole and trimethoprim in some synthetic, pharmaceutical formulation and biological fluid samples.

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... I submit reports and additional information? (a) You must submit any written report or additional information required under this part to FDA, CDRH, Medical Device Reporting, P.O. Box 3002, Rockville, MD...

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

Code of Federal Regulations, 2011 CFR

2011-04-01

... information? 803.12 Section 803.12 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN... I submit reports and additional information? (a) You must submit any written report or additional information required under this part to FDA, CDRH, Medical Device Reporting, P.O. Box 3002, Rockville, MD...

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

Code of Federal Regulations, 2012 CFR

2012-04-01

... information? 803.12 Section 803.12 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN... I submit reports and additional information? (a) You must submit any written report or additional information required under this part to FDA, CDRH, Medical Device Reporting, P.O. Box 3002, Rockville, MD...

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.

34 CFR 222.185 - What additional information must be included in an emergency grant application?

Code of Federal Regulations, 2011 CFR

2011-07-01

... 34 Education 1 2011-07-01 2011-07-01 false What additional information must be included in an... for A Grant § 222.185 What additional information must be included in an emergency grant application? In addition to the information specified in § 222.184, an application for an emergency grant must...

25 CFR 103.14 - Can BIA request additional information?

Code of Federal Regulations, 2010 CFR

2010-04-01

... 25 Indians 1 2010-04-01 2010-04-01 false Can BIA request additional information? 103.14 Section 103.14 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR FINANCIAL ACTIVITIES LOAN GUARANTY, INSURANCE, AND INTEREST SUBSIDY How a Lender Obtains a Loan Guaranty or Insurance Coverage § 103.14 Can BIA...

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 TRANSMITTAL RULES § 803.20 Requests for additional...

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 TRANSMITTAL RULES § 803.20 Requests for additional...

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 TRANSMITTAL RULES § 803.20 Requests for additional...

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 TRANSMITTAL RULES § 803.20 Requests for additional...

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

Code of Federal Regulations, 2011 CFR

2011-01-01

... 16 Commercial Practices 1 2011-01-01 2011-01-01 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 TRANSMITTAL RULES § 803.20 Requests for additional...

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.

A theory of pragmatic information and its application to the quasi-species model of biological evolution.

PubMed

Weinberger, Edward D

2002-01-01

'Standard' information theory says nothing about the semantic content of information. Nevertheless, applications such as evolutionary theory demand consideration of precisely this aspect of information, a need that has motivated a largely unsuccessful search for a suitable measure of an 'amount of meaning'. This paper represents an attempt to move beyond this impasse, based on the observation that the meaning of a message can only be understood relative to its receiver. Positing that the semantic value of information is its usefulness in making an informed decision, we define pragmatic information as the information gain in the probability distributions of the receiver's actions, both before and after receipt of a message in some pre-defined ensemble. We then prove rigorously that our definition is the only one that satisfies obvious desiderata, such as the additivity of information from logically independent messages. This definition, when applied to the information 'learned' by the time evolution of a process, defies the intuitions of the few previous researchers thinking along these lines by being monotonic in the uncertainty that remains after receipt of the message, but non-monotonic in the Shannon entropy of the input ensemble. It also follows that the pragmatic information of the genetic 'messages' in an evolving population is a global Lyapunov function for Eigen's quasi-species model of biological evolution. A concluding section argues that a theory such as ours must explicitly acknowledge purposeful action, or 'agency', in such diverse fields as evolutionary theory and finance.

Perceptions of patients with rheumatic diseases treated with subcutaneous biologicals on their level of information: RHEU-LIFE Survey.

PubMed

de Toro, Javier; Cea-Calvo, Luis; Battle, Enrique; Carmona, Loreto; Arteaga, María J; Fernández, Sabela; González, Carlos M

2017-12-22

To investigate, in Spanish patients with rheumatic diseases treated with subcutaneous biological drugs, their sources of information, which sources they consider most relevant, and their satisfaction with the information received in the hospital. Rheumatologists from 50 hospitals handed out an anonymous survey to 20 consecutive patients with rheumatoid arthritis, axial spondyloarthritis or psoriatic arthritis treated with subcutaneous biologicals. The survey was developed ad hoc by 4 rheumatologists and 3 patients, and included questions with closed-ended responses on sources of information and satisfaction. The survey was handed-out to 1,000 patients, 592 of whom completed it (response rate: 59.2%). The rheumatologist was mentioned as the most important source of information (75%), followed by the primary care physician, nurses, and electronic resources; 45.2% received oral and written information about the biological, 46.1% oral only, and 6.0% written only; 8.7% stated that they had not been taught to inject the biological. The percentage of patients satisfied with the information received was high (87.2%), although the satisfaction was lower in relation to safety. If the information came from the rheumatologist, the satisfaction was higher (89.6%) than when coming from other sources (59.6%; P<.001). Satisfaction was also higher if the information was provided orally and written (92.8%) than if provided only orally (86.1%; P=.013); 45.2% reported having sought information from sources outside the hospital. The rheumatologist is key in transmitting satisfactory information on biological treatment to patients. He or she must also act as a guide, since a high percentage of patients seeks information in other different sources. Copyright © 2017. Publicado por Elsevier España, S.L.U.

43 CFR 2884.22 - Can BLM ask me for additional information?

Code of Federal Regulations, 2013 CFR

2013-10-01

... 43 Public Lands: Interior 2 2013-10-01 2013-10-01 false Can BLM ask me for additional information? 2884.22 Section 2884.22 Public Lands: Interior Regulations Relating to Public Lands (Continued) BUREAU... THE MINERAL LEASING ACT Applying for MLA Grants or TUPs § 2884.22 Can BLM ask me for additional...

43 CFR 2884.22 - Can BLM ask me for additional information?

Code of Federal Regulations, 2011 CFR

2011-10-01

... 43 Public Lands: Interior 2 2011-10-01 2011-10-01 false Can BLM ask me for additional information? 2884.22 Section 2884.22 Public Lands: Interior Regulations Relating to Public Lands (Continued) BUREAU... THE MINERAL LEASING ACT Applying for MLA Grants or TUPs § 2884.22 Can BLM ask me for additional...

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. © 2014 Royal Australian and New Zealand College of Ophthalmologists.

[Effect of biologically active food additives on energy metabolism and human body weight].

PubMed

Gapparov, M M

1999-01-01

Review is devoted to analysis of human energy requirements depending on age, sex, occupational and living condition. Special attention was paid to importance of strict balance in organism between consumption and expense of energy. Modern views on mechanism of action food supplements as additional instrument of regulation of energy metabolism for correction of surplus body weight is given. Review is the first attempt of systematisation of biologically active food supplements according to their mechanism of action both on nutrition processes and on biochemical mechanisms of assimilation and utilisation of macronutrients, in particular of fats and carbohydrates.

Multiplicative and additive modulation of neuronal tuning with population activity affects encoded information

PubMed Central

Arandia-Romero, Iñigo; Tanabe, Seiji; Drugowitsch, Jan; Kohn, Adam; Moreno-Bote, Rubén

2016-01-01

Numerous studies have shown that neuronal responses are modulated by stimulus properties, and also by the state of the local network. However, little is known about how activity fluctuations of neuronal populations modulate the sensory tuning of cells and affect their encoded information. We found that fluctuations in ongoing and stimulus-evoked population activity in primate visual cortex modulate the tuning of neurons in a multiplicative and additive manner. While distributed on a continuum, neurons with stronger multiplicative effects tended to have less additive modulation, and vice versa. The information encoded by multiplicatively-modulated neurons increased with greater population activity, while that of additively-modulated neurons decreased. These effects offset each other, so that population activity had little effect on total information. Our results thus suggest that intrinsic activity fluctuations may act as a `traffic light' that determines which subset of neurons are most informative. PMID:26924437

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. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Developing information fluency in introductory biology students in the context of an investigative laboratory.

PubMed

Lindquester, Gary J; Burks, Romi L; Jaslow, Carolyn R

2005-01-01

Students of biology must learn the scientific method for generating information in the field. Concurrently, they should learn how information is reported and accessed. We developed a progressive set of exercises for the undergraduate introductory biology laboratory that combine these objectives. Pre- and postassessments of approximately 100 students suggest that increases occurred, some statistically significant, in the number of students using various library-related resources, in the numbers and confidence level of students using various technologies, and in the numbers and confidence levels of students involved in various activities related to the scientific method. Following this course, students should be better prepared for more advanced and independent study.

Developing Information Fluency in Introductory Biology Students in the Context of an Investigative Laboratory

PubMed Central

2005-01-01

Students of biology must learn the scientific method for generating information in the field. Concurrently, they should learn how information is reported and accessed. We developed a progressive set of exercises for the undergraduate introductory biology laboratory that combine these objectives. Pre- and postassessments of approximately 100 students suggest that increases occurred, some statistically significant, in the number of students using various library-related resources, in the numbers and confidence level of students using various technologies, and in the numbers and confidence levels of students involved in various activities related to the scientific method. Following this course, students should be better prepared for more advanced and independent study. PMID:15746979

75 FR 68608 - Information Collection; Request for Authorization of Additional Classification and Rate, Standard...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-11-08

... Authorization of Additional Classification and Rate, Standard Form 1444 AGENCY: Department of Defense (DOD... of Additional Classification and Rate, Standard Form 1444. DATES: Comments may be submitted on or.../or business confidential information provided. FOR FURTHER INFORMATION CONTACT: Mr. Ernest Woodson...

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. © 2014 Nordic Association for the Publication of BCPT (former Nordic Pharmacological Society).

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

Federal Register 2010, 2011, 2012, 2013, 2014

2012-11-13

...] Agency Information Collection Activities; Proposed Collection; Comment Request; Food Additive Petitions and Investigational Food Additive Exemptions; Extension AGENCY: Food and Drug Administration, HHS... solicits comments on food additive petitions regarding animal food. DATES: Submit electronic or written...

H-point standard additions method for simultaneous determination of sulfamethoxazole and trimethoprim in pharmaceutical formulations and biological fluids with simultaneous addition of two analytes.

PubMed

Givianrad, M H; Saber-Tehrani, M; Aberoomand-Azar, P; Mohagheghian, M

2011-03-01

The applicability of H-point standard additions method (HPSAM) to the resolving of overlapping spectra corresponding to the sulfamethoxazole and trimethoprim is verified by UV-vis spectrophotometry. The results show that the H-point standard additions method with simultaneous addition of both analytes is suitable for the simultaneous determination of sulfamethoxazole and trimethoprim in aqueous media. The results of applying the H-point standard additions method showed that the two drugs could be determined simultaneously with the concentration ratios of sulfamethoxazole to trimethoprim varying from 1:18 to 16:1 in the mixed samples. Also, the limits of detections were 0.58 and 0.37 μmol L(-1) for sulfamethoxazole and trimethoprim, respectively. In addition the means of the calculated RSD (%) were 1.63 and 2.01 for SMX and TMP, respectively in synthetic mixtures. The proposed method has been successfully applied to the simultaneous determination of sulfamethoxazole and trimethoprim in some synthetic, pharmaceutical formulation and biological fluid samples. Copyright © 2011 Elsevier B.V. All rights reserved.

An ontology-driven semantic mashup of gene and biological pathway information: application to the domain of nicotine dependence.

PubMed

Sahoo, Satya S; Bodenreider, Olivier; Rutter, Joni L; Skinner, Karen J; Sheth, Amit P

2008-10-01

This paper illustrates how Semantic Web technologies (especially RDF, OWL, and SPARQL) can support information integration and make it easy to create semantic mashups (semantically integrated resources). In the context of understanding the genetic basis of nicotine dependence, we integrate gene and pathway information and show how three complex biological queries can be answered by the integrated knowledge base. We use an ontology-driven approach to integrate two gene resources (Entrez Gene and HomoloGene) and three pathway resources (KEGG, Reactome and BioCyc), for five organisms, including humans. We created the Entrez Knowledge Model (EKoM), an information model in OWL for the gene resources, and integrated it with the extant BioPAX ontology designed for pathway resources. The integrated schema is populated with data from the pathway resources, publicly available in BioPAX-compatible format, and gene resources for which a population procedure was created. The SPARQL query language is used to formulate queries over the integrated knowledge base to answer the three biological queries. Simple SPARQL queries could easily identify hub genes, i.e., those genes whose gene products participate in many pathways or interact with many other gene products. The identification of the genes expressed in the brain turned out to be more difficult, due to the lack of a common identification scheme for proteins. Semantic Web technologies provide a valid framework for information integration in the life sciences. Ontology-driven integration represents a flexible, sustainable and extensible solution to the integration of large volumes of information. Additional resources, which enable the creation of mappings between information sources, are required to compensate for heterogeneity across namespaces. RESOURCE PAGE: http://knoesis.wright.edu/research/lifesci/integration/structured_data/JBI-2008/

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 purposes...

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 purposes...

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 purposes...

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 purposes...

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 purposes...

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…

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. Copyright © 2015 Elsevier Ltd. All rights reserved.

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…

"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. © 2015 Society for Risk Analysis.

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.

Impaired visual recognition of biological motion in schizophrenia.

PubMed

Kim, Jejoong; Doop, Mikisha L; Blake, Randolph; Park, Sohee

2005-09-15

Motion perception deficits have been suggested to be an important feature of schizophrenia but the behavioral consequences of such deficits are unknown. Biological motion refers to the movements generated by living beings. The human visual system rapidly and effortlessly detects and extracts socially relevant information from biological motion. A deficit in biological motion perception may have significant consequences for detecting and interpreting social information. Schizophrenia patients and matched healthy controls were tested on two visual tasks: recognition of human activity portrayed in point-light animations (biological motion task) and a perceptual control task involving detection of a grouped figure against the background noise (global-form task). Both tasks required detection of a global form against background noise but only the biological motion task required the extraction of motion-related information. Schizophrenia patients performed as well as the controls in the global-form task, but were significantly impaired on the biological motion task. In addition, deficits in biological motion perception correlated with impaired social functioning as measured by the Zigler social competence scale [Zigler, E., Levine, J. (1981). Premorbid competence in schizophrenia: what is being measured? Journal of Consulting and Clinical Psychology, 49, 96-105.]. The deficit in biological motion processing, which may be related to the previously documented deficit in global motion processing, could contribute to abnormal social functioning in schizophrenia.

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

An ontology-driven semantic mash-up of gene and biological pathway information: Application to the domain of nicotine dependence

PubMed Central

Sahoo, Satya S.; Bodenreider, Olivier; Rutter, Joni L.; Skinner, Karen J.; Sheth, Amit P.

2008-01-01

Objectives This paper illustrates how Semantic Web technologies (especially RDF, OWL, and SPARQL) can support information integration and make it easy to create semantic mashups (semantically integrated resources). In the context of understanding the genetic basis of nicotine dependence, we integrate gene and pathway information and show how three complex biological queries can be answered by the integrated knowledge base. Methods We use an ontology-driven approach to integrate two gene resources (Entrez Gene and HomoloGene) and three pathway resources (KEGG, Reactome and BioCyc), for five organisms, including humans. We created the Entrez Knowledge Model (EKoM), an information model in OWL for the gene resources, and integrated it with the extant BioPAX ontology designed for pathway resources. The integrated schema is populated with data from the pathway resources, publicly available in BioPAX-compatible format, and gene resources for which a population procedure was created. The SPARQL query language is used to formulate queries over the integrated knowledge base to answer the three biological queries. Results Simple SPARQL queries could easily identify hub genes, i.e., those genes whose gene products participate in many pathways or interact with many other gene products. The identification of the genes expressed in the brain turned out to be more difficult, due to the lack of a common identification scheme for proteins. Conclusion Semantic Web technologies provide a valid framework for information integration in the life sciences. Ontology-driven integration represents a flexible, sustainable and extensible solution to the integration of large volumes of information. Additional resources, which enable the creation of mappings between information sources, are required to compensate for heterogeneity across namespaces. Resource page http://knoesis.wright.edu/research/lifesci/integration/structured_data/JBI-2008/ PMID:18395495

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

Code of Federal Regulations, 2013 CFR

2013-07-01

... provided by the additive manufacturer. 79.21 Section 79.21 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) REGISTRATION OF FUELS AND FUEL ADDITIVES Additive Registration Procedures § 79.21 Information and assurances to be provided by the additive manufacturer. Each...

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

Code of Federal Regulations, 2010 CFR

2010-07-01

... provided by the additive manufacturer. 79.21 Section 79.21 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) REGISTRATION OF FUELS AND FUEL ADDITIVES Additive Registration Procedures § 79.21 Information and assurances to be provided by the additive manufacturer. Each...

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

Code of Federal Regulations, 2014 CFR

2014-07-01

... provided by the additive manufacturer. 79.21 Section 79.21 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) REGISTRATION OF FUELS AND FUEL ADDITIVES Additive Registration Procedures § 79.21 Information and assurances to be provided by the additive manufacturer. Each...

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

Code of Federal Regulations, 2012 CFR

2012-07-01

... provided by the additive manufacturer. 79.21 Section 79.21 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) REGISTRATION OF FUELS AND FUEL ADDITIVES Additive Registration Procedures § 79.21 Information and assurances to be provided by the additive manufacturer. Each...

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

Code of Federal Regulations, 2011 CFR

2011-07-01

... provided by the additive manufacturer. 79.21 Section 79.21 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) REGISTRATION OF FUELS AND FUEL ADDITIVES Additive Registration Procedures § 79.21 Information and assurances to be provided by the additive manufacturer. Each...

NCRETURN Computer Program for Evaluating Investments Revised to Provide Additional Information

Treesearch

Allen L. Lundgren; Dennis L. Schweitzer

1971-01-01

Reports a modified version of NCRETURN, a computer program for evauating forestry investments. The revised version, RETURN, provides additional information about each investment, including future net worths and benefit-cost ratios, with no added input.

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…

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.

Using the Viking biology experimental results to obtain chemical information about Martian regolith

NASA Technical Reports Server (NTRS)

Plumb, Robert C.

1992-01-01

Although initially formulated as biology experiments, most of the results produced by the Viking Labeled Release (LR), Gas Exchange (GEX), and Pyrolytic Release (PR) experiments have been reproduced by chemical means. The experiments do not need more study as 'biological' phenomena, but they do deserve much more careful consideration from a chemical viewpoint. They are the only 'wet-chemical' experiments that scientists have performed on another planet, but they have not found very general use as sources of scientific information. There is a large set of potentially useful chemical observations, e.g., the three resolvable and precisely measured kinetic components of the release of C-14-labeled gases, the thermal sensitivity and magnitudes of the oxidation reaction(s) of the LR experiments, the kinetics and magnitude of the O2 and CO2 release of the GEX experiments, the thermal sensitivity of the GEX results, the differences between the thermal sensitivity of the GEX and the thermal sensitivity of the LR responses, and the kinetics and magnitudes of the LR successive injection reabsorption effect. It should be possible to test many chemical aspects of hypothetical martian phenomena in experiments using the biology experimental configurations and derive much valuable information by comparisons with the Viking observations.

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…

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

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-13

... DEPARTMENT OF HEALTH AND HUMAN SERVICES Food and Drug Administration [Docket No. FDA-2010-N-0622] Agency Information Collection Activities; Proposed Collection; Comment Request; Color Additive... collection provisions of FDA's regulations governing batch certification of color additives manufactured for...

Systems biology: the case for a systems science approach to diabetes.

PubMed

Petrasek, Danny

2008-01-01

The unprecedented accumulation of biological data in recent decades has underscored the need to organize and integrate the massive collection of information. In addition, there is rising agreement among biologists that a complete understanding of a single cell will not lead directly to a complete understanding of a system of cells. The success of a systems science approach in engineering and physics may be of great value in the evolution of biological science. This article reviews some examples that suggest the importance of a systems biology approach and, in addition, advance one specific systems science principle, the conservation of uncertainty, which may give insight into the emergent behavior of numerous biological and physiological phenomena.

Stream biological surveys - self-defense for coal mine operators

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hampton, E.L.; Pennington, W.L.; Lackey, J.L.

1979-12-01

According to Section 779.20 of the Permanent Regulatory Program Regulations, Surface Coal Mining and Reclamation Operations, Department of the Interior, office of Surface Mining Reclamation and Enforcement, coal mine operators must provide information on fish and wildlife resources in order to obtain mining permits. Although considered to be a liability by many mine operators, stream biological surveys can, in reality, become a significant asset. When combined with appropriate water quality measurements, stream biological surveys can adequately assess a stream's health. Although initially adding cost, stream biological surveys can actually save money and potential litigation during the mining period. However, streammore » biological surveys must be conducted before any mining activity is initiated and should continue on a periodic basis thereafter. Only in this manner can mine operators be assured that biological measurements made on streams affected by their operation are accurate reflections of pre- and post-mining conditions. Armed with this vital information, mine operators have a basis to defend against any unjustified claims that their operations are having deleterious effects on the stream in question. This paper addresses the purpose, scope, methodology, and interpretation of results of stream biological surveys. Additionally, methods for utilizing information from stream biological surveys will be stressed.« less

Online information seeking practices of biology teachers and the perceived influences on instructional planning

NASA Astrophysics Data System (ADS)

Perrault, Anne Marie

The purpose of this study was to examine biology teachers' perceptions of how their online information seeking practices influence their instructional planning. When teachers engage in activities to locate, evaluate, and use online information and resources, a myriad of inter-related and often inseparable consequences follows. These influences may be any combination of direct/indirect, desirable/undesirable, or anticipated/unanticipated (Rogers, 2003). This exploratory study collected baseline data regarding teachers' online practices and its influence on their practice. There were two phases of data collection in this study. Phase I was an online survey of more than seventy New York State biology teachers. The survey was intended to capture (1) a snapshot of the biology teachers' online information seeking practices during the summer and fall 2004, and (2) their perceptions regarding how their online practices influenced their instructional planning. In Phase II, ten study participants were interviewed in order to explore in greater detail the consequences of their online information seeking practices on their instructional planning. Four themes reflecting the consequences of teachers' information seeking practices emerged from the data analysis: Currency of Information; Sparking of Ideas and Gaining Personal Knowledge; Resource Management and the Role of Time; and Webs of Sharing. Each theme encompassed both the purposeful and the indirect actions by teachers to access knowledge and resources to refine and improve their instructional planning. This study's findings show that teachers are using a greater number and wider range of current and multi-modal resources than pre-Internet and they perceive this as an advantage in creating authentic, inquiry-based learning experiences. A notable discovery was of the under-use by teachers of educational online resources specifically designed to support teaching and learning activities (e.g., digital libraries, online

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.

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.

Integrating biological knowledge into variable selection: an empirical Bayes approach with an application in cancer biology

PubMed Central

2012-01-01

Background An important question in the analysis of biochemical data is that of identifying subsets of molecular variables that may jointly influence a biological response. Statistical variable selection methods have been widely used for this purpose. In many settings, it may be important to incorporate ancillary biological information concerning the variables of interest. Pathway and network maps are one example of a source of such information. However, although ancillary information is increasingly available, it is not always clear how it should be used nor how it should be weighted in relation to primary data. Results We put forward an approach in which biological knowledge is incorporated using informative prior distributions over variable subsets, with prior information selected and weighted in an automated, objective manner using an empirical Bayes formulation. We employ continuous, linear models with interaction terms and exploit biochemically-motivated sparsity constraints to permit exact inference. We show an example of priors for pathway- and network-based information and illustrate our proposed method on both synthetic response data and by an application to cancer drug response data. Comparisons are also made to alternative Bayesian and frequentist penalised-likelihood methods for incorporating network-based information. Conclusions The empirical Bayes method proposed here can aid prior elicitation for Bayesian variable selection studies and help to guard against mis-specification of priors. Empirical Bayes, together with the proposed pathway-based priors, results in an approach with a competitive variable selection performance. In addition, the overall procedure is fast, deterministic, and has very few user-set parameters, yet is capable of capturing interplay between molecular players. The approach presented is general and readily applicable in any setting with multiple sources of biological prior knowledge. PMID:22578440

Radiation Information for Designing and Interpreting Biological Experiments Onboard Missions Beyond Low Earth Orbit

NASA Technical Reports Server (NTRS)

Straume, T.; Slaba, T.; Bhattacharya, S.; Braby, L. A.

2017-01-01

There is growing interest in flying biological experiments beyond low-Earth orbit (LEO) to measure biological responses potentially relevant to those expected during a human mission to Mars. Such experiments could be payloads onboard precursor missions, including unmanned private-public partnerships, as well as small low-cost spacecraft (satellites) designed specifically for biosentinel type missions. Designing such experiments requires knowledge of the radiation environment and its interactions with both the spacecraft and the experimental payload. Information is provided here that is useful for designing such experiments.

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 Development...

Defining the Synthetic Biology Supply Chain

DOE Office of Scientific and Technical Information (OSTI.GOV)

Frazar, Sarah L.; Hund, Gretchen E.; Bonheyo, George T.

In this article, a team of experts in synthetic biology, data analytics, and national security describe the overall supply chain surrounding synthetic biology. The team analyzes selected interactions within that network to better understand the risks raised by synthetic biology and identifies opportunities for risk mitigation. To introduce the concept, the article will briefly describe how an understanding of supply chains has been important in promoting nuclear nonproliferation objectives. The article concludes by assessing the structure and networks identified in the supply chains to reveal potential opportunities for future biodefense research and development; options for additional information exchange; and meansmore » to interdict, detect, or deter suspicious activity.« less

An efficient biological pathway layout algorithm combining grid-layout and spring embedder for complicated cellular location information

PubMed Central

2010-01-01

Background Graph drawing is one of the important techniques for understanding biological regulations in a cell or among cells at the pathway level. Among many available layout algorithms, the spring embedder algorithm is widely used not only for pathway drawing but also for circuit placement and www visualization and so on because of the harmonized appearance of its results. For pathway drawing, location information is essential for its comprehension. However, complex shapes need to be taken into account when torus-shaped location information such as nuclear inner membrane, nuclear outer membrane, and plasma membrane is considered. Unfortunately, the spring embedder algorithm cannot easily handle such information. In addition, crossings between edges and nodes are usually not considered explicitly. Results We proposed a new grid-layout algorithm based on the spring embedder algorithm that can handle location information and provide layouts with harmonized appearance. In grid-layout algorithms, the mapping of nodes to grid points that minimizes a cost function is searched. By imposing positional constraints on grid points, location information including complex shapes can be easily considered. Our layout algorithm includes the spring embedder cost as a component of the cost function. We further extend the layout algorithm to enable dynamic update of the positions and sizes of compartments at each step. Conclusions The new spring embedder-based grid-layout algorithm and a spring embedder algorithm are applied to three biological pathways; endothelial cell model, Fas-induced apoptosis model, and C. elegans cell fate simulation model. From the positional constraints, all the results of our algorithm satisfy location information, and hence, more comprehensible layouts are obtained as compared to the spring embedder algorithm. From the comparison of the number of crossings, the results of the grid-layout-based algorithm tend to contain more crossings than those of the

DNASU plasmid and PSI:Biology-Materials repositories: resources to accelerate biological research

PubMed Central

Seiler, Catherine Y.; Park, Jin G.; Sharma, Amit; Hunter, Preston; Surapaneni, Padmini; Sedillo, Casey; Field, James; Algar, Rhys; Price, Andrea; Steel, Jason; Throop, Andrea; Fiacco, Michael; LaBaer, Joshua

2014-01-01

The mission of the DNASU Plasmid Repository is to accelerate research by providing high-quality, annotated plasmid samples and online plasmid resources to the research community through the curated DNASU database, website and repository (http://dnasu.asu.edu or http://dnasu.org). The collection includes plasmids from grant-funded, high-throughput cloning projects performed in our laboratory, plasmids from external researchers, and large collections from consortia such as the ORFeome Collaboration and the NIGMS-funded Protein Structure Initiative: Biology (PSI:Biology). Through DNASU, researchers can search for and access detailed information about each plasmid such as the full length gene insert sequence, vector information, associated publications, and links to external resources that provide additional protein annotations and experimental protocols. Plasmids can be requested directly through the DNASU website. DNASU and the PSI:Biology-Materials Repositories were previously described in the 2010 NAR Database Issue (Cormier, C.Y., Mohr, S.E., Zuo, D., Hu, Y., Rolfs, A., Kramer, J., Taycher, E., Kelley, F., Fiacco, M., Turnbull, G. et al. (2010) Protein Structure Initiative Material Repository: an open shared public resource of structural genomics plasmids for the biological community. Nucleic Acids Res., 38, D743–D749.). In this update we will describe the plasmid collection and highlight the new features in the website redesign, including new browse/search options, plasmid annotations and a dynamic vector mapping feature that was developed in collaboration with LabGenius. Overall, these plasmid resources continue to enable research with the goal of elucidating the role of proteins in both normal biological processes and disease. PMID:24225319

[Information value of "additional tasks" method to evaluate pilot's work load].

PubMed

Gorbunov, V V

2005-01-01

"Additional task" method was used to evaluate pilot's work load in prolonged flight. Calculated through durations of latent periods of motor responses, quantitative criterion of work load is more informative for objective evaluation of pilot's involvement in his piloting functions rather than of other registered parameters.

Moving beyond a descriptive aquatic toxicology: the value of biological process and trait information.

PubMed

Segner, Helmut

2011-10-01

In order to improve the ability to link chemical exposure to toxicological and ecological effects, aquatic toxicology will have to move from observing what chemical concentrations induce adverse effects to more explanatory approaches, that are concepts which build on knowledge of biological processes and pathways leading from exposure to adverse effects, as well as on knowledge on stressor vulnerability as given by the genetic, physiological and ecological (e.g., life history) traits of biota. Developing aquatic toxicology in this direction faces a number of challenges, including (i) taking into account species differences in toxicant responses on the basis of the evolutionarily developed diversity of phenotypic vulnerability to environmental stressors, (ii) utilizing diversified biological response profiles to serve as biological read across for prioritizing chemicals, categorizing them according to modes of action, and for guiding targeted toxicity evaluation; (iii) prediction of ecological consequences of toxic exposure from knowledge of how biological processes and phenotypic traits lead to effect propagation across the levels of biological hierarchy; and (iv) the search for concepts to assess the cumulative impact of multiple stressors. An underlying theme in these challenges is that, in addition to the question of what the chemical does to the biological receptor, we should give increasing emphasis to the question how the biological receptor handles the chemicals, i.e., through which pathways the initial chemical-biological interaction extends to the adverse effects, how this extension is modulated by adaptive or compensatory processes as well as by phenotypic traits of the biological receptor. 2011 Elsevier B.V. All rights reserved.

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 concern...

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

Code of Federal Regulations, 2012 CFR

2012-07-01

... 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 concern...

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

Code of Federal Regulations, 2014 CFR

2014-07-01

... 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 concern...

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

Code of Federal Regulations, 2013 CFR

2013-07-01

... 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 concern...

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

Informed consent should be obtained from patients to use products (skin substitutes) and dressings containing biological material.

PubMed

Enoch, S; Shaaban, H; Dunn, K W

2005-01-01

Biological products (tissue engineered skin, allograft and xenograft, and biological dressings) are widely used in the treatment of burns, chronic wounds, and other forms of acute injury. However, the religious and ethical issues, including consent, arising from their use have never been addressed in the medical literature. This study was aimed to ascertain the views of religious leaders about the acceptability of biological products and to evaluate awareness among healthcare professionals about their constituents. The religious groups that make up about 75% of the United Kingdom population were identified and a questionnaire on 11 biological products was sent to its leaders. Another questionnaire concerning 17 products (11 biological and 6 synthetic dressings) was sent to 100 healthcare professionals working in seven specialist units in the UK. All religious leaders (100% response rate) replied, some after consultation with international bodies. Among them, 77% said that patients should be informed of the constituents of the biological products and consent obtained. Some leaders expressed concerns about particular products including the transmission of viral and prion diseases, cruelty to animals, and material derived from neonates. None of the healthcare professionals (73% response rate) surveyed knew the constituents of all the products correctly. Ignoring religious sensitivities and neglecting consent in the usage of biological products could have very serious implications, including litigation. Hospitals and manufacturers should take immediate measures to enlighten healthcare professionals of the constituents of these products so that they can obtain informed consent from patients.

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.

43 CFR 3515.23 - May BLM require me to submit additional information?

Code of Federal Regulations, 2011 CFR

2011-10-01

... require me to submit additional information? Yes. You must be willing to provide geologic and economic data we need to determine the fair market value of your preference right or lease to be relinquished. ...

Biological Agents

MedlinePlus

... E-Tools Safety and Health Topics / Biological Agents Biological Agents This page requires that javascript be enabled ... 202) 693-2300 if additional assistance is required. Biological Agents Menu Overview In Focus: Ebola Frederick A. ...

76 FR 51125 - Additional Identifying Information Associated With Persons Whose Property and Interests in...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-08-17

... Transnational Criminal Organizations.'' FOR FURTHER INFORMATION CONTACT: Assistant Director, Sanctions... DEPARTMENT OF THE TREASURY Office of Foreign Assets Control Additional Identifying Information... 13581of July 24, 2011, ``Blocking Property of Transnational Criminal Organizations.'' AGENCY: Office of...

Quantum entanglement and quantum information in biological systems (DNA)

NASA Astrophysics Data System (ADS)

Hubač, Ivan; Švec, Miloslav; Wilson, Stephen

2017-12-01

Recent studies of DNA show that the hydrogen bonds between given base pairs can be treated as diabatic systems with spin-orbit coupling. For solid state systems strong diabaticity and spin-orbit coupling the possibility of forming Majorana fermions has been discussed. We analyze the hydrogen bonds in the base pairs in DNA from this perspective. Our analysis is based on a quasiparticle supersymmetric transformation which couples electronic and vibrational motion and includes normal coordinates and the corresponding momenta. We define qubits formed by Majorana fermions in the hydrogen bonds and also discuss the entangled states in base pairs. Quantum information and quantum entropy are introduced. In addition to the well-known classical information connected with the DNA base pairs, we also consider quantum information and show that the classical and quantum information are closely connected.

Data-intensive drug development in the information age: applications of Systems Biology/Pharmacology/Toxicology.

PubMed

Kiyosawa, Naoki; Manabe, Sunao

2016-01-01

Pharmaceutical companies continuously face challenges to deliver new drugs with true medical value. R&D productivity of drug development projects depends on 1) the value of the drug concept and 2) data and in-depth knowledge that are used rationally to evaluate the drug concept's validity. A model-based data-intensive drug development approach is a key competitive factor used by innovative pharmaceutical companies to reduce information bias and rationally demonstrate the value of drug concepts. Owing to the accumulation of publicly available biomedical information, our understanding of the pathophysiological mechanisms of diseases has developed considerably; it is the basis for identifying the right drug target and creating a drug concept with true medical value. Our understanding of the pathophysiological mechanisms of disease animal models can also be improved; it can thus support rational extrapolation of animal experiment results to clinical settings. The Systems Biology approach, which leverages publicly available transcriptome data, is useful for these purposes. Furthermore, applying Systems Pharmacology enables dynamic simulation of drug responses, from which key research questions to be addressed in the subsequent studies can be adequately informed. Application of Systems Biology/Pharmacology to toxicology research, namely Systems Toxicology, should considerably improve the predictability of drug-induced toxicities in clinical situations that are difficult to predict from conventional preclinical toxicology studies. Systems Biology/Pharmacology/Toxicology models can be continuously improved using iterative learn-confirm processes throughout preclinical and clinical drug discovery and development processes. Successful implementation of data-intensive drug development approaches requires cultivation of an adequate R&D culture to appreciate this approach.

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

Code of Federal Regulations, 2010 CFR

2010-10-01

... service agents release information? 40.331 Section 40.331 Transportation Office of the Secretary of... Release of Information § 40.331 To what additional parties must employers and service agents release information? As an employer or service agent you must release information under the following circumstances...

20 CFR 30.518 - Can OWCP require the recipient of the overpayment to submit additional financial information?

Code of Federal Regulations, 2010 CFR

2010-04-01

... overpayment to submit additional financial information? 30.518 Section 30.518 Employees' Benefits OFFICE OF... OWCP require the recipient of the overpayment to submit additional financial information? (a) The... specified by OWCP. This information is needed to determine whether or not recovery of an overpayment would...

20 CFR 30.518 - Can OWCP require the recipient of the overpayment to submit additional financial information?

Code of Federal Regulations, 2012 CFR

2012-04-01

... overpayment to submit additional financial information? 30.518 Section 30.518 Employees' Benefits OFFICE OF... OWCP require the recipient of the overpayment to submit additional financial information? (a) The... specified by OWCP. This information is needed to determine whether or not recovery of an overpayment would...

20 CFR 30.518 - Can OWCP require the recipient of the overpayment to submit additional financial information?

Code of Federal Regulations, 2011 CFR

2011-04-01

... overpayment to submit additional financial information? 30.518 Section 30.518 Employees' Benefits OFFICE OF... OWCP require the recipient of the overpayment to submit additional financial information? (a) The... specified by OWCP. This information is needed to determine whether or not recovery of an overpayment would...

How Information Literate Are Junior and Senior Class Biology Students?

NASA Astrophysics Data System (ADS)

Schiffl, Iris

2018-03-01

Information literacy—i.e. obtaining, evaluating and using information—is a key element of scientific literacy. However, students are frequently equipped with poor information literacy skills—even at university level—as information literacy is often not explicitly taught in schools. Little is known about students' information skills in science at junior and senior class level, and about teachers' competences in dealing with information literacy in science class. This study examines the information literacy of Austrian 8th, 10th and 12th grade students. Information literacy is important for science education in Austria, because it is listed as a basic competence in Austria's science standards. Two different aspects of information literacy are examined: obtaining information and extracting information from texts. An additional research focus of this study is teachers' competences in diagnosing information skills. The results reveal that students mostly rely on online sources for obtaining information. However, they also use books and consult with people they trust. The younger the students, the more they rely on personal sources. Students' abilities to evaluate sources are poor, especially among younger students. Although teachers claim to use information research in class, their ability to assess their students' information competences is limited.

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)

Biological imaging with coherent Raman scattering microscopy: a tutorial

PubMed Central

Alfonso-García, Alba; Mittal, Richa; Lee, Eun Seong; Potma, Eric O.

2014-01-01

Abstract. Coherent Raman scattering (CRS) microscopy is gaining acceptance as a valuable addition to the imaging toolset of biological researchers. Optimal use of this label-free imaging technique benefits from a basic understanding of the physical principles and technical merits of the CRS microscope. This tutorial offers qualitative explanations of the principles behind CRS microscopy and provides information about the applicability of this nonlinear optical imaging approach for biological research. PMID:24615671

21 CFR 640.61 - Informed consent.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 7 2010-04-01 2010-04-01 false Informed consent. 640.61 Section 640.61 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) BIOLOGICS ADDITIONAL STANDARDS FOR HUMAN BLOOD AND BLOOD PRODUCTS Source Plasma § 640.61 Informed consent. The written...

21 CFR 640.61 - Informed consent.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 7 2012-04-01 2012-04-01 false Informed consent. 640.61 Section 640.61 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) BIOLOGICS ADDITIONAL STANDARDS FOR HUMAN BLOOD AND BLOOD PRODUCTS Source Plasma § 640.61 Informed consent. The written...

21 CFR 640.61 - Informed consent.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 7 2011-04-01 2010-04-01 true Informed consent. 640.61 Section 640.61 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) BIOLOGICS ADDITIONAL STANDARDS FOR HUMAN BLOOD AND BLOOD PRODUCTS Source Plasma § 640.61 Informed consent. The written...

21 CFR 640.61 - Informed consent.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 7 2013-04-01 2013-04-01 false Informed consent. 640.61 Section 640.61 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) BIOLOGICS ADDITIONAL STANDARDS FOR HUMAN BLOOD AND BLOOD PRODUCTS Source Plasma § 640.61 Informed consent. The written...

21 CFR 640.61 - Informed consent.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 7 2014-04-01 2014-04-01 false Informed consent. 640.61 Section 640.61 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) BIOLOGICS ADDITIONAL STANDARDS FOR HUMAN BLOOD AND BLOOD PRODUCTS Source Plasma § 640.61 Informed consent. The written...

“Gestaltomics”: Systems Biology Schemes for the Study of Neuropsychiatric Diseases

PubMed Central

Gutierrez Najera, Nora A.; Resendis-Antonio, Osbaldo; Nicolini, Humberto

2017-01-01

The integration of different sources of biological information about what defines a behavioral phenotype is difficult to unify in an entity that reflects the arithmetic sum of its individual parts. In this sense, the challenge of Systems Biology for understanding the “psychiatric phenotype” is to provide an improved vision of the shape of the phenotype as it is visualized by “Gestalt” psychology, whose fundamental axiom is that the observed phenotype (behavior or mental disorder) will be the result of the integrative composition of every part. Therefore, we propose the term “Gestaltomics” as a term from Systems Biology to integrate data coming from different sources of information (such as the genome, transcriptome, proteome, epigenome, metabolome, phenome, and microbiome). In addition to this biological complexity, the mind is integrated through multiple brain functions that receive and process complex information through channels and perception networks (i.e., sight, ear, smell, memory, and attention) that in turn are programmed by genes and influenced by environmental processes (epigenetic). Today, the approach of medical research in human diseases is to isolate one disease for study; however, the presence of an additional disease (co-morbidity) or more than one disease (multimorbidity) adds complexity to the study of these conditions. This review will present the challenge of integrating psychiatric disorders at different levels of information (Gestaltomics). The implications of increasing the level of complexity, for example, studying the co-morbidity with another disease such as cancer, will also be discussed. PMID:28536537

Synthetic biology: insights into biological computation.

PubMed

Manzoni, Romilde; Urrios, Arturo; Velazquez-Garcia, Silvia; de Nadal, Eulàlia; Posas, Francesc

2016-04-18

Organisms have evolved a broad array of complex signaling mechanisms that allow them to survive in a wide range of environmental conditions. They are able to sense external inputs and produce an output response by computing the information. Synthetic biology attempts to rationally engineer biological systems in order to perform desired functions. Our increasing understanding of biological systems guides this rational design, while the huge background in electronics for building circuits defines the methodology. In this context, biocomputation is the branch of synthetic biology aimed at implementing artificial computational devices using engineered biological motifs as building blocks. Biocomputational devices are defined as biological systems that are able to integrate inputs and return outputs following pre-determined rules. Over the last decade the number of available synthetic engineered devices has increased exponentially; simple and complex circuits have been built in bacteria, yeast and mammalian cells. These devices can manage and store information, take decisions based on past and present inputs, and even convert a transient signal into a sustained response. The field is experiencing a fast growth and every day it is easier to implement more complex biological functions. This is mainly due to advances in in vitro DNA synthesis, new genome editing tools, novel molecular cloning techniques, continuously growing part libraries as well as other technological advances. This allows that digital computation can now be engineered and implemented in biological systems. Simple logic gates can be implemented and connected to perform novel desired functions or to better understand and redesign biological processes. Synthetic biological digital circuits could lead to new therapeutic approaches, as well as new and efficient ways to produce complex molecules such as antibiotics, bioplastics or biofuels. Biological computation not only provides possible biomedical and

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

... Designated Nationals and Blocked Persons (``SDN List'') on September 13, 2012. FOR FURTHER INFORMATION... and Facsimile Availability The SDN List and additional information concerning OFAC are available from...

Towards the prediction of essential genes by integration of network topology, cellular localization and biological process information

PubMed Central

2009-01-01

Background The identification of essential genes is important for the understanding of the minimal requirements for cellular life and for practical purposes, such as drug design. However, the experimental techniques for essential genes discovery are labor-intensive and time-consuming. Considering these experimental constraints, a computational approach capable of accurately predicting essential genes would be of great value. We therefore present here a machine learning-based computational approach relying on network topological features, cellular localization and biological process information for prediction of essential genes. Results We constructed a decision tree-based meta-classifier and trained it on datasets with individual and grouped attributes-network topological features, cellular compartments and biological processes-to generate various predictors of essential genes. We showed that the predictors with better performances are those generated by datasets with integrated attributes. Using the predictor with all attributes, i.e., network topological features, cellular compartments and biological processes, we obtained the best predictor of essential genes that was then used to classify yeast genes with unknown essentiality status. Finally, we generated decision trees by training the J48 algorithm on datasets with all network topological features, cellular localization and biological process information to discover cellular rules for essentiality. We found that the number of protein physical interactions, the nuclear localization of proteins and the number of regulating transcription factors are the most important factors determining gene essentiality. Conclusion We were able to demonstrate that network topological features, cellular localization and biological process information are reliable predictors of essential genes. Moreover, by constructing decision trees based on these data, we could discover cellular rules governing essentiality. PMID:19758426

HOW CAN BIOLOGICALLY-BASED MODELING OF ARSENIC KINETICS AND DYNAMICS INFORM THE RISK ASSESSMENT PROCESS?

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 met...

CyBy(2): a structure-based data management tool for chemical and biological data.

PubMed

Höck, Stefan; Riedl, Rainer

2012-01-01

We report the development of a powerful data management tool for chemical and biological data: CyBy(2). CyBy(2) is a structure-based information management tool used to store and visualize structural data alongside additional information such as project assignment, physical information, spectroscopic data, biological activity, functional data and synthetic procedures. The application consists of a database, an application server, used to query and update the database, and a client application with a rich graphical user interface (GUI) used to interact with the server.

Telomeres and age-related disease: how telomere biology informs clinical paradigms

PubMed Central

Armanios, Mary

2013-01-01

Telomere length shortens with age and predicts the onset of replicative senescence. Recently, short telomeres have been linked to the etiology of degenerative diseases such as idiopathic pulmonary fibrosis, bone marrow failure, and cryptogenic liver cirrhosis. These disorders have recognizable clinical manifestations, and the telomere defect explains their genetics and informs the approach to their treatment. Here, I review how telomere biology has become intimately connected to clinical paradigms both for understanding pathophysiology and for individualizing therapy decisions. I also critically examine nuances of interpreting telomere length measurement in clinical studies. PMID:23454763

Biological aerosol background characterization

NASA Astrophysics Data System (ADS)

Blatny, Janet; Fountain, Augustus W., III

2011-05-01

To provide useful information during military operations, or as part of other security situations, a biological aerosol detector has to respond within seconds or minutes to an attack by virulent biological agents, and with low false alarms. Within this time frame, measuring virulence of a known microorganism is extremely difficult, especially if the microorganism is of unknown antigenic or nucleic acid properties. Measuring "live" characteristics of an organism directly is not generally an option, yet only viable organisms are potentially infectious. Fluorescence based instruments have been designed to optically determine if aerosol particles have viability characteristics. Still, such commercially available biological aerosol detection equipment needs to be improved for their use in military and civil applications. Air has an endogenous population of microorganisms that may interfere with alarm software technologies. To design robust algorithms, a comprehensive knowledge of the airborne biological background content is essential. For this reason, there is a need to study ambient live bacterial populations in as many locations as possible. Doing so will permit collection of data to define diverse biological characteristics that in turn can be used to fine tune alarm algorithms. To avoid false alarms, improving software technologies for biological detectors is a crucial feature requiring considerations of various parameters that can be applied to suppress alarm triggers. This NATO Task Group will aim for developing reference methods for monitoring biological aerosol characteristics to improve alarm algorithms for biological detection. Additionally, they will focus on developing reference standard methodology for monitoring biological aerosol characteristics to reduce false alarm rates.

Evaluating Drugs and Food Additives for Public Use: A Case Studies Approach.

ERIC Educational Resources Information Center

Merritt, Sheridan V.

1980-01-01

Described is a case study used in an introductory college biology course that provides a basis for generating debate on an issue concerning the regulation of controversial food additives and prescription drugs. The case study contained within this article deals with drug screening, specifically with information related to thalidomide. (CS)

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

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 > ).

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

... whether: (1) The information requested is essential for processing the license application; and (2) The... or other interested party requests additional information? 148.108 Section 148.108 Navigation and... requests additional information? (a) Any Federal or State agency or other interested person may recommend...

Defining the "like" in "begetting the like": The development of inductive inference in the domain of biology

NASA Astrophysics Data System (ADS)

Lo, Ya-Fen

There are evidences that very young children consider linguistic labels when making similarity judgment and inductive inferences. However, it remains unclear how labels contribute to young children's similarity judgment and inductive inferences. It has been demonstrated that labels facilitate categorical memberships about objects in young children's similarity judgment and inductive inferences. It is also suggested that young children should rely on several sources of information when making similarity judgment and inductive inferences. Three experiments were conducted to examine these interpretations, in which biological information, labeling information, and perceptual similarity information were varied in a systematic manner. Three- to eleven-year-old children were asked to judge which of two Test animals a baby animals would share biological properties with. In Experiment 1, preschool children demonstrated a basic understanding of the importance of biological information for generalizing biological properties. In Experiment 2, when the labeling information became available, young children relied on linguistic labels rather than on biological information when generalizing biological properties. At the same time, 9- to 11-year-old children relied consistently on biological information. Experiment 3 supported the results of Experiment 2 and suggested that in addition to labels, perceptual similarity also contributed to children's inductive inferences.

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

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. © 2016 The Author(s).

26 CFR 1.852-7 - Additional information required in returns of shareholders.

Code of Federal Regulations, 2014 CFR

2014-04-01

... (CONTINUED) INCOME TAX (CONTINUED) INCOME TAXES (CONTINUED) Regulated Investment Companies and Real Estate Investment Trusts § 1.852-7 Additional information required in returns of shareholders. Any person who fails or refuses to comply with the demand of a regulated investment company for the written statements...

26 CFR 1.852-7 - Additional information required in returns of shareholders.

Code of Federal Regulations, 2012 CFR

2012-04-01

... (CONTINUED) INCOME TAX (CONTINUED) INCOME TAXES (CONTINUED) Regulated Investment Companies and Real Estate Investment Trusts § 1.852-7 Additional information required in returns of shareholders. Any person who fails or refuses to comply with the demand of a regulated investment company for the written statements...

26 CFR 1.852-7 - Additional information required in returns of shareholders.

Code of Federal Regulations, 2011 CFR

2011-04-01

... (CONTINUED) INCOME TAX (CONTINUED) INCOME TAXES (CONTINUED) Regulated Investment Companies and Real Estate Investment Trusts § 1.852-7 Additional information required in returns of shareholders. Any person who fails or refuses to comply with the demand of a regulated investment company for the written statements...

26 CFR 1.852-7 - Additional information required in returns of shareholders.

Code of Federal Regulations, 2013 CFR

2013-04-01

... (CONTINUED) INCOME TAX (CONTINUED) INCOME TAXES (CONTINUED) Regulated Investment Companies and Real Estate Investment Trusts § 1.852-7 Additional information required in returns of shareholders. Any person who fails or refuses to comply with the demand of a regulated investment company for the written statements...

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

Code of Federal Regulations, 2010 CFR

2010-04-01

... § 20.61 of this chapter. (3) Adverse reaction reports, product experience reports, consumer complaints... or action on a particular lot of a certifiable color additive. (b) The following data and information...

Quantitation and detection of vanadium in biologic and pollution materials

NASA Technical Reports Server (NTRS)

Gordon, W. A.

1974-01-01

A review is presented of special considerations and methodology for determining vanadium in biological and air pollution materials. In addition to descriptions of specific analysis procedures, general sections are included on quantitation of analysis procedures, sample preparation, blanks, and methods of detection of vanadium. Most of the information presented is applicable to the determination of other trace elements in addition to vanadium.

The application of biological motion research: biometrics, sport, and the military.

PubMed

Steel, Kylie; Ellem, Eathan; Baxter, David

2015-02-01

The body of research that examines the perception of biological motion is extensive and explores the factors that are perceived from biological motion and how this information is processed. This research demonstrates that individuals are able to use relative (temporal and spatial) information from a person's movement to recognize factors, including gender, age, deception, emotion, intention, and action. The research also demonstrates that movement presents idiosyncratic properties that allow individual discrimination, thus providing the basis for significant exploration in the domain of biometrics and social signal processing. Medical forensics, safety garments, and victim selection domains also have provided a history of research on the perception of biological motion applications; however, a number of additional domains present opportunities for application that have not been explored in depth. Therefore, the purpose of this paper is to present an overview of the current applications of biological motion-based research and to propose a number of areas where biological motion research, specific to recognition, could be applied in the future.

Understanding pictorial information in biology: students' cognitive activities and visual reading strategies

NASA Astrophysics Data System (ADS)

Brandstetter, Miriam; Sandmann, Angela; Florian, Christine

2017-06-01

In classroom, scientific contents are increasingly communicated through visual forms of representations. Students' learning outcomes rely on their ability to read and understand pictorial information. Understanding pictorial information in biology requires cognitive effort and can be challenging to students. Yet evidence-based knowledge about students' visual reading strategies during the process of understanding pictorial information is pending. Therefore, 42 students at the age of 14-15 were asked to think aloud while trying to understand visual representations of the blood circulatory system and the patellar reflex. A category system was developed differentiating 16 categories of cognitive activities. A Principal Component Analysis revealed two underlying patterns of activities that can be interpreted as visual reading strategies: 1. Inferences predominated by using a problem-solving schema; 2. Inferences predominated by recall of prior content knowledge. Each pattern consists of a specific set of cognitive activities that reflect selection, organisation and integration of pictorial information as well as different levels of expertise. The results give detailed insights into cognitive activities of students who were required to understand the pictorial information of complex organ systems. They provide an evidence-based foundation to derive instructional aids that can promote students pictorial-information-based learning on different levels of expertise.

Fostering synergy between cell biology and systems biology.

PubMed

Eddy, James A; Funk, Cory C; Price, Nathan D

2015-08-01

In the shared pursuit of elucidating detailed mechanisms of cell function, systems biology presents a natural complement to ongoing efforts in cell biology. Systems biology aims to characterize biological systems through integrated and quantitative modeling of cellular information. The process of model building and analysis provides value through synthesizing and cataloging information about cells and molecules, predicting mechanisms and identifying generalizable themes, generating hypotheses and guiding experimental design, and highlighting knowledge gaps and refining understanding. In turn, incorporating domain expertise and experimental data is crucial for building towards whole cell models. An iterative cycle of interaction between cell and systems biologists advances the goals of both fields and establishes a framework for mechanistic understanding of the genome-to-phenome relationship. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

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

Code of Federal Regulations, 2013 CFR

2013-04-01

... chapter. (8) All records showing the testing of and action on a particular lot by the Food and Drug... of a biological product on animals and humans and all studies and tests on the drug for identity... 21 Food and Drugs 7 2013-04-01 2013-04-01 false Confidentiality of data and information in...

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

Code of Federal Regulations, 2012 CFR

2012-04-01

... chapter. (8) All records showing the testing of and action on a particular lot by the Food and Drug... of a biological product on animals and humans and all studies and tests on the drug for identity... 21 Food and Drugs 7 2012-04-01 2012-04-01 false Confidentiality of data and information in...

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

Code of Federal Regulations, 2014 CFR

2014-04-01

... chapter. (8) All records showing the testing of and action on a particular lot by the Food and Drug... of a biological product on animals and humans and all studies and tests on the drug for identity... 21 Food and Drugs 7 2014-04-01 2014-04-01 false Confidentiality of data and information in...

Analysis of arsenical metabolites in biological samples.

PubMed

Hernandez-Zavala, Araceli; Drobna, Zuzana; Styblo, Miroslav; Thomas, David J

2009-11-01

Quantitation of iAs and its methylated metabolites in biological samples provides dosimetric information needed to understand dose-response relations. Here, methods are described for separation of inorganic and mono-, di-, and trimethylated arsenicals by thin layer chromatography. This method has been extensively used to track the metabolism of the radionuclide [(73)As] in a variety of in vitro assay systems. In addition, a hydride generation-cryotrapping-gas chromatography-atomic absorption spectrometric method is described for the quantitation of arsenicals in biological samples. This method uses pH-selective hydride generation to differentiate among arsenicals containing trivalent or pentavalent arsenic.

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.

Additional Support for the Information Systems Analyst Exam as a Valid Program Assessment Tool

ERIC Educational Resources Information Center

Carpenter, Donald A.; Snyder, Johnny; Slauson, Gayla Jo; Bridge, Morgan K.

2011-01-01

This paper presents a statistical analysis to support the notion that the Information Systems Analyst (ISA) exam can be used as a program assessment tool in addition to measuring student performance. It compares ISA exam scores earned by students in one particular Computer Information Systems program with scores earned by the same students on the…

Traversing the conceptual divide between biological and statistical epistasis: systems biology and a more modern synthesis.

PubMed

Moore, Jason H; Williams, Scott M

2005-06-01

Epistasis plays an important role in the genetic architecture of common human diseases and can be viewed from two perspectives, biological and statistical, each derived from and leading to different assumptions and research strategies. Biological epistasis is the result of physical interactions among biomolecules within gene regulatory networks and biochemical pathways in an individual such that the effect of a gene on a phenotype is dependent on one or more other genes. In contrast, statistical epistasis is defined as deviation from additivity in a mathematical model summarizing the relationship between multilocus genotypes and phenotypic variation in a population. The goal of this essay is to review definitions and examples of biological and statistical epistasis and to explore the relationship between the two. Specifically, we present and discuss the following two questions in the context of human health and disease. First, when does statistical evidence of epistasis in human populations imply underlying biomolecular interactions in the etiology of disease? Second, when do biomolecular interactions produce patterns of statistical epistasis in human populations? Answers to these two reciprocal questions will provide an important framework for using genetic information to improve our ability to diagnose, prevent and treat common human diseases. We propose that systems biology will provide the necessary information for addressing these questions and that model systems such as bacteria, yeast and digital organisms will be a useful place to start.

Design and analysis of large-scale biological rhythm studies: a comparison of algorithms for detecting periodic signals in biological data

PubMed Central

Deckard, Anastasia; Anafi, Ron C.; Hogenesch, John B.; Haase, Steven B.; Harer, John

2013-01-01

Motivation: To discover and study periodic processes in biological systems, we sought to identify periodic patterns in their gene expression data. We surveyed a large number of available methods for identifying periodicity in time series data and chose representatives of different mathematical perspectives that performed well on both synthetic data and biological data. Synthetic data were used to evaluate how each algorithm responds to different curve shapes, periods, phase shifts, noise levels and sampling rates. The biological datasets we tested represent a variety of periodic processes from different organisms, including the cell cycle and metabolic cycle in Saccharomyces cerevisiae, circadian rhythms in Mus musculus and the root clock in Arabidopsis thaliana. Results: From these results, we discovered that each algorithm had different strengths. Based on our findings, we make recommendations for selecting and applying these methods depending on the nature of the data and the periodic patterns of interest. Additionally, these results can also be used to inform the design of large-scale biological rhythm experiments so that the resulting data can be used with these algorithms to detect periodic signals more effectively. Contact: anastasia.deckard@duke.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24058056

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

... Collection Request; Comment Request; Regulation of Fuels and Fuel Additives: 2011 Renewable Fuel Standards... collection request (ICR), ``Regulation of Fuels and Fuel Additives: 2011 Renewable Fuel Standards--Petition... whose disclosure is restricted by statute. FOR FURTHER INFORMATION CONTACT: Geanetta Heard, Fuels...

47 CFR 25.111 - Additional information.

Code of Federal Regulations, 2010 CFR

2010-10-01

... information it requires for the Advance Publication, Coordination and Notification of frequency assignments... information required by the ITU Radiocommunication Bureau to advance publish, coordinate and notify the frequencies to be used for tracking, telemetry and control functions of DBS systems. [56 FR 24016, May 28...

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...

Using biological-physical modelling for informing sea lice dispersal in Loch Linnhe, Scotland.

PubMed

Salama, N K G; Dale, A C; Ivanov, V V; Cook, P F; Pert, C C; Collins, C M; Rabe, B

2018-06-01

Sea lice are a constraint on the sustainable growth of Scottish marine salmonid aquaculture. As part of an integrated pest management approach, farms coordinate procedures within spatial units. We present observations of copepodids being at relatively greater density than nauplii in upper waters, which informs the development of surface layer sea lice transmission modelling of Loch Linnhe, Scotland, for informing farm parasite management. A hydrodynamic model is coupled with a biological particle-tracking model, with characteristics of plankton sea lice. Simulations are undertaken for May and October 2011-2013, forced by local wind data collected for those periods. Particles are continually released from positions representing farm locations, weighted by relative farm counts, over a 2-week period and tracked for a further 5 days. A comparison is made between modelled relative concentrations against physical and biological surveys to provide confidence in model outputs. Connectivity between farm locations is determined in order to propose potential coordination areas. Generally, connectivity depends on flow patterns in the loch and decreases with increased farm separation. The connectivity indices are used to estimate the origins of the sea lice population composition at each site, which may influence medicinal regimens to avoid loss of efficacy. © 2017 John Wiley & Sons Ltd.

Organic Matter in SNC Meteorites: Is It Time to Re-Evaluate the Viking Biology Experimental Data?

NASA Technical Reports Server (NTRS)

Warmflash, D.; Clemett, S. J.; McKay, D. S.

2001-01-01

New data from SNC meteorites suggests that organic material may be present in the martian upper crust. This adds to possibility that the Viking biology experiments may have plausible biological interpretations as well as inorganic chemical interpretations Additional information is contained in the original extended abstract..

Plant Biology: From the Classroom to the Internet

ERIC Educational Resources Information Center

Bradley, Lucy K.; Stutz, Jean C.; Towill, Leslie R.

2009-01-01

The lecture content of a Plant Biology class for non-majors was transformed from a traditional on-campus lecture to an asynchronous website for use both as a stand-alone internet-based course and as an adjunct to the on-campus course. Additional information and examples of the online interactive activities included in PLB 108, Concepts in Plant…

Estimating the biological value of soft-bottom sediments with sediment profile imaging and grab sampling

NASA Astrophysics Data System (ADS)

Van Hoey, Gert; Birchenough, Silvana N. R.; Hostens, Kris

2014-02-01

Biological value estimation is based on a set of assessment questions and several thresholds to delineate areas of ecological importance (e.g. biodiversity). An existing framework, that was specifically designed to assess the ecosystem biodiversity, was expanded by adding new questions on the productivity, functionality and biogeochemical status of benthic habitats. The additional ecological and sedimentological information was collected by using sediment profile imagery (SPI) and grab sampling. Additionally, information on the performance and comparability of both techniques is provided in this study. The research idea was tested at a site near the harbor of Zeebrugge, an area under consideration as a new disposal site for dredged material from the harbor entrance. The sedimentology of the area can be adequately described based on the information from both SPI and Van Veen grab samples, but only the SPI revealed structural information on the physical habitat (layering, a-RPD). The latter information represented the current status of the benthic habitat, which was confirmed by the Van Veen grab samples. All information was summarized through the biological valuation framework, and provided clear evidence of the differences in biological value for the different sediment types within the area. We concluded that the installation of a new dredged material disposal site in this area was not in conflict with the benthic ecology. This area has a low biological value and the benthic system is adapted to changing conditions, which was signaled by the dominance of mobile, short living and opportunistic species. This study showed that suitable sedimentological and ecological information can be gathered by these traditional and complementary techniques, to estimate the biological value of an area in the light of marine spatial planning and environmental impact assessments.

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

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…

Biological and health effects of exposure to kerosene-based jet fuels and performance additives.

PubMed

Ritchie, Glenn; Still, Kenneth; Rossi, John; Bekkedal, Marni; Bobb, Andrew; Arfsten, Darryl

2003-01-01

performance additives, and other environmental exposure factors may result in unpredicted toxicity. While there is little epidemiological evidence for fuel-induced death, cancer, or other serious organic disease in fuel-exposed workers, large numbers of self-reported health complaints in this cohort appear to justify study of more subtle health consequences. A number of recently published studies reported acute or persisting biological or health effects from acute, subchronic, or chronic exposure of humans or animals to kerosene-based hydrocarbon fuels, to constituent chemicals of these fuels, or to fuel combustion products. This review provides an in-depth summary of human, animal, and in vitro studies of biological or health effects from exposure to JP-8, JP-8 +100, JP-5, Jet A, Jet A-1, or kerosene.

Attention, biological motion, and action recognition.

PubMed

Thompson, James; Parasuraman, Raja

2012-01-02

Interacting with others in the environment requires that we perceive and recognize their movements and actions. Neuroimaging and neuropsychological studies have indicated that a number of brain regions, particularly the superior temporal sulcus, are involved in a number of processes essential for action recognition, including the processing of biological motion and processing the intentions of actions. We review the behavioral and neuroimaging evidence suggesting that while some aspects of action recognition might be rapid and effective, they are not necessarily automatic. Attention is particularly important when visual information about actions is degraded or ambiguous, or if competing information is present. We present evidence indicating that neural responses associated with the processing of biological motion are strongly modulated by attention. In addition, behavioral and neuroimaging evidence shows that drawing inferences from the actions of others is attentionally demanding. The role of attention in action observation has implications for everyday social interactions and workplace applications that depend on observing, understanding and interpreting actions. Published by Elsevier Inc.

Gap analysis on the biology of Mediterranean marine fishes

PubMed Central

Dimarchopoulou, Donna; Stergiou, Konstantinos I.

2017-01-01

We estimated the current level of knowledge concerning several biological characteristics of the Mediterranean marine fishes by carrying out a gap analysis based on information extracted from the literature, aiming to identify research trends and future needs in the field of Mediterranean fish biology that can be used in stock assessments, ecosystem modeling and fisheries management. Based on the datasets that emerged from the literature review, there is no information on any biological characteristic for 43% (n = 310) of the Mediterranean fish species, whereas for an additional 15% (n = 109) of them there is information about just one characteristic. The gap between current and desired knowledge (defined here as having information on most biological characteristics for at least half of the Mediterranean marine fishes) is smaller in length-weight relationships, which have been studied for 43% of the species, followed by spawning (39%), diet (29%), growth (25%), maturity (24%), lifespan (19%) and fecundity (17%). The gap is larger in natural mortality for which information is very scarce (8%). European hake (Merluccius merluccius), red mullet (Mullus barbatus), annular seabream (Diplodus annularis), common pandora (Pagellus erythrinus), European anchovy (Engraulis encrasicolus), European pilchard (Sardina pilchardus) and bogue (Boops boops) were the most studied species, while sharks and rays were among the least studied ones. Only 25 species were fully studied, i.e. there was available information on all their biological characteristics. The knowledge gaps per characteristic varied among the western, central and eastern Mediterranean subregions. The number of available records per species was positively related to total landings, while no relationship emerged with its maximum reported length, trophic level and commercial value. Future research priorities that should be focused on less studied species (e.g. sharks and rays) and mortality/fecundity instead of length

Gap analysis on the biology of Mediterranean marine fishes.

PubMed

Dimarchopoulou, Donna; Stergiou, Konstantinos I; Tsikliras, Athanassios C

2017-01-01

We estimated the current level of knowledge concerning several biological characteristics of the Mediterranean marine fishes by carrying out a gap analysis based on information extracted from the literature, aiming to identify research trends and future needs in the field of Mediterranean fish biology that can be used in stock assessments, ecosystem modeling and fisheries management. Based on the datasets that emerged from the literature review, there is no information on any biological characteristic for 43% (n = 310) of the Mediterranean fish species, whereas for an additional 15% (n = 109) of them there is information about just one characteristic. The gap between current and desired knowledge (defined here as having information on most biological characteristics for at least half of the Mediterranean marine fishes) is smaller in length-weight relationships, which have been studied for 43% of the species, followed by spawning (39%), diet (29%), growth (25%), maturity (24%), lifespan (19%) and fecundity (17%). The gap is larger in natural mortality for which information is very scarce (8%). European hake (Merluccius merluccius), red mullet (Mullus barbatus), annular seabream (Diplodus annularis), common pandora (Pagellus erythrinus), European anchovy (Engraulis encrasicolus), European pilchard (Sardina pilchardus) and bogue (Boops boops) were the most studied species, while sharks and rays were among the least studied ones. Only 25 species were fully studied, i.e. there was available information on all their biological characteristics. The knowledge gaps per characteristic varied among the western, central and eastern Mediterranean subregions. The number of available records per species was positively related to total landings, while no relationship emerged with its maximum reported length, trophic level and commercial value. Future research priorities that should be focused on less studied species (e.g. sharks and rays) and mortality/fecundity instead of length

NanoSIMS for biological applications: Current practices and analyses

DOE PAGES

Nunez, Jamie R.; Renslow, Ryan S.; Cliff, III, John B.; ...

2017-09-27

Secondary ion mass spectrometry (SIMS) has become an increasingly utilized tool in biologically-relevant studies. Of these, high lateral resolution methodologies using the NanoSIMS 50/50L have been especially powerful within many biological fields over the past decade. Here, we provide a review of this technology, sample preparation and analysis considerations, examples of recent biological studies, data analysis, and current outlooks. Specifically, we offer an overview of SIMS and development of the NanoSIMS. We describe the major experimental factors that should be considered prior to NanoSIMS analysis and then provide information on best practices for data analysis and image generation, which includesmore » an in-depth discussion of appropriate colormaps. Additionally, we provide an open-source method for data representation that allows simultaneous visualization of secondary electron and ion information within a single image. Lastly, we present a perspective on the future of this technology and where we think it will have the greatest impact in near future.« less

NanoSIMS for biological applications: Current practices and analyses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nunez, Jamie R.; Renslow, Ryan S.; Cliff, III, John B.

Secondary ion mass spectrometry (SIMS) has become an increasingly utilized tool in biologically-relevant studies. Of these, high lateral resolution methodologies using the NanoSIMS 50/50L have been especially powerful within many biological fields over the past decade. Here, we provide a review of this technology, sample preparation and analysis considerations, examples of recent biological studies, data analysis, and current outlooks. Specifically, we offer an overview of SIMS and development of the NanoSIMS. We describe the major experimental factors that should be considered prior to NanoSIMS analysis and then provide information on best practices for data analysis and image generation, which includesmore » an in-depth discussion of appropriate colormaps. Additionally, we provide an open-source method for data representation that allows simultaneous visualization of secondary electron and ion information within a single image. Lastly, we present a perspective on the future of this technology and where we think it will have the greatest impact in near future.« less

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.

Digital and biological computing in organizations.

PubMed

Kampfner, Roberto R

2002-01-01

Michael Conrad unveiled many of the fundamental characteristics of biological computing. Underlying the behavioral variability and the adaptability of biological systems are these characteristics, including the ability of biological information processing to exploit quantum features at the atomic level, the powerful 3-D pattern recognition capabilities of macromolecules, the computational efficiency, and the ability to support biological function. Among many other things, Conrad formalized and explicated the underlying principles of biological adaptability, characterized the differences between biological and digital computing in terms of a fundamental tradeoff between adaptability and programmability of information processing, and discussed the challenges of interfacing digital computers and human society. This paper is about the encounter of biological and digital computing. The focus is on the nature of the biological information processing infrastructure of organizations and how it can be extended effectively with digital computing. In order to achieve this goal effectively, however, we need to embed properly digital computing into the information processing aspects of human and social behavior and intelligence, which are fundamentally biological. Conrad's legacy provides a firm, strong, and inspiring foundation for this endeavor.

The technology and biology of single-cell RNA sequencing.

PubMed

Kolodziejczyk, Aleksandra A; Kim, Jong Kyoung; Svensson, Valentine; Marioni, John C; Teichmann, Sarah A

2015-05-21

The differences between individual cells can have profound functional consequences, in both unicellular and multicellular organisms. Recently developed single-cell mRNA-sequencing methods enable unbiased, high-throughput, and high-resolution transcriptomic analysis of individual cells. This provides an additional dimension to transcriptomic information relative to traditional methods that profile bulk populations of cells. Already, single-cell RNA-sequencing methods have revealed new biology in terms of the composition of tissues, the dynamics of transcription, and the regulatory relationships between genes. Rapid technological developments at the level of cell capture, phenotyping, molecular biology, and bioinformatics promise an exciting future with numerous biological and medical applications. Copyright © 2015 Elsevier Inc. All rights reserved.

Design and implementation of a library-based information service in molecular biology and genetics at the University of Pittsburgh

PubMed Central

Chattopadhyay, Ansuman; Tannery, Nancy Hrinya; Silverman, Deborah A. L.; Bergen, Phillip; Epstein, Barbara A.

2006-01-01

Setting: In summer 2002, the Health Sciences Library System (HSLS) at the University of Pittsburgh initiated an information service in molecular biology and genetics to assist researchers with identifying and utilizing bioinformatics tools. Program Components: This novel information service comprises hands-on training workshops and consultation on the use of bioinformatics tools. The HSLS also provides an electronic portal and networked access to public and commercial molecular biology databases and software packages. Evaluation Mechanisms: Researcher feedback gathered during the first three years of workshops and individual consultation indicate that the information service is meeting user needs. Next Steps/Future Directions: The service's workshop offerings will expand to include emerging bioinformatics topics. A frequently asked questions database is also being developed to reuse advice on complex bioinformatics questions. PMID:16888665

Clerodane diterpenes: sources, structures, and biological activities†

PubMed Central

Li, Rongtao; Morris-Natschke, Susan L.; Lee, Kuo-Hsiung

2016-01-01

The clerodane diterpenoids are a widespread class of secondary metabolites and have been found in several hundreds of plant species from various families and in organisms from other taxonomic groups. These substances have attracted interest in recent years due to their notable biological activities, particularly insect antifeedant properties. In addition, the major active clerodanes of Salvia divinorum can be used as novel opioid receptor probes, allowing greater insight into opioid receptor-mediated phenomena, as well as opening additional areas for chemical investigation. This article provides extensive coverage of naturally occurring clerodane diterpenes discovered from 1990 until 2015, and follows up on the 1992 review by Merritt and Ley in this same journal. The distribution, chemotaxonomic significance, chemical structures, and biological activities of clerodane diterpenes are summarized. In the cases where sufficient information is available, structure activity relationship (SAR) correlations and mode of action of active clerodanes have been presented. PMID:27433555

Computational systems chemical biology.

PubMed

Oprea, Tudor I; May, Elebeoba E; Leitão, Andrei; Tropsha, Alexander

2011-01-01

There is a critical need for improving the level of chemistry awareness in systems biology. The data and information related to modulation of genes and proteins by small molecules continue to accumulate at the same time as simulation tools in systems biology and whole body physiologically based pharmacokinetics (PBPK) continue to evolve. We called this emerging area at the interface between chemical biology and systems biology systems chemical biology (SCB) (Nat Chem Biol 3: 447-450, 2007).The overarching goal of computational SCB is to develop tools for integrated chemical-biological data acquisition, filtering and processing, by taking into account relevant information related to interactions between proteins and small molecules, possible metabolic transformations of small molecules, as well as associated information related to genes, networks, small molecules, and, where applicable, mutants and variants of those proteins. There is yet an unmet need to develop an integrated in silico pharmacology/systems biology continuum that embeds drug-target-clinical outcome (DTCO) triplets, a capability that is vital to the future of chemical biology, pharmacology, and systems biology. Through the development of the SCB approach, scientists will be able to start addressing, in an integrated simulation environment, questions that make the best use of our ever-growing chemical and biological data repositories at the system-wide level. This chapter reviews some of the major research concepts and describes key components that constitute the emerging area of computational systems chemical biology.

Computational Systems Chemical Biology

PubMed Central

Oprea, Tudor I.; May, Elebeoba E.; Leitão, Andrei; Tropsha, Alexander

2013-01-01

There is a critical need for improving the level of chemistry awareness in systems biology. The data and information related to modulation of genes and proteins by small molecules continue to accumulate at the same time as simulation tools in systems biology and whole body physiologically-based pharmacokinetics (PBPK) continue to evolve. We called this emerging area at the interface between chemical biology and systems biology systems chemical biology, SCB (Oprea et al., 2007). The overarching goal of computational SCB is to develop tools for integrated chemical-biological data acquisition, filtering and processing, by taking into account relevant information related to interactions between proteins and small molecules, possible metabolic transformations of small molecules, as well as associated information related to genes, networks, small molecules and, where applicable, mutants and variants of those proteins. There is yet an unmet need to develop an integrated in silico pharmacology / systems biology continuum that embeds drug-target-clinical outcome (DTCO) triplets, a capability that is vital to the future of chemical biology, pharmacology and systems biology. Through the development of the SCB approach, scientists will be able to start addressing, in an integrated simulation environment, questions that make the best use of our ever-growing chemical and biological data repositories at the system-wide level. This chapter reviews some of the major research concepts and describes key components that constitute the emerging area of computational systems chemical biology. PMID:20838980

Informing DSM-5: biological boundaries between bipolar I disorder, schizoaffective disorder, and schizophrenia

PubMed Central

2013-01-01

Background The fifth version of the Diagnostic and Statistical Manual of Mental Disorders (DSM-5) opted to retain existing diagnostic boundaries between bipolar I disorder, schizoaffective disorder, and schizophrenia. The debate preceding this decision focused on understanding the biologic basis of these major mental illnesses. Evidence from genetics, neuroscience, and pharmacotherapeutics informed the DSM-5 development process. The following discussion will emphasize some of the key factors at the forefront of the debate. Discussion Family studies suggest a clear genetic link between bipolar I disorder, schizoaffective disorder, and schizophrenia. However, large-scale genome-wide association studies have not been successful in identifying susceptibility genes that make substantial etiological contributions. Boundaries between psychotic disorders are not further clarified by looking at brain morphology. The fact that symptoms of bipolar I disorder, but not schizophrenia, are often responsive to medications such as lithium and other anticonvulsants must be interpreted within a larger framework of biological research. Summary For DSM-5, existing nosological boundaries between bipolar I disorder and schizophrenia were retained and schizoaffective disorder preserved as an independent diagnosis since the biological data are not yet compelling enough to justify a move to a more neurodevelopmentally continuous model of psychosis. PMID:23672587

Exogenous addition of H2 for an in situ biogas upgrading through biological reduction of carbon dioxide into methane.

PubMed

Mulat, Daniel Girma; Mosbæk, Freya; Ward, Alastair James; Polag, Daniela; Greule, Markus; Keppler, Frank; Nielsen, Jeppe Lund; Feilberg, Anders

2017-10-01

Biological reduction of CO 2 into CH 4 by exogenous addition of H 2 is a promising technology for upgrading biogas into higher CH 4 content. The aim of this work was to study the feasibility of exogenous H 2 addition for an in situ biogas upgrading through biological conversion of the biogas CO 2 into CH 4. Moreover, this study employed systematic study with isotope analysis for providing comprehensive evidence on the underlying pathways of CH 4 production and upstream processes. Batch reactors were inoculated with digestate originating from a full-scale biogas plant and fed once with maize leaf substrate. Periodic addition of H 2 into the headspace resulted in a completely consumption of CO 2 and a concomitant increase in CH 4 content up to 89%. The microbial community and isotope analysis shows an enrichment of hydrogenotrophic Methanobacterium and the key role of hydrogenotrophic methanogenesis for biogas upgrading to higher CH 4 content. Excess H 2 was also supplied to evaluate its effect on overall process performance. The results show that excess H 2 addition resulted in accumulation of H 2 , depletion of CO 2 and inhibition of the degradation of acetate and other volatile fatty acids (VFA). A systematic isotope analysis revealed that excess H 2 supply led to an increase in dissolved H 2 to the level that thermodynamically inhibit the degradation of VFA and stimulate homo-acetogens for production of acetate from CO 2 and H 2 . The inhibition was a temporary effect and acetate degradation resumed when the excess H 2 was removed as well as in the presence of stoichiometric amount of H 2 and CO 2 . This inhibition mechanism underlines the importance of carefully regulating the H 2 addition rate and gas retention time to the CO 2 production rate, H 2 -uptake rate and growth of hydrogenotrophic methanogens in order to achieve higher CH 4 content without the accumulation of acetate and other VFA. Copyright © 2017 Elsevier Ltd. All rights reserved.

Physical, chemical, and biological properties of white MTA with additions of AlF3.

PubMed

Marciano, Marina Angélica; Camilleri, Josette; Lucateli, Ribamar Lazanha; Costa, Reginaldo Mendonça; Matsumoto, Mariza Akemi; Duarte, Marco Antonio Hungaro

2018-04-13

Addition of aluminum fluoride (AlF 3 ) to MTA was tested to inhibit dental discoloration. MTA Angelus with 0, 5, 15, and 45% AlF 3 were tested. The set cements were characterized using scanning electron microscopy, energy-dispersive spectroscopy, and X-ray diffraction. Radiopacity and setting time were analyzed according to ANSI/ADA 57 and ASTM C266-08. Volume change was evaluated using volumetric micro-CT analysis. The pH and calcium ion release were assessed after 3 and 24 h and 28 days. Dental discoloration in contact with the cements was assessed after 24 h and 28 and 90 days of contact with bovine and human dentine. Tissue reaction to subcutaneous implantation in rats was examined after 30 and 60 days. AlF 3 altered the microstructure of MTA. The addition of 5% AlF 3 did not significantly alter the radiopacity, setting time, and volume change (p > 0.05). pH and calcium ion release significantly increased with addition of AlF 3 (p > 0.05). All the tested proportions of AlF 3 prevented the dental darkening verified for MTA Angelus in bovine and human teeth. AlF 3 did not interfere in inflammatory response of MTA in all periods of analysis; otherwise, lower amounts showed less intense inflammatory infiltrate. AlF 3 prevents destabilization of bismuth oxide and consequent tooth darkening, frequently verified in clinical practice when using white MTA. The use of 5% of AlF 3 in combination to MTA resulted in a cement that did not result in dental discoloration and did not affect significantly physical, chemical, and biological properties.

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).

The Chemical Information Ontology: Provenance and Disambiguation for Chemical Data on the Biological Semantic Web

PubMed Central

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). PMID:21991315

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

Code of Federal Regulations, 2011 CFR

2011-07-01

... 30 Mineral Resources 2 2011-07-01 2011-07-01 false What biological, physical, and socioeconomic information must accompany the DPP or DOCD? 250.247 Section 250.247 Mineral Resources BUREAU OF OCEAN ENERGY... species, marine mammals protected under the MMPA, sensitive underwater features, marine sanctuaries...

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 requirements for applications involving vertical competitive impacts. 33.4 Section 33.4 Conservation of Power... electricity products (i.e., downstream relevant products) in the same geographic markets or that the extent of...

78 FR 22937 - 60-Day Notice of Proposed Information Collection: Application for Additional Visa Pages or...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-17

...: Application for Additional Visa Pages or Miscellaneous Passport Services ACTION: Notice of request for public... Information Collection: Application for Additional Visa Pages or Miscellaneous Passport Services. OMB Control...: Bureau of Consular Affairs, Passport Services, Office of Program Management and Operational Support...

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)

Integrating data from biological experiments into metabolic networks with the DBE information system.

PubMed

Borisjuk, Ljudmilla; Hajirezaei, Mohammad-Reza; Klukas, Christian; Rolletschek, Hardy; Schreiber, Falk

2005-01-01

Modern 'omics'-technologies result in huge amounts of data about life processes. For analysis and data mining purposes this data has to be considered in the context of the underlying biological networks. This work presents an approach for integrating data from biological experiments into metabolic networks by mapping the data onto network elements and visualising the data enriched networks automatically. This methodology is implemented in DBE, an information system that supports the analysis and visualisation of experimental data in the context of metabolic networks. It consists of five parts: (1) the DBE-Database for consistent data storage, (2) the Excel-Importer application for the data import, (3) the DBE-Website as the interface for the system, (4) the DBE-Pictures application for the up- and download of binary (e. g. image) files, and (5) DBE-Gravisto, a network analysis and graph visualisation system. The usability of this approach is demonstrated in two examples.

A generic standard additions based method to determine endogenous analyte concentrations by immunoassays to overcome complex biological matrix interference.

PubMed

Pang, Susan; Cowen, Simon

2017-12-13

We describe a novel generic method to derive the unknown endogenous concentrations of analyte within complex biological matrices (e.g. serum or plasma) based upon the relationship between the immunoassay signal response of a biological test sample spiked with known analyte concentrations and the log transformed estimated total concentration. If the estimated total analyte concentration is correct, a portion of the sigmoid on a log-log plot is very close to linear, allowing the unknown endogenous concentration to be estimated using a numerical method. This approach obviates conventional relative quantification using an internal standard curve and need for calibrant diluent, and takes into account the individual matrix interference on the immunoassay by spiking the test sample itself. This technique is based on standard additions for chemical analytes. Unknown endogenous analyte concentrations within even 2-fold diluted human plasma may be determined reliably using as few as four reaction wells.

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 major...

BioCreative V track 4: a shared task for the extraction of causal network information using the Biological Expression Language.

PubMed

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. © The Author(s) 2016. Published by Oxford University Press.

Why Are There Old People? Senescence as Biological and Cultural Preparedness for the Transmission of Information.

ERIC Educational Resources Information Center

Mergler, N.L.; Goldstein, M.D.

1983-01-01

Biological theories of adaptation are used to generate a model of human cognitive development in which physiological and cognitive change in aged persons can be understood as an adaptive stage of development. Related literature is reviewed that focuses on the elderly as information transmitters and on the psychology of "telling."…

News from the Biological Stain Commission No. 5.

PubMed

Lyon, H O; Dapson, R W

2009-06-01

In this fifth issue of News from the Biological Stain Commission (BSC), under the heading of Regulatory Affairs, the BSC's International Affairs Committee provides more information from the meeting of the International Standards Organization ISO/TC 212 Committee that took place on June 2-4, 2008 at Vancouver, Canada. In addition, we give an update on the current situation regarding the supplies of hematoxylin.

Curriculum and course materials for a forensic DNA biology course.

PubMed

Elkins, Kelly M

2014-01-01

The Forensic Science Education Programs Accreditation Commission (FEPAC) requires accredited programs offer a "coherent curriculum" to ensure each student gains a "thorough grounding of the natural…sciences." Part of this curriculum includes completion of a minimum of 15 semester-hours forensic science coursework, nine of which can involve a class in forensic DNA biology. Departments that have obtained or are pursuing FEPAC accreditation can meet this requirement by offering a stand-alone forensic DNA biology course; however, materials necessary to instruct students are often homegrown and not standardized; in addition, until recently, the community lacked commercially available books, lab manuals, and teaching materials, and many of the best pedagogical resources were scattered across various peer-reviewed journals. The curriculum discussed below is an attempt to synthesize this disparate information, and although certainly not the only acceptable methodology, the below discussion represents "a way" for synthesizing and aggregating this information into a cohesive, comprehensive whole. Copyright © 2013 by The International Union of Biochemistry and Molecular Biology.

On the search for design principles in biological systems.

PubMed

Poyatos, Juan F

2012-01-01

The search for basic concepts and underlying principles was at the core of the systems approach to science and technology. This approach was somehow abandoned in mainstream biology after its initial proposal, due to the rise and success of molecular biology. This situation has changed. The accumulated knowledge of decades of molecular studies in combination with new technological advances, while further highlighting the intricacies of natural systems, is also bringing back the quest-for-principles research program. Here, I present two lessons that I derived from my own quest: the importance of studying biological information processing to identify common principles in seemingly unrelated contexts and the adequacy of using known design principles at one level of biological organization as a valuable tool to help recognizing principles at an alternative one. These and additional lessons should contribute to the ultimate goal of establishing principles able to integrate the many scales of biological complexity.

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 rig...

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 rig...

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 rig...

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... 21 Food and Drugs 1 2012-04-01 2012-04-01 false Confidentiality of data and information in color additive petitions. 71.15 Section 71.15 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH...

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

Code of Federal Regulations, 2014 CFR

2014-04-01

... established in § 20.61 of this chapter. (6) All records showing the Food and Drug Administration's testing of... 21 Food and Drugs 1 2014-04-01 2014-04-01 false Confidentiality of data and information in color additive petitions. 71.15 Section 71.15 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH...

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

Code of Federal Regulations, 2013 CFR

2013-04-01

... established in § 20.61 of this chapter. (6) All records showing the Food and Drug Administration's testing of... 21 Food and Drugs 1 2013-04-01 2013-04-01 false Confidentiality of data and information in color additive petitions. 71.15 Section 71.15 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH...

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

Code of Federal Regulations, 2011 CFR

2011-04-01

... established in § 20.61 of this chapter. (6) All records showing the Food and Drug Administration's testing of... 21 Food and Drugs 1 2011-04-01 2011-04-01 false Confidentiality of data and information in color additive petitions. 71.15 Section 71.15 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH...

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... Integrated Workplace concepts? The GSA Office of Governmentwide Policy provides additional guidance in its...

Standard Biological Parts Knowledgebase

PubMed Central

Galdzicki, Michal; Rodriguez, Cesar; Chandran, Deepak; Sauro, Herbert M.; Gennari, John H.

2011-01-01

We have created the Knowledgebase of Standard Biological Parts (SBPkb) as a publically accessible Semantic Web resource for synthetic biology (sbolstandard.org). The SBPkb allows researchers to query and retrieve standard biological parts for research and use in synthetic biology. Its initial version includes all of the information about parts stored in the Registry of Standard Biological Parts (partsregistry.org). SBPkb transforms this information so that it is computable, using our semantic framework for synthetic biology parts. This framework, known as SBOL-semantic, was built as part of the Synthetic Biology Open Language (SBOL), a project of the Synthetic Biology Data Exchange Group. SBOL-semantic represents commonly used synthetic biology entities, and its purpose is to improve the distribution and exchange of descriptions of biological parts. In this paper, we describe the data, our methods for transformation to SBPkb, and finally, we demonstrate the value of our knowledgebase with a set of sample queries. We use RDF technology and SPARQL queries to retrieve candidate “promoter” parts that are known to be both negatively and positively regulated. This method provides new web based data access to perform searches for parts that are not currently possible. PMID:21390321

Standard biological parts knowledgebase.

PubMed

Galdzicki, Michal; Rodriguez, Cesar; Chandran, Deepak; Sauro, Herbert M; Gennari, John H

2011-02-24

We have created the Knowledgebase of Standard Biological Parts (SBPkb) as a publically accessible Semantic Web resource for synthetic biology (sbolstandard.org). The SBPkb allows researchers to query and retrieve standard biological parts for research and use in synthetic biology. Its initial version includes all of the information about parts stored in the Registry of Standard Biological Parts (partsregistry.org). SBPkb transforms this information so that it is computable, using our semantic framework for synthetic biology parts. This framework, known as SBOL-semantic, was built as part of the Synthetic Biology Open Language (SBOL), a project of the Synthetic Biology Data Exchange Group. SBOL-semantic represents commonly used synthetic biology entities, and its purpose is to improve the distribution and exchange of descriptions of biological parts. In this paper, we describe the data, our methods for transformation to SBPkb, and finally, we demonstrate the value of our knowledgebase with a set of sample queries. We use RDF technology and SPARQL queries to retrieve candidate "promoter" parts that are known to be both negatively and positively regulated. This method provides new web based data access to perform searches for parts that are not currently possible.

Biological effects of anthropogenic contaminants in the San Francisco Estuary

USGS Publications Warehouse

Thompson, B.; Adelsbach, T.; Brown, C.; Hunt, J.; Kuwabara, J.; Neale, J.; Ohlendorf, H.; Schwarzbach, S.; Spies, R.; Taberski, K.

2007-01-01

Concentrations of many anthropogenic contaminants in the San Francisco Estuary exist at levels that have been associated with biological effects elsewhere, so there is a potential for them to cause biological effects in the Estuary. The purpose of this paper is to summarize information about biological effects on the Estuary's plankton, benthos, fish, birds, and mammals, gathered since the early 1990s, focusing on key accomplishments. These studies have been conducted at all levels of biological organization (sub-cellular through communities), but have included only a small fraction of the organisms and contaminants of concern in the region. The studies summarized provide a body of evidence that some contaminants are causing biological impacts in some biological resources in the Estuary. However, no general patterns of effects were apparent in space and time, and no single contaminant was consistently related to effects among the biota considered. These conclusions reflect the difficulty in demonstrating biological effects due specifically to contamination because there is a wide range of sensitivity to contaminants among the Estuary's many organisms. Additionally, the spatial and temporal distribution of contamination in the Estuary is highly variable, and levels of contamination covary with other environmental factors, such as freshwater inflow or sediment-type. Federal and State regulatory agencies desire to develop biological criteria to protect the Estuary's biological resources. Future studies of biological effects in San Francisco Estuary should focus on the development of meaningful indicators of biological effects, and on key organism and contaminants of concern in long-term, multifaceted studies that include laboratory and field experiments to determine cause and effect to adequately inform management and regulatory decisions. ?? 2006 Elsevier Inc. All rights reserved.

Silicon photonics for neuromorphic information processing

NASA Astrophysics Data System (ADS)

Bienstman, Peter; Dambre, Joni; Katumba, Andrew; Freiberger, Matthias; Laporte, Floris; Lugnan, Alessio

2018-02-01

We present our latest results on silicon photonics neuromorphic information processing based a.o. on techniques like reservoir computing. We will discuss aspects like scalability, novel architectures for enhanced power efficiency, as well as all-optical readout. Additionally, we will touch upon new machine learning techniques to operate these integrated readouts. Finally, we will show how these systems can be used for high-speed low-power information processing for applications like recognition of biological cells.

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. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Designing mental health interventions informed by child development and human biology theory: A social ecology intervention for child soldiers in Nepal

PubMed Central

Kohrt, Brandon A.; Jordans, Mark J.D.; Koirala, Suraj; Worthman, Carol M.

2017-01-01

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. PMID:25380194

Getting the most out of additional guidance information in deformable image registration by leveraging multi-objective optimization

NASA Astrophysics Data System (ADS)

Alderliesten, Tanja; Bosman, Peter A. N.; Bel, Arjan

2015-03-01

Incorporating additional guidance information, e.g., landmark/contour correspondence, in deformable image registration is often desirable and is typically done by adding constraints or cost terms to the optimization function. Commonly, deciding between a "hard" constraint and a "soft" additional cost term as well as the weighting of cost terms in the optimization function is done on a trial-and-error basis. The aim of this study is to investigate the advantages of exploiting guidance information by taking a multi-objective optimization perspective. Hereto, next to objectives related to match quality and amount of deformation, we define a third objective related to guidance information. Multi-objective optimization eliminates the need to a-priori tune a weighting of objectives in a single optimization function or the strict requirement of fulfilling hard guidance constraints. Instead, Pareto-efficient trade-offs between all objectives are found, effectively making the introduction of guidance information straightforward, independent of its type or scale. Further, since complete Pareto fronts also contain less interesting parts (i.e., solutions with near-zero deformation effort), we study how adaptive steering mechanisms can be incorporated to automatically focus more on solutions of interest. We performed experiments on artificial and real clinical data with large differences, including disappearing structures. Results show the substantial benefit of using additional guidance information. Moreover, compared to the 2-objective case, additional computational cost is negligible. Finally, with the same computational budget, use of the adaptive steering mechanism provides superior solutions in the area of interest.

Human development VII: a spiral fractal model of fine structure of physical energy could explain central aspects of biological information, biological organization and biological creativity.

PubMed

Ventegodt, Søren; Hermansen, Tyge Dahl; Flensborg-Madsen, Trine; Rald, Erik; Nielsen, Maj Lyck; Merrick, Joav

2006-11-14

In this paper we have made a draft of a physical fractal essence of the universe, a sketch of a new cosmology, which we believe to lay at the root of our new holistic biological paradigm. We present the fractal roomy spiraled structures and the energy-rich dancing "infinite strings" or lines of the universe that our hypothesis is based upon. The geometric language of this cosmology is symbolic and both pre-mathematical and pre-philosophical. The symbols are both text and figures, and using these we step by step explain the new model that at least to some extent is able to explain the complex informational system behind morphogenesis, ontogenesis, regeneration and healing. We suggest that it is from this highly dynamic spiraled structure that organization of cells, organs, and the wholeness of the human being including consciousness emerge. The model of "dancing fractal spirals" carries many similarities to premodern cultures descriptions of the energy of the life and universe. Examples are the Native American shamanistic descriptions of their perception of energy and the old Indian Yogis descriptions of the life-energy within the body and outside. Similar ideas of energy and matter are found in the modern superstring theories. The model of the informational system of the organism gives new meaning to Bateson's definition of information: "A difference that makes a difference", and indicates how information-directed self-organization can exist on high structural levels in living organisms, giving birth to their subjectivity and consciousness.

Phylogenetically informed logic relationships improve detection of biological network organization

PubMed Central

2011-01-01

Background A "phylogenetic profile" refers to the presence or absence of a gene across a set of organisms, and it has been proven valuable for understanding gene functional relationships and network organization. Despite this success, few studies have attempted to search beyond just pairwise relationships among genes. Here we search for logic relationships involving three genes, and explore its potential application in gene network analyses. Results Taking advantage of a phylogenetic matrix constructed from the large orthologs database Roundup, we invented a method to create balanced profiles for individual triplets of genes that guarantee equal weight on the different phylogenetic scenarios of coevolution between genes. When we applied this idea to LAPP, the method to search for logic triplets of genes, the balanced profiles resulted in significant performance improvement and the discovery of hundreds of thousands more putative triplets than unadjusted profiles. We found that logic triplets detected biological network organization and identified key proteins and their functions, ranging from neighbouring proteins in local pathways, to well separated proteins in the whole pathway, and to the interactions among different pathways at the system level. Finally, our case study suggested that the directionality in a logic relationship and the profile of a triplet could disclose the connectivity between the triplet and surrounding networks. Conclusion Balanced profiles are superior to the raw profiles employed by traditional methods of phylogenetic profiling in searching for high order gene sets. Gene triplets can provide valuable information in detection of biological network organization and identification of key genes at different levels of cellular interaction. PMID:22172058

75 FR 6401 - Medical Devices Regulated by the Center for Biologics Evaluation and Research; Availability of...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-02-09

... premarket approval applications (PMAs) that have been approved by the Center for Biologics Evaluation and Research (CBER). This list is intended to inform the public of the availability through the Internet and... post this information on the Internet at http://www.fda.gov . In addition, the regulations provide that...

At a glance: cellular biology for engineers.

PubMed

Khoshmanesh, K; Kouzani, A Z; Nahavandi, S; Baratchi, S; Kanwar, J R

2008-10-01

Engineering contributions have played an important role in the rise and evolution of cellular biology. Engineering technologies have helped biologists to explore the living organisms at cellular and molecular levels, and have created new opportunities to tackle the unsolved biological problems. There is now a growing demand to further expand the role of engineering in cellular biology research. For an engineer to play an effective role in cellular biology, the first essential step is to understand the cells and their components. However, the stumbling block of this step is to comprehend the information given in the cellular biology literature because it best suits the readers with a biological background. This paper aims to overcome this bottleneck by describing the human cell components as micro-plants that form cells as micro-bio-factories. This concept can accelerate the engineers' comprehension of the subject. In this paper, first the structure and function of different cell components are described. In addition, the engineering attempts to mimic various cell components through numerical modelling or physical implementation are highlighted. Next, the interaction of different cell components that facilitate complicated chemical processes, such as energy generation and protein synthesis, are described. These complex interactions are translated into simple flow diagrams, generally used by engineers to represent multi-component processes.

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.

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

50 CFR 23.25 - What additional information is required on a non-Party CITES document?

Code of Federal Regulations, 2010 CFR

2010-10-01

....25 What additional information is required on a non-Party CITES document? (a) Purpose. Under Article... Certification (1) Export (i) For Appendix-I and -II specimens, the Scientific Authority has advised that the...

Using biological factors to individualize interventions for youth with conduct problems: Current state and ethical issues.

PubMed

Glenn, Andrea L

2018-04-16

A growing body of evidence suggests that biological factors such as genes, hormone levels, brain structure, and brain functioning influence the development and trajectory of conduct problems in youth. In addition, biological factors affect how individuals respond to the environment, including how individuals respond to programs designed to prevent or treat conduct problems. Programs designed to reduce behavior problems in youth would have the greatest impact if they were targeted toward youth who need it the most (e.g., who are mostly likely to demonstrate persistent behavior problems) as well as youth who may benefit the most from the program. Biological information may improve our ability to make decisions about which type or level of intervention is best for a particular child, thus maximizing overall effectiveness, but it also raises a number of ethical concerns. These include the idea that we may be providing fewer services to some youth based on biological factors, and that information about biological risk could potentially lead to discrimination or labeling. In this article, I discuss the risks and benefits of using biological information to individualize interventions for youth with conduct problems. Copyright © 2018 Elsevier Ltd. All rights reserved.

[Biologically active food additives: their role in human body sanitation and in prophylaxis of alimentary-dependent diseases].

PubMed

Maev, E Z; Zaĭtseva, V P

2002-09-01

The different aspects of the problem of health maintaining and strengthening are discussed. The special attention is devoted to the problem of diet that at present is characterized by deficiency of macro- and micronutrients. It is supposed that this factor together with the change in ecological condition promotes the development of different somatic diseases and their atypical course. To correct the dietary regimen, to strengthen the body functional reserves and to improve its nonspecific resistance to the influence of environmental unfavorable and pathogenic factors the possibility of wide use of biologically active food additives (BAA) is discussed. The examples of BAAs based on plant materials and results of their use in health resort conditions are given.

Biological consequences of ENSO: What have we learned recently?

NASA Astrophysics Data System (ADS)

Chavez, F.; Messié, M.

2013-12-01

A comprehensive theory regarding the biological response to El Niño was developed from observations during the 1982-83 event. The theory has withstood the test of time but additional information from remote sensing and growing in situ databases has allowed for a more comprehensive evaluation of the biological consequences of the full ENSO cycle on global scales and in relation to other climatic variability and change. Here we review the major developments over the past few decades that include a greater appreciation for the cool or La Niña phase and the relation of ENSO to other climatic variability including the Pacific Decadal Oscillation and the North Pacific Gyre Oscillation. The use of ENSO as an analog for biological consequences of a warmer world is also discussed.

75 FR 35119 - 60-Day Notice of Proposed Information Collection: Form DS-4085 Application for Additional Visa...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-21

... DS-4085 Application for Additional Visa Pages or Miscellaneous Passport Services, OMB Control Number... of Information Collection: Application for Additional Visa Pages or Miscellaneous Passport Services.... Originating Office: Bureau of Consular Affairs, Passport Services CA/PPT. Form Number: DS-4085. Respondents...

21 CFR 71.4 - Samples; additional information.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 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 in... additive, or articles used as components thereof, or of the food, drug, or cosmetic in which the color...

21 CFR 71.4 - Samples; additional information.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 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 in... additive, or articles used as components thereof, or of the food, drug, or cosmetic in which the color...

21 CFR 71.4 - Samples; additional information.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 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 in... additive, or articles used as components thereof, or of the food, drug, or cosmetic in which the color...

21 CFR 71.4 - Samples; additional information.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 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 in... additive, or articles used as components thereof, or of the food, drug, or cosmetic in which the color...

21 CFR 71.4 - Samples; additional information.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 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 in... additive, or articles used as components thereof, or of the food, drug, or cosmetic in which the color...

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. © 2014 Wiley Periodicals, Inc.

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

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.

Methods of Collection of Biological Information for Fatigue Evaluation during Visual Display Terminals (VDT) Operation

NASA Astrophysics Data System (ADS)

Hachiya, Yuriko; Ogai, Harutoshi; Okazaki, Hiroko; Fujisaki, Takeshi; Uchida, Kazuhiko; Oda, Susumu; Wada, Futoshi; Mori, Koji

A method for the analysis of fatigue parameters has been rarely researched in VDT operation. Up to now, fatigue was evaluated by changing of biological information. If signals regarding fatigue are detected, fatigue can be measured. The purpose of this study proposed experiment and analysis method to extract parameters related to fatigue from the biological information during VDT operation using the Independent Component Analysis (ICA). An experiment had 11 subjects. As for the experiment were light loaded VDT operation and heavy loaded VDT operation. A measurement item were amount of work, a mistake number, subjective symptom, surface skin temperature (forehead and apex nasi), heart rate, skin blood flow of forearm and respiratory rate. In the heavy loaded operation group, mistake number and subjective symptom score were increased to compare with the other. And Two-factor ANOVA was used for analysis. The result of mistake number was confirmed that heavy loaded. After the moving averages of waveshape were calculated, it was made to extract independent components by using the ICA. The results of the ICA suggest that the independent components increase according to accumulation of fatigue. Thus, the independent components would be a possible parameter of fatigue. However, further experiments should continue in order to obtain the conclusive finding of our research.

Biological baseline data Youngs Bay, Oregon, 1974

DOE Office of Scientific and Technical Information (OSTI.GOV)

McMechan, K.J.; Higley, D.L.; Holton, R.L.

1975-04-01

This report presents biological baseline information gathered during the research project, Physical, Chemical and Biological Studies on Youngs Bay.'' Youngs Bay is a shallow embayment located on the south shore of the Columbia River, near Astoria, Oregon. Research on Youngs Bay was motivated by the proposed construction by Alumax Pacific Aluminum Corporation of an aluminum reduction plant at Warrenton, Oregon. The research was designed to provide biological baseline information on Youngs Bay in anticipation of potential harmful effects from plant effluents. The information collected concerns the kinds of animals found in the Youngs Bay area, and their distribution and seasonalmore » patterns of abundance. In addition, information was collected on the feeding habits of selected fish species, and on the life history and behavioral characteristics of the most abundant benthic amphipod, Corophium salmonis. Sampling was conducted at approximately three-week intervals, using commonly accepted methods of animal collection. Relatively few stations were sampled for fish, because of the need to standardize conditions of capture. Data on fish capture are reported in terms of catch-per-unit effort by a particular sampling gear at a specific station. Methods used in sampling invertebrates were generally more quantitative, and allowed sampling at a greater variety of places, as well as a valid basis for the computation of densities. Checklists of invertebrate species and fish species were developed from these samples, and are referred to throughout the report. The invertebrate checklist is more specific taxonomically than are tables reporting invertebrate densities. This is because the methods employed in identification were more precise than those used in counts. 9 refs., 27 figs., 25 tabs.« less

Can we manage for biological diversity in the absence of science?

USGS Publications Warehouse

Trauger, D.L.; Hall, R.J.

1995-01-01

Conservation of biological diversity is dependent on sound scientific information about underlying ecological processes. Current knowledge of the composition, distribution, abundance and life cycles of most species of plants and animals is incomplete, insufficient, unreliable, or nonexistent. Contemporary managers are also confronted with additional levels of complexity related to varying degrees of knowledge and understanding about interactions of species and ecosystems. Consequently, traditional species-oriented management schemes may have unintended consequences and ecosystem-oriented management initiatives may fail in the face of inadequate or fragmentary information on the structure, function, and dynamics of biotic communities and ecological systems. Nevertheless, resource managers must make decisions and manage based on the best biological information currently available. Adaptive resource management may represent a management paradigm that allows managers to learn something about the species or systems that they are managing while they are managing, but potential pitfalls lurk for such approaches. In addition to lack of control over the primary physical, chemical, and ecological processes, managers also lack control over social, economic, and political parameters affecting resource management options. Moreover, appropriate goals may be difficult to identify and criteria for determining success may be elusive. Some management responsibilities do not lend themselves to adaptive strategies. Finally, the lessons learned from adaptive management are usually obtained from a highly situational context that may limit applicability in a wider range of situations or undermine confidence that problems and solutions were properly diagnosed and addressed. Several scenarios are critically examined where adaptive management approaches may be inappropriate or ineffective and where management for biological diversity may be infeasible or inefficient without a sound

Current Trends in Biology Education.

ERIC Educational Resources Information Center

Wivagg, Daniel E.; Moore, Randy

1987-01-01

This newsletter reports on the status of biology education in the United States. It states that biology has entered its "golden age" because of the emergence of biotechnology, ecology, agricultural productivity, and human biology as major societal issues. This report discusses the status of the informal national curriculum of biology, involving…

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)

Decontamination formulation with sorbent additive

DOEpatents

Tucker; Mark D. , Comstock; Robert H.

2007-10-16

A decontamination formulation and method of making that neutralizes the adverse health effects of both chemical and biological compounds, especially chemical warfare (CW) and biological warfare (BW) agents, and toxic industrial chemicals. The formulation provides solubilizing compounds that serve to effectively render the chemical and biological compounds, particularly CW and BW compounds, susceptible to attack, and at least one reactive compound that serves to attack (and detoxify or kill) the compound. The formulation includes at least one solubilizing agent, a reactive compound, a bleaching activator, a sorbent additive, and water. The highly adsorbent, water-soluble sorbent additive (e.g., sorbitol or mannitol) is used to "dry out" one or more liquid ingredients, such as the liquid bleaching activator (e.g., propylene glycol diacetate or glycerol diacetate) and convert the activator into a dry, free-flowing powder that has an extended shelf life, and is more convenient to handle and mix in the field.

Regression analysis of informative current status data with the additive hazards model.

PubMed

Zhao, Shishun; Hu, Tao; Ma, Ling; Wang, Peijie; Sun, Jianguo

2015-04-01

This paper discusses regression analysis of current status failure time data arising from the additive hazards model in the presence of informative censoring. Many methods have been developed for regression analysis of current status data under various regression models if the censoring is noninformative, and also there exists a large literature on parametric analysis of informative current status data in the context of tumorgenicity experiments. In this paper, a semiparametric maximum likelihood estimation procedure is presented and in the method, the copula model is employed to describe the relationship between the failure time of interest and the censoring time. Furthermore, I-splines are used to approximate the nonparametric functions involved and the asymptotic consistency and normality of the proposed estimators are established. A simulation study is conducted and indicates that the proposed approach works well for practical situations. An illustrative example is also provided.

Towards a semantic lexicon for biological language processing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Verspoor, K.

It is well understood that natural language processing (NLP) applications require sophisticated lexical resources to support their processing goals. In the biomedical domain, we are privileged to have access to extensive terminological resources in the form of controlled vocabularies and ontologies, which have been integrated into the framework of the National Library of Medicine's Unified Medical Language System's (UMLS) Metathesaurus. However, the existence of such terminological resources does not guarantee their utility for NLP. In particular, we have two core requirements for lexical resources for NLP in addition to the basic enumeration of important domain terms: representation of morphosyntactic informationmore » about those terms, specifically part of speech information and inflectional patterns to support parsing and lemma assignment, and representation of semantic information indicating general categorical information about terms, and significant relations between terms to support text understanding and inference (Hahn et at, 1999). Biomedical vocabularies by and large commonly leave out morphosyntactic information, and where they address semantic considerations, they often do so in an unprincipled manner, for instance by indicating a relation between two concepts without indicating the type of that relation. But all is not lost. The UMLS knowledge sources include two additional resources which are relevant - the SPECIALIST lexicon, a lexicon addressing our morphosyntactic requirements, and the Semantic Network, a representation of core conceptual categories in the biomedical domain. The coverage of these two knowledge sources with respect to the full coverage of the Metathesaurus is, however, not entirely clear. Furthermore, when our goals are specifically to process biological text - and often more specifically, text in the molecular biology domain - it is difficult to say whether the coverage of these resources is meaningful. The utility of the UMLS

Cation Selectivity in Biological Cation Channels Using Experimental Structural Information and Statistical Mechanical Simulation.

PubMed

Finnerty, Justin John; Peyser, Alexander; Carloni, Paolo

2015-01-01

Cation selective channels constitute the gate for ion currents through the cell membrane. Here we present an improved statistical mechanical model based on atomistic structural information, cation hydration state and without tuned parameters that reproduces the selectivity of biological Na+ and Ca2+ ion channels. The importance of the inclusion of step-wise cation hydration in these results confirms the essential role partial dehydration plays in the bacterial Na+ channels. The model, proven reliable against experimental data, could be straightforwardly used for designing Na+ and Ca2+ selective nanopores.

Cation Selectivity in Biological Cation Channels Using Experimental Structural Information and Statistical Mechanical Simulation

PubMed Central

Finnerty, Justin John

2015-01-01

Cation selective channels constitute the gate for ion currents through the cell membrane. Here we present an improved statistical mechanical model based on atomistic structural information, cation hydration state and without tuned parameters that reproduces the selectivity of biological Na+ and Ca2+ ion channels. The importance of the inclusion of step-wise cation hydration in these results confirms the essential role partial dehydration plays in the bacterial Na+ channels. The model, proven reliable against experimental data, could be straightforwardly used for designing Na+ and Ca2+ selective nanopores. PMID:26460827

Learning Cell Biology as a Team: A Project-Based Approach to Upper-Division Cell Biology

ERIC Educational Resources Information Center

Wright, Robin; Boggs, James

2002-01-01

To help students develop successful strategies for learning how to learn and communicate complex information in cell biology, we developed a quarter-long cell biology class based on team projects. Each team researches a particular human disease and presents information about the cellular structure or process affected by the disease, the cellular…

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. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

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.

Connecting Biology to Electronics: Molecular Communication via Redox Modality.

PubMed

Liu, Yi; Li, Jinyang; Tschirhart, Tanya; Terrell, Jessica L; Kim, Eunkyoung; Tsao, Chen-Yu; Kelly, Deanna L; Bentley, William E; Payne, Gregory F

2017-12-01

Biology and electronics are both expert at for accessing, analyzing, and responding to information. Biology uses ions, small molecules, and macromolecules to receive, analyze, store, and transmit information, whereas electronic devices receive input in the form of electromagnetic radiation, process the information using electrons, and then transmit output as electromagnetic waves. Generating the capabilities to connect biology-electronic modalities offers exciting opportunities to shape the future of biosensors, point-of-care medicine, and wearable/implantable devices. Redox reactions offer unique opportunities for bio-device communication that spans the molecular modalities of biology and electrical modality of devices. Here, an approach to search for redox information through an interactive electrochemical probing that is analogous to sonar is adopted. The capabilities of this approach to access global chemical information as well as information of specific redox-active chemical entities are illustrated using recent examples. An example of the use of synthetic biology to recognize external molecular information, process this information through intracellular signal transduction pathways, and generate output responses that can be detected by electrical modalities is also provided. Finally, exciting results in the use of redox reactions to actuate biology are provided to illustrate that synthetic biology offers the potential to guide biological response through electrical cues. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Biology, Bionomics and Molecular Biology of Anopheles sinensis Wiedemann 1828 (Diptera: Culicidae), Main Malaria Vector in China

PubMed Central

Feng, Xinyu; Zhang, Shaosen; Huang, Fang; Zhang, Li; Feng, Jun; Xia, Zhigui; Zhou, Hejun; Hu, Wei; Zhou, Shuisen

2017-01-01

China has set a goal to eliminate all malaria in the country by 2020, but it is unclear if current understanding of malaria vectors and transmission is sufficient to achieve this objective. Anopheles sinensis is the most widespread malaria vector specie in China, which is also responsible for vivax malaria outbreak in central China. We reviewed literature from 1954 to 2016 on An. sinensis with emphasis on biology, bionomics, and molecular biology. A total of 538 references were relevant and included. An. sienesis occurs in 29 Chinese provinces. Temperature can affect most life-history parameters. Most An. sinensis are zoophilic, but sometimes they are facultatively anthropophilic. Sporozoite analysis demonstrated An. sinensis efficacy on Plasmodium vivax transmission. An. sinensis was not stringently refractory to P. falciparum under experimental conditions, however, sporozoite was not found in salivary glands of field collected An. sinensis. The literature on An. sienesis biology and bionomics was abundant, but molecular studies, such as gene functions and mechanisms, were limited. Only 12 molecules (genes, proteins or enzymes) have been studied. In addition, there were considerable untapped omics resources for potential vector control tools. Existing information on An. sienesis could serve as a baseline for advanced research on biology, bionomics and genetics relevant to vector control strategies. PMID:28848504

Biology, Bionomics and Molecular Biology of Anopheles sinensis Wiedemann 1828 (Diptera: Culicidae), Main Malaria Vector in China.

PubMed

Feng, Xinyu; Zhang, Shaosen; Huang, Fang; Zhang, Li; Feng, Jun; Xia, Zhigui; Zhou, Hejun; Hu, Wei; Zhou, Shuisen

2017-01-01

China has set a goal to eliminate all malaria in the country by 2020, but it is unclear if current understanding of malaria vectors and transmission is sufficient to achieve this objective. Anopheles sinensis is the most widespread malaria vector specie in China, which is also responsible for vivax malaria outbreak in central China. We reviewed literature from 1954 to 2016 on An. sinensis with emphasis on biology, bionomics, and molecular biology. A total of 538 references were relevant and included. An. sienesis occurs in 29 Chinese provinces. Temperature can affect most life-history parameters. Most An. sinensis are zoophilic, but sometimes they are facultatively anthropophilic. Sporozoite analysis demonstrated An. sinensis efficacy on Plasmodium vivax transmission. An. sinensis was not stringently refractory to P. falciparum under experimental conditions, however, sporozoite was not found in salivary glands of field collected An. sinensis . The literature on An. sienesis biology and bionomics was abundant, but molecular studies, such as gene functions and mechanisms, were limited. Only 12 molecules (genes, proteins or enzymes) have been studied. In addition, there were considerable untapped omics resources for potential vector control tools. Existing information on An. sienesis could serve as a baseline for advanced research on biology, bionomics and genetics relevant to vector control strategies.

An Examination of the Addition of Video Informed Reflective Practice to the Active Support Toolkit

ERIC Educational Resources Information Center

Baker, Peter; Appleton, Philippa; Williams, Rosie

2017-01-01

Background: This study evaluated a package of Active Support (AS), which included standard training with additional video informed reflective practice. Materials & Methods: The training package was implemented as part of a service improvement initiative in four residential intellectual disability homes, using a concurrent multiple baseline…

Informed Additive Literacy Instruction for ELLs

ERIC Educational Resources Information Center

Bauer, Eurydice Bouchereau

2009-01-01

There are numerous reasons why schools struggle to provide English-language learners (ELLs) with additive literacy instruction. One reason for this is the lack of available trained bilingual teachers, mainstream teachers who have not received adequate training on how to teach ELLs, and the current political climate that appears to support an…

Glycoprotein Biochemistry (Biosynthesis)--A Vehicle for Teaching Many Aspects of Biochemistry and Molecular Biology.

ERIC Educational Resources Information Center

Cole, Clair R.; Smith, Christopher A.

1990-01-01

Information about the biosynthesis of the carbohydrate portions or glycans of glycoproteins is presented. The teaching of glycosylation can be used to develop and emphasize many general aspects of biosynthesis, in addition to explaining specific biochemical and molecular biological features associated with producing the oligosaccharide portions of…

Covalent Modifiers: A Chemical Perspective on the Reactivity of α,β-Unsaturated Carbonyls with Thiols via Hetero-Michael Addition Reactions.

PubMed

Jackson, Paul A; Widen, John C; Harki, Daniel A; Brummond, Kay M

2017-02-09

Although Michael acceptors display a potent and broad spectrum of bioactivity, they have largely been ignored in drug discovery because of their presumed indiscriminate reactivity. As such, a dearth of information exists relevant to the thiol reactivity of natural products and their analogues possessing this moiety. In the midst of recently approved acrylamide-containing drugs, it is clear that a good understanding of the hetero-Michael addition reaction and the relative reactivities of biological thiols with Michael acceptors under physiological conditions is needed for the design and use of these compounds as biological tools and potential therapeutics. This Perspective provides information that will contribute to this understanding, such as kinetics of thiol addition reactions, bioactivities, as well as steric and electronic factors that influence the electrophilicity and reversibility of Michael acceptors. This Perspective is focused on α,β-unsaturated carbonyls given their preponderance in bioactive natural products.

Covalent Modifiers: A Chemical Perspective on the Reactivity of α,β-Unsaturated Carbonyls with Thiols via Hetero-Michael Addition Reactions

PubMed Central

Jackson, Paul A.; Widen, John C.; Harki, Daniel A.; Brummond, Kay M.

2017-01-01

Although Michael acceptors display a potent and broad spectrum of bioactivity, they have largely been ignored in drug discovery because of their presumed indiscriminate reactivity. As such, a dearth of information exists relevant to the thiol reactivity of natural products and their analogs possessing this moiety. In the midst of recently approved acrylamide-containing drugs, it is clear that a good understanding of the hetero-Michael addition reaction and the relative reactivities of biological thiols with Michael acceptors under physiological conditions is needed for the design and use of these compounds as biological tools and potential therapeutics. This perspective provides information that will contribute to this understanding, such as kinetics of thiol addition reactions, bioactivities, as well as steric and electronic factors that influence the electrophilicity and reversibility of Michael acceptors. This perspective is focused on α,β-unsaturated carbonyls given their preponderance in bioactive natural products. PMID:27996267

A Converter from the Systems Biology Markup Language to the Synthetic Biology Open Language.

PubMed

Nguyen, Tramy; Roehner, Nicholas; Zundel, Zach; Myers, Chris J

2016-06-17

Standards are important to synthetic biology because they enable exchange and reproducibility of genetic designs. This paper describes a procedure for converting between two standards: the Systems Biology Markup Language (SBML) and the Synthetic Biology Open Language (SBOL). SBML is a standard for behavioral models of biological systems at the molecular level. SBOL describes structural and basic qualitative behavioral aspects of a biological design. Converting SBML to SBOL enables a consistent connection between behavioral and structural information for a biological design. The conversion process described in this paper leverages Systems Biology Ontology (SBO) annotations to enable inference of a designs qualitative function.

Addition products of alpha-tocopherol with lipid-derived free radicals.

PubMed

Yamauchi, Ryo

2007-01-01

The addition products of alpha-tocopherol with lipid-derived free radicals have been reviewed. Free radical scavenging reactions of alpha-tocopherol take place via the alpha-tocopheroxyl radical as an intermediate. If a suitable free radical is present, an addition product can be formed from the coupling of the free radical with the alpha-tocopheroxyl radical. The addition products of alpha-tocopherol with lipid-peroxyl radicals are 8a-(lipid-dioxy)-alpha-tocopherones, which are hydrolyzed to alpha-tocopherylquinone. On the other hand, the carbon-centered radicals of lipids prefer to react with the phenoxyl radical of alpha-tocopherol to form 6-O-lipid-alpha-tocopherol under anaerobic conditions. The addition products of alpha-tocopherol with peroxyl radicals (epoxylinoleoyl-peroxyl radicals) produced from cholesteryl ester and phosphatidylcholine were detected in the peroxidized human plasma using a high-sensitive HPLC procedure with postcolumn reduction and electrochemical detection. Thus, the formation of these addition products provides us with much information on the antioxidant function of vitamin E in biological systems.

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.

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.

Zsyntax: a formal language for molecular biology with projected applications in text mining and biological prediction.

PubMed

Boniolo, Giovanni; D'Agostino, Marcello; Di Fiore, Pier Paolo

2010-03-03

We propose a formal language that allows for transposing biological information precisely and rigorously into machine-readable information. This language, which we call Zsyntax (where Z stands for the Greek word zetaomegaeta, life), is grounded on a particular type of non-classical logic, and it can be used to write algorithms and computer programs. We present it as a first step towards a comprehensive formal language for molecular biology in which any biological process can be written and analyzed as a sort of logical "deduction". Moreover, we illustrate the potential value of this language, both in the field of text mining and in that of biological prediction.

The value of mechanistic biophysical information for systems-level understanding of complex biological processes such as cytokinesis.

PubMed

Pollard, Thomas D

2014-12-02

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. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Biology of Skin Color.

ERIC Educational Resources Information Center

Corcos, Alain

1983-01-01

Information from scientific journals on the biology of skin color is discussed. Major areas addressed include: (1) biology of melanin, melanocytes, and melanosomes; (2) melanosome and human diversity; (3) genetics of skin color; and (4) skin color, geography, and natural selection. (JN)

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

Indices of polarimetric purity for biological tissues inspection

NASA Astrophysics Data System (ADS)

Van Eeckhout, Albert; Lizana, Angel; Garcia-Caurel, Enric; Gil, José J.; Sansa, Adrià; Rodríguez, Carla; Estévez, Irene; González, Emilio; Escalera, Juan C.; Moreno, Ignacio; Campos, Juan

2018-02-01

We highlight the interest of using the Indices of Polarimetric Purity (IPPs) for the biological tissue inspection. These are three polarimetric metrics focused on the study of the depolarizing behaviour of the sample. The IPPs have been recently proposed in the literature and provide different and synthetized information than the commonly used depolarizing indices, as depolarization index (PΔ) or depolarization power (Δ). Compared with the standard polarimetric images of biological samples, IPPs enhance the contrast between different tissues of the sample and show differences between similar tissues which are not observed using the other standard techniques. Moreover, they present further physical information related to the depolarization mechanisms inherent to different tissues. In addition, the algorithm does not require advanced calculations (as in the case of polar decompositions), being the indices of polarimetric purity fast and easy to implement. We also propose a pseudo-coloured image method which encodes the sample information as a function of the different indices weights. These images allow us to customize the visualization of samples and to highlight certain of their constitutive structures. The interest and potential of the IPP approach are experimentally illustrated throughout the manuscript by comparing polarimetric images of different ex-vivo samples obtained with standard polarimetric methods with those obtained from the IPPs analysis. Enhanced contrast and retrieval of new information are experimentally obtained from the different IPP based images.

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.

Synergy of understanding dermatologic disease and epidermal biology.

PubMed

Stanley, John R

2012-02-01

Dermatologic disease, although seldom life threatening, can be extremely disfiguring and interfere with the quality of life. In addition, as opposed to other organs, just the aging of skin and its adnexal structure the hair follicle can result in cosmetic concerns that affect most of us. The articles in this dermatology Review Series demonstrate recent progress in understanding the cell biology and molecular pathophysiology of the epidermis and hair follicles, which harbor keratinocyte and melanocyte stem cells. They reveal a dynamic relationship between research and clinical care: knowledge of dermatologic disease has facilitated the understanding of the biology of the epidermis and, in turn, progress in basic science has informed our understanding of disease. This type of synergy is a profound strength of clinical research of the type that the JCI is dedicated to publishing.

MushBase: A Mushroom Information Database Application

PubMed Central

Le, Vang Quy; Lee, Hyun-Sook

2007-01-01

A database application, namely MushBase, has been built based on Microsoft Access in order to store and manage different kinds of data about mushroom biological information of species, strains and their physiological characteristics such as geometries and growth condition(s). In addition, it is also designed to store another group of information that is experimental data about mushroom classification by Random Amplification of Polymorphic DNA (RAPD). These two groups of information are stored and managed in the way so that it is convenient to retrieve each group of data and to cross-refer between them as well. PMID:24015087

Patients retrieving additional information via the Internet: a trend analysis in a Swedish population, 2000-05.

PubMed

Rahmqvist, Mikael; Bara, Ana-Claudia

2007-01-01

To examine the trends over five years for patients' seeking online additional health information about their disease/health problem to what the doctor has been giving, and investigate any differences in information-seeking behaviour according to age, gender, self-perceived health status, living area, and type of medical encounter. Data from three independent surveys conducted in 2000, 2002, and 2005 of a population with a recent experience of outpatient care[n]typesetter: please remove blue shading here and elsewhere[/n], including 24,800 respondents aged between 20 and 95, were analysed in a trend analysis and a logistic regression regarding background factors that may influence the seeking behaviour. During the study period, there was a significant increase in Internet use in most age groups. The total use among men 20-95 years old increased from 7% in 2000 to 18% in 2005 and from 9% to 25% for women respectively. The predictors for using the Internet as a source of information were: age, gender, self-perceived health status, living area, and the type of medical encounter (first or repeated). In 2005, women aged 20-49 used the Internet as a source to a significantly greater extent than men, even when all background factors were controlled for (OR 1.46 and CI 1.21-1.77). Swedish patients, especially the young and middle-aged, are to a substantial degree using the Internet to gather additional information on their disease. The benefits of this increase include more informed patients; however, there are inherent quality issues that require strategies for ensuring public access to high-quality health information online.

An efficient grid layout algorithm for biological networks utilizing various biological attributes

PubMed Central

Kojima, Kaname; Nagasaki, Masao; Jeong, Euna; Kato, Mitsuru; Miyano, Satoru

2007-01-01

Background Clearly visualized biopathways provide a great help in understanding biological systems. However, manual drawing of large-scale biopathways is time consuming. We proposed a grid layout algorithm that can handle gene-regulatory networks and signal transduction pathways by considering edge-edge crossing, node-edge crossing, distance measure between nodes, and subcellular localization information from Gene Ontology. Consequently, the layout algorithm succeeded in drastically reducing these crossings in the apoptosis model. However, for larger-scale networks, we encountered three problems: (i) the initial layout is often very far from any local optimum because nodes are initially placed at random, (ii) from a biological viewpoint, human layouts still exceed automatic layouts in understanding because except subcellular localization, it does not fully utilize biological information of pathways, and (iii) it employs a local search strategy in which the neighborhood is obtained by moving one node at each step, and automatic layouts suggest that simultaneous movements of multiple nodes are necessary for better layouts, while such extension may face worsening the time complexity. Results We propose a new grid layout algorithm. To address problem (i), we devised a new force-directed algorithm whose output is suitable as the initial layout. For (ii), we considered that an appropriate alignment of nodes having the same biological attribute is one of the most important factors of the comprehension, and we defined a new score function that gives an advantage to such configurations. For solving problem (iii), we developed a search strategy that considers swapping nodes as well as moving a node, while keeping the order of the time complexity. Though a naïve implementation increases by one order, the time complexity, we solved this difficulty by devising a method that caches differences between scores of a layout and its possible updates. Conclusion Layouts of the new

On Crowd-verification of Biological Networks

PubMed Central

Ansari, Sam; Binder, Jean; Boue, Stephanie; Di Fabio, Anselmo; Hayes, William; Hoeng, Julia; Iskandar, Anita; Kleiman, Robin; Norel, Raquel; O’Neel, Bruce; Peitsch, Manuel C.; Poussin, Carine; Pratt, Dexter; Rhrissorrakrai, Kahn; Schlage, Walter K.; Stolovitzky, Gustavo; Talikka, Marja

2013-01-01

Biological networks with a structured syntax are a powerful way of representing biological information generated from high density data; however, they can become unwieldy to manage as their size and complexity increase. This article presents a crowd-verification approach for the visualization and expansion of biological networks. Web-based graphical interfaces allow visualization of causal and correlative biological relationships represented using Biological Expression Language (BEL). Crowdsourcing principles enable participants to communally annotate these relationships based on literature evidences. Gamification principles are incorporated to further engage domain experts throughout biology to gather robust peer-reviewed information from which relationships can be identified and verified. The resulting network models will represent the current status of biological knowledge within the defined boundaries, here processes related to human lung disease. These models are amenable to computational analysis. For some period following conclusion of the challenge, the published models will remain available for continuous use and expansion by the scientific community. PMID:24151423

40 CFR 141.154 - Required additional health information.

Code of Federal Regulations, 2014 CFR

2014-07-01

... skin damage and circulatory problems. (2) May write its own educational statement, but only in... MCL: (1) Must include a short informational statement about the impacts of nitrate on children using... its effects on children. The statement must include the following information: If present, elevated...

Synthetic biology: Novel approaches for microbiology.

PubMed

Padilla-Vaca, Felipe; Anaya-Velázquez, Fernando; Franco, Bernardo

2015-06-01

In the past twenty years, molecular genetics has created powerful tools for genetic manipulation of living organisms. Whole genome sequencing has provided necessary information to assess knowledge on gene function and protein networks. In addition, new tools permit to modify organisms to perform desired tasks. Gene function analysis is speed up by novel approaches that couple both high throughput data generation and mining. Synthetic biology is an emerging field that uses tools for generating novel gene networks, whole genome synthesis and engineering. New applications in biotechnological, pharmaceutical and biomedical research are envisioned for synthetic biology. In recent years these new strategies have opened up the possibilities to study gene and genome editing, creation of novel tools for functional studies in virus, parasites and pathogenic bacteria. There is also the possibility to re-design organisms to generate vaccine subunits or produce new pharmaceuticals to combat multi-drug resistant pathogens. In this review we provide our opinion on the applicability of synthetic biology strategies for functional studies of pathogenic organisms and some applications such as genome editing and gene network studies to further comprehend virulence factors and determinants in pathogenic organisms. We also discuss what we consider important ethical issues for this field of molecular biology, especially for potential misuse of the new technologies. Copyright© by the Spanish Society for Microbiology and Institute for Catalan Studies.

Addition of a Fluoride-containing Radiopacifier Improves Micromechanical and Biological Characteristics of Modified Calcium Silicate Cements.

PubMed

Antonijevic, Djordje; Jeschke, Anke; Colovic, Bozana; Milovanovic, Petar; Jevremovic, Danimir; Kisic, Danilo; vom Scheidt, Annika; Hahn, Michael; Amling, Michael; Jokanovic, Vukoman; Busse, Björn; Djuric, Marija

2015-12-01

Calcium silicate cements (CSCs) with the addition of nanohydroxyapatite and calcium carbonate play a critical role in dental applications. To further improve their properties, particularly radiopacity and biointeractivity, the fluoride-containing radiopacifier ytterbium trifluoride (YbF3) was added to their composition, and biological and mechanical characteristics were evaluated. YbF3 was added to 3 different CSCs: cement I (CSC + calcium carbonate), cement II (CSC + nanohydroxyapatite), and Portland cement. Material characterization encompassed measurements of pH, calcium, ytterbium, and fluoride ion release; radiopacity; setting time; porosity; microindentation properties; wettability; and Fourier transform infrared spectroscopic, x-ray diffraction, and scanning electron microscopic analyses. Osteoblast- and osteoclast-like cells were grown on the materials' surface to evaluate their adherence. The addition of calcium carbonate, nanohydroxyapatite, and 30 wt% of YbF3 improved radiopacity and the setting time of experimental cements. The pH values did not differ among the groups. The greatest ytterbium and fluoride releases occurred in the Portland cement + YbF3 group. Combined x-ray diffraction and Fourier transform infrared spectroscopic analysis showed the presence of calcium hydroxide and calcium silicate hydrates. In addition, the presence of calcium ytterbium fluoride and ytterbium oxide proved that YbF3 reacted with cement compounds. Wettability of cement I + YbF3 was superior to other formulations, but its porosity and microindentation properties were weaker than in the Portland cement + YbF3 mixture. Cement II + YbF3 presented micromechanical indentation and porosity characteristics similar to the Portland-based cement formulation. Osteoclast- and osteoblast-like cells adhered to the cements' surfaces without alteration of the cell structural integrity. YbF3-containing CSCs with nanostructured hydroxyapatite and calcium carbonate are well suited for

Current food chain information provides insufficient information for modern meat inspection of pigs.

PubMed

Felin, Elina; Jukola, Elias; Raulo, Saara; Heinonen, Jaakko; Fredriksson-Ahomaa, Maria

2016-05-01

Meat inspection now incorporates a more risk-based approach for protecting human health against meat-borne biological hazards. Official post-mortem meat inspection of pigs has shifted to visual meat inspection. The official veterinarian decides on additional post-mortem inspection procedures, such as incisions and palpations. The decision is based on declarations in the food chain information (FCI), ante-mortem inspection and post-mortem inspection. However, a smooth slaughter and inspection process is essential. Therefore, one should be able to assess prior to slaughter which pigs are suitable for visual meat inspection only, and which need more profound inspection procedures. This study evaluates the usability of the FCI provided by pig producers and considered the possibility for risk ranking of incoming slaughter batches according to the previous meat inspection data and the current FCI. Eighty-five slaughter batches comprising 8954 fattening pigs were randomly selected at a slaughterhouse that receives animals from across Finland. The mortality rate, the FCI and the meat inspection results for each batch were obtained. The current FCI alone provided insufficient and inaccurate information for risk ranking purposes for meat inspection. The partial condemnation rate for a batch was best predicted by the partial condemnation rate calculated for all the pigs sent for slaughter from the same holding in the previous year (p<0.001) and by prior information on cough declared in the current FCI (p=0.02) statement. Training and information to producers are needed to make the FCI reporting procedures more accurate. Historical meat inspection data on pigs slaughtered from the same holdings and well-chosen symptoms/signs for reporting, should be included in the FCI to facilitate the allocation of pigs for visual inspection. The introduced simple scoring system can be easily used for additional information for directing batches to appropriate meat inspection procedures. To

Logic Gate Operation by DNA Translocation through Biological Nanopores.

PubMed

Yasuga, Hiroki; Kawano, Ryuji; Takinoue, Masahiro; Tsuji, Yutaro; Osaki, Toshihisa; Kamiya, Koki; Miki, Norihisa; Takeuchi, Shoji

2016-01-01

Logical operations using biological molecules, such as DNA computing or programmable diagnosis using DNA, have recently received attention. Challenges remain with respect to the development of such systems, including label-free output detection and the rapidity of operation. Here, we propose integration of biological nanopores with DNA molecules for development of a logical operating system. We configured outputs "1" and "0" as single-stranded DNA (ssDNA) that is or is not translocated through a nanopore; unlabeled DNA was detected electrically. A negative-AND (NAND) operation was successfully conducted within approximately 10 min, which is rapid compared with previous studies using unlabeled DNA. In addition, this operation was executed in a four-droplet network. DNA molecules and associated information were transferred among droplets via biological nanopores. This system would facilitate linking of molecules and electronic interfaces. Thus, it could be applied to molecular robotics, genetic engineering, and even medical diagnosis and treatment.

Logic Gate Operation by DNA Translocation through Biological Nanopores

PubMed Central

Takinoue, Masahiro; Tsuji, Yutaro; Osaki, Toshihisa; Kamiya, Koki; Miki, Norihisa; Takeuchi, Shoji

2016-01-01

Logical operations using biological molecules, such as DNA computing or programmable diagnosis using DNA, have recently received attention. Challenges remain with respect to the development of such systems, including label-free output detection and the rapidity of operation. Here, we propose integration of biological nanopores with DNA molecules for development of a logical operating system. We configured outputs “1” and “0” as single-stranded DNA (ssDNA) that is or is not translocated through a nanopore; unlabeled DNA was detected electrically. A negative-AND (NAND) operation was successfully conducted within approximately 10 min, which is rapid compared with previous studies using unlabeled DNA. In addition, this operation was executed in a four-droplet network. DNA molecules and associated information were transferred among droplets via biological nanopores. This system would facilitate linking of molecules and electronic interfaces. Thus, it could be applied to molecular robotics, genetic engineering, and even medical diagnosis and treatment. PMID:26890568

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

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

... 41 Public Contracts and Property Management 3 2013-07-01 2013-07-01 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) FEDERAL...

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

... 41 Public Contracts and Property Management 3 2011-01-01 2011-01-01 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) FEDERAL...

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

... 41 Public Contracts and Property Management 3 2014-01-01 2014-01-01 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) FEDERAL...

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

... 41 Public Contracts and Property Management 3 2012-01-01 2012-01-01 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) FEDERAL...

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

... 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 an Executive agency transmit with the Report of Excess Real Property (Standard Form 118)? 102-75.140 Section 102-75.140 Public Contracts and Property...

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

Code of Federal Regulations, 2014 CFR

2014-01-01

... 41 Public Contracts and Property Management 3 2014-01-01 2014-01-01 false In addition to the title report, and all necessary environmental information and certifications, what information must an Executive agency transmit with the Report of Excess Real Property (Standard Form 118)? 102-75.140 Section 102-75.140 Public Contracts and Property...

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

Code of Federal Regulations, 2011 CFR

2011-01-01

... 41 Public Contracts and Property Management 3 2011-01-01 2011-01-01 false In addition to the title report, and all necessary environmental information and certifications, what information must an Executive agency transmit with the Report of Excess Real Property (Standard Form 118)? 102-75.140 Section 102-75.140 Public Contracts and Property...

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

Code of Federal Regulations, 2013 CFR

2013-07-01

... 41 Public Contracts and Property Management 3 2013-07-01 2013-07-01 false In addition to the title report, and all necessary environmental information and certifications, what information must an Executive agency transmit with the Report of Excess Real Property (Standard Form 118)? 102-75.140 Section 102-75.140 Public Contracts and Property...

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

Code of Federal Regulations, 2012 CFR

2012-01-01

... 41 Public Contracts and Property Management 3 2012-01-01 2012-01-01 false In addition to the title report, and all necessary environmental information and certifications, what information must an Executive agency transmit with the Report of Excess Real Property (Standard Form 118)? 102-75.140 Section 102-75.140 Public Contracts and Property...

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

Social networks to biological networks: systems biology of Mycobacterium tuberculosis.

PubMed

Vashisht, Rohit; Bhardwaj, Anshu; Osdd Consortium; Brahmachari, Samir K

2013-07-01

Contextualizing relevant information to construct a network that represents a given biological process presents a fundamental challenge in the network science of biology. The quality of network for the organism of interest is critically dependent on the extent of functional annotation of its genome. Mostly the automated annotation pipelines do not account for unstructured information present in volumes of literature and hence large fraction of genome remains poorly annotated. However, if used, this information could substantially enhance the functional annotation of a genome, aiding the development of a more comprehensive network. Mining unstructured information buried in volumes of literature often requires manual intervention to a great extent and thus becomes a bottleneck for most of the automated pipelines. In this review, we discuss the potential of scientific social networking as a solution for systematic manual mining of data. Focusing on Mycobacterium tuberculosis, as a case study, we discuss our open innovative approach for the functional annotation of its genome. Furthermore, we highlight the strength of such collated structured data in the context of drug target prediction based on systems level analysis of pathogen.

Data warehousing in molecular biology.

PubMed

Schönbach, C; Kowalski-Saunders, P; Brusic, V

2000-05-01

In the business and healthcare sectors data warehousing has provided effective solutions for information usage and knowledge discovery from databases. However, data warehousing applications in the biological research and development (R&D) sector are lagging far behind. The fuzziness and complexity of biological data represent a major challenge in data warehousing for molecular biology. By combining experiences in other domains with our findings from building a model database, we have defined the requirements for data warehousing in molecular biology.

BSCS BIOLOGY--IMPLEMENTATION IN THE SCHOOLS.

ERIC Educational Resources Information Center

GROBMAN, ARNOLD B.; AND OTHERS

INFORMATION FOR TEACHERS AND PRINCIPALS IMPLEMENTING BIOLOGICAL SCIENCE CURRICULUM STUDY (BSCS) BIOLOGY IN THE SCHOOL PROGRAM IS INCLUDED IN THIS GUIDE. THE RATIONALE AND CONTENT OF THE BSCS VERSIONS ARE EXPLAINED. PHYSICAL FACILITIES, LABORATORY EQUIPMENT, AND LABORATORY MATERIALS THAT FACILITATE TEACHING BSCS BIOLOGY ARE ANALYZED. ADMINISTRATIVE…

Managing biological diversity

USGS Publications Warehouse

Samson, Fred B.; Knopf, Fritz L.

1993-01-01

viewing issues across biological, spatial, and temporal scales (Knopf and Smith 1992), natural resource managers find much conflicting information in the literature on strategies and programs for the conservation of biological diversity (Ehrlich 1992). Moreover, recommendations provided in much of the published information available for planning or decisions not only can be debated but may prove counterproductive if implemented. Current operational efforts beg for clearer focus on fundamental concepts central to daily decisions that impact native biological diversity. Recognizing that many biologists would provide different council and at the risk of oversimplification, we offer the following 4 topical issues as fundamental guidance to wise conservation action. These recommendations are based on our collective experiences working within conservation agencies since our original, collaborative essay (Samson and Knopf 1982). They are offered as initial, rather than authoritative, steps to better align research and management decisions with what we perceive as the critical issues in conserving biological diversity at the landscape and ecosystem levels of resolution.

An investigation of the efficacy of biological additives for the suppression of pyritic sulphur during simulated froth flotation of coal.

PubMed

Stainthorpe, A C

1989-02-05

The biological molecule responsible for the suppression of pyritic sulfur in fine coal simulated froth flotation treated with bacteria was identified. Protein was found to be the most effective agent in pyrite suppression of the three cell components (protein, lipid, and carbohydrate) assayed. Coal recovery and ash removal of the flotation process were only slightly reduced by this treatment. Other protein-containing materials were evaluated for their ability to suppress pyrite flotation. Whey was found to be the most cost-effective flotation additive of those assayed. The sulfur content of the whey-treated float was reduced by 84.0% in a synthetically prepared fractionated coal (10.7% sulfur), by a raw whey dosage of 20 microL/g coal. The inorganic sulfur component of a natural high sulfur coal fraction (10.9%) was completely depressed by this whey addition. The effect of particle size and pulp density upon the process were investigated.

Data Integration and Mining for Synthetic Biology Design.

PubMed

Mısırlı, Göksel; Hallinan, Jennifer; Pocock, Matthew; Lord, Phillip; McLaughlin, James Alastair; Sauro, Herbert; Wipat, Anil

2016-10-21

One aim of synthetic biologists is to create novel and predictable biological systems from simpler modular parts. This approach is currently hampered by a lack of well-defined and characterized parts and devices. However, there is a wealth of existing biological information, which can be used to identify and characterize biological parts, and their design constraints in the literature and numerous biological databases. However, this information is spread among these databases in many different formats. New computational approaches are required to make this information available in an integrated format that is more amenable to data mining. A tried and tested approach to this problem is to map disparate data sources into a single data set, with common syntax and semantics, to produce a data warehouse or knowledge base. Ontologies have been used extensively in the life sciences, providing this common syntax and semantics as a model for a given biological domain, in a fashion that is amenable to computational analysis and reasoning. Here, we present an ontology for applications in synthetic biology design, SyBiOnt, which facilitates the modeling of information about biological parts and their relationships. SyBiOnt was used to create the SyBiOntKB knowledge base, incorporating and building upon existing life sciences ontologies and standards. The reasoning capabilities of ontologies were then applied to automate the mining of biological parts from this knowledge base. We propose that this approach will be useful to speed up synthetic biology design and ultimately help facilitate the automation of the biological engineering life cycle.

RNA and RNP as Building Blocks for Nanotechnology and Synthetic Biology.

PubMed

Ohno, Hirohisa; Saito, Hirohide

2016-01-01

Recent technologies that aimed to elucidate cellular function have revealed essential roles for RNA molecules in living systems. Our knowledge concerning functional and structural information of naturally occurring RNA and RNA-protein (RNP) complexes is increasing rapidly. RNA and RNP interaction motifs are structural units that function as building blocks to constitute variety of complex structures. RNA-central synthetic biology and nanotechnology are constructive approaches that employ the accumulated information and build synthetic RNA (RNP)-based circuits and nanostructures. Here, we describe how to design and construct synthetic RNA (RNP)-based devices and structures at the nanometer-scale for biological and future therapeutic applications. RNA/RNP nanostructures can also be utilized as the molecular scaffold to control the localization or interactions of target molecule(s). Moreover, RNA motifs recognized by RNA-binding proteins can be applied to make protein-responsive translational "switches" that can turn gene expression "on" or "off" depending on the intracellular environment. This "synthetic RNA and RNP world" will expand tools for nanotechnology and synthetic biology. In addition, these reconstructive approaches would lead to a greater understanding of building principle in naturally occurring RNA/RNP molecules and systems. Copyright © 2016 Elsevier Inc. All rights reserved.

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

Code of Federal Regulations, 2011 CFR

2011-07-01

... Notification of Compliance Status 42 Table 42 to Subpart UUU of Part 63 Protection of Environment ENVIRONMENTAL... Refineries: Catalytic Cracking Units, Catalytic Reforming Units, and Sulfur Recovery Units Pt. 63, Subpt. UUU, Table 42 Table 42 to Subpart UUU of Part 63—Additional Information for Initial Notification of...

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

Code of Federal Regulations, 2010 CFR

2010-07-01

... Notification of Compliance Status 42 Table 42 to Subpart UUU of Part 63 Protection of Environment ENVIRONMENTAL... Refineries: Catalytic Cracking Units, Catalytic Reforming Units, and Sulfur Recovery Units Pt. 63, Subpt. UUU, Table 42 Table 42 to Subpart UUU of Part 63—Additional Information for Initial Notification of...

The Relationships Between Epistemic Beliefs in Biology and Approaches to Learning Biology Among Biology-Major University Students in Taiwan

NASA Astrophysics Data System (ADS)

Lin, Yi-Chun; Liang, Jyh-Chong; Tsai, Chin-Chung

2012-12-01

The aim of this study was to investigate the relationships between students' epistemic beliefs in biology and their approaches to learning biology. To this end, two instruments, the epistemic beliefs in biology and the approaches to learning biology surveys, were developed and administered to 520 university biology students, respectively. By and large, it was found that the students reflected "mixed" motives in biology learning, while those who had more sophisticated epistemic beliefs tended to employ deep strategies. In addition, the results of paired t tests revealed that the female students were more likely to possess beliefs about biological knowledge residing in external authorities, to believe in a right answer, and to utilize rote learning as a learning strategy. Moreover, compared to juniors and seniors, freshmen and sophomores tended to hold less mature views on all factors of epistemic beliefs regarding biology. Another comparison indicated that theoretical biology students (e.g. students majoring in the Department of Biology) tended to have more mature beliefs in learning biology and more advanced strategies for biology learning than those students studying applied biology (e.g. in the Department of Biotechnology). Stepwise regression analysis, in general, indicated that students who valued the role of experiments and justify epistemic assumptions and knowledge claims based on evidence were more oriented towards having mixed motives and utilizing deep strategies to learn biology. In contrast, students who believed in the certainty of biological knowledge were more likely to adopt rote learning strategies and to aim to qualify in biology.

An integrative approach to inferring biologically meaningful gene modules.

PubMed

Cho, Ji-Hoon; Wang, Kai; Galas, David J

2011-07-26

The ability to construct biologically meaningful gene networks and modules is critical for contemporary systems biology. Though recent studies have demonstrated the power of using gene modules to shed light on the functioning of complex biological systems, most modules in these networks have shown little association with meaningful biological function. We have devised a method which directly incorporates gene ontology (GO) annotation in construction of gene modules in order to gain better functional association. We have devised a method, Semantic Similarity-Integrated approach for Modularization (SSIM) that integrates various gene-gene pairwise similarity values, including information obtained from gene expression, protein-protein interactions and GO annotations, in the construction of modules using affinity propagation clustering. We demonstrated the performance of the proposed method using data from two complex biological responses: 1. the osmotic shock response in Saccharomyces cerevisiae, and 2. the prion-induced pathogenic mouse model. In comparison with two previously reported algorithms, modules identified by SSIM showed significantly stronger association with biological functions. The incorporation of semantic similarity based on GO annotation with gene expression and protein-protein interaction data can greatly enhance the functional relevance of inferred gene modules. In addition, the SSIM approach can also reveal the hierarchical structure of gene modules to gain a broader functional view of the biological system. Hence, the proposed method can facilitate comprehensive and in-depth analysis of high throughput experimental data at the gene network level.

An integrative approach to inferring biologically meaningful gene modules

PubMed Central

2011-01-01

Background The ability to construct biologically meaningful gene networks and modules is critical for contemporary systems biology. Though recent studies have demonstrated the power of using gene modules to shed light on the functioning of complex biological systems, most modules in these networks have shown little association with meaningful biological function. We have devised a method which directly incorporates gene ontology (GO) annotation in construction of gene modules in order to gain better functional association. Results We have devised a method, Semantic Similarity-Integrated approach for Modularization (SSIM) that integrates various gene-gene pairwise similarity values, including information obtained from gene expression, protein-protein interactions and GO annotations, in the construction of modules using affinity propagation clustering. We demonstrated the performance of the proposed method using data from two complex biological responses: 1. the osmotic shock response in Saccharomyces cerevisiae, and 2. the prion-induced pathogenic mouse model. In comparison with two previously reported algorithms, modules identified by SSIM showed significantly stronger association with biological functions. Conclusions The incorporation of semantic similarity based on GO annotation with gene expression and protein-protein interaction data can greatly enhance the functional relevance of inferred gene modules. In addition, the SSIM approach can also reveal the hierarchical structure of gene modules to gain a broader functional view of the biological system. Hence, the proposed method can facilitate comprehensive and in-depth analysis of high throughput experimental data at the gene network level. PMID:21791051

Greek Secondary School Students' Views about Biology

ERIC Educational Resources Information Center

Mavrikaki, Evangelia; Koumparou, Helen; Kyriakoudi, Margarita; Papacharalampous, Irene; Trimandili, Maria

2012-01-01

This paper aims to give a picture of Greek students' views about biology and some of the factors that affect them. A questionnaire measuring students' intrinsic motivation to learn biology, individual interest in biology and perceived difficulty of biology, along with information about students' gender, level, parents' occupation and educational…

It's more than stamp collecting: how genome sequencing can unify biological research.

PubMed

Richards, Stephen

2015-07-01

The availability of reference genome sequences, especially the human reference, has revolutionized the study of biology. However, while the genomes of some species have been fully sequenced, a wide range of biological problems still cannot be effectively studied for lack of genome sequence information. Here, I identify neglected areas of biology and describe how both targeted species sequencing and more broad taxonomic surveys of the tree of life can address important biological questions. I enumerate the significant benefits that would accrue from sequencing a broader range of taxa, as well as discuss the technical advances in sequencing and assembly methods that would allow for wide-ranging application of whole-genome analysis. Finally, I suggest that in addition to 'big science' survey initiatives to sequence the tree of life, a modified infrastructure-funding paradigm would better support reference genome sequence generation for research communities most in need. Copyright © 2015 Elsevier Ltd. All rights reserved.

Titanium dioxide nanotubes addition to self-adhesive resin cement: Effect on physical and biological properties.

PubMed

Ramos-Tonello, Carla M; Lisboa-Filho, Paulo N; Arruda, Larisa B; Tokuhara, Cintia K; Oliveira, Rodrigo C; Furuse, Adilson Y; Rubo, José H; Borges, Ana Flávia S

2017-07-01

This study has investigated the influence of Titanium dioxide nanotubes (TiO 2 -nt) addition to self-adhesive resin cement on the degree of conversion, water sorption, and water solubility, mechanical and biological properties. A commercially available auto-adhesive resin cement (RelyX U200™, 3M ESPE) was reinforced with varying amounts of nanotubes (0.3, 0.6, 0.9wt%) and evaluated at different curing modes (self- and dual cure). The DC in different times (3, 6, 9, 12 and 15min), water sorption (Ws) and solubility (Sl), 3-point flexural strength (σf), elastic modulus (E), Knoop microhardness (H) and viability of NIH/3T3 fibroblasts were performed to characterize the resin cement. Reinforced self-adhesive resin cement, regardless of concentration, increased the DC for the self- and dual-curing modes at all times studied. The concentration of the TiO 2 -nt and the curing mode did not influence the Ws and Sl. Regarding σf, concentrations of both 0.3 and 0.9wt% for self-curing mode resulted in data similar to that of dual-curing unreinforced cement. The E increased with the addition of 0.9wt% for self-cure mode and H increased with 0.6 and 0.9wt% for both curing modes. Cytotoxicity assays revealed that reinforced cements were biocompatible. TiO 2 -nt reinforced self-adhesive resin cement are promising materials for use in indirect dental restorations. Taken together, self-adhesive resin cement reinforced with TiO 2 -nt exhibited physicochemical and mechanical properties superior to those of unreinforced cements, without compromising their cellular viability. Copyright © 2017 The Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

Using Biology Education Research and Qualitative Inquiry to Inform Genomic Nursing Education.

PubMed

Ward, Linda D

Decades of research in biology education show that learning genetics is difficult and reveals specific sources of learning difficulty. Little is known about how nursing students learn in this domain, although they likely encounter similar difficulties as nonnursing students. Using qualitative approaches, this study investigated challenges to learning genetics among nursing students. Findings indicate that nursing students face learning difficulties already identified among biology students, suggesting that nurse educators might benefit from biology education research.

It’s More Than Stamp Collecting: How Genome Sequencing Can Unify Biological Research

PubMed Central

Richards, Stephen

2015-01-01

The availability of reference genome sequences, especially the human reference, has revolutionized the study of biology. However, whilst the genomes of some species have been fully sequenced, a wide range of biological problems still cannot be effectively studied for lack of genome sequence information. Here, I identify neglected areas of biology and describe how both targeted species sequencing and more broad taxonomic surveys of the tree of life can address important biological questions. I enumerate the significant benefits that would accrue from sequencing a broader range of taxa, as well as discuss the technical advances in sequencing and assembly methods that would allow for wide-ranging application of whole-genome analysis. Finally, I suggest that in addition to “Big Science” survey initiatives to sequence the tree of life, a modified infrastructure-funding paradigm would better support reference genome sequence generation for research communities most in need. PMID:26003218

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

... Notification of Compliance Status 42 Table 42 to Subpart UUU of Part 63 Protection of Environment ENVIRONMENTAL..., Subpt. UUU, Table 42 Table 42 to Subpart UUU of Part 63—Additional Information for Initial Notification... source or vent associated with an affected source not subject to the requirements of subpart UUU. 2...

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

Code of Federal Regulations, 2014 CFR

2014-07-01

... Notification of Compliance Status 42 Table 42 to Subpart UUU of Part 63 Protection of Environment ENVIRONMENTAL..., Subpt. UUU, Table 42 Table 42 to Subpart UUU of Part 63—Additional Information for Initial Notification... source or vent associated with an affected source not subject to the requirements of subpart UUU. 2...

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

Code of Federal Regulations, 2013 CFR

2013-07-01

... Notification of Compliance Status 42 Table 42 to Subpart UUU of Part 63 Protection of Environment ENVIRONMENTAL..., Subpt. UUU, Table 42 Table 42 to Subpart UUU of Part 63—Additional Information for Initial Notification... source or vent associated with an affected source not subject to the requirements of subpart UUU. 2...

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

A comparative approach for the investigation of biological information processing: an examination of the structure and function of computer hard drives and DNA.

PubMed

D'Onofrio, David J; An, Gary

2010-01-21

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. 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. 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 systems do not have an

A standard-enabled workflow for synthetic biology.

PubMed

Myers, Chris J; Beal, Jacob; Gorochowski, Thomas E; Kuwahara, Hiroyuki; Madsen, Curtis; McLaughlin, James Alastair; Mısırlı, Göksel; Nguyen, Tramy; Oberortner, Ernst; Samineni, Meher; Wipat, Anil; Zhang, Michael; Zundel, Zach

2017-06-15

A synthetic biology workflow is composed of data repositories that provide information about genetic parts, sequence-level design tools to compose these parts into circuits, visualization tools to depict these designs, genetic design tools to select parts to create systems, and modeling and simulation tools to evaluate alternative design choices. Data standards enable the ready exchange of information within such a workflow, allowing repositories and tools to be connected from a diversity of sources. The present paper describes one such workflow that utilizes, among others, the Synthetic Biology Open Language (SBOL) to describe genetic designs, the Systems Biology Markup Language to model these designs, and SBOL Visual to visualize these designs. We describe how a standard-enabled workflow can be used to produce types of design information, including multiple repositories and software tools exchanging information using a variety of data standards. Recently, the ACS Synthetic Biology journal has recommended the use of SBOL in their publications. © 2017 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society.

Response of the bacterial community in oil-contaminated marine water to the addition of chemical and biological dispersants.

PubMed

Couto, Camila Rattes de Almeida; Jurelevicius, Diogo de Azevedo; Alvarez, Vanessa Marques; van Elsas, Jan Dirk; Seldin, Lucy

2016-12-15

The use of dispersants in different stages of the oil production chain and for the remediation of water and soil is a well established practice. However, the choice for a chemical or biological dispersant is still a controversial subject. Chemical surfactants that persist long in the environment may pose problems of toxicity themselves; therefore, biosurfactants are considered to constitute an environmentally friendly and effective alternative. Nevertheless, the putative effects of such agents on the microbiomes of oil-contaminated and uncontaminated marine environments have not been sufficiently evaluated. Here, we studied the effects of the surfactant Ultrasperse II ® and the surfactin (biosurfactant) produced by Bacillus sp. H2O-1 on the bacterial communities of marine water. Specifically, we used quantitative PCR and genetic fingerprint analyses to study the abundance and structure of the bacterial communities in marine water collected from two regions with contrasting climatic conditions. The addition of either chemical surfactant or biosurfactant influenced the structure and abundance of total and oil-degrading bacterial communities of oil-contaminated and uncontaminated marine waters. Remarkably, the bacterial communities responded similarly to the addition of oil and/or either the surfactant or the biosurfactant in both set of microcosms. After 30 days of incubation, the addition of surfactin enhanced the oil-degrading bacteria more than the chemical surfactant. However, no increase of hydrocarbon biodegradation values was observed, irrespective of the dispersant used. These data contribute to an increased understanding of the impact of novel dispersants on marine bacteriomes before commercial release into the environment. Copyright © 2016 Elsevier Ltd. All rights reserved.

Synthetic Biology Open Language (SBOL) Version 2.0.0.

PubMed

Bartley, Bryan; Beal, Jacob; Clancy, Kevin; Misirli, Goksel; Roehner, Nicholas; Oberortner, Ernst; Pocock, Matthew; Bissell, Michael; Madsen, Curtis; Nguyen, Tramy; Zhang, Zhen; Gennari, John H; Myers, Chris; Wipat, Anil; Sauro, Herbert

2015-09-04

Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. One method to ameliorate these problems would be to improve the exchange of information about designed systems between laboratories. The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, filling a need not satisfied by other pre-existing standards. This document details version 2.0 of SBOL, introducing a standardized format for the electronic exchange of information on the structural and functional aspects of biological designs. The standard has been designed to support the explicit and unambiguous description of biological designs by means of a well defined data model. The standard also includes rules and best practices on how to use this data model and populate it with relevant design details. The publication of this specification is intended to make these capabilities more widely accessible to potential developers and users in the synthetic biology community and beyond.

An information maximization model of eye movements

NASA Technical Reports Server (NTRS)

Renninger, Laura Walker; Coughlan, James; Verghese, Preeti; Malik, Jitendra

2005-01-01

We propose a sequential information maximization model as a general strategy for programming eye movements. The model reconstructs high-resolution visual information from a sequence of fixations, taking into account the fall-off in resolution from the fovea to the periphery. From this framework we get a simple rule for predicting fixation sequences: after each fixation, fixate next at the location that minimizes uncertainty (maximizes information) about the stimulus. By comparing our model performance to human eye movement data and to predictions from a saliency and random model, we demonstrate that our model is best at predicting fixation locations. Modeling additional biological constraints will improve the prediction of fixation sequences. Our results suggest that information maximization is a useful principle for programming eye movements.

Social inclusion enhances biological motion processing: A functional near-infrared spectroscopy study

PubMed Central

Bolling, Danielle Z.; Pelphrey, Kevin A.; Kaiser, Martha D.

2012-01-01

Humans are especially tuned to the movements of other people. Neural correlates of this social attunement have been proposed to lie in and around the right posterior superior temporal sulcus (STS) region, which robustly responds to biological motion in contrast to a variety of non-biological motions. This response persists even when no form information is provided, as in point-light displays (PLDs). The aim of the current study was to assess the ability of functional near-infrared spectroscopy (fNIRS) to reliably measure brain responses to PLDs of biological motion, and determine the sensitivity of these responses to interpersonal contextual factors. To establish reliability, we measured brain activation to biological motion with fNIRS and functional magnetic resonance imaging (fMRI) during two separate sessions in an identical group of 12 participants. To establish sensitivity, brain responses to biological motion measured with fNIRS were subjected to an additional social manipulation where participants were either socially included or excluded before viewing PLDs of biological motion. Results revealed comparable brain responses to biological motion using fMRI and fNIRS in the right supramarginal gyrus. Further, social inclusion increased brain responses to biological motion in right supramarginal gyrus and posterior STS. Thus, fNIRS can reliably measure brain responses to biological motion and can detect social experience-dependent modulations of these brain responses. PMID:22941501

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

News from the Biological Stain Commission.

PubMed

Lyon, H O; Kiernan, J A

2008-12-01

In the three earlier editions of News from the Biological Stain Commission (BSC), under the heading of "Regulatory affairs," the BSC's International Affairs Committee reported on the work of Technical Committee 212, Clinical Laboratory Testing and in Vitro Diagnostic Test Systems of the International Standards Organization (ISO/TC 212) and its working groups, WG 1, WG 2 and WG 3. In this issue of News from the BSC, H.O. Lyon provides information from the annual meeting of ISO/TC 212 that took place June 2-4, 2008 in Vancouver, British Columbia, Canada. In addition, under the heading of "Certification," J.A. Kiernan examines the certification procedure for thionine used by the BSC laboratory in Rochester, NY.

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)

Promoting a structural view of biology for varied audiences: an overview of RCSB PDB resources and experiences.

PubMed

Dutta, Shuchismita; Zardecki, Christine; Goodsell, David S; Berman, Helen M

2010-10-01

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) supports scientific research and education worldwide by providing an essential resource of information on biomolecular structures. In addition to serving as a deposition, data-processing and distribution center for PDB data, the RCSB PDB offers resources and online materials that different audiences can use to customize their structural biology instruction. These include resources for general audiences that present macromolecular structure in the context of a biological theme, method-based materials for researchers who take a more traditional approach to the presentation of structural science, and materials that mix theme-based and method-based approaches for educators and students. Through these efforts the RCSB PDB aims to enable optimal use of structural data by researchers, educators and students designing and understanding experiments in biology, chemistry and medicine, and by general users making informed decisions about their life and health.

Promoting a structural view of biology for varied audiences: an overview of RCSB PDB resources and experiences

PubMed Central

Dutta, Shuchismita; Zardecki, Christine; Goodsell, David S.; Berman, Helen M.

2010-01-01

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) supports scientific research and education worldwide by providing an essential resource of information on biomolecular structures. In addition to serving as a deposition, data-processing and distribution center for PDB data, the RCSB PDB offers resources and online materials that different audiences can use to customize their structural biology instruction. These include resources for general audiences that present macromolecular structure in the context of a biological theme, method-based materials for researchers who take a more traditional approach to the presentation of structural science, and materials that mix theme-based and method-based approaches for educators and students. Through these efforts the RCSB PDB aims to enable optimal use of structural data by researchers, educators and students designing and understanding experiments in biology, chemistry and medicine, and by general users making informed decisions about their life and health. PMID:20877496

Using argument notation to engineer biological simulations with increased confidence

PubMed Central

Alden, Kieran; Andrews, Paul S.; Polack, Fiona A. C.; Veiga-Fernandes, Henrique; Coles, Mark C.; Timmis, Jon

2015-01-01

The application of computational and mathematical modelling to explore the mechanics of biological systems is becoming prevalent. To significantly impact biological research, notably in developing novel therapeutics, it is critical that the model adequately represents the captured system. Confidence in adopting in silico approaches can be improved by applying a structured argumentation approach, alongside model development and results analysis. We propose an approach based on argumentation from safety-critical systems engineering, where a system is subjected to a stringent analysis of compliance against identified criteria. We show its use in examining the biological information upon which a model is based, identifying model strengths, highlighting areas requiring additional biological experimentation and providing documentation to support model publication. We demonstrate our use of structured argumentation in the development of a model of lymphoid tissue formation, specifically Peyer's Patches. The argumentation structure is captured using Artoo (www.york.ac.uk/ycil/software/artoo), our Web-based tool for constructing fitness-for-purpose arguments, using a notation based on the safety-critical goal structuring notation. We show how argumentation helps in making the design and structured analysis of a model transparent, capturing the reasoning behind the inclusion or exclusion of each biological feature and recording assumptions, as well as pointing to evidence supporting model-derived conclusions. PMID:25589574

Using argument notation to engineer biological simulations with increased confidence.

PubMed

Alden, Kieran; Andrews, Paul S; Polack, Fiona A C; Veiga-Fernandes, Henrique; Coles, Mark C; Timmis, Jon

2015-03-06

The application of computational and mathematical modelling to explore the mechanics of biological systems is becoming prevalent. To significantly impact biological research, notably in developing novel therapeutics, it is critical that the model adequately represents the captured system. Confidence in adopting in silico approaches can be improved by applying a structured argumentation approach, alongside model development and results analysis. We propose an approach based on argumentation from safety-critical systems engineering, where a system is subjected to a stringent analysis of compliance against identified criteria. We show its use in examining the biological information upon which a model is based, identifying model strengths, highlighting areas requiring additional biological experimentation and providing documentation to support model publication. We demonstrate our use of structured argumentation in the development of a model of lymphoid tissue formation, specifically Peyer's Patches. The argumentation structure is captured using Artoo (www.york.ac.uk/ycil/software/artoo), our Web-based tool for constructing fitness-for-purpose arguments, using a notation based on the safety-critical goal structuring notation. We show how argumentation helps in making the design and structured analysis of a model transparent, capturing the reasoning behind the inclusion or exclusion of each biological feature and recording assumptions, as well as pointing to evidence supporting model-derived conclusions.

Genetically-Based Biologic Technologies. Biology and Human Welfare.