Science.gov

Sample records for defense identification code

  1. Color code identification in coded structured light.

    PubMed

    Zhang, Xu; Li, Youfu; Zhu, Limin

    2012-08-01

    Color code is widely employed in coded structured light to reconstruct the three-dimensional shape of objects. Before determining the correspondence, a very important step is to identify the color code. Until now, the lack of an effective evaluation standard has hindered the progress in this unsupervised classification. In this paper, we propose a framework based on the benchmark to explore the new frontier. Two basic facets of the color code identification are discussed, including color feature selection and clustering algorithm design. First, we adopt analysis methods to evaluate the performance of different color features, and the order of these color features in the discriminating power is concluded after a large number of experiments. Second, in order to overcome the drawback of K-means, a decision-directed method is introduced to find the initial centroids. Quantitative comparisons affirm that our method is robust with high accuracy, and it can find or closely approach the global peak. PMID:22859022

  2. Secure surface identification codes

    NASA Astrophysics Data System (ADS)

    Beekhof, F.; Voloshynovskiy, S.; Koval, O.; Villan, R.; Pun, T.

    2008-02-01

    This paper introduces an identification framework for random microstructures of material surfaces. These microstructures represent a kind of unique fingerprints that can be used to track and trace an item as well as for anti-counterfeiting. We first consider the architecture for mobile phone-based item identification and then introduce a practical identification algorithm enabling fast searching in large databases. The proposed algorithm is based on reference list decoding. The link to digital communications and robust perceptual hashing is shown. We consider a practical construction of reference list decoding, which comprizes computational complexity, security, memory storage and performance requirements. The efficiency of the proposed algorithm is demonstrated on experimental data obtained from natural paper surfaces.

  3. 76 FR 38046 - Defense Federal Acquisition Regulation Supplement (DFARS); Assignment of Order Codes (DFARS Case...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-29

    ... Logistics Agency with Defense Procurement and Acquisition Policy, Program Development and Implementation, as... Regulation Supplement (DFARS); Assignment of Order Codes (DFARS Case 2011-D004) AGENCY: Defense Acquisition... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF...

  4. 49 CFR 178.502 - Identification codes for packagings.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 2 2010-10-01 2010-10-01 false Identification codes for packagings. 178.502... FOR PACKAGINGS Non-bulk Performance-Oriented Packaging Standards § 178.502 Identification codes for packagings. (a) Identification codes for designating kinds of packagings consist of the following: (1)...

  5. 49 CFR 178.905 - Large Packaging identification codes.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 49 Transportation 3 2011-10-01 2011-10-01 false Large Packaging identification codes. 178.905... PACKAGINGS Large Packagings Standards § 178.905 Large Packaging identification codes. Large packaging code... letter(s) specified in paragraph (b) of this section. (a) Large packaging code number designations are...

  6. 49 CFR 178.905 - Large Packaging identification codes.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 49 Transportation 3 2012-10-01 2012-10-01 false Large Packaging identification codes. 178.905... PACKAGINGS Large Packagings Standards § 178.905 Large Packaging identification codes. Large packaging code... letter(s) specified in paragraph (b) of this section. (a) Large packaging code number designations are...

  7. 49 CFR 178.905 - Large Packaging identification codes.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 49 Transportation 3 2013-10-01 2013-10-01 false Large Packaging identification codes. 178.905... PACKAGINGS Large Packagings Standards § 178.905 Large Packaging identification codes. Large packaging code... letter(s) specified in paragraph (b) of this section. (a) Large packaging code number designations are...

  8. 49 CFR 178.905 - Large Packaging identification codes.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 49 Transportation 3 2014-10-01 2014-10-01 false Large Packaging identification codes. 178.905... PACKAGINGS Large Packagings Standards § 178.905 Large Packaging identification codes. Large packaging code... letter(s) specified in paragraph (b) of this section. (a) Large packaging code number designations are...

  9. 49 CFR 178.905 - Large Packaging identification codes.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 2 2010-10-01 2010-10-01 false Large Packaging identification codes. 178.905... FOR PACKAGINGS Large Packagings Standards § 178.905 Large Packaging identification codes. Large packaging code designations consist of: two numerals specified in paragraph (a) of this section; followed...

  10. 49 CFR 178.1005 - Flexible Bulk Container identification code.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 49 Transportation 3 2014-10-01 2014-10-01 false Flexible Bulk Container identification code. 178... FOR PACKAGINGS Flexible Bulk Container Standards § 178.1005 Flexible Bulk Container identification code. The Flexible Bulk Container code designation is BK3....

  11. 49 CFR 178.1005 - Flexible Bulk Container identification code.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 49 Transportation 3 2013-10-01 2013-10-01 false Flexible Bulk Container identification code. 178... FOR PACKAGINGS Flexible Bulk Container Standards § 178.1005 Flexible Bulk Container identification code. The Flexible Bulk Container code designation is BK3....

  12. 33 CFR 181.31 - Manufacturer identification code assignment.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... types and sizes of boats that will be imported. If a nation has a hull identification number system... 33 Navigation and Navigable Waters 2 2012-07-01 2012-07-01 false Manufacturer identification code... SECURITY (CONTINUED) BOATING SAFETY MANUFACTURER REQUIREMENTS Identification of Boats § 181.31...

  13. 33 CFR 181.31 - Manufacturer identification code assignment.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... be imported. If a nation has a hull identification number system which has been accepted by the U.S... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false Manufacturer identification code... SECURITY (CONTINUED) BOATING SAFETY MANUFACTURER REQUIREMENTS Identification of Boats § 181.31...

  14. 33 CFR 181.31 - Manufacturer identification code assignment.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... be imported. If a nation has a hull identification number system which has been accepted by the U.S... 33 Navigation and Navigable Waters 2 2011-07-01 2011-07-01 false Manufacturer identification code... SECURITY (CONTINUED) BOATING SAFETY MANUFACTURER REQUIREMENTS Identification of Boats § 181.31...

  15. 76 FR 9714 - Defense Federal Acquisition Regulation Supplement; Passive Radio Frequency Identification (DFARS...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-02-22

    ... Regulation Supplement; Passive Radio Frequency Identification (DFARS Case 2010-D014) AGENCY: Defense... to amend the Defense Federal Acquisition Regulation Supplement (DFARS) to update requirements..., Chapter 203, for marking of 463L System pallets. Passive RFID tag means a tag that reflects energy...

  16. Improving the Use of Self-Generated Identification Codes

    ERIC Educational Resources Information Center

    Schnell, Rainer; Bachteler, Tobias; Reiher, Jorg

    2010-01-01

    In panel studies on sensitive topics, respondent-generated identification codes are often used to link records across surveys. However, usually a substantial number of cases are lost due to the codes. These losses may cause biased estimates. Using more components and linking the codes by the Levenshtein string distance function will reduce the…

  17. Identification of a Maize Locus that Modulates the Hypersensitive Defense Response, Using Mutant-Assisted Gene Identification and Characterization (MAGIC)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The hypersensitive response (HR) is the most visible and arguably the most important defense response in plants, although the details of how it is controlled and executed remain patchy. In this paper a novel genetic technique called MAGIC (Mutant-Assisted Gene Identification and Characterization) i...

  18. Identification coding schemes for modulated reflectance systems

    DOEpatents

    Coates, Don M.; Briles, Scott D.; Neagley, Daniel L.; Platts, David; Clark, David D.

    2006-08-22

    An identifying coding apparatus employing modulated reflectance technology involving a base station emitting a RF signal, with a tag, located remotely from the base station, and containing at least one antenna and predetermined other passive circuit components, receiving the RF signal and reflecting back to the base station a modulated signal indicative of characteristics related to the tag.

  19. 41 CFR 102-34.95 - What motor vehicle identification must the Department of Defense (DOD) display on motor vehicles...

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 41 Public Contracts and Property Management 3 2012-01-01 2012-01-01 false What motor vehicle identification must the Department of Defense (DOD) display on motor vehicles it owns or leases commercially? 102... identification must the Department of Defense (DOD) display on motor vehicles it owns or leases...

  20. Bar code technology improves positive patient identification and transfusion safety.

    PubMed

    Sandler, S G; Langeberg, A; Dohnalek, L

    2005-01-01

    As a result of human error, an estimated 1 in 12,000 blood transfusions is given to the wrong patient. The cause of nearly all of these errors is failure of hospital personnel to identify positively intended transfusion recipients, their blood samples for cross-matching, or their correct blood components. We describe our experience using a point-of-care bar code transfusion safety system that links patients' bar-coded wristbands, with bar-coded labels on blood sample tubes, blood component bags, and nurses' identification badges. The result was 100 % accuracy of matching patients, their blood samples, and components for transfusions. For verifying information before starting blood transfusions, nurses preferred bar code "double checks" to conventional visual "double checks" by a second nurse. Methods are needed to reinforce nurses' proficiency with technological approaches to transfusion safety, such as software-driven bar code scanning, in situations where transfusions are administered infrequently. PMID:16050151

  1. Adaptive error correction codes for face identification

    NASA Astrophysics Data System (ADS)

    Hussein, Wafaa R.; Sellahewa, Harin; Jassim, Sabah A.

    2012-06-01

    Face recognition in uncontrolled environments is greatly affected by fuzziness of face feature vectors as a result of extreme variation in recording conditions (e.g. illumination, poses or expressions) in different sessions. Many techniques have been developed to deal with these variations, resulting in improved performances. This paper aims to model template fuzziness as errors and investigate the use of error detection/correction techniques for face recognition in uncontrolled environments. Error correction codes (ECC) have recently been used for biometric key generation but not on biometric templates. We have investigated error patterns in binary face feature vectors extracted from different image windows of differing sizes and for different recording conditions. By estimating statistical parameters for the intra-class and inter-class distributions of Hamming distances in each window, we encode with appropriate ECC's. The proposed approached is tested for binarised wavelet templates using two face databases: Extended Yale-B and Yale. We shall demonstrate that using different combinations of BCH-based ECC's for different blocks and different recording conditions leads to in different accuracy rates, and that using ECC's results in significantly improved recognition results.

  2. Identification of Drosophila Mutants Affecting Defense to an Entomopathogenic Fungus

    PubMed Central

    Lu, Hsiao-Ling; Wang, Jonathan B.; Brown, Markus A.; Euerle, Christopher; St. Leger, Raymond J.

    2015-01-01

    Fungi cause the majority of insect disease. However, to date attempts to model host–fungal interactions with Drosophila have focused on opportunistic human pathogens. Here, we performed a screen of 2,613 mutant Drosophila lines to identify host genes affecting susceptibility to the natural insect pathogen Metarhizium anisopliae (Ma549). Overall, 241 (9.22%) mutant lines had altered resistance to Ma549. Life spans ranged from 3.0 to 6.2 days, with females being more susceptible than males in all lines. Speed of kill correlated with within-host growth and onset of sporulation, but total spore production is decoupled from host genotypes. Results showed that mutations affected the ability of Drosophila to restrain rather than tolerate infections and suggested trade-offs between antifungal and antibacterial genes affecting cuticle and gut structural barriers. Approximately, 13% of mutations where in genes previously associated with host pathogen interactions. These encoded fast-acting immune responses including coagulation, phagocytosis, encapsulation and melanization but not the slow-response induction of anti-fungal peptides. The non-immune genes impact a wide variety of biological functions, including behavioral traits. Many have human orthologs already implicated in human disorders; while others were mutations in protein and non-protein coding genes for which disease resistance was the first biological annotation. PMID:26202798

  3. Predictive Fallout Composition Modeling: Improvements and Applications of the Defense Land Fallout Interpretive Code

    SciTech Connect

    Hooper, David A; Jodoin, Vincent J; Lee, Ronald W; Monterial, Mateusz

    2012-01-01

    This paper outlines several improvements to the Particle Activity Module of the Defense Land Fallout Interpretive Code (DELFIC). The modeling of each phase of the fallout process is discussed within DELFIC to demonstrate the capabilities and limitations with the code for modeling and simulation. Expansion of the DELFIC isotopic library to include actinides and light elements is shown. Several key features of the new library are demonstrated, including compliance with ENDF/B-VII standards, augmentation of hardwired activated soil and actinide decay calculations with exact Bateman calculations, and full physical and chemical fractionation of all material inventories. Improvements to the radionuclide source term are demonstrated, including the ability to specify heterogeneous fission types and the ability to import source terms from irradiation calculations using the Oak Ridge Isotope Generation (ORIGEN) code. Additionally, the dose, kerma, and effective dose conversion factors are revised. Finally, the application of DELFIC for consequence management planning and forensic analysis is presented. For consequence management, DELFIC is shown to provide disaster recovery teams with simulations of real-time events, including the location, composition, time of arrival, activity rates, and dose rates of fallout, accounting for site-specific atmospheric effects. The results from DELFIC are also demonstrated for use by nuclear forensics teams to plan collection routes (including the determination of optimal collection locations), estimate dose rates to collectors, and anticipate the composition of material at collection sites. These capabilities give mission planners the ability to maximize their effectiveness in the field while minimizing risk to their collectors.

  4. 21 CFR 11.300 - Controls for identification codes/passwords.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 1 2013-04-01 2013-04-01 false Controls for identification codes/passwords. 11... identification codes/passwords. Persons who use electronic signatures based upon use of identification codes in combination with passwords shall employ controls to ensure their security and integrity. Such controls...

  5. 21 CFR 11.300 - Controls for identification codes/passwords.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 1 2014-04-01 2014-04-01 false Controls for identification codes/passwords. 11... identification codes/passwords. Persons who use electronic signatures based upon use of identification codes in combination with passwords shall employ controls to ensure their security and integrity. Such controls...

  6. 21 CFR 11.300 - Controls for identification codes/passwords.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 1 2012-04-01 2012-04-01 false Controls for identification codes/passwords. 11... identification codes/passwords. Persons who use electronic signatures based upon use of identification codes in combination with passwords shall employ controls to ensure their security and integrity. Such controls...

  7. 21 CFR 11.300 - Controls for identification codes/passwords.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 1 2011-04-01 2011-04-01 false Controls for identification codes/passwords. 11... identification codes/passwords. Persons who use electronic signatures based upon use of identification codes in combination with passwords shall employ controls to ensure their security and integrity. Such controls...

  8. 21 CFR 11.300 - Controls for identification codes/passwords.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 1 2010-04-01 2010-04-01 false Controls for identification codes/passwords. 11... identification codes/passwords. Persons who use electronic signatures based upon use of identification codes in combination with passwords shall employ controls to ensure their security and integrity. Such controls...

  9. Bar Coding MS(2) Spectra for Metabolite Identification.

    PubMed

    Spalding, Jonathan L; Cho, Kevin; Mahieu, Nathaniel G; Nikolskiy, Igor; Llufrio, Elizabeth M; Johnson, Stephen L; Patti, Gary J

    2016-03-01

    Metabolite identifications are most frequently achieved in untargeted metabolomics by matching precursor mass and full, high-resolution MS(2) spectra to metabolite databases and standards. Here we considered an alternative approach for establishing metabolite identifications that does not rely on full, high-resolution MS(2) spectra. First, we select mass-to-charge regions containing the most informative metabolite fragments and designate them as bins. We then translate each metabolite fragmentation pattern into a binary code by assigning 1's to bins containing fragments and 0's to bins without fragments. With 20 bins, this binary-code system is capable of distinguishing 96% of the compounds in the METLIN MS(2) library. A major advantage of the approach is that it extends untargeted metabolomics to low-resolution triple quadrupole (QqQ) instruments, which are typically less expensive and more robust than other types of mass spectrometers. We demonstrate a method of acquiring MS(2) data in which the third quadrupole of a QqQ instrument cycles over 20 wide isolation windows (coinciding with the location and width of our bins) for each precursor mass selected by the first quadrupole. Operating the QqQ instrument in this mode yields diagnostic bar codes for each precursor mass that can be matched to the bar codes of metabolite standards. Furthermore, our data suggest that using low-resolution bar codes enables QqQ instruments to make MS(2)-based identifications in untargeted metabolomics with a specificity and sensitivity that is competitive to high-resolution time-of-flight technologies. PMID:26837423

  10. CRITICA: coding region identification tool invoking comparative analysis

    NASA Technical Reports Server (NTRS)

    Badger, J. H.; Olsen, G. J.; Woese, C. R. (Principal Investigator)

    1999-01-01

    Gene recognition is essential to understanding existing and future DNA sequence data. CRITICA (Coding Region Identification Tool Invoking Comparative Analysis) is a suite of programs for identifying likely protein-coding sequences in DNA by combining comparative analysis of DNA sequences with more common noncomparative methods. In the comparative component of the analysis, regions of DNA are aligned with related sequences from the DNA databases; if the translation of the aligned sequences has greater amino acid identity than expected for the observed percentage nucleotide identity, this is interpreted as evidence for coding. CRITICA also incorporates noncomparative information derived from the relative frequencies of hexanucleotides in coding frames versus other contexts (i.e., dicodon bias). The dicodon usage information is derived by iterative analysis of the data, such that CRITICA is not dependent on the existence or accuracy of coding sequence annotations in the databases. This independence makes the method particularly well suited for the analysis of novel genomes. CRITICA was tested by analyzing the available Salmonella typhimurium DNA sequences. Its predictions were compared with the DNA sequence annotations and with the predictions of GenMark. CRITICA proved to be more accurate than GenMark, and moreover, many of its predictions that would seem to be errors instead reflect problems in the sequence databases. The source code of CRITICA is freely available by anonymous FTP (rdp.life.uiuc.edu in/pub/critica) and on the World Wide Web (http:/(/)rdpwww.life.uiuc.edu).

  11. Identification of protein coding regions in RNA transcripts

    PubMed Central

    Tang, Shiyuyun; Lomsadze, Alexandre; Borodovsky, Mark

    2015-01-01

    Massive parallel sequencing of RNA transcripts by next-generation technology (RNA-Seq) generates critically important data for eukaryotic gene discovery. Gene finding in transcripts can be done by statistical (alignment-free) as well as by alignment-based methods. We describe a new tool, GeneMarkS-T, for ab initio identification of protein-coding regions in RNA transcripts. The algorithm parameters are estimated by unsupervised training which makes unnecessary manually curated preparation of training sets. We demonstrate that (i) the unsupervised training is robust with respect to the presence of transcripts assembly errors and (ii) the accuracy of GeneMarkS-T in identifying protein-coding regions and, particularly, in predicting translation initiation sites in modelled as well as in assembled transcripts compares favourably to other existing methods. PMID:25870408

  12. Identification of a Maize Locus That Modulates the Hypersensitive Defense Response, Using Mutant-Assisted Gene Identification and Characterization

    PubMed Central

    Chintamanani, Satya; Hulbert, Scot H.; Johal, Gurmukh S.; Balint-Kurti, Peter J.

    2010-01-01

    Potentially useful naturally occurring genetic variation is often difficult to identify as the effects of individual genes are subtle and difficult to observe. In this study, a novel genetic technique called Mutant-Assisted Gene Identification and Characterization is used to identify naturally occurring loci modulating the hypersensitive defense response (HR) in maize. Mutant-Assisted Gene Identification and Characterization facilitates the identification of naturally occurring alleles underlying phenotypic variation from diverse germplasm, using a mutant phenotype as a “reporter.” In this study the reporter phenotype was caused by a partially dominant autoactive disease resistance gene, Rp1-D21, which caused HR lesions to form spontaneously all over the plant. Here it is demonstrated that the Rp1-D21 phenotype is profoundly affected by genetic background. By crossing the Rp1-D21 gene into the IBM mapping population, it was possible to map and identify Hrml1 on chromosome 10, a locus responsible for modulating the HR phenotype conferred by Rp1-D21. Other loci with smaller effects were identified on chromosomes 1 and 9. These results demonstrate that Mutant-Assisted Gene Identification and Characterization is a viable approach for identifying naturally occurring useful genetic variation. PMID:20176981

  13. Amino acids and our genetic code: a highly adaptive and interacting defense system.

    PubMed

    Verheesen, R H; Schweitzer, C M

    2012-04-01

    Since the discovery of the genetic code, Mendel's heredity theory and Darwin's evolution theory, science believes that adaptations to the environment are processes in which the adaptation of the genes is a matter of probability, in which finally the specie will survive which is evolved by chance. We hypothesize that evolution and the adaptation of the genes is a well-organized fully adaptive system in which there is no rigidity of the genes. The dividing of the genes will take place in line with the environment to be expected, sensed through the mother. The encoding triplets can encode for more than one amino acid depending on the availability of the amino acids and the needed micronutrients. Those nutrients can cause disease but also prevent diseases, even cancer and auto immunity. In fact we hypothesize that auto immunity is an effective process of the organism to clear suboptimal proteins, formed due to amino acid and micronutrient deficiencies. Only when deficiencies sustain, disease will develop, otherwise the autoantibodies will function as all antibodies function, in a protective way. Furthermore, we hypothesize that essential amino acids are less important than nonessential amino acid (NEA). Species developed the ability to produce the nonessential amino acids themselves because they were not provided by food sufficiently. In contrast essential amino acids are widely available, without any evolutionary pressure. Since we can only produce small amounts of NEA and the availability in food can be reasoned to be too low they are still our main concern in amino acid availability. In conclusion, we hypothesize that increasing health will only be possible by improving our natural environment and living circumstances, not by changing the genes, since they are our last line of defense in surviving our environmental changes. PMID:22289341

  14. Proposing national identification number on dental prostheses as universal personal identification code - A revolution in forensic odontology

    PubMed Central

    Baad, Rajendra K.; Belgaumi, Uzma; Vibhute, Nupura; Kadashetti, Vidya; Chandrappa, Pramod Redder; Gugwad, Sushma

    2015-01-01

    The proper identification of a decedent is not only important for humanitarian and emotional reasons, but also for legal and administrative purposes. During the reconstructive identification process, all necessary information is gathered from the unknown body of the victim and hence that an objective reconstructed profile can be established. Denture marking systems are being used in various situations, and a number of direct and indirect methods are reported. We propose that national identification numbers be incorporated in all removable and fixed prostheses, so as to adopt a single and definitive universal personal identification code with the aim of achieving a uniform, standardized, easy, and fast identification method worldwide for forensic identification. PMID:26005294

  15. Proposing national identification number on dental prostheses as universal personal identification code - A revolution in forensic odontology.

    PubMed

    Baad, Rajendra K; Belgaumi, Uzma; Vibhute, Nupura; Kadashetti, Vidya; Chandrappa, Pramod Redder; Gugwad, Sushma

    2015-01-01

    The proper identification of a decedent is not only important for humanitarian and emotional reasons, but also for legal and administrative purposes. During the reconstructive identification process, all necessary information is gathered from the unknown body of the victim and hence that an objective reconstructed profile can be established. Denture marking systems are being used in various situations, and a number of direct and indirect methods are reported. We propose that national identification numbers be incorporated in all removable and fixed prostheses, so as to adopt a single and definitive universal personal identification code with the aim of achieving a uniform, standardized, easy, and fast identification method worldwide for forensic identification. PMID:26005294

  16. Identification of putative TAL effector targets of the citrus canker pathogens shows functional convergence underlying disease development and defense response

    PubMed Central

    2014-01-01

    Background Transcriptional activator-like (TAL) effectors, formerly known as the AvrBs3/PthA protein family, are DNA-binding effectors broadly found in Xanthomonas spp. that transactivate host genes upon injection via the bacterial type three-secretion system. Biologically relevant targets of TAL effectors, i.e. host genes whose induction is vital to establish a compatible interaction, have been reported for xanthomonads that colonize rice and pepper; however, citrus genes modulated by the TAL effectors PthA“s” and PthC“s” of the citrus canker bacteria Xanthomonas citri (Xc) and Xanthomonas aurantifolii pathotype C (XaC), respectively, are poorly characterized. Of particular interest, XaC causes canker disease in its host lemon (Citrus aurantifolia), but triggers a defense response in sweet orange. Results Based on, 1) the TAL effector-DNA binding code, 2) gene expression data of Xc and XaC-infiltrated sweet orange leaves, and 3) citrus hypocotyls transformed with PthA2, PthA4 or PthC1, we have identified a collection of Citrus sinensis genes potentially targeted by Xc and XaC TAL effectors. Our results suggest that similar with other strains of Xanthomonas TAL effectors, PthA2 and PthA4, and PthC1 to some extent, functionally converge. In particular, towards induction of genes involved in the auxin and gibberellin synthesis and response, cell division, and defense response. We also present evidence indicating that the TAL effectors act as transcriptional repressors and that the best scoring predicted DNA targets of PthA“s” and PthC“s” in citrus promoters predominantly overlap with or localize near to TATA boxes of core promoters, supporting the idea that TAL effectors interact with the host basal transcriptional machinery to recruit the RNA pol II and start transcription. Conclusions The identification of PthA“s” and PthC“s” targets, such as the LOB (LATERAL ORGAN BOUNDARY) and CCNBS genes that we report here, is key for the understanding

  17. We Are Not Numbers: The Use of Identification Codes in Online Learning

    ERIC Educational Resources Information Center

    Francis-Poscente, Krista; Moisey, Susan Darlene

    2012-01-01

    This paper discusses students' experiences with the use of identification codes in a graduate course delivered asynchronously via the Internet. While teaching an introductory masters level graduate course in distance learning, the authors discovered that the learning management system, Moodle, was programmed to display identification codes rather…

  18. 22 CFR 228.03 - Identification of principal geographic code numbers.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... codes: (a) Code 000—The United States: The United States of America, any State(s) of the United States... 22 Foreign Relations 1 2011-04-01 2011-04-01 false Identification of principal geographic code..., ORIGIN AND NATIONALITY FOR COMMODITIES AND SERVICES FINANCED BY USAID Definitions and Scope of This...

  19. PROBCON-HDW: A probability and consequence system of codes for long-term analysis of Hanford defense wastes

    SciTech Connect

    Piepho, M.G.; Nguyen, T.H.

    1988-12-01

    The PROBCON-HDW (PROBability and CONsequence analysis for Hanford defense waste) computer code system calculates the long-term cumulative releases of radionuclides from the Hanford defense wastes (HDW) to the accessible environment and compares the releases to environmental release limits as defined in 40 CFR 191. PROBCON-HDW takes into account the variability of input parameter values used in models to calculate HDW release and transport in the vadose zone to the accessible environment (taken here as groundwater). A human intrusion scenario, which consists of drilling boreholes into the waste beneath the waste sites and bringing waste to the surface, is also included in PROBCON-HDW. PROBCON-HDW also includes the capability to combine the cumulative releases according to various long-term (10,000 year) scenarios into a composite risk curve or complementary cumulative distribution function (CCDF). The system structure of the PROBCON-HDW codes, the mathematical models in PROBCON-HDW, the input files, the input formats, the command files, and the graphical output results of several HDW release scenarios are described in the report. 3 refs., 7 figs., 9 tabs.

  20. Identification codes for organizations listed in computerized data systems of the U.S. Geological Survey

    USGS Publications Warehouse

    Edwards, Melvin D.; Drilleau, Margery O.

    1976-01-01

    This report contains codes for the identification of public and private organizations listed in computerized data systems. These codes are used by the U.S. Geological Survey 's National Water Data Exchange (NAWDEX), National Water Data Storage and Retrieval System (WATSTORE), and National Cartographic Information Center (NCIC). The format structure of the codes is discussed and instructions are given for requesting new codes. (Woodard-USGS)

  1. Identification codes for organizations listed in computerized data systems of the U.S. Geological Survey

    USGS Publications Warehouse

    Edwards, Melvin D.; Josefson, Beverly M.

    1982-01-01

    This report contains codes for the identification of public and private organizations listed in computerized data systems. These codes are used by the U.S. Geological Survey 's National Water Data Exchange (NAWDEX), National Water Data Storage and Retrieval System (WATSTORE), National Cartographic Information Center (NCIC), Office of Water Data Coordination (OWDC). The format structure of the codes is discussed and instructions are given for requesting new codes. (USGS)

  2. Identification codes for organizations listed in computerized data systems of the U.S. Geological Survey

    USGS Publications Warehouse

    Edwards, Melvin D.; Myers, Beverly M.

    1979-01-01

    This report contains codes for the identification of public and private organizations listed in computerized data systems. These codes are used by the U.S. Geological Survey 's National Water Data Exchange (NAWDEX), National Water Data Storage and Retrieval System (WATSTORE), National Cartographic Information Center (NCIC), and Office of Water Data Coordination (OWDC). The format structure of the codes is discussed and instructions are given for requesting new codes. (Woodard-USGS)

  3. Identification codes for organizations listed in computerized data systems of the U.S. Geological Survey

    USGS Publications Warehouse

    Edwards, Melvin D.; Drilleau, Margery O.

    1978-01-01

    This report contains codes for the identification of public and private organizations listed in computerized data systems. These codes are used by the U.S. Geological Survey 's National Water Data Exchange (NAWDEX), National Water Data Storage and Retrieval System (WATSTORE), National Cartographic Information Center (NCIC), and Office of Water Data Coordination (OWDC). The format structure of the codes is discussed and instructions are given for requesting new codes. (Woodard-USGS)

  4. Identification codes for organizations listed in computerized data systems of the U.S. Geological Survey

    USGS Publications Warehouse

    Edwards, Melvin D.; Myers, Beverly M.

    1981-01-01

    This report contains codes for the identification of public and private organizations listed in computerized data systems. These codes are used by the U.S. Geological Survey 's National Water Data Exchange (NAWDEX), National Water Data Storage and Retrieval System (WATSTORE), National Cartographic Information Center (NCIC), and Office of Water Data Coordination (OWDC). The format structure of the codes is discussed and instructions are given for requesting new codes. (USGS)

  5. The Use of Self-Generated Identification Codes in Longitudinal Research

    ERIC Educational Resources Information Center

    Yurek, Leo A.; Vasey, Joseph; Sullivan Havens, Donna

    2008-01-01

    Longitudinal research designs involve data collection at multiple time points to measure change over time. Therefore, identification of the same respondents is essential at each time point so that data from the same respondents can be matched for comparison over time. Subject-generated identification codes permit an anonymous means to track…

  6. Identification of ICD Codes Suggestive of Child Maltreatment

    ERIC Educational Resources Information Center

    Schnitzer, Patricia G.; Slusher, Paula L.; Kruse, Robin L.; Tarleton, Molly M.

    2011-01-01

    Objective: In order to be reimbursed for the care they provide, hospitals in the United States are required to use a standard system to code all discharge diagnoses: the International Classification of Disease, 9th Revision, Clinical Modification (ICD-9). Although ICD-9 codes specific for child maltreatment exist, they do not identify all…

  7. Identification of Novel Defense Response Genes in Medicago truncatula for Improving Disease Resistance in Alfalfa

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Infection of plants by pathogens initiates a cascade of defense responses that halt or limit pathogen growth. However, the role of many of the genes induced by pathogens is unknown. Transcript profiling was used to identify genes associated with defense responses in the model legume Medicago truncat...

  8. Identification codes for organizations listed in computerized data systems of the U.S. Geological Survey

    USGS Publications Warehouse

    Blackwell, C.D.

    1988-01-01

    Codes for the unique identification of public and private organizations listed in computerized data systems are presented. These codes are used by the U.S. Geological Survey 's National Water Data Exchange (NAWDEX), National Water Data Storage and Retrieval System (WATSTORE), National Cartographic Information Center (NCIC), and Office of Water Data Coordination (OWDC). The format structure of the codes is discussed and instructions are given for requesting new books. (Author 's abstract)

  9. The effect of a redundant color code on an overlearned identification task

    NASA Technical Reports Server (NTRS)

    Obrien, Kevin

    1992-01-01

    The possibility of finding redundancy gains with overlearned tasks was examined using a paradigm varying familiarity with the stimulus set. Redundant coding in a multidimensional stimulus was demonstrated to result in increased identification accuracy and decreased latency of identification when compared to stimuli varying on only one dimension. The advantages attributable to redundant coding are referred to as redundancy gain and were found for a variety of stimulus dimension combinations, including the use of hue or color as one of the dimensions. Factors that have affected redundancy gain include the discriminability of the levels of one stimulus dimension and the level of stimulus-to-response association. The results demonstrated that response time is in part a function of familiarity, but no effect of redundant color coding was demonstrated. Implications of research on coding in identification tasks for display design are discussed.

  10. 48 CFR 204.7005 - Assignment of order codes.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... Identification Numbers 204.7005 Assignment of order codes. (a) The Defense Logistics Agency, Acquisition Policy...-1000 Air Force: SAF/AQCI, 1060 Air Force Pentagon, Washington, DC 20330-1060 Defense Logistics Agency: Defense Logistics Agency, Acquisition Policy Branch (J-3311), John J. Kingman Road, Fort Belvoir, VA...

  11. 48 CFR 204.7005 - Assignment of order codes.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 48 Federal Acquisition Regulations System 3 2014-10-01 2014-10-01 false Assignment of order codes. 204.7005 Section 204.7005 Federal Acquisition Regulations System DEFENSE ACQUISITION REGULATIONS SYSTEM, DEPARTMENT OF DEFENSE GENERAL ADMINISTRATIVE MATTERS Uniform Procurement Instrument Identification Numbers 204.7005 Assignment of order codes....

  12. Identification of transcriptional regulatory nodes in soybean defense networks using transient co-transactivation assays

    PubMed Central

    Wang, Yongli; Wang, Hui; Ma, Yujie; Du, Haiping; Yang, Qing; Yu, Deyue

    2015-01-01

    Plant responses to major environmental stressors, such as insect feeding, not only occur via the functions of defense genes but also involve a series of regulatory factors. Our previous transcriptome studies proposed that, in addition to two defense-related genes, GmVSPβ and GmN:IFR, a high proportion of transcription factors (TFs) participate in the incompatible soybean-common cutworm interaction networks. However, the regulatory mechanisms and effects of these TFs on those induced defense-related genes remain unknown. In the present work, we isolated and identified 12 genes encoding MYB, WRKY, NAC, bZIP, and DREB TFs from a common cutworm-induced cDNA library of a resistant soybean line. Sequence analysis of the promoters of three co-expressed genes, including GmVSPα, GmVSPβ, and GmN:IFR, revealed the enrichment of various TF-binding sites for defense and stress responses. To further identify the regulatory nodes composed of these TFs and defense gene promoters, we performed extensive transient co-transactivation assays to directly test the transcriptional activity of the 12 TFs binding at different levels to the three co-expressed gene promoters. The results showed that all 12 TFs were able to transactivate the GmVSPβ and GmN:IFR promoters. GmbZIP110 and GmMYB75 functioned as distinct regulators of GmVSPα/β and GmN:IFR expression, respectively, while GmWRKY39 acted as a common central regulator of GmVSPα/β and GmN:IFR expression. These corresponding TFs play crucial roles in coordinated plant defense regulation, which provides valuable information for understanding the molecular mechanisms involved in insect-induced transcriptional regulation in soybean. More importantly, the identified TFs and suitable promoters can be used to engineer insect-resistant plants in molecular breeding studies. PMID:26579162

  13. Computational identification of genetic subnetwork modules associated with maize defense response to Fusarium verticillioides

    PubMed Central

    2015-01-01

    Background Maize, a crop of global significance, is vulnerable to a variety of biotic stresses resulting in economic losses. Fusarium verticillioides (teleomorph Gibberella moniliformis) is one of the key fungal pathogens of maize, causing ear rots and stalk rots. To better understand the genetic mechanisms involved in maize defense as well as F. verticillioides virulence, a systematic investigation of the host-pathogen interaction is needed. The aim of this study was to computationally identify potential maize subnetwork modules associated with its defense response against F. verticillioides. Results We obtained time-course RNA-seq data from B73 maize inoculated with wild type F. verticillioides and a loss-of-virulence mutant, and subsequently established a computational pipeline for network-based comparative analysis. Specifically, we first analyzed the RNA-seq data by a cointegration-correlation-expression approach, where maize genes were jointly analyzed with known F. verticillioides virulence genes to find candidate maize genes likely associated with the defense mechanism. We predicted maize co-expression networks around the selected maize candidate genes based on partial correlation, and subsequently searched for subnetwork modules that were differentially activated when inoculated with two different fungal strains. Based on our analysis pipeline, we identified four potential maize defense subnetwork modules. Two were directly associated with maize defense response and were associated with significant GO terms such as GO:0009817 (defense response to fungus) and GO:0009620 (response to fungus). The other two predicted modules were indirectly involved in the defense response, where the most significant GO terms associated with these modules were GO:0046914 (transition metal ion binding) and GO:0046686 (response to cadmium ion). Conclusion Through our RNA-seq data analysis, we have shown that a network-based approach can enhance our understanding of the

  14. A simple and inexpensive bar-coding technique for denture identification.

    PubMed

    Nalawade, Sonali N; Lagdive, Sanjay B; Gangadhar, Sa; Bhandari, Aruna J

    2011-07-01

    A number of commercial methods for identifying dentures are available. They can be either invasive or noninvasive techniques. The less sophisticated procedures include simple engraving with bur, and more sophisticated procedures use labels or chips. Bar coding system is a way of transferring data to the computer and huge data can be stored as a record. Bar coding can be easily incorporated during acrylization of the denture and thus could be used in individual identification. PMID:22408329

  15. A simple and inexpensive bar-coding technique for denture identification

    PubMed Central

    Nalawade, Sonali N; Lagdive, Sanjay B; Gangadhar, SA; Bhandari, Aruna J

    2011-01-01

    A number of commercial methods for identifying dentures are available. They can be either invasive or noninvasive techniques. The less sophisticated procedures include simple engraving with bur, and more sophisticated procedures use labels or chips. Bar coding system is a way of transferring data to the computer and huge data can be stored as a record. Bar coding can be easily incorporated during acrylization of the denture and thus could be used in individual identification. PMID:22408329

  16. Identification of defense-related genes newly-associated with tomato flower abscission

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The current abscission model suggests the formation of a post-abscission trans-differentiation of a protective layer as the last step of the process. The present report expands the repertoire of genes activated in the tomato flower abscission zone (AZ), which are likely to be involved in defense res...

  17. 76 FR 14641 - Defense Federal Acquisition Regulation Supplement; Identification of Critical Safety Items (DFARS...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-17

    ... the ``Submit a Comment'' screen. Please include your name, company name (if any), and ``DFARS Case... This DFARS case was initiated at the request of the Defense Contract Management Agency so that when DoD... joint agency instructions, such as Management of Aviation Critical Safety Items (dated January 25,...

  18. Machine readable identification systems: An overview. [Bar code and other labeling methods

    SciTech Connect

    Smith, F.J.; Cantor, S.

    1987-09-01

    The application of automated identification of an item by the use of machine readable methods is improving the accuracy and speed of data capture. Bar codes, optical character recognition, magnetic strips, and magnetic-ink recognition are all current machine readable methods which are used for data collection. Bar code data collection is the most used technology for real time inventory control, tracking, and point of sale applications. Magnetic strip coding is used for highly compact data identification on ID cards and on tags. Optical character recognition is generally used today to capture documents for computer storage and recall. Magnetic-ink character recognition, though used widely in banking, has limited applications elsewhere. Bar code methods are currently experiencing a faster rate of growth than the other technologies. Emphasis of this paper is on bar coding because of its popularity. The fundamentals of bar coding are discussed and labeling and scanning techniques are presented. New, automatic data-collection techniques are being developed, utilizing microcircuits and compact-disk memory media. The greatly increased memory capacity of these systems will likely lead to identification in terms of definitive characteristics of the item.

  19. Identification and function of long non-coding RNA

    PubMed Central

    Ernst, Carl; Morton, Cynthia C.

    2013-01-01

    Long non-coding (lnc) RNAs are defined as non-protein coding RNAs distinct from housekeeping RNAs such as tRNAs, rRNAs, and snRNAs, and independent from small RNAs with specific molecular processing machinery such as micro- or piwi-RNAs. Recent studies of lncRNAs across different species have revealed a diverse population of RNA molecules of differing size and function. RNA sequencing studies suggest transcription throughout the genome, so there is a need to understand how sequence relates to functional and structural relationships amongst RNA molecules. Our synthesis of recent studies suggests that neither size, presence of a poly-A tail, splicing, direction of transcription, nor strand specificity are of importance to lncRNA function. Rather, relative genomic position in relation to a target is fundamentally important. In this review, we describe issues of key importance in functional assessment of lncRNA and how this might apply to lncRNAs important in neurodevelopment. PMID:24106460

  20. 47 CFR 3.22 - Number of accounting authority identification codes per applicant.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... AUTHORIZATION AND ADMINISTRATION OF ACCOUNTING AUTHORITIES IN MARITIME AND MARITIME MOBILE-SATELLITE RADIO SERVICES Application Procedures § 3.22 Number of accounting authority identification codes per applicant... assign U.S. AAICs for entities settling accounts of U.S. licensed vessels in the maritime mobile...

  1. 27 CFR 73.12 - What security controls must I use for identification codes and passwords?

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 2 2014-04-01 2014-04-01 false What security controls must I use for identification codes and passwords? 73.12 Section 73.12 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY (CONTINUED) PROCEDURES...

  2. 27 CFR 73.12 - What security controls must I use for identification codes and passwords?

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 2 2012-04-01 2011-04-01 true What security controls must I use for identification codes and passwords? 73.12 Section 73.12 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY (CONTINUED) PROCEDURES...

  3. 27 CFR 73.12 - What security controls must I use for identification codes and passwords?

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 2 2011-04-01 2011-04-01 false What security controls must I use for identification codes and passwords? 73.12 Section 73.12 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY (CONTINUED) PROCEDURES...

  4. 27 CFR 73.12 - What security controls must I use for identification codes and passwords?

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 2 2010-04-01 2010-04-01 false What security controls must I use for identification codes and passwords? 73.12 Section 73.12 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY (CONTINUED) PROCEDURES...

  5. 27 CFR 73.12 - What security controls must I use for identification codes and passwords?

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 2 2013-04-01 2013-04-01 false What security controls must I use for identification codes and passwords? 73.12 Section 73.12 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY (CONTINUED) PROCEDURES...

  6. One-time collision arbitration algorithm in radio-frequency identification based on the Manchester code

    NASA Astrophysics Data System (ADS)

    Liu, Chen-Chung; Chan, Yin-Tsung

    2011-02-01

    In radio-requency identification (RFID) systems, when multiple tags transmit data to a reader simultaneously, these data may collide and create unsuccessful identifications; hence, anticollision algorithms are needed to reduce collisions (collision cycles) to improve the tag identification speed. We propose a one-time collision arbitration algorithm to reduce both the number of collisions and the time consumption for tags' identification in RFID. The proposed algorithm uses Manchester coding to detect the locations of collided bits, uses the divide-and-conquer strategy to find the structure of colliding bits to generate 96-bit query strings as the 96-bit candidate query strings (96BCQSs), and uses query-tree anticollision schemes with 96BCQSs to identify tags. The performance analysis and experimental results show that the proposed algorithm has three advantages: (i) reducing the number of collisions to only one, so that the time complexity of tag identification is the simplest O(1), (ii) storing identified identification numbers (IDs) and the 96BCQSs in a register to save the used memory, and (iii) resulting in the number of bits transmitted by both the reader and tags being evidently less than the other algorithms in one-tag identification or in all tags identification.

  7. 76 FR 52138 - Defense Federal Acquisition Regulation Supplement; Identification of Critical Safety Items (DFARS...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-19

    ... a proposed rule at 76 FR 14641 on March 17, 2011, to add a contract clause that clearly identifies... published at 76 FR 14642 on March 17, 2011. Briefly, the combination of the actions of the design control... Regulation Supplement; Identification of Critical Safety Items (DFARS Case 2010-D022) AGENCY:...

  8. Department of Defense picture archiving and communication system acceptance testing: results and identification of problem components.

    PubMed

    Allison, Scott A; Sweet, Clifford F; Beall, Douglas P; Lewis, Thomas E; Monroe, Thomas

    2005-09-01

    The PACS implementation process is complicated requiring a tremendous amount of time, resources, and planning. The Department of Defense (DOD) has significant experience in developing and refining PACS acceptance testing (AT) protocols that assure contract compliance, clinical safety, and functionality. The DOD's AT experience under the initial Medical Diagnostic Imaging Support System contract led to the current Digital Imaging Network-Picture Archiving and Communications Systems (DIN-PACS) contract AT protocol. To identify the most common system and component deficiencies under the current DIN-PACS AT protocol, 14 tri-service sites were evaluated during 1998-2000. Sixteen system deficiency citations with 154 separate types of limitations were noted with problems involving the workstation, interfaces, and the Radiology Information System comprising more than 50% of the citations. Larger PACS deployments were associated with a higher number of deficiencies. The most commonly cited systems deficiencies were among the most expensive components of the PACS. PMID:15924273

  9. Evidence for a Nest Defense Pheromone in Bald-Faced Hornets, Dolichovespula Maculata, and Identification of Components.

    PubMed

    Jimenez, Sebastian Ibarra; Gries, Regine; Zhai, Huimin; Derstine, Nathan; McCann, Sean; Gries, Gerhard

    2016-05-01

    In eusocial insects like Bald-faced hornets, Dolichovespula maculata, nest defense is essential because nests contain a large number of protein-rich larvae and pupae, and thus are attractive to nest predators. Our objectives were to investigate whether D. maculata exhibit pheromone-mediated nest defense, and to identify and field test any pheromone components. We tested for pheromone-mediated nest defense behavior of D. maculata by placing a paired box-apparatus near the entrance of D. maculata nests, and treating both boxes with a solvent control, or one of the two boxes with a solvent control and the other with either venom sac extract, the putative source of nest defense pheromone, or synthetic pheromone. The sound impulses caused by nest mates attempting to sting or strike the boxes were recorded for 3 min. Compared to the double-control treatment, the number of strikes increased 27-fold when one of the two boxes was treated with venom sac extract, providing evidence for an alarm response. The box treated with venom sac extract also induced a significantly greater proportion of strikes than the corresponding control box, providing evidence for a target-oriented response. Analyzing venom sac extract by gas chromatographic-electroantennographic detection (GC-EAD) and GC-mass spectrometry resulted in the identification of seven candidate pheromone components: (a) dimethylaminoethanol, (b) dimethylamino ethyl acetate, (c) 2,5-dimethylpyrazine, (d) N-3-methylbutylacetamide, (e) 2-heptadecanone, (f) (Z)-8-heptadecen-2-one, and (g) (Z)-10-nonadecen-2-one. Testing in paired-box bioassays blends of the nitrogen-containing volatile components a-d, the less volatile ketones e-g, or both (a-g), indicated that a-d primarily have an alarm function. The ketones e-g, in contrast, induced target-oriented responses, possibly marking the box, or potential nest predators, for guided and concerted attacks, or enhancing the alarm-inducing effect of the volatile pheromone components

  10. Identification and Validation of Reference Genes for Transcript Normalization in Strawberry (Fragaria × ananassa) Defense Responses

    PubMed Central

    Amil-Ruiz, Francisco; Garrido-Gala, José; Blanco-Portales, Rosario; Folta, Kevin M.; Muñoz-Blanco, Juan; Caballero, José L.

    2013-01-01

    Strawberry (Fragaria spp) is an emerging model for the development of basic genomics and recombinant DNA studies among rosaceous crops. Functional genomic and molecular studies involve relative quantification of gene expression under experimental conditions of interest. Accuracy and reliability are dependent upon the choice of an optimal reference control transcript. There is no information available on validated endogenous reference genes for use in studies testing strawberry-pathogen interactions. Thirteen potential pre-selected strawberry reference genes were tested against different tissues, strawberry cultivars, biotic stresses, ripening and senescent conditions, and SA/JA treatments. Evaluation of reference candidate’s suitability was analyzed by five different methodologies, and information was merged to identify best reference transcripts. A combination of all five methods was used for selective classification of reference genes. The resulting superior reference genes, FaRIB413, FaACTIN, FaEF1α and FaGAPDH2 are strongly recommended as control genes for relative quantification of gene expression in strawberry. This report constitutes the first systematic study to identify and validate optimal reference genes for accurate normalization of gene expression in strawberry plant defense response studies. PMID:23940602

  11. Identification and characterization of the gene expression profiles for protein coding and non-coding RNAs of pancreatic ductal adenocarcinomas

    PubMed Central

    Gutiérrez, María Laura; Corchete, Luis; Teodosio, Cristina; Sarasquete, María Eugenia; Abad, María del Mar; Iglesias, Manuel; Esteban, Carmen

    2015-01-01

    Significant advances have been achieved in recent years in the identification of the genetic and the molecular alterations of pancreatic ductal adenocarcinoma (PDAC). Despite this, at present the understanding of the precise mechanisms involved in the development and malignant transformation of PDAC remain relatively limited. Here, we evaluated for the first time, the molecular heterogeneity of PDAC tumors, through simultaneous assessment of the gene expression profile (GEP) for both coding and non-coding genes of tumor samples from 27 consecutive PDAC patients. Overall, we identified a common GEP for all PDAC tumors, characterized by an increased expression of genes involved in PDAC cell proliferation, local invasion and metastatic capacity, together with a significant alteration of the early steps of the cellular immune response. At the same time, we confirm and extend on previous observations about the genetic complexity of PDAC tumors as revealed by the demonstration of two clearly distinct and unique GEPs (e.g. epithelial-like vs. mesenchymal-like) reflecting the alteration of different signaling pathways involved in the oncogenesis and progression of these tumors. Our results also highlight the potential role of the immune system microenvironment in these tumors, with potential diagnostic and therapeutic implications. PMID:26053098

  12. Analytical qualification of system identification (modal analysis) codes for use in the dynamic testing of nuclear power plant structures

    SciTech Connect

    Weaver, H.J.; Ng, D.; Lager, D.

    1980-01-02

    The analytical evaluation of two particular system identification codes used at Lawrence Livermore Laboratory is presented. Both codes are eigenparameter identification codes; however, one uses a time domain approach while the other a frequency domain approach. The evaluation was accomplished by analytically generating several time history signals in which the true modal parameters were known. These time histories ranged from widely spaced modes with spacing factors of 100 percent to closely spaced modes with spacing factors of 6 percent. These signals were then polluted with various levels of simulated measurement noise and the ability of our computer codes to extract the parameters from this noisy data was evaluated.

  13. Violations of Temporary Flight Restrictions and Air Defense Identification Zones: An Analysis of Airspace Violations and Pilot Report Data

    NASA Technical Reports Server (NTRS)

    Zuschlag, Michael

    2005-01-01

    This document provides the results from a study into the apparent factors and causes of violations of restricted airspace, particularly temporary flight restrictions (TFRs) and air defense identification zones (ADIZs). By illuminating the reasons for these violations, this study aims to take the first step towards reducing them. The study assesses the basic characteristics of restricted airspace violations as well as the probable causes and factors contributing to violations. Results from the study imply most violations occur where the restriction has been in place for a significant amount of time prior to the violation. Additionally, the study results imply most violations are not due to the pilot simply being unaware of the airspace at the time of violation. In most violations, pilots are aware of the presence of the restricted airspace but have incorrect information about it, namely, its exact boundaries or procedures for authorized penetration. These results imply that the best means to reduce violations of restricted airspace is to improve the effectiveness of providing pilots the details required to avoid the airspace.

  14. Wind turbine control systems: Dynamic model development using system identification and the fast structural dynamics code

    SciTech Connect

    Stuart, J.G.; Wright, A.D.; Butterfield, C.P.

    1996-10-01

    Mitigating the effects of damaging wind turbine loads and responses extends the lifetime of the turbine and, consequently, reduces the associated Cost of Energy (COE). Active control of aerodynamic devices is one option for achieving wind turbine load mitigation. Generally speaking, control system design and analysis requires a reasonable dynamic model of {open_quotes}plant,{close_quotes} (i.e., the system being controlled). This paper extends the wind turbine aileron control research, previously conducted at the National Wind Technology Center (NWTC), by presenting a more detailed development of the wind turbine dynamic model. In prior research, active aileron control designs were implemented in an existing wind turbine structural dynamics code, FAST (Fatigue, Aerodynamics, Structures, and Turbulence). In this paper, the FAST code is used, in conjunction with system identification, to generate a wind turbine dynamic model for use in active aileron control system design. The FAST code is described and an overview of the system identification technique is presented. An aileron control case study is used to demonstrate this modeling technique. The results of the case study are then used to propose ideas for generalizing this technique for creating dynamic models for other wind turbine control applications.

  15. Genome Wide Identification and Functional Prediction of Long Non-Coding RNAs Responsive to Sclerotinia sclerotiorum Infection in Brassica napus.

    PubMed

    Joshi, Raj Kumar; Megha, Swati; Basu, Urmila; Rahman, Muhammad H; Kav, Nat N V

    2016-01-01

    Sclerotinia stem rot caused by Sclerotinia sclerotiorum affects canola production worldwide. Emerging evidence suggests that long non-coding RNAs (lncRNAs) play important roles in the regulation of gene expression in plants, in response to both abiotic and biotic stress. So far, identification of lncRNAs has been limited to a few model plant species, and their roles in mediating responses to biotic stresses are yet to be characterized in Brassica napus. The present study reports the identification of novel lncRNAs responsive to S. sclerotiorum infection in B. napus at two time points after infection (24 hpi and 48 hpi) using a stranded RNA-Sequencing technique and a detection pipeline for lncRNAs. Of the total 3,181 lncRNA candidates, 2,821 lncRNAs were intergenic, 111 were natural antisense transcripts, 76 possessed exonic overlap with the reference coding transcripts while the remaining 173 represented novel lnc- isoforms. Forty one lncRNAs were identified as the precursors for microRNAs (miRNAs) including miR156, miR169 and miR394, with significant roles in mediating plant responses to fungal phytopathogens. A total of 931 differentially expressed lncRNAs were identified in response to S. sclerotiorum infection and the expression of 12 such lncRNAs was further validated using qRT-PCR. B. napus antisense lncRNA, TCONS_00000966, having 90% overlap with a plant defensin gene, showed significant induction at both infection stages, suggesting its involvement in the transcriptional regulation of defense responsive genes under S. sclerotiorum infection. Additionally, nine lncRNAs showed overlap with cis-regulatory regions of differentially expressed genes of B. napus. Quantitative RT-PCR verification of a set of S. sclerotiorum responsive sense/antisense transcript pairs revealed contrasting expression patterns, supporting the hypothesis that steric clashes of transcriptional machinery may lead to inactivation of sense promoter. Our findings highlight the potential

  16. Genome Wide Identification and Functional Prediction of Long Non-Coding RNAs Responsive to Sclerotinia sclerotiorum Infection in Brassica napus

    PubMed Central

    Joshi, Raj Kumar; Megha, Swati; Basu, Urmila; Rahman, Muhammad H.; Kav, Nat N. V.

    2016-01-01

    Sclerotinia stem rot caused by Sclerotinia sclerotiorum affects canola production worldwide. Emerging evidence suggests that long non-coding RNAs (lncRNAs) play important roles in the regulation of gene expression in plants, in response to both abiotic and biotic stress. So far, identification of lncRNAs has been limited to a few model plant species, and their roles in mediating responses to biotic stresses are yet to be characterized in Brassica napus. The present study reports the identification of novel lncRNAs responsive to S. sclerotiorum infection in B. napus at two time points after infection (24 hpi and 48 hpi) using a stranded RNA-Sequencing technique and a detection pipeline for lncRNAs. Of the total 3,181 lncRNA candidates, 2,821 lncRNAs were intergenic, 111 were natural antisense transcripts, 76 possessed exonic overlap with the reference coding transcripts while the remaining 173 represented novel lnc- isoforms. Forty one lncRNAs were identified as the precursors for microRNAs (miRNAs) including miR156, miR169 and miR394, with significant roles in mediating plant responses to fungal phytopathogens. A total of 931 differentially expressed lncRNAs were identified in response to S. sclerotiorum infection and the expression of 12 such lncRNAs was further validated using qRT-PCR. B. napus antisense lncRNA, TCONS_00000966, having 90% overlap with a plant defensin gene, showed significant induction at both infection stages, suggesting its involvement in the transcriptional regulation of defense responsive genes under S. sclerotiorum infection. Additionally, nine lncRNAs showed overlap with cis-regulatory regions of differentially expressed genes of B. napus. Quantitative RT-PCR verification of a set of S. sclerotiorum responsive sense/antisense transcript pairs revealed contrasting expression patterns, supporting the hypothesis that steric clashes of transcriptional machinery may lead to inactivation of sense promoter. Our findings highlight the potential

  17. Identification of several inducible defense-related genes in mechanically damaged soybean (glycine max l. merr) stems

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Multiple defense-related genes have been identified in soybean (Glycine max L. Merr), however, research has primarily focused on the plant leaves, and despite the numerous insects and pathogens that feed on soybean stem tissues, relatively little is known about the stem defense response. In the curr...

  18. Identification of long non-coding RNAs involved in neuronal development and intellectual disability.

    PubMed

    D'haene, Eva; Jacobs, Eva Z; Volders, Pieter-Jan; De Meyer, Tim; Menten, Björn; Vergult, Sarah

    2016-01-01

    Recently, exome sequencing led to the identification of causal mutations in 16-31% of patients with intellectual disability (ID), leaving the underlying cause for many patients unidentified. In this context, the noncoding part of the human genome remains largely unexplored. For many long non-coding RNAs (lncRNAs) a crucial role in neurodevelopment and hence the human brain is anticipated. Here we aimed at identifying lncRNAs associated with neuronal development and ID. Therefore, we applied an integrated genomics approach, harnessing several public epigenetic datasets. We found that the presence of neuron-specific H3K4me3 confers the highest specificity for genes involved in neurodevelopment and ID. Based on the presence of this feature and GWAS hits for CNS disorders, we identified 53 candidate lncRNA genes. Extensive expression profiling on human brain samples and other tissues, followed by Gene Set Enrichment Analysis indicates that at least 24 of these lncRNAs are indeed implicated in processes such as synaptic transmission, nervous system development and neurogenesis. The bidirectional or antisense overlapping orientation relative to multiple coding genes involved in neuronal processes supports these results. In conclusion, we identified several lncRNA genes putatively involved in neurodevelopment and CNS disorders, providing a resource for functional studies. PMID:27319317

  19. Identification of long non-coding RNAs involved in neuronal development and intellectual disability

    PubMed Central

    D’haene, Eva; Jacobs, Eva Z.; Volders, Pieter-Jan; De Meyer, Tim; Menten, Björn; Vergult, Sarah

    2016-01-01

    Recently, exome sequencing led to the identification of causal mutations in 16–31% of patients with intellectual disability (ID), leaving the underlying cause for many patients unidentified. In this context, the noncoding part of the human genome remains largely unexplored. For many long non-coding RNAs (lncRNAs) a crucial role in neurodevelopment and hence the human brain is anticipated. Here we aimed at identifying lncRNAs associated with neuronal development and ID. Therefore, we applied an integrated genomics approach, harnessing several public epigenetic datasets. We found that the presence of neuron-specific H3K4me3 confers the highest specificity for genes involved in neurodevelopment and ID. Based on the presence of this feature and GWAS hits for CNS disorders, we identified 53 candidate lncRNA genes. Extensive expression profiling on human brain samples and other tissues, followed by Gene Set Enrichment Analysis indicates that at least 24 of these lncRNAs are indeed implicated in processes such as synaptic transmission, nervous system development and neurogenesis. The bidirectional or antisense overlapping orientation relative to multiple coding genes involved in neuronal processes supports these results. In conclusion, we identified several lncRNA genes putatively involved in neurodevelopment and CNS disorders, providing a resource for functional studies. PMID:27319317

  20. [Evaluation of the GNF computer-coding system for the identification of non-fermentative Gram-negative bacilli].

    PubMed

    Tarng, C M; Chen, M M; Tsai, W C

    1983-05-01

    In order to evaluate the effectiveness of the GNF computer-coding system for the identification of glucose non-fermenting gram-negative bacilli, we employed 406 strains of bacteria including 367 clinical isolates and 39 standard strains for testing. These strains were inoculated into the following eleven conventional biochemical test media: Triple Sugar Iron Agar, Simmon's Citrate Agar, Christensen's Urea Agar, Sulfide-Indole-Motility Medium, Semisolid Voges-Proskauer Test Medium, Moeller's Ornithine Decarboxylase Test Medium, Pyocyanin Test Medium, Oxidation/Fermentation (O/F) Glucose, O/F Fructose, Nitrate Broth, Moeller's Arginine Dihydrolase Test Medium. The results of these tests plus those from the hanging drop motility test and the oxidase test were converted into bacterial code number and then checked with the GNF computer-coding system. It was found that the first preference of agreement was 75.6%, second 15.3%, third 5.9%, and fourth or more 3.2%. In regard to the speed of bacterial identification by using the GNF system and information from hemolysis pattern and flagella stain, it was indicated that 84.7% would be correctly identified within 36-48 hours after isolation. If more confirmational tests were employed, the accurate identification rate would reach to 98.7% after 4 days of isolation. In addition, the use of the GNF computer-coding system can standardize identification procedures, shorten the identification period, and save cost in terms of materials supply, inoculation time, media preparation and media-storing space. Therefore, we conclude that the GNF computer-coding system is an effective tool in the identification of the glucose non-fermenting gram-negative bacilli. PMID:6617315

  1. Codes for the identification of aquifer names and geologic units in the United States and the Caribbean outlying areas

    USGS Publications Warehouse

    U.S. Geological Survey

    1988-01-01

    This standard provides codes to be used for the identification of aquifer names and geologic units in the United States, the Caribbean and other outlying areas. Outlying areas include Puerto Rico, the Virgin Islands, American Samoa, the Midway Islands, Trust Territories of the Pacific Islands, and miscellaneous Pacific Islands. Each code identifies an aquifer or rock-stratigraphic unit and its age designation. The codes provide a standardized base for use by organizations in the storage, retrieval, and exchange of ground-water data; the indexing and inventory of ground-water data and information; the cataloging of ground-water data acquisition activities; and a variety of other applications.

  2. Codes for the identification of aquifer names and geologic units in the United States and the Caribbean outlying areas

    USGS Publications Warehouse

    U.S. Geological Survey

    1985-01-01

    This standard provides codes to be used for the identification of aquifer names and geologic units in the United States, the Caribbean and other outlying areas. Outlying areas include Puerto Rico, the Virgin Islands, American Samoa, the Midway Islands, Trust Territories of the Pacific Islands, and miscellaneous Pacific Islands. Each code identifies an aquifer or rock-stratigraphic unit and its age designation. The codes provide a standardized base for use by organizations in the storage, retrieval, and exchange of ground-water data; the indexing and inventory of ground-water data and information; the cataloging of ground-water data acquisition activities; and a variety of other applications.

  3. Partial kindling of the ventral hippocampus: identification of changes in limbic physiology which accompany changes in feline aggression and defense.

    PubMed

    Adamec, R E

    1991-03-01

    This study examined the interictal consequences of partial kindling of the ventral perforant path on attack and defensive behavior in the domestic cat. Partial kindling produced a lasting increase in defense response of cats to both rats and conspecific threat howls. In addition, there was a lasting suppression of approach-attack behaviors directed toward rats. The suppression of some components of approach-attack were shown to be independent of the increases in defensive response. The effects of partial kindling of the ventral perforant path on spread of seizure activity into the amygdala, and on the output of the amygdala to both the ventromedial hypothalamus (VMH) and bed nucleus of the stria terminalis (BNST) were also examined. In addition, the effects of repeated hippocampal seizures on recurrent inhibition in the trisynaptic circuit (areas CA1 and CA3) were investigated. Growth of seizure activity in the amygdala and VMH as partial kindling progressed was essential for behavioral change. In addition, interictal long-term potentiation of potentials evoked in the VMH and in the BNST by pulsed stimulation of the amygdala followed partial kindling or afterdischarge threshold determination in the ventral perforant path. A lasting interictal increase in inhibition in area CA3 and a lasting interictal failure of inhibition in area CA1 of the ventral hippocampus also followed partial kindling. These changes in limbic physiology were related to the behavioral changes produced by partial kindling. The analysis revealed the importance of the amygdalo-VMH pathway in increased defensive response to rats. The amygdalo-BNST pathway is not important in mediating defensive response to prey, but it is implicated in suppression of some types of predatory aggression. Finally, changes in neural inhibition in the ventral hippocampus in areas CA1 and CA3 are associated with changes in both defensiveness and predatory aggression. PMID:1648239

  4. Defense styles of pedophilic offenders.

    PubMed

    Drapeau, Martin; Beretta, Véronique; de Roten, Yves; Koerner, Annett; Despland, Jean-Nicolas

    2008-04-01

    This pilot study investigated the defense styles of pedophile sexual offenders. Interviews with 20 pedophiles and 20 controls were scored using the Defense Mechanisms Rating Scales. Results showed that pedophiles had a significantly lower overall defensive functioning score than the controls. Pedophiles used significantly fewer obsessional-level defenses but more major image-distorting and action-level defenses. Results also suggested differences in the prevalence of individual defenses where pedophiles used more dissociation, displacement, denial, autistic fantasy, splitting of object, projective identification, acting out, and passive aggressive behavior but less intellectualization and rationalization. PMID:17875603

  5. Genome defense against exogenous nucleic acids in eukaryotes by non-coding DNA occurs through CRISPR-like mechanisms in the cytosol and the bodyguard protection in the nucleus.

    PubMed

    Qiu, Guo-Hua

    2016-01-01

    In this review, the protective function of the abundant non-coding DNA in the eukaryotic genome is discussed from the perspective of genome defense against exogenous nucleic acids. Peripheral non-coding DNA has been proposed to act as a bodyguard that protects the genome and the central protein-coding sequences from ionizing radiation-induced DNA damage. In the proposed mechanism of protection, the radicals generated by water radiolysis in the cytosol and IR energy are absorbed, blocked and/or reduced by peripheral heterochromatin; then, the DNA damage sites in the heterochromatin are removed and expelled from the nucleus to the cytoplasm through nuclear pore complexes, most likely through the formation of extrachromosomal circular DNA. To strengthen this hypothesis, this review summarizes the experimental evidence supporting the protective function of non-coding DNA against exogenous nucleic acids. Based on these data, I hypothesize herein about the presence of an additional line of defense formed by small RNAs in the cytosol in addition to their bodyguard protection mechanism in the nucleus. Therefore, exogenous nucleic acids may be initially inactivated in the cytosol by small RNAs generated from non-coding DNA via mechanisms similar to the prokaryotic CRISPR-Cas system. Exogenous nucleic acids may enter the nucleus, where some are absorbed and/or blocked by heterochromatin and others integrate into chromosomes. The integrated fragments and the sites of DNA damage are removed by repetitive non-coding DNA elements in the heterochromatin and excluded from the nucleus. Therefore, the normal eukaryotic genome and the central protein-coding sequences are triply protected by non-coding DNA against invasion by exogenous nucleic acids. This review provides evidence supporting the protective role of non-coding DNA in genome defense. PMID:27036064

  6. Systematic Identification and Characterization of Long Non-Coding RNAs in the Silkworm, Bombyx mori

    PubMed Central

    Wu, Yuqian; Cheng, Tingcai; Liu, Chun; Liu, Duolian; Zhang, Quan; Long, Renwen; Zhao, Ping; Xia, Qingyou

    2016-01-01

    Long noncoding RNAs (lncRNAs) are emerging as important regulators in various biological processes. However, to date, no systematic characterization of lncRNAs has been reported in the silkworm Bombyx mori. In the present study, we generated eighteen RNA-seq datasets with relatively high depth. Using an in-house designed lncRNA identification pipeline, 11,810 lncRNAs were identified for 5,556 loci. Among these lncRNAs, 474 transcripts were intronic lncRNAs (ilncRNAs), 6,250 transcripts were intergenic lncRNAs (lincRNAs), and 5,086 were natural antisense lncRNAs (lncNATs). Compared with protein-coding mRNAs, silkworm lncRNAs are shorter in terms of full length but longer in terms of exon and intron length. In addition, lncRNAs exhibit a lower level of sequence conservation, more repeat sequences overlapped and higher tissue specificity than protein-coding mRNAs in the silkworm. We found that 69 lncRNA transcripts from 33 gene loci may function as miRNA precursors, and 104 lncRNA transcripts from 72 gene loci may act as competing endogenous RNAs (ceRNAs). In total, 49.47% of all gene loci (2,749/5,556) for which lncRNAs were identified showed sex-biased expression. Co-expression network analysis resulted in 19 modules, 12 of which revealed relatively high tissue specificity. The highlighted darkgoldenrod module was specifically associated with middle and posterior silk glands, and the hub lncRNAs within this module were co-expressed with proteins involved in translation, translocation, and secretory processes, suggesting that these hub lncRNAs may function as regulators of the biosynthesis, translocation, and secretion of silk proteins. This study presents the first comprehensive genome-wide analysis of silkworm lncRNAs and provides an invaluable resource for genetic, evolutionary, and genomic studies of B. mori. PMID:26771876

  7. Systematic Identification and Characterization of Long Non-Coding RNAs in the Silkworm, Bombyx mori.

    PubMed

    Wu, Yuqian; Cheng, Tingcai; Liu, Chun; Liu, Duolian; Zhang, Quan; Long, Renwen; Zhao, Ping; Xia, Qingyou

    2016-01-01

    Long noncoding RNAs (lncRNAs) are emerging as important regulators in various biological processes. However, to date, no systematic characterization of lncRNAs has been reported in the silkworm Bombyx mori. In the present study, we generated eighteen RNA-seq datasets with relatively high depth. Using an in-house designed lncRNA identification pipeline, 11,810 lncRNAs were identified for 5,556 loci. Among these lncRNAs, 474 transcripts were intronic lncRNAs (ilncRNAs), 6,250 transcripts were intergenic lncRNAs (lincRNAs), and 5,086 were natural antisense lncRNAs (lncNATs). Compared with protein-coding mRNAs, silkworm lncRNAs are shorter in terms of full length but longer in terms of exon and intron length. In addition, lncRNAs exhibit a lower level of sequence conservation, more repeat sequences overlapped and higher tissue specificity than protein-coding mRNAs in the silkworm. We found that 69 lncRNA transcripts from 33 gene loci may function as miRNA precursors, and 104 lncRNA transcripts from 72 gene loci may act as competing endogenous RNAs (ceRNAs). In total, 49.47% of all gene loci (2,749/5,556) for which lncRNAs were identified showed sex-biased expression. Co-expression network analysis resulted in 19 modules, 12 of which revealed relatively high tissue specificity. The highlighted darkgoldenrod module was specifically associated with middle and posterior silk glands, and the hub lncRNAs within this module were co-expressed with proteins involved in translation, translocation, and secretory processes, suggesting that these hub lncRNAs may function as regulators of the biosynthesis, translocation, and secretion of silk proteins. This study presents the first comprehensive genome-wide analysis of silkworm lncRNAs and provides an invaluable resource for genetic, evolutionary, and genomic studies of B. mori. PMID:26771876

  8. Five-way smoking status classification using text hot-spot identification and error-correcting output codes.

    PubMed

    Cohen, Aaron M

    2008-01-01

    We participated in the i2b2 smoking status classification challenge task. The purpose of this task was to evaluate the ability of systems to automatically identify patient smoking status from discharge summaries. Our submission included several techniques that we compared and studied, including hot-spot identification, zero-vector filtering, inverse class frequency weighting, error-correcting output codes, and post-processing rules. We evaluated our approaches using the same methods as the i2b2 task organizers, using micro- and macro-averaged F1 as the primary performance metric. Our best performing system achieved a micro-F1 of 0.9000 on the test collection, equivalent to the best performing system submitted to the i2b2 challenge. Hot-spot identification, zero-vector filtering, classifier weighting, and error correcting output coding contributed additively to increased performance, with hot-spot identification having by far the largest positive effect. High performance on automatic identification of patient smoking status from discharge summaries is achievable with the efficient and straightforward machine learning techniques studied here. PMID:17947623

  9. Identification of a key role for permeability glycoprotein in enhancing the cellular defense mechanisms of fertilized oocytes.

    PubMed

    Martin, Jacinta H; Nixon, Brett; Lord, Tessa; Bromfield, Elizabeth G; Aitken, R John

    2016-09-01

    Double strand breaks (DSBs) are highly damaging DNA lesions that can destabilize the genome and generate a suite of adverse physiological outcomes in the oocyte and early embryo. While it is therefore likely that these cells possess a sophisticated suite of protective mechanisms to ameliorate such damage, the precise nature of these defense systems are yet to be fully elucidated. This study characterizes the sensitivity of the oocyte to etoposide, a chemotherapeutic agent with the ability to elicit DSBs. We demonstrate significant developmental changes in etoposide vulnerability, with fertilization of the oocyte leading to an enhancement of its cellular defense machinery. Using a parthenogenic model we show that this response is mediated, at least in part, by permeability glycoprotein (PGP), an endogenous multidrug efflux transporter that is up-regulated, translocated to the oolemma and phosphorylated upon oocyte activation. Moreover, evidence from dye exclusion assays in the presence of a specific PGP pharmacological inhibitor (PSC833), illustrates that these events effectively increase oocyte efflux activity, thereby enhancing the ability of these cells to exclude genotoxicants capable of eliciting DSB formation. PMID:27397031

  10. Self-Reported Pleasantness Ratings and Examiner-Coded Defensiveness in Response to Touch in Children with ASD: Effects of Stimulus Material and Bodily Location

    ERIC Educational Resources Information Center

    Cascio, Carissa J.; Lorenzi, Jill; Baranek, Grace T.

    2016-01-01

    Tactile defensiveness, characterized by behavioral hyperresponsiveness and negative emotional responses to touch, is a common manifestation of aberrant sensory processing in autism spectrum disorders (ASD) and other developmental disabilities (DD). Variations in tactile defensiveness with the properties of the stimulus and the bodily site of…

  11. The identification and characterization of non-coding and coding RNAs and their modified nucleosides by mass spectrometry

    PubMed Central

    Gaston, Kirk W; Limbach, Patrick A

    2014-01-01

    The analysis of ribonucleic acids (RNA) by mass spectrometry has been a valuable analytical approach for more than 25 years. In fact, mass spectrometry has become a method of choice for the analysis of modified nucleosides from RNA isolated out of biological samples. This review summarizes recent progress that has been made in both nucleoside and oligonucleotide mass spectral analysis. Applications of mass spectrometry in the identification, characterization and quantification of modified nucleosides are discussed. At the oligonucleotide level, advances in modern mass spectrometry approaches combined with the standard RNA modification mapping protocol enable the characterization of RNAs of varying lengths ranging from low molecular weight short interfering RNAs (siRNAs) to the extremely large 23 S rRNAs. New variations and improvements to this protocol are reviewed, including top-down strategies, as these developments now enable qualitative and quantitative measurements of RNA modification patterns in a variety of biological systems. PMID:25616408

  12. Coupling scanning electronc microscopy with DNA bar coding: A novel approach for thrips identification

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The small size and cryptic nature of thrips pests help them acquire microhabitats of a plant and in the field, often making their monitoring and the identification process difficult. Accurate identification of such pests is a fundamental requirement in development of any effective quarantine and man...

  13. Molecular identification of three novel glutaredoxin genes that play important roles in antioxidant defense in Helicoverpa armigera.

    PubMed

    Zhang, Song-Dou; Shen, Zhong-Jian; Liu, Xiao-Ming; Li, Zhen; Zhang, Qing-Wen; Liu, Xiao-Xia

    2016-08-01

    Glutaredoxins (Grxs), also known as thioltransferases, play key roles in maintaining intracellular redox balance and protecting cells from oxidative damage in plants and mammals. We tested whether Grxs play important roles in antioxidant defense in insects using the moth, Helicoverpa armigera. We obtained the full-length cDNA sequences of three novel Grx genes, named HaGrx, HaGrx3, and HaGrx5. Sequence analysis indicated that HaGrx shared a high amino acid identity (58%-78%) and a CPYC motif of conserved redox activity with homologues from other selected insect species. In contrast, HaGrx3 and HaGrx5 both shared a CGF(S/G) motif, a conserved catalytic domain, with other orthologous genes. Quantitative real-time PCR results revealed that HaGrx, HaGrx3, and HaGrx5 exhibited temporally- and spatially-dependent patterns of expression. The mRNA expression of HaGrx, HaGrx3, and HaGrx5 was induced by various temperature stresses and H2O2 treatments. We further investigated the knockdown of HaGrx, HaGrx3, and HaGrx5 in H. armigera larvae and found that most of the selected antioxidant genes were up regulated. However, Tpx was down regulated, and further interpretation of the complementary functions of these antioxidant genes is still required. We also determined the effect of HaGrx, HaGrx3, and HaGrx5 knockdown on antioxidant enzymatic activity and metabolite content. The enzymatic activities of SOD, CAT, and POD, and the metabolite contents of hydrogen peroxide, ascorbate, protein carbonyl, and total GSH increased after RNAi mediated knockdown of HaGrx, HaGrx3, and HaGrx5. These results supported our hypothesis that HaGrx, HaGrx3, and HaGrx5 play important roles in antioxidant defense of Helicoverpa armigera and provided a theoretical basis for further in-depth study of physiological function in the insect glutaredoxin family genes. PMID:27339760

  14. Identification and analysis of mouse non-coding RNA using transcriptome data.

    PubMed

    Zhao, Yuhui; Liu, Wanfei; Zeng, Jingyao; Liu, Shoucheng; Tan, Xinyu; Aljohi, Hasanawad; Hu, Songnian

    2016-06-01

    Transcripts are expressed spatially and temporally and they are very complicated, precise and specific; however, most studies are focused on protein-coding related genes. Recently, massively parallel cDNA sequencing (RNA-seq) has emerged to be a new and promising tool for transcriptome research, and numbers of non-coding RNAs, especially lincRNAs, have been widely identified and well characterized as important regulators of diverse biological processes. In this study, we used ultra-deep RNA-seq data from 15 mouse tissues to study the diversity and dynamic of non-coding RNAs in mouse. Using our own criteria, we identified totally 16,249 non-coding genes (21,569 non-coding RNAs) in mouse. We annotated these non-coding RNAs by diverse properties and found non-coding RNAs are generally shorter, have fewer exons, express in lower level and are more strikingly tissue-specific compared with protein-coding genes. Moreover, these non-coding RNAs show significant enrichment with transcriptional initiation and elongation signals including histone modifications (H3K4me3, H3K27me3 and H3K36me3), RNAPII binding sites and CAGE tags. The gene set enrichment analysis (GSEA) result revealed several sets of lincRNAs associated with diverse biological processes such as immune effector process, muscle development and sexual reproduction. Taken together, this study provides a more comprehensive annotation of mouse non-coding RNAs and gives an opportunity for future functional and evolutionary study of mouse non-coding RNAs. PMID:26944582

  15. Identification of Defense Compounds in Barbarea vulgaris against the Herbivore Phyllotreta nemorum by an Ecometabolomic Approach1[W

    PubMed Central

    Kuzina, Vera; Ekstrøm, Claus Thorn; Andersen, Sven Bode; Nielsen, Jens Kvist; Olsen, Carl Erik; Bak, Søren

    2009-01-01

    Winter cress (Barbarea vulgaris) is resistant to a range of insect species. Some B. vulgaris genotypes are resistant, whereas others are susceptible, to herbivory by flea beetle larvae (Phyllotreta nemorum). Metabolites involved in resistance to herbivory by flea beetles were identified using an ecometabolomic approach. An F2 population representing the whole range from full susceptibility to full resistance to flea beetle larvae was generated by a cross between a susceptible and a resistant B. vulgaris plant. This F2 offspring was evaluated with a bioassay measuring the ability of susceptible flea beetle larvae to survive on each plant. Metabolites that correlated negatively with larvae survival were identified through correlation, cluster, and principal component analyses. Two main clusters of metabolites that correlate negatively with larvae survival were identified. Principal component analysis grouped resistant and susceptible plants as well as correlated metabolites. Known saponins, such as hederagenin cellobioside and oleanolic acid cellobioside, as well as two other saponins correlated significantly with plant resistance. This study shows the potential of metabolomics to identify bioactive compounds involved in plant defense. PMID:19819983

  16. Identification and Analysis of Critical Gaps in Nuclear Fuel Cycle Codes Required by the SINEMA Program

    SciTech Connect

    Adrian Miron; Joshua Valentine; John Christenson; Majd Hawwari; Santosh Bhatt; Mary Lou Dunzik-Gougar: Michael Lineberry

    2009-10-01

    The current state of the art in nuclear fuel cycle (NFC) modeling is an eclectic mixture of codes with various levels of applicability, flexibility, and availability. In support of the advanced fuel cycle systems analyses, especially those by the Advanced Fuel Cycle Initiative (AFCI), Unviery of Cincinnati in collaboration with Idaho State University carried out a detailed review of the existing codes describing various aspects of the nuclear fuel cycle and identified the research and development needs required for a comprehensive model of the global nuclear energy infrastructure and the associated nuclear fuel cycles. Relevant information obtained on the NFC codes was compiled into a relational database that allows easy access to various codes' properties. Additionally, the research analyzed the gaps in the NFC computer codes with respect to their potential integration into programs that perform comprehensive NFC analysis.

  17. 78 FR 78163 - Eligibility of the Gulf Cooperation Council To Receive Defense Articles and Defense Services...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-24

    ..., Washington, December 16, 2013. [FR Doc. 2013-30984 Filed 12-23-13; 11:15 am] Billing code 4710-10 ... Cooperation Council To Receive Defense Articles and Defense Services Under the Foreign Assistance Act of 1961... that the furnishing of defense articles and defense services to the Gulf Cooperation Council...

  18. Combining subproteome enrichment and Rubisco depletion enables identification of low abundance proteins differentially regulated during plant defense.

    PubMed

    Widjaja, Ivy; Naumann, Kai; Roth, Udo; Wolf, Noreen; Mackey, David; Dangl, Jeffery L; Scheel, Dierk; Lee, Justin

    2009-01-01

    Transgenic Arabidopsis conditionally expressing the bacterial avrRpm1 type III effector under the control of a dexamethasone-responsive promoter were used for proteomics studies. This model system permits study of an individual effector without interference from additional bacterial components. Coupling of different prefractionation approaches to high resolution 2-DE facilitated the discovery of low abundance proteins - enabling the identification of proteins that have escaped detection in similar experiments. A total of 34 differentially regulated protein spots were identified. Four of these (a remorin, a protein phosphatase 2C (PP2C), an RNA-binding protein, and a C2-domain-containing protein) are potentially early signaling components in the interaction between AvrRpm1 and the cognate disease resistance gene product, resistance to Pseudomonas syringae pv. maculicola 1 (RPM1). For the remorin and RNA-binding protein, involvement of PTM and post-transcriptional regulation are implicated, respectively. PMID:19053141

  19. The identification of the first molluscan Akirin2 with immune defense function in the Hong Kong oyster Crassostrea hongkongensis.

    PubMed

    Qu, Fufa; Xiang, Zhiming; Zhang, Yang; Li, Jun; Zhang, Yuehuan; Yu, Ziniu

    2014-12-01

    The Akirin protein is a nuclear factor in the innate immune system that is highly conserved from insects to mammals and plays key roles in diverse biological processes, including immunity, myogenesis, development and the cellular stress response. However, the function of Akirins in mollusk, the second most diverse group of animals, is still poorly understood. In this study, we report the discovery of an Akirin2 gene homolog (ChAkirin2) and its biological functions in the Hong Kong oyster Crassostrea hongkongensis. ChAkirin2 is 189 amino acids in length and shares significant homology with invertebrate homologs. Phylogenetic analysis results revealed that ChAkirin2 is clustered with invertebrate Akirin2s. A sequence analysis of the 5' flanking regions of ChAkirin2 indicated that it harbors several potential PAMP-activated transcription factor binding sites (TFB), including sites for NF-κB, C/EBPα, AP-1, SRF, Oct-1 and GATA-1. An RT-PCR analysis showed that ChAkirin2 mRNA was ubiquitously expressed in various tissues and at different embryonic and larval stages. Additionally, upon infection by pathogens (Vibrio alginolyticus, Staphylococcus haemolyticus and Saccharomyces cerevisiae) and pathogen-associated molecular patterns (PAMPs: LPS, PGN and polyI:C), the expression of ChAkirin2 was significantly up-regulated. Moreover, fluorescence microscopy observations show that ChAkirin2 is located in the nuclei of HeLa cells, and the overexpression of ChAkirin2 activated the transcriptional activities of the NF-κB reporter gene in HEK293T cells. Altogether, this report provided the first experimental demonstration that mollusks possess a functional Akirin2 that is involved in the innate defense and embryogenesis processes of the oyster. PMID:25284180

  20. HYPERSENSITIVE RESPONSE-LIKE LESIONS 1 Codes for AtPPT1 and Regulates Accumulation of ROS and Defense Against Bacterial Pathogen Pseudomonas syringae in Arabidopsis thaliana

    PubMed Central

    Dutta, Aditya; Chan, Samuel H.P.; Pauli, Noel T.

    2015-01-01

    Abstract Aims: Plants employ both basal and resistance gene (R gene)-mediated defenses in response to pathogens. Reactive oxygen species (ROS) are widely reported to play a central role in both basal and R gene-mediated defense; however, the nature of ROS has been less well established for basal defense. In addition, spatial distribution of redox moieties and mechanisms of plant responses during basal defense are poorly understood. We investigated redox signaling in Arabidopsis thaliana in response to virulent bacterial pathogen, focusing on the role of the mitochondria in balancing energy demands against generation of physiologically relevant ROS. Results: Positional cloning of an Arabidopsis lesion mimic mutant identified a polyprenyl transferase involved in the biosynthesis of Coenzyme Q10 (CoQ), which leads to novel insights into physiological ROS levels and their role in basal resistance. Gain- and loss-of-function studies identified Coenzyme Q10 redox state to be a key determinant of ROS levels. These Coenzyme Q10 redox state-mediated ROS levels had a direct bearing on both response against pathogen and ability to thrive in high oxidative stress environments. Innovation: We demonstrate that Coenzyme Q10 redox state generates an ROS threshold for a successful basal resistance response. Perturbation of the Coenzyme Q10 redox state has the potential to disrupt plant defense responses against bacterial pathogens. Conclusions: Coenzyme Q10 redox state is a key regulator of Arabidopsis basal resistance against bacterial pathogens. Antioxid. Redox Signal. 22, 785–796. PMID:25557512

  1. Identification and Characterization of Long Non-Coding RNAs Related to Mouse Embryonic Brain Development from Available Transcriptomic Data

    PubMed Central

    He, Hongjuan; Xiu, Youcheng; Guo, Jing; Liu, Hui; Liu, Qi; Zeng, Tiebo; Chen, Yan; Zhang, Yan; Wu, Qiong

    2013-01-01

    Long non-coding RNAs (lncRNAs) as a key group of non-coding RNAs have gained widely attention. Though lncRNAs have been functionally annotated and systematic explored in higher mammals, few are under systematical identification and annotation. Owing to the expression specificity, known lncRNAs expressed in embryonic brain tissues remain still limited. Considering a large number of lncRNAs are only transcribed in brain tissues, studies of lncRNAs in developmental brain are therefore of special interest. Here, publicly available RNA-sequencing (RNA-seq) data in embryonic brain are integrated to identify thousands of embryonic brain lncRNAs by a customized pipeline. A significant proportion of novel transcripts have not been annotated by available genomic resources. The putative embryonic brain lncRNAs are shorter in length, less spliced and show less conservation than known genes. The expression of putative lncRNAs is in one tenth on average of known coding genes, while comparable with known lncRNAs. From chromatin data, putative embryonic brain lncRNAs are associated with active chromatin marks, comparable with known lncRNAs. Embryonic brain expressed lncRNAs are also indicated to have expression though not evident in adult brain. Gene Ontology analysis of putative embryonic brain lncRNAs suggests that they are associated with brain development. The putative lncRNAs are shown to be related to possible cis-regulatory roles in imprinting even themselves are deemed to be imprinted lncRNAs. Re-analysis of one knockdown data suggests that four regulators are associated with lncRNAs. Taken together, the identification and systematic analysis of putative lncRNAs would provide novel insights into uncharacterized mouse non-coding regions and the relationships with mammalian embryonic brain development. PMID:23967161

  2. TPASS: a gamma-ray spectrum analysis and isotope identification computer code

    SciTech Connect

    Dickens, J.K.

    1981-03-01

    The gamma-ray spectral data-reduction and analysis computer code TPASS is described. This computer code is used to analyze complex Ge(Li) gamma-ray spectra to obtain peak areas corrected for detector efficiencies, from which are determined gamma-ray yields. These yields are compared with an isotope gamma-ray data file to determine the contributions to the observed spectrum from decay of specific radionuclides. A complete FORTRAN listing of the code and a complex test case are given.

  3. Self-identification of protein-coding regions in microbial genomes.

    PubMed

    Audic, S; Claverie, J M

    1998-08-18

    A new method for predicting protein-coding regions in microbial genomic DNA sequences is presented. It uses an ab initio iterative Markov modeling procedure to automatically perform the partition of genomic sequences into three subsets shown to correspond to coding, coding on the opposite strand, and noncoding segments. In contrast to current methods, such as GENEMARK [Borodovsky, M. & McIninch, J. D. (1993) Comput. Chem. 17, 123-133], no training set or prior knowledge of the statistical properties of the studied genome are required. This new method tolerates error rates of 1-2% and can process unassembled sequences. It is thus ideal for the analysis of genome survey and/or fragmented sequence data from uncharacterized microorganisms. The method was validated on 10 complete bacterial genomes (from four major phylogenetic lineages). The results show that protein-coding regions can be identified with an accuracy of up to 90% with a totally automated and objective procedure. PMID:9707594

  4. Validation of coding algorithms for the identification of patients with primary biliary cirrhosis using administrative data

    PubMed Central

    Myers, Robert P; Shaheen, Abdel Aziz M; Fong, Andrew; Wan, Alex F; Swain, Mark G; Hilsden, Robert J; Sutherland, Lloyd; Quan, Hude

    2010-01-01

    BACKGROUND: Large-scale epidemiological studies of primary biliary cirrhosis (PBC) have been hindered by difficulties in case ascertainment. OBJECTIVE: To develop coding algorithms for identifying PBC patients using administrative data – a widely available data source. METHODS: Population-based administrative databases were used to identify patients with a diagnosis code for PBC from 1994 to 2002. Coding algorithms for confirmed PBC (two or more of antimitochondrial antibody positivity, cholestatic liver biochemistry and/or compatible liver histology) were derived using chart abstraction data as the reference. Patients with a recorded PBC diagnosis but insufficient confirmatory data were classified as ‘suspected PBC’. RESULTS: Of 189 potential PBC cases, 119 (60%) had confirmed PBC and 28 (14%) had suspected PBC. The optimal algorithm including two or more uses of a PBC code had a sensitivity of 94% (95% CI 71% to 100%) and positive predictive values of 73% (95% CI 61% to 75%) for confirmed PBC, and 89% (95% CI 82% to 94%) for confirmed or suspected PBC. Sensitivity analyses revealed greater accuracy among women, and with the use of multiple data sources and one or more years of data. Inclusion of diagnosis codes for conditions frequently misclassified as PBC did not improve algorithm performance. CONCLUSIONS: Administrative databases can reliably identify patients with PBC and may facilitate epidemiological investigations of this condition. PMID:20352146

  5. Identification of internal transcribed spacer sequence motifs in truffles: a first step toward their DNA bar coding.

    PubMed

    El Karkouri, Khalid; Murat, Claude; Zampieri, Elisa; Bonfante, Paola

    2007-08-01

    This work presents DNA sequence motifs from the internal transcribed spacer (ITS) of the nuclear rRNA repeat unit which are useful for the identification of five European and Asiatic truffles (Tuber magnatum, T. melanosporum, T. indicum, T. aestivum, and T. mesentericum). Truffles are edible mycorrhizal ascomycetes that show similar morphological characteristics but that have distinct organoleptic and economic values. A total of 36 out of 46 ITS1 or ITS2 sequence motifs have allowed an accurate in silico distinction of the five truffles to be made (i.e., by pattern matching and/or BLAST analysis on downloaded GenBank sequences and directly against GenBank databases). The motifs considered the intraspecific genetic variability of each species, including rare haplotypes, and assigned their respective species from either the ascocarps or ectomycorrhizas. The data indicate that short ITS1 or ITS2 motifs (< or = 50 bp in size) can be considered promising tools for truffle species identification. A dot blot hybridization analysis of T. magnatum and T. melanosporum compared with other close relatives or distant lineages allowed at least one highly specific motif to be identified for each species. These results were confirmed in a blind test which included new field isolates. The current work has provided a reliable new tool for a truffle oligonucleotide bar code and identification in ecological and evolutionary studies. PMID:17601808

  6. Inter-STOP symbol distances for the identification of coding regions.

    PubMed

    Bastos, Carlos A C; Afreixo, Vera; Garcia, Sara P; Pinho, Armando J

    2013-01-01

    In this study we explore the potential of inter-STOP symbol distances for finding coding regions in DNA sequences. We use the distance between STOP symbols in the DNA sequence and a chi-square statistic to evaluate the nonhomogeneity of the three possible reading frames and the occurrence of one long distance in one of the frames. The results of this exploratory study suggest that inter-STOP symbol distances have strong ability to discriminate coding regions in prokaryotes and simple eukaryotes. PMID:24231144

  7. Genome-Wide Identification and Characterization of Long Non-Coding RNAs from Mulberry (Morus notabilis) RNA-seq Data.

    PubMed

    Song, Xiaobo; Sun, Liang; Luo, Haitao; Ma, Qingguo; Zhao, Yi; Pei, Dong

    2016-01-01

    Numerous sources of evidence suggest that most of the eukaryotic genome is transcribed into protein-coding mRNAs and also into a large number of non-coding RNAs (ncRNAs). Long ncRNAs (lncRNAs), a group consisting of ncRNAs longer than 200 nucleotides, have been found to play critical roles in transcriptional, post-transcriptional, and epigenetic gene regulation across all kingdoms of life. However, lncRNAs and their regulatory roles remain poorly characterized in plants, especially in woody plants. In this paper, we used a computational approach to identify novel lncRNAs from a published RNA-seq data set and analyzed their sequences and expression patterns. In total, 1133 novel lncRNAs were identified in mulberry, and 106 of these lncRNAs displayed a predominant tissue-specific expression in the five major tissues investigated. Additionally, functional predictions revealed that tissue-specific lncRNAs adjacent to protein-coding genes might play important regulatory roles in the development of floral organ and root in mulberry. The pipeline used in this study would be useful for the identification of lncRNAs obtained from other deep sequencing data. Furthermore, the predicted lncRNAs would be beneficial towards an understanding of the variations in gene expression in plants. PMID:26938562

  8. Genome-Wide Identification and Characterization of Long Non-Coding RNAs from Mulberry (Morus notabilis) RNA-seq Data

    PubMed Central

    Song, Xiaobo; Sun, Liang; Luo, Haitao; Ma, Qingguo; Zhao, Yi; Pei, Dong

    2016-01-01

    Numerous sources of evidence suggest that most of the eukaryotic genome is transcribed into protein-coding mRNAs and also into a large number of non-coding RNAs (ncRNAs). Long ncRNAs (lncRNAs), a group consisting of ncRNAs longer than 200 nucleotides, have been found to play critical roles in transcriptional, post-transcriptional, and epigenetic gene regulation across all kingdoms of life. However, lncRNAs and their regulatory roles remain poorly characterized in plants, especially in woody plants. In this paper, we used a computational approach to identify novel lncRNAs from a published RNA-seq data set and analyzed their sequences and expression patterns. In total, 1133 novel lncRNAs were identified in mulberry, and 106 of these lncRNAs displayed a predominant tissue-specific expression in the five major tissues investigated. Additionally, functional predictions revealed that tissue-specific lncRNAs adjacent to protein-coding genes might play important regulatory roles in the development of floral organ and root in mulberry. The pipeline used in this study would be useful for the identification of lncRNAs obtained from other deep sequencing data. Furthermore, the predicted lncRNAs would be beneficial towards an understanding of the variations in gene expression in plants. PMID:26938562

  9. Identification and characterization of long non-coding RNAs in rainbow trout eggs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Long non-coding RNAs (lncRNAs) are in general considered as a diverse class of transcripts longer than 200 nucleotides that structurally resemble mRNAs but do not encode proteins. Recent advances in RNA sequencing (RNA-Seq) and bioinformatics methods have provided an opportunity to indentify and ana...

  10. Identification of a Rare Coding Variant in Complement 3 Associated with Age-related Macular Degeneration

    PubMed Central

    Zhan, Xiaowei; Larson, David E.; Wang, Chaolong; Koboldt, Daniel C.; Sergeev, Yuri V.; Fulton, Robert S.; Fulton, Lucinda L.; Fronick, Catrina C.; Branham, Kari E.; Bragg-Gresham, Jennifer; Jun, Goo; Hu, Youna; Kang, Hyun Min; Liu, Dajiang; Othman, Mohammad; Brooks, Matthew; Ratnapriya, Rinki; Boleda, Alexis; Grassmann, Felix; von Strachwitz, Claudia; Olson, Lana M.; Buitendijk, Gabriëlle H.S.; Hofman, Albert; van Duijn, Cornelia M.; Cipriani, Valentina; Moore, Anthony T.; Shahid, Humma; Jiang, Yingda; Conley, Yvette P.; Morgan, Denise J.; Kim, Ivana K.; Johnson, Matthew P.; Cantsilieris, Stuart; Richardson, Andrea J.; Guymer, Robyn H.; Luo, Hongrong; Ouyang, Hong; Licht, Christoph; Pluthero, Fred G.; Zhang, Mindy M.; Zhang, Kang; Baird, Paul N.; Blangero, John; Klein, Michael L.; Farrer, Lindsay A.; DeAngelis, Margaret M.; Weeks, Daniel E.; Gorin, Michael B.; Yates, John R.W.; Klaver, Caroline C.W.; Pericak-Vance, Margaret A.; Haines, Jonathan L.; Weber, Bernhard H.F.; Wilson, Richard K.; Heckenlively, John R.; Chew, Emily Y.; Stambolian, Dwight; Mardis, Elaine R.; Swaroop, Anand; Abecasis, Goncalo R.

    2013-01-01

    Macular degeneration is a common cause of blindness in the elderly. To identify rare coding variants associated with a large increase in risk of age-related macular degeneration (AMD), we sequenced 2,335 cases and 789 controls in 10 candidate loci (57 genes). To increase power, we augmented our control set with ancestry-matched exome sequenced controls. An analysis of coding variation in 2,268 AMD cases and 2,268 ancestry matched controls revealed two large-effect rare variants; previously described R1210C in the CFH gene (fcase = 0.51%, fcontrol = 0.02%, OR = 23.11), and newly identified K155Q in the C3 gene (fcase = 1.06%, fcontrol = 0.39%, OR = 2.68). The variants suggest decreased inhibition of C3 by Factor H, resulting in increased activation of the alternative complement pathway, as a key component of disease biology. PMID:24036949

  11. Key for protein coding sequences identification: computer analysis of codon strategy.

    PubMed Central

    Rodier, F; Gabarro-Arpa, J; Ehrlich, R; Reiss, C

    1982-01-01

    The signal qualifying an AUG or GUG as an initiator in mRNAs processed by E. coli ribosomes is not found to be a systematic, literal homology sequence. In contrast, stability analysis reveals that initiators always occur within nucleic acid domains of low stability, for which a high A/U content is observed. Since no aminoacid selection pressure can be detected at N-termini of the proteins, the A/U enrichment results from a biased usage of the code degeneracy. A computer analysis is presented which allows easy detection of the codon strategy. N-terminal codons carry rather systematically A or U in third position, which suggests a mechanism for translation initiation and helps to detect protein coding sequences in sequenced DNA. PMID:7038623

  12. Identification of Genes Coding Aminoglycoside Modifying Enzymes in E. coli of UTI Patients in India

    PubMed Central

    Bashir, Yasir; Dar, Firdous Ahmad; Sekhar, M.

    2016-01-01

    This study is to probe the pattern of antibiotic resistance against aminoglycosides and its mechanism in E. coli obtained from patients from Chennai, India. Isolation and identification of pathogens were done on MacConkey agar. Antimicrobial sensitivity testing was done by disc diffusion test. The identification of genes encoding aminoglycoside modifying enzymes was done by Polymerase Chain Reaction (PCR). Out of 98 isolates, 71 (72.45%) isolates were identified as E. coli and the remaining 27 (27.55%) as other bacteria. Disc diffusion method results showed a resistance level of 72.15% for streptomycin, 73.4% for gentamicin, 63.26% for neomycin, 57.14% for tobramycin, 47.9% for netilmicin, and 8.16% for amikacin in E. coli. PCR screening showed the presence of four genes, namely, rrs, aacC2, aacA-aphD, and aphA3, in their plasmid DNA. The results point towards the novel mechanism of drug resistance in E. coli from UTI patients in India as they confirm the presence of genes encoding enzymes that cause resistance to aminoglycoside drugs. This could be an alarm for drug prescription to UTI patients. PMID:27403451

  13. Identification of a Novel Small Non-Coding RNA Modulating the Intracellular Survival of Brucella melitensis.

    PubMed

    Wang, Yufei; Ke, Yuehua; Xu, Jie; Wang, Ligui; Wang, Tongkun; Liang, Hui; Zhang, Wei; Gong, Chunli; Yuan, Jiuyun; Zhuang, Yubin; An, Chang; Lei, Shuangshuang; Du, Xinying; Wang, Zhoujia; Li, Wenna; Yuan, Xitong; Huang, Liuyu; Yang, Xiaoli; Chen, Zeliang

    2015-01-01

    Bacterial small non-coding RNAs (sRNAs) are gene expression modulators respond to environmental changes, stressful conditions, and pathogenesis. In this study, by using a combined bioinformatic and experimental approach, eight novel sRNA genes were identified in intracellular pathogen Brucella melitensis. BSR0602, one sRNA that was highly induced in stationary phase, was further examined and found to modulate the intracellular survival of B. melitensis. BSR0602 was present at very high levels in vitro under stresses similar to those encountered during infection in host macrophages. Furthermore, BSR0602 was found to be highly expressed in the spleens of infected mice, suggesting its potential role in the control of pathogenesis. BSR0602 targets the mRNAs coding for gntR, a global transcriptional regulator, which is required for B. melitensis virulence. Overexpression of BSR0602 results in distinct reduction in the gntR mRNA level. B. melitensis with high level of BSR0602 is defective in bacteria intracellular survival in macrophages and defective in growth in the spleens of infected mice. Therefore, BSR0602 may directly inhibit the expression of gntR, which then impairs Brucellae intracellular survival and contributes to Brucella infection. Our findings suggest that BSR0602 is responsible for bacterial adaptation to stress conditions and thus modulate B. melitensis intracellular survival. PMID:25852653

  14. Identification of a Novel Small Non-Coding RNA Modulating the Intracellular Survival of Brucella melitensis

    PubMed Central

    Wang, Yufei; Ke, Yuehua; Xu, Jie; Wang, Ligui; Wang, Tongkun; Liang, Hui; Zhang, Wei; Gong, Chunli; Yuan, Jiuyun; Zhuang, Yubin; An, Chang; Lei, Shuangshuang; Du, Xinying; Wang, Zhoujia; Li, Wenna; Yuan, Xitong; Huang, Liuyu; Yang, Xiaoli; Chen, Zeliang

    2015-01-01

    Bacterial small non-coding RNAs (sRNAs) are gene expression modulators respond to environmental changes, stressful conditions, and pathogenesis. In this study, by using a combined bioinformatic and experimental approach, eight novel sRNA genes were identified in intracellular pathogen Brucella melitensis. BSR0602, one sRNA that was highly induced in stationary phase, was further examined and found to modulate the intracellular survival of B. melitensis. BSR0602 was present at very high levels in vitro under stresses similar to those encountered during infection in host macrophages. Furthermore, BSR0602 was found to be highly expressed in the spleens of infected mice, suggesting its potential role in the control of pathogenesis. BSR0602 targets the mRNAs coding for gntR, a global transcriptional regulator, which is required for B. melitensis virulence. Overexpression of BSR0602 results in distinct reduction in the gntR mRNA level. B. melitensis with high level of BSR0602 is defective in bacteria intracellular survival in macrophages and defective in growth in the spleens of infected mice. Therefore, BSR0602 may directly inhibit the expression of gntR, which then impairs Brucellae intracellular survival and contributes to Brucella infection. Our findings suggest that BSR0602 is responsible for bacterial adaptation to stress conditions and thus modulate B. melitensis intracellular survival. PMID:25852653

  15. [Identification of the open reading frame coding transposase of Bordetella pertussis RS-element].

    PubMed

    Vorontsov, V V; Sivov, I G; Umiarov, A M; Siniashina, L N; Bol'shakova, T N; Dobrynina, O Iu; Molchanova, M L; Amelina, I P; Rudnev, I A; Karataev, G I

    2004-01-01

    A computer-aided analysis of the repeating sequence of Bordetella pertussis chromosome (RSBP3) revealed 3 open reading frames, one of whose (ORF1) can code a protein whose structure and properties are similar to those of transposasas, i.e. enzymes in charges for the traveling of migrating genetic elements of pro- and eukaryote. Mutants of the RSBP3 insertion sequence with the affected and unaffected ORF1 sequence were constructed in order to substantiate the above assumption. Two independent experimental models (formation of inter-plasmid co-integrates and of co-integrates between plasmid and E. coli chromosome) were used to show that the RSBP3-stimulated formation of co-integrates is only true for plasmids containing RSBP3 with the unaffected ORF1 sequence. An activity of the Hpr protein (a component of the phosphoenolpyruvate-dependent phosphotransferase) was proven to influence the formation process of inter-plasmid co-integrates. PMID:15164716

  16. Enteropathogenic Escherichia coli: identification of a gene cluster coding for bundle-forming pilus morphogenesis.

    PubMed Central

    Sohel, I; Puente, J L; Ramer, S W; Bieber, D; Wu, C Y; Schoolnik, G K

    1996-01-01

    Sequence flanking the bfpA locus on the enteroadherent factor plasmid of the enteropathogenic Escherichia coli (EPEC) strain B171-8 (O111:NM) was obtained to identify genes that might be required for bundle-forming pilus (BFP) biosynthesis. Deletion experiments led to the identification of a contiguous cluster of at least 12 open reading frames, including bfpA, that could direct the synthesis of a morphologically normal BFP filament. Within the bfp gene cluster, we identified open reading frames that share homology with other type IV pilus accessory genes and with genes required for transformation competence and protein secretion. Immediately upstream of the bfp gene cluster, we identified a potential replication origin including genes that are predicted to encode proteins homologous with replicase and resolvase. Restriction fragment length polymorphism analysis of DNA from six additional EPEC serotypes showed that the organization of the bfp gene cluster and its juxtaposition with a potential plasmid origin of replication are highly conserved features of the EPEC biotype. PMID:8626330

  17. Rat hepatic glutaminase: identification of the full coding sequence and characterization of a functional promoter.

    PubMed Central

    Chung-Bok, M I; Vincent, N; Jhala, U; Watford, M

    1997-01-01

    Glutamine catabolism in mammalian liver is catalysed by a unique isoenzyme of phosphate-activated glutaminase. The full coding and 5' untranslated sequence for rat hepatic glutaminase was isolated by screening lambda ZAP cDNA libraries and a Charon 4a rat genomic library. The sequence produces a mRNA 2225 nt in length, encoding a polypeptide of 535 amino acid residues with a calculated molecular mass of 59.2 kDa. The deduced amino acid sequence of rat liver glutaminase shows 86% similarity to that of rat kidney glutaminase and 65% similarity to a putative glutaminase from Caenorhabditis elegans. A genomic clone to rat liver glutaminase was isolated that contains 3.5 kb of the gene and 7.5 kb of the 5' flanking region. The 1 kb immediately upstream of the hepatic glutaminase gene (from -1022 to +48) showed functional promoter activity in HepG2 hepatoma cells. This promoter region did not respond to treatment with cAMP, but was highly responsive (10-fold stimulation) to the synthetic glucocorticoid dexamethasone. Subsequent 5' deletion analysis indicated that the promoter region between -103 and +48 was sufficient for basal promoter activity. This region does not contain an identifiable TATA element, indicating that transcription of the glutaminase gene is driven by a TATA-less promoter. The region responsive to glucocorticoids was mapped to -252 to -103 relative to the transcription start site. PMID:9164856

  18. Experimental identification and analysis of macronuclear non-coding RNAs from the ciliate Tetrahymena thermophila

    PubMed Central

    Andersen, Kasper L.; Nielsen, Henrik

    2012-01-01

    The ciliate Tetrahymena thermophila is an important eukaryotic model organism that has been used in pioneering studies of general phenomena, such as ribozymes, telomeres, chromatin structure and genome reorganization. Recent work has shown that Tetrahymena has many classes of small RNA molecules expressed during vegetative growth or sexual reorganization. In order to get an overview of medium-sized (40–500 nt) RNAs expressed from the Tetrahymena genome, we created a size-fractionated cDNA library from macronuclear RNA and analyzed 80 RNAs, most of which were previously unknown. The most abundant class was small nucleolar RNAs (snoRNAs), many of which are formed by an unusual maturation pathway. The modifications guided by the snoRNAs were analyzed bioinformatically and experimentally and many Tetrahymena-specific modifications were found, including several in an essential, but not conserved domain of ribosomal RNA. Of particular interest, we detected two methylations in the 5′-end of U6 small nuclear RNA (snRNA) that has an unusual structure in Tetrahymena. Further, we found a candidate for the first U8 outside metazoans, and an unusual U14 candidate. In addition, a number of candidates for new non-coding RNAs were characterized by expression analysis at different growth conditions. PMID:21967850

  19. Identification of novel long non-coding RNAs in triple-negative breast cancer

    PubMed Central

    Yu, Wenjie; Wang, Wenmin; Xu, Dong; Yan, Xinqiang; Chen, Beibei; Yu, Longyao; Li, Jicheng; Chen, Xiaobing; Ding, Kan; Cao, Feilin

    2015-01-01

    Triple-negative breast carcinomas (TNBC) are characterized by particularly poor outcomes, and there are no established markers significantly associated with prognosis. Long non-coding RNAs (lncRNAs) are subclass of noncoding RNAs that have been recently shown to play critical roles in cancer biology. However, little is known about their mechanistic role in TNBC pathogenesis. In this report, we investigated the expression patterns of lncRNAs from TNBC tissues and matched normal tissues with Agilent Human lncRNA array. We identified 1,758 lncRNAs and 1,254 mRNAs that were differentially expressed (≥ 2-fold change), indicating that many lncRNAs are significantly upregulated or downregulated in TNBC. Among these, XR_250621.1 and NONHSAT125629 were the most upregulated and downregulated lncRNAs respectively. qRT-PCR was employed to validate the microarray analysis findings, and results were consistent with the data from the microarrays. GO and KEGG pathway analysis were applied to explore the potential lncRNAs functions, some pathways including microtubule motor activity and DNA replication were identified in TNBC pathogenesis. Our study revealed that a set of lncRNAs were differentially expressed in TNBC tissues, suggesting that they may play role in TNBC. These results shed light on lncRNAs’ biological functions and provide useful information for exploring potential therapeutic targets for breast cancer. PMID:26078338

  20. Defense Mechanisms: Discussions and Bibliographies; General or Multiple, and Specific.

    ERIC Educational Resources Information Center

    Pedrini, D. T.; Pedrini, Bonnie C.

    This publication considers some Freudian ego mechanisms. The first discussion and bibliography concerns defense mechanisms, in general or in multiple; after which, the discussions and bibliographies concern specific defense mechanisms: denial; displacement, substitution, sublimation; fixation; identification, introjection, incorporation,…

  1. Identification of neural firing patterns, frequency and temporal coding mechanisms in individual aortic baroreceptors

    PubMed Central

    Gu, Huaguang; Pan, Baobao

    2015-01-01

    In rabbit depressor nerve fibers, an on-off firing pattern, period-1 firing, and integer multiple firing with quiescent state were observed as the static pressure level was increased. A bursting pattern with bursts at the systolic phase of blood pressure, continuous firing, and bursting with burst at diastolic phase and quiescent state at systolic phase were observed as the mean level of the dynamic blood pressure was increased. For both static and dynamic pressures, the firing frequency of the first two firing patterns increased and of the last firing pattern decreased due to the quiescent state. If the quiescent state is disregarded, the spike frequency becomes an increasing trend. The instantaneous spike frequency of the systolic phase bursting, continuous firing, and diastolic phase bursting can reflect the temporal process of the systolic phase, whole procedure, and diastolic phase of the dynamic blood pressure signal, respectively. With increasing the static current corresponding to pressure level, the deterministic Hodgkin-Huxley (HH) model manifests a process from a resting state first to period-1 firing via a subcritical Hopf bifurcation and then to a resting state via a supercritical Hopf bifurcation, and the firing frequency increases. The on-off firing and integer multiple firing were here identified as noise-induced firing patterns near the subcritical and supercritical Hopf bifurcation points, respectively, using the stochastic HH model. The systolic phase bursting and diastolic phase bursting were identified as pressure-induced firings near the subcritical and supercritical Hopf bifurcation points, respectively, using an HH model with a dynamic signal. The firing, spike frequency, and instantaneous spike frequency observed in the experiment were simulated and explained using HH models. The results illustrate the dynamics of different firing patterns and the frequency and temporal coding mechanisms of aortic baroreceptor. PMID:26379539

  2. Identification of Differentially Expressed Long Non-coding RNAs in Polarized Macrophages

    PubMed Central

    Huang, Zikun; Luo, Qing; Yao, Fangyi; Qing, Cheng; Ye, Jianqing; Deng, Yating; Li, Junming

    2016-01-01

    Macrophages display remarkable plasticity, with the ability to undergo dynamic transition between classically and alternatively activated phenotypes. Long non-coding RNAs (lncRNAs) are more than 200 nucleotides in length and play roles in various biological pathways. However, the role of lncRNAs in regulating macrophage polarization has yet to be explored. In this study, lncRNAs expression profiles were determined in human monocyte-derived macrophages (MDMs) incubated in conditions causing activation toward M(IFN-γ + LPS) or M(IL-4) phenotypes. Compared with primary MDMs, 9343 lncRNAs and 5903 mRNAs were deregulated in M(IFN-γ + LPS) group (fold change ≥2.0, P < 0.05), 4592 lncRNAs and 3122 mRNAs were deregulated in M(IL-4) group. RT-qPCR results were generally consistent with the microarray data. Furthermore, we found that TCONS_00019715 is expressed at a higher level in M(IFN-γ + LPS) macrophages than in M(IL-4) macrophages. TCONS_00019715 expression was decreased when M(IFN-γ + LPS) converted to M(IL-4) whereas increased when M(IL-4) converted to M(IFN-γ + LPS). Knockdown of TCONS_00019715 following the activation of THP-1 cellls using IFN-γ and LPS diminished the expression of M(IFN-γ + LPS) markers, and elevated the expression of M(IL-4) markers. These data show a significantly altered lncRNA and mRNA expression profile in macrophages exposure to different activating conditions. Dysregulation of some of these lncRNAs may play important roles in regulating macrophage polarization. PMID:26796525

  3. Identification of Differentially Expressed Long Non-coding RNAs in Polarized Macrophages.

    PubMed

    Huang, Zikun; Luo, Qing; Yao, Fangyi; Qing, Cheng; Ye, Jianqing; Deng, Yating; Li, Junming

    2016-01-01

    Macrophages display remarkable plasticity, with the ability to undergo dynamic transition between classically and alternatively activated phenotypes. Long non-coding RNAs (lncRNAs) are more than 200 nucleotides in length and play roles in various biological pathways. However, the role of lncRNAs in regulating macrophage polarization has yet to be explored. In this study, lncRNAs expression profiles were determined in human monocyte-derived macrophages (MDMs) incubated in conditions causing activation toward M(IFN-γ + LPS) or M(IL-4) phenotypes. Compared with primary MDMs, 9343 lncRNAs and 5903 mRNAs were deregulated in M(IFN-γ + LPS) group (fold change ≥ 2.0, P < 0.05), 4592 lncRNAs and 3122 mRNAs were deregulated in M(IL-4) group. RT-qPCR results were generally consistent with the microarray data. Furthermore, we found that TCONS_00019715 is expressed at a higher level in M(IFN-γ + LPS) macrophages than in M(IL-4) macrophages. TCONS_00019715 expression was decreased when M(IFN-γ + LPS) converted to M(IL-4) whereas increased when M(IL-4) converted to M(IFN-γ + LPS). Knockdown of TCONS_00019715 following the activation of THP-1 cellls using IFN-γ and LPS diminished the expression of M(IFN-γ + LPS) markers, and elevated the expression of M(IL-4) markers. These data show a significantly altered lncRNA and mRNA expression profile in macrophages exposure to different activating conditions. Dysregulation of some of these lncRNAs may play important roles in regulating macrophage polarization. PMID:26796525

  4. Phosphoprotein Isotope-coded Affinity Tags: Application to the Enrichment and Identification of Low-Abundance Phosphoproteins

    SciTech Connect

    Goshe, Michael; Veenstra, Timothy D. ); Panisko, Ellen A.; Conrads, Thomas P. ); Angell, Nicolas H.; Smith, Richard D. )

    2002-02-01

    A novel approach using different isotopic labeling and biotinylation has been developed for the enrichment and quantitation of phosphoseryl and phosphothreonyl-peptides. The phosphoprotein isotope-coded affinity tag (PhIAT) exploits the high affinity biotin-avidin interaction to isolate modified phosphopeptides from a complex mixture of peptides. The PhIAT strategy for quantifying and enriching mixtures for phosphopeptides was demonstrated using a commercially available sample of the phosphoprotein B-casein. A denatured solution of B-casein was labeled using the PhIAT method and after proteolytic digestion, the labeled peptides were isolated using immobilize avidin. The recovered peptides were separated by capillary reversed-phase liquid chromatography and identified by tandem mass spectrometry. PhIAT-labeled peptides corresponding to known O-phosphorylated peptides from B-casein were identified as were phosphorylated peptides from as1-casein and ase-casein, known low-level (< 5%) contaminants of commercially available B-casein. All of the identified phosphopeptides from these caseins have been previously documented to be phosphorylated at the sites elucidated by the PhIAT approach. The results illustrate the efficancy of the PhIAT-labeling strategy to enrich mixtures for phosphopeptides and permit the detection and identification of low abundance phosphopeptides. In addition, experiments using light and heavy isotopic version of the PhIAT reagents demonstrated that a 10% difference in phosphorylation state could be determined between phosphopeptides in comparative samples.

  5. Analysis of putative apoplastic effectors from the nematode, Globodera rostochiensis, and identification of an expansin-like protein that can induce and suppress host defenses.

    PubMed

    Ali, Shawkat; Magne, Maxime; Chen, Shiyan; Côté, Olivier; Stare, Barbara Gerič; Obradovic, Natasa; Jamshaid, Lubna; Wang, Xiaohong; Bélair, Guy; Moffett, Peter

    2015-01-01

    The potato cyst nematode, Globodera rostochiensis, is an important pest of potato. Like other pathogens, plant parasitic nematodes are presumed to employ effector proteins, secreted into the apoplast as well as the host cytoplasm, to alter plant cellular functions and successfully infect their hosts. We have generated a library of ORFs encoding putative G. rostochiensis putative apoplastic effectors in vectors for expression in planta. These clones were assessed for morphological and developmental effects on plants as well as their ability to induce or suppress plant defenses. Several CLAVATA3/ESR-like proteins induced developmental phenotypes, whereas predicted cell wall-modifying proteins induced necrosis and chlorosis, consistent with roles in cell fate alteration and tissue invasion, respectively. When directed to the apoplast with a signal peptide, two effectors, an ubiquitin extension protein (GrUBCEP12) and an expansin-like protein (GrEXPB2), suppressed defense responses including NB-LRR signaling induced in the cytoplasm. GrEXPB2 also elicited defense response in species- and sequence-specific manner. Our results are consistent with the scenario whereby potato cyst nematodes secrete effectors that modulate host cell fate and metabolism as well as modifying host cell walls. Furthermore, we show a novel role for an apoplastic expansin-like protein in suppressing intra-cellular defense responses. PMID:25606855

  6. Analysis of Putative Apoplastic Effectors from the Nematode, Globodera rostochiensis, and Identification of an Expansin-Like Protein That Can Induce and Suppress Host Defenses

    PubMed Central

    Ali, Shawkat; Magne, Maxime; Chen, Shiyan; Côté, Olivier; Stare, Barbara Gerič; Obradovic, Natasa; Jamshaid, Lubna; Wang, Xiaohong; Bélair, Guy; Moffett, Peter

    2015-01-01

    The potato cyst nematode, Globodera rostochiensis, is an important pest of potato. Like other pathogens, plant parasitic nematodes are presumed to employ effector proteins, secreted into the apoplast as well as the host cytoplasm, to alter plant cellular functions and successfully infect their hosts. We have generated a library of ORFs encoding putative G. rostochiensis putative apoplastic effectors in vectors for expression in planta. These clones were assessed for morphological and developmental effects on plants as well as their ability to induce or suppress plant defenses. Several CLAVATA3/ESR-like proteins induced developmental phenotypes, whereas predicted cell wall-modifying proteins induced necrosis and chlorosis, consistent with roles in cell fate alteration and tissue invasion, respectively. When directed to the apoplast with a signal peptide, two effectors, an ubiquitin extension protein (GrUBCEP12) and an expansin-like protein (GrEXPB2), suppressed defense responses including NB-LRR signaling induced in the cytoplasm. GrEXPB2 also elicited defense response in species- and sequence-specific manner. Our results are consistent with the scenario whereby potato cyst nematodes secrete effectors that modulate host cell fate and metabolism as well as modifying host cell walls. Furthermore, we show a novel role for an apoplastic expansin-like protein in suppressing intra-cellular defense responses. PMID:25606855

  7. Identification of a positive transcription regulatory element within the coding region of the nifLA operon in Azotobacter vinelandii.

    PubMed

    Mitra, Ranjana; Das, Hirendra K; Dixit, Aparna

    2005-07-01

    Nitrogen fixation in Azotobacter vinelandii is regulated by the nifLA operon. NifA activates the transcription of nif genes, while NifL antagonizes the transcriptional activator NifA in response to fixed nitrogen and molecular oxygen levels. However, transcriptional regulation of the nifLA operon of A. vinelandii itself is not fully understood. Using the S1 nuclease assay, we mapped the transcription start site of the nifLA operon, showing it to be similar to the sigma54-dependent promoters. We also identified a positive cis-acting regulatory element (+134 to +790) of the nifLA operon within the coding region of the nifL gene of A. vinelandii. Deletion of this element results in complete loss of promoter activity. Several protein factors bind to this region, and the specific binding sites have been mapped by DNase I foot printing. Two of these sites, namely dR1 (+134 to +204) and dR2 (+745 to +765), are involved in regulating the nifLA promoter activity. The absence of NtrC-like binding sites in the upstream region of the nifLA operon in A. vinelandii makes the identification of these downstream elements a highly significant finding. The interaction of the promoter with the proteins binding to the dR2 region spanning +745 to +765 appears to be dependent on the face of the helix as introduction of 4 bases just before this region completely disrupts promoter activity. Thus, the positive regulatory element present within the BglII-BglII fragment may play, in part; an important role in nifLA regulation in A. vinelandii. PMID:16000781

  8. Primitive defenses: cognitive aspects and therapeutic handling.

    PubMed

    Groh, L S

    In this paper the primitive defenses first described by Melanie Klein under the label of "schizoid mechanisms" are examined. The defenses considered are splitting the pathological uses of identification and projective identification, and the psychotic forms of denial. This examination is twofold: (1) the cognitive aspects of these defenses as described in terms of concepts developed by Jean Piaget; (2) concrete examples of the operation of these defenses during the treatment of schizophrenic patients are given and the effects of interventions based on the cognitive analysis are described. It is stressed that at times interventions, such as interpretation and confrontation, based on cognitive analysis, can temporarily and in some instances even permanently stop the operation of these defenses, allowing emotionally meaningful material to emerge which expedites the therapeutic process. PMID:7429737

  9. Identification of Predictive Markers for Response to Neoadjuvant Chemoradiation in Rectal Carcinomas by Proteomic Isotope Coded Protein Label (ICPL) Analysis

    PubMed Central

    Croner, Roland S.; Sevim, Müzeyyen; Metodiev, Metodi V.; Jo, Peter; Ghadimi, Michael; Schellerer, Vera; Brunner, Maximillian; Geppert, Carol; Rau, Tilman; Stürzl, Michael; Naschberger, Elisabeth; Matzel, Klaus E.; Hohenberger, Werner; Lottspeich, Friedrich; Kellermann, Josef

    2016-01-01

    Neoadjuvant chemoradiation (nCRT) is an established procedure in stage union internationale contre le cancer (UICC) II/III rectal carcinomas. Around 53% of the tumours present with good tumor regression after nCRT, and 8%–15% are complete responders. Reliable selection markers would allow the identification of poor or non-responders prior to therapy. Tumor biopsies were harvested from 20 patients with rectal carcinomas, and stored in liquid nitrogen prior to therapy after obtaining patients’ informed consent (Erlangen-No.3784). Patients received standardized nCRT with 5-Fluoruracil (nCRT I) or 5-Fluoruracil ± Oxaliplatin (nCRT II) according to the CAO/ARO/AIO-04 protocol. After surgery, regression grading (Dworak) of the tumors was performed during histopathological examination of the specimens. Tumors were classified as poor (Dworak 1 + 2) or good (Dworak 3 + 4) responders. Laser capture microdissection (LCM) for tumor enrichment was performed on preoperative biopsies. Differences in expressed proteins between poor and good responders to nCRT I and II were identified by proteomic analysis (Isotope Coded Protein Label, ICPL™) and selected markers were validated by immunohistochemistry. Tumors of 10 patients were classified as histopathologically poor (Dworak 1 or 2) and the other 10 tumor samples as histopathologically good (Dworak 3 or 4) responders to nCRT after surgery. Sufficient material in good quality was harvested for ICPL analysis by LCM from all biopsies. We identified 140 differentially regulated proteins regarding the selection criteria and the response to nCRT. Fourteen of these proteins were synchronously up-regulated at least 1.5-fold after nCRT I or nCRT II (e.g., FLNB, TKT, PKM2, SERINB1, IGHG2). Thirty-five proteins showed a complete reciprocal regulation (up or down) after nCRT I or nCRT II and the rest was regulated either according to nCRT I or II. The protein expression of regulated proteins such as PLEC1, TKT, HADHA and TAGLN was

  10. The Fusion Protein Signal-Peptide-Coding Region of Canine Distemper Virus: A Useful Tool for Phylogenetic Reconstruction and Lineage Identification

    PubMed Central

    Sarute, Nicolás; Calderón, Marina Gallo; Pérez, Ruben; La Torre, José; Hernández, Martín; Francia, Lourdes; Panzera, Yanina

    2013-01-01

    Canine distemper virus (CDV; Paramyxoviridae, Morbillivirus) is the etiologic agent of a multisystemic infectious disease affecting all terrestrial carnivore families with high incidence and mortality in domestic dogs. Sequence analysis of the hemagglutinin (H) gene has been widely employed to characterize field strains, permitting the identification of nine CDV lineages worldwide. Recently, it has been established that the sequences of the fusion protein signal-peptide (Fsp) coding region are extremely variable, suggesting that analysis of its sequence might be useful for strain characterization studies. However, the divergence of Fsp sequences among worldwide strains and its phylogenetic resolution has not yet been evaluated. We constructed datasets containing the Fsp-coding region and H gene sequences of the same strains belonging to eight CDV lineages. Both datasets were used to evaluate their phylogenetic resolution. The phylogenetic analysis revealed that both datasets clustered the same strains into eight different branches, corresponding to CDV lineages. The inter-lineage amino acid divergence was fourfold greater for the Fsp peptide than for the H protein. The likelihood mapping revealed that both datasets display strong phylogenetic signals in the region of well-resolved topologies. These features indicate that Fsp-coding region sequence analysis is suitable for evolutionary studies as it allows for straightforward identification of CDV lineages. PMID:23675493

  11. Identification and Expression Analysis of Candidate Genes Associated with Defense Responses to Phytophthora capsici in Pepper Line “PI 201234”

    PubMed Central

    Wang, Pingyong; Liu, Xiaodan; Guo, Jinju; Liu, Chen; Fu, Nan; Shen, Huolin

    2015-01-01

    Phytophthora capsici (Leonian), classified as an oomycete, seriously threatens the production of pepper (Capsicum annuum). Current understanding of the defense responses in pepper to P. capsici is limited. In this study, RNA-sequencing analysis was utilized to identify differentially expressed genes in the resistant line “PI 201234”, with 1220 differentially expressed genes detected. Of those genes, 480 were up-regulated and 740 were down-regulated, with 211 candidate genes found to be involved in defense responses based on the gene annotations. Furthermore, the expression patterns of 12 candidate genes were further validated via quantitative real-time PCR (qPCR). These genes were found to be significantly up-regulated at different time points post-inoculation (6 hpi, 24 hpi, and 5 dpi) in the resistant line “PI 201234” and susceptible line “Qiemen”. Seven genes were found to be involved in cell wall modification, phytoalexin biosynthesis, symptom development, and phytohormone signaling pathways, thus possibly playing important roles in combating exogenous pathogens. The genes identified herein will provide a basis for further gene cloning and functional verification studies and will aid in an understanding of the regulatory mechanism of pepper resistance to P. capsici. PMID:25993303

  12. 32 CFR 32.42 - Codes of conduct.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 32 National Defense 1 2010-07-01 2010-07-01 false Codes of conduct. 32.42 Section 32.42 National Defense Department of Defense OFFICE OF THE SECRETARY OF DEFENSE DoD GRANT AND AGREEMENT REGULATIONS... NON-PROFIT ORGANIZATIONS Post-Award Requirements Procurement Standards § 32.42 Codes of conduct....

  13. A Global Identification and Analysis of Small Nucleolar RNAs and Possible Intermediate-Sized Non-Coding RNAs in Oryza sativa

    PubMed Central

    Liu, Ting-Ting; Zhu, Danmeng; Chen, Wei; Deng, Xing Wang

    2013-01-01

    Accumulating evidence suggests that non-coding RNAs (ncRNAs) are both widespread and functionally important in many eukaryotic organisms. In this study, we employed a special size fractionation and cDNA library construction method followed by 454 deep sequencing to systematically profile rice intermediate-size ncRNAs. Our analysis resulted in the identification of 1349 ncRNAs in total, including 754 novel ncRNAs of an unknown functional category. Chromosome distribution of all identified ncRNAs showed no strand bias, and displayed a pattern similar to that observed in protein-coding genes with few chromosome dependencies. More than half of the ncRNAs were centered around the plus-strand of the 5’ and 3’ termini of the coding regions. The majority of the novel ncRNAs were rice specific, while 78% of the small nucleolar RNAs (snoRNAs) were conserved. Tandem duplication drove the expansion of over half of the snoRNA gene families. Furthermore, 90% of the snoRNA candidates were shown to produce small RNAs between 20–30 nt, 80% of which were associated with ARGONAUT proteins generally, and AGO1b in particular. Overall, our findings provide a comprehensive view of an intermediate-size non-coding transcriptome in a monocot species, which will serve as a useful platform for an in-depth analysis of ncRNA functions. PMID:22986792

  14. Identification of a long non-coding RNA gene, growth hormone secretagogue receptor opposite strand, which stimulates cell migration in non-small cell lung cancer cell lines.

    PubMed

    Whiteside, Eliza J; Seim, Inge; Pauli, Jana P; O'Keeffe, Angela J; Thomas, Patrick B; Carter, Shea L; Walpole, Carina M; Fung, Jenny N T; Josh, Peter; Herington, Adrian C; Chopin, Lisa K

    2013-08-01

    The molecular mechanisms involved in non‑small cell lung cancer tumourigenesis are largely unknown; however, recent studies have suggested that long non-coding RNAs (lncRNAs) are likely to play a role. In this study, we used public databases to identify an mRNA-like, candidate long non-coding RNA, GHSROS (GHSR opposite strand), transcribed from the antisense strand of the ghrelin receptor gene, growth hormone secretagogue receptor (GHSR). Quantitative real-time RT-PCR revealed higher expression of GHSROS in lung cancer tissue compared to adjacent, non-tumour lung tissue. In common with many long non-coding RNAs, GHSROS is 5' capped and 3' polyadenylated (mRNA-like), lacks an extensive open reading frame and harbours a transposable element. Engineered overexpression of GHSROS stimulated cell migration in the A549 and NCI-H1299 non-small cell lung cancer cell lines, but suppressed cell migration in the Beas-2B normal lung-derived bronchoepithelial cell line. This suggests that GHSROS function may be dependent on the oncogenic context. The identification of GHSROS, which is expressed in lung cancer and stimulates cell migration in lung cancer cell lines, contributes to the growing number of non-coding RNAs that play a role in the regulation of tumourigenesis and metastatic cancer progression. PMID:23722988

  15. Values as Defenses

    ERIC Educational Resources Information Center

    Hultman, Kenneth E.

    1976-01-01

    The author outlines a cognitive approach for explaining how and why people use values as defenses. He examines the relationship between defensive values and irrational beliefs, suggests a number of criteria for diagnosing the presence of defensive values, and proposes some strategies for dealing with defensive values in counseling. (Author)

  16. Construction of a full-length cDNA library of Solen grandis dunker and identification of defense- and immune-related genes

    NASA Astrophysics Data System (ADS)

    Sun, Guohua; Liu, Xiangquan; Ren, Lihua; Yang, Jianmin; Wei, Xiumei; Yang, Jialong

    2013-11-01

    The basic genetic characteristics, important functional genes, and entire transcriptome of Solen grandis Dunker were investigated by constructing a full-length cDNA library with the `switching mechanism at the 5'-end of the RNA transcript' (SMART) technique. Total RNA was isolated from the immune-relevant tissues, gills and hemocytes, using the Trizol reagent, and cDNA fragments were digested with Sfi I before being ligated to the pBluescript II SK* vector. The cDNA library had a titer of 1048 cfu μL-1 and a storage capacity of 1.05×106 cfu. Approximately 98% of the clones in the library were recombinants, and the fragment lengths of insert cDNA ranged from 0.8 kb to 3.0 kb. A total of 2038 expressed sequence tags were successfully sequenced and clustered into 965 unigenes. BLASTN analysis showed that 240 sequences were highly similar to the known genes (E-value < 1e -5; percent identity >80%), accounting for 25% of the total unigenes. According to the Gene Ontology, these unigenes were related to several biological processes, including cell structure, signal transport, protein synthesis, transcription, energy metabolism, and immunity. Fifteen of the identified sequences were related to defense and immunity. The full-length cDNA sequence of HSC70 was obtained. The cDNA library of S. grandis provided a useful resource for future researches of functional genomics related to stress tolerance, immunity, and other physiological activities.

  17. PCR assay based on DNA coding for 16S rRNA for detection and identification of mycobacteria in clinical samples.

    PubMed Central

    Kox, L F; van Leeuwen, J; Knijper, S; Jansen, H M; Kolk, A H

    1995-01-01

    A PCR and a reverse cross blot hybridization assay were developed for the detection and identification of mycobacteria in clinical samples. The PCR amplifies a part of the DNA coding for 16S rRNA with a set of primers that is specific for the genus Mycobacterium and that flanks species-specific sequences within the genes coding for 16S rRNA. The PCR product is analyzed in a reverse cross blot hybridization assay with probes specific for M. tuberculosis complex (pTub1), M. avium (pAvi3), M. intracellulare (pInt5 and pInt7), M. kansasii complex-M. scrofulaceum complex (pKan1), M. xenopi (pXen1), M. fortuitum (pFor1), M. smegmatis (pSme1), and Mycobacterium spp. (pMyc5a). The PCR assay can detect 10 fg of DNA, the equivalent of two mycobacteria. The specificities of the probes were tested with 108 mycobacterial strains (33 species) and 31 nonmycobacterial strains (of 17 genera). The probes pAvi3, pInt5, pInt7, pKan1, pXen1, and pMyc5a were specific. With probes pTub1, pFor1, and pSme1, slight cross hybridization occurred. However, the mycobacterial strains from which the cross-hybridizing PCR products were derived belonged to nonpathogenic or nonopportunistic species which do not occur in clinical samples. The test was used on 31 different clinical specimens obtained from patients suspected of having mycobacterial disease, including a patient with a double mycobacterial infection. The samples included sputum, bronchoalveolar lavage, tissue biopsy samples, cerebrospinal fluid, pus, peritoneal fluid, pleural fluid, and blood. The results of the PCR assay agreed with those of conventional identification methods or with clinical data, showing that the test can be used for the direct and rapid detection and identification of mycobacteria in clinical samples. PMID:8586707

  18. 32 CFR Appendix A to Part 169a - Codes and Definitions of Functional Areas

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 32 National Defense 1 2010-07-01 2010-07-01 false Codes and Definitions of Functional Areas A Appendix A to Part 169a National Defense Department of Defense OFFICE OF THE SECRETARY OF DEFENSE DEFENSE CONTRACTING COMMERCIAL ACTIVITIES PROGRAM PROCEDURES Pt. 169a, App. A Appendix A to Part 169a—Codes and Definitions of Functional Areas This list...

  19. 32 CFR Appendix A to Part 169a - Codes and Definitions of Functional Areas

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 32 National Defense 1 2011-07-01 2011-07-01 false Codes and Definitions of Functional Areas A Appendix A to Part 169a National Defense Department of Defense OFFICE OF THE SECRETARY OF DEFENSE DEFENSE CONTRACTING COMMERCIAL ACTIVITIES PROGRAM PROCEDURES Pt. 169a, App. A Appendix A to Part 169a—Codes and Definitions of Functional Areas This list...

  20. 32 CFR Appendix A to Part 169a - Codes and Definitions of Functional Areas

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 32 National Defense 1 2012-07-01 2012-07-01 false Codes and Definitions of Functional Areas A Appendix A to Part 169a National Defense Department of Defense OFFICE OF THE SECRETARY OF DEFENSE DEFENSE CONTRACTING COMMERCIAL ACTIVITIES PROGRAM PROCEDURES Pt. 169a, App. A Appendix A to Part 169a—Codes and Definitions of Functional Areas This list...

  1. 32 CFR Appendix A to Part 169a - Codes and Definitions of Functional Areas

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 32 National Defense 1 2014-07-01 2014-07-01 false Codes and Definitions of Functional Areas A Appendix A to Part 169a National Defense Department of Defense OFFICE OF THE SECRETARY OF DEFENSE DEFENSE CONTRACTING COMMERCIAL ACTIVITIES PROGRAM PROCEDURES Pt. 169a, App. A Appendix A to Part 169a—Codes and Definitions of Functional Areas This list...

  2. 32 CFR Appendix A to Part 169a - Codes and Definitions of Functional Areas

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 32 National Defense 1 2013-07-01 2013-07-01 false Codes and Definitions of Functional Areas A Appendix A to Part 169a National Defense Department of Defense OFFICE OF THE SECRETARY OF DEFENSE DEFENSE CONTRACTING COMMERCIAL ACTIVITIES PROGRAM PROCEDURES Pt. 169a, App. A Appendix A to Part 169a—Codes and Definitions of Functional Areas This list...

  3. Improving the identification of people with dementia in primary care: evaluation of the impact of primary care dementia coding guidance on identified prevalence

    PubMed Central

    Russell, Paul; Banerjee, Sube; Watt, Jen; Adleman, Rosalyn; Agoe, Belinda; Burnie, Nerida; Carefull, Alex; Chandan, Kiran; Constable, Dominie; Daniels, Mark; Davies, David; Deshmukh, Sid; Huddart, Martin; Jabin, Ashrafi; Jarrett, Penelope; King, Jenifer; Koch, Tamar; Kumar, Sanjoy; Lees, Stavroula; Mir, Sinan; Naidoo, Dominic; Nyame, Sylvia; Sasae, Ryuichiro; Sharma, Tushar; Thormod, Clare; Vedavanam, Krish; Wilton, Anja; Flaherty, Breda

    2013-01-01

    Objective Improving dementia care is a policy priority nationally and internationally; there is a ‘diagnosis gap’ with less than half of the cases of dementia ever diagnosed. The English Health Department's Quality and Outcomes Framework (QOF) encourages primary care recognition and recording of dementia. The codes for dementia are complex with the possibility of underidentification through miscoding. We developed guidance on coding of dementia; we report the impact of applying this to ‘clean up’ dementia coding and records at a practice level. Design The guidance had five elements: (1) identify Read Codes for dementia; (2) access QOF dementia register; (3) generate lists of patients who may have dementia; (4) compare search with QOF data and (5) review cases. In each practice, one general practitioner conducted the exercise. The number of dementia QOF registers before and after the exercise was recorded with the hours taken to complete the exercise. Setting London primary care. Participants 23 (85%) of 27 practices participated, covering 79 312 (19 562 over 65 s) participants. Outcomes The number on dementia QOF registers; time taken. Results The number of people with dementia on QOF registers increased from 1007 to 1139 (χ2=8.17, p=0.004), raising identification rates by 8.8%. It took 4.7 h per practice, on an average. Conclusions These data demonstrate the potential of a simple primary care coding exercise, requiring no specific training, to increase the dementia identification rate. An improvement of 8.8% between 2011 and 2012 is equivalent to that of the fourth most improved primary care trust in the UK. In absolute terms, if this effects were mirrored across the UK primary care, the number of cases with dementia identified would rise by over 70 000 from 364 329 to 434 488 raising the recognition rate from 46% to 54.8%. Implementing this exercise appears to be a simple and effective way to improve recognition rates in primary care. PMID

  4. Identification of Genes Potentially Responsible for extra-Oral Digestion and Overcoming Plant Defense from Salivary Glands of the Tarnished Plant Bug (Hemiptera: Miridae) Using cDNA Sequencing

    PubMed Central

    Zhu, Yu-Cheng; Yao, Jianxiu; Luttrell, Randall

    2016-01-01

    Saliva is known to play a crucial role in tarnished plant bug (TPB, Lygus lineolaris [Palisot de Beauvois]) feeding. By facilitating the piercing, the enzyme-rich saliva may be used for extra-oral digestion and for overcoming plant defense before the plant fluids are ingested by TPBs. To identify salivary gland genes, mRNA was extracted from salivary glands and cDNA library clones were sequenced. A de novo-assembling of 7,000 Sanger sequences revealed 666 high-quality unique cDNAs with an average size of 624 bp, in which the identities of 347 cDNAs were determined using Blast2GO. Kyoto Encyclopedia of Genes and Genomes analysis indicated that these genes participate in eighteen metabolic pathways. Identifications of large number of enzyme genes in TPB salivary glands evidenced functions for extra-oral digestion and feeding damage mechanism, including 45 polygalacturonase, two α- amylase, one glucosidase, one glycan enzyme, one aminopeptidase, four lipase, and many serine protease cDNAs. The presence of multiple transcripts, multigene members, and high abundance of cell wall degradation enzymes (polygalacturonases) indicated that the enzyme-rich saliva may cause damage to plants by breaking down plant cell walls to make nutrients available for feeding. We also identified genes potentially involved in insect adaptation and detoxifying xenobiotics that may allow insects to overcome plant defense responses, including four glutathione S-transferases, three esterases, one cytochrome P450, and several serine proteases. The gene profiles of TPB salivary glands revealed in this study provides a foundation for further understanding and potential development of novel enzymatic inhibitors, or other RNAi approaches that may interrupt or minimize TPB feeding damage. PMID:27324587

  5. Identification of Genes Potentially Responsible for extra-Oral Digestion and Overcoming Plant Defense from Salivary Glands of the Tarnished Plant Bug (Hemiptera: Miridae) Using cDNA Sequencing.

    PubMed

    Zhu, Yu-Cheng; Yao, Jianxiu; Luttrell, Randall

    2016-01-01

    Saliva is known to play a crucial role in tarnished plant bug (TPB, Lygus lineolaris [Palisot de Beauvois]) feeding. By facilitating the piercing, the enzyme-rich saliva may be used for extra-oral digestion and for overcoming plant defense before the plant fluids are ingested by TPBs. To identify salivary gland genes, mRNA was extracted from salivary glands and cDNA library clones were sequenced. A de novo-assembling of 7,000 Sanger sequences revealed 666 high-quality unique cDNAs with an average size of 624 bp, in which the identities of 347 cDNAs were determined using Blast2GO. Kyoto Encyclopedia of Genes and Genomes analysis indicated that these genes participate in eighteen metabolic pathways. Identifications of large number of enzyme genes in TPB salivary glands evidenced functions for extra-oral digestion and feeding damage mechanism, including 45 polygalacturonase, two α- amylase, one glucosidase, one glycan enzyme, one aminopeptidase, four lipase, and many serine protease cDNAs. The presence of multiple transcripts, multigene members, and high abundance of cell wall degradation enzymes (polygalacturonases) indicated that the enzyme-rich saliva may cause damage to plants by breaking down plant cell walls to make nutrients available for feeding. We also identified genes potentially involved in insect adaptation and detoxifying xenobiotics that may allow insects to overcome plant defense responses, including four glutathione S-transferases, three esterases, one cytochrome P450, and several serine proteases. The gene profiles of TPB salivary glands revealed in this study provides a foundation for further understanding and potential development of novel enzymatic inhibitors, or other RNAi approaches that may interrupt or minimize TPB feeding damage. PMID:27324587

  6. High resolution methylome map of rat indicates role of intragenic DNA methylation in identification of coding region.

    PubMed

    Sati, Satish; Tanwar, Vinay Singh; Kumar, K Anand; Patowary, Ashok; Jain, Vaibhav; Ghosh, Sourav; Ahmad, Shadab; Singh, Meghna; Reddy, S Umakar; Chandak, Giriraj Ratan; Raghunath, Manchala; Sivasubbu, Sridhar; Chakraborty, Kausik; Scaria, Vinod; Sengupta, Shantanu

    2012-01-01

    DNA methylation is crucial for gene regulation and maintenance of genomic stability. Rat has been a key model system in understanding mammalian systemic physiology, however detailed rat methylome remains uncharacterized till date. Here, we present the first high resolution methylome of rat liver generated using Methylated DNA immunoprecipitation and high throughput sequencing (MeDIP-Seq) approach. We observed that within the DNA/RNA repeat elements, simple repeats harbor the highest degree of methylation. Promoter hypomethylation and exon hypermethylation were common features in both RefSeq genes and expressed genes (as evaluated by proteomic approach). We also found that although CpG islands were generally hypomethylated, about 6% of them were methylated and a large proportion (37%) of methylated islands fell within the exons. Notably, we obeserved significant differences in methylation of terminal exons (UTRs); methylation being more pronounced in coding/partially coding exons compared to the non-coding exons. Further, events like alternate exon splicing (cassette exon) and intron retentions were marked by DNA methylation and these regions are retained in the final transcript. Thus, we suggest that DNA methylation could play a crucial role in marking coding regions thereby regulating alternative splicing. Apart from generating the first high resolution methylome map of rat liver tissue, the present study provides several critical insights into methylome organization and extends our understanding of interplay between epigenome, gene expression and genome stability. PMID:22355382

  7. Identification of a Conserved Non-Protein-Coding Genomic Element that Plays an Essential Role in Alphabaculovirus Pathogenesis

    PubMed Central

    Kikhno, Irina

    2014-01-01

    Highly homologous sequences 154–157 bp in length grouped under the name of “conserved non-protein-coding element” (CNE) were revealed in all of the sequenced genomes of baculoviruses belonging to the genus Alphabaculovirus. A CNE alignment led to the detection of a set of highly conserved nucleotide clusters that occupy strictly conserved positions in the CNE sequence. The significant length of the CNE and conservation of both its length and cluster architecture were identified as a combination of characteristics that make this CNE different from known viral non-coding functional sequences. The essential role of the CNE in the Alphabaculovirus life cycle was demonstrated through the use of a CNE-knockout Autographa californica multiple nucleopolyhedrovirus (AcMNPV) bacmid. It was shown that the essential function of the CNE was not mediated by the presumed expression activities of the protein- and non-protein-coding genes that overlap the AcMNPV CNE. On the basis of the presented data, the AcMNPV CNE was categorized as a complex-structured, polyfunctional genomic element involved in an essential DNA transaction that is associated with an undefined function of the baculovirus genome. PMID:24740153

  8. Radiological Defense. Textbook.

    ERIC Educational Resources Information Center

    Defense Civil Preparedness Agency (DOD), Washington, DC.

    This textbook has been prepared under the direction of the Defense Civil Preparedness Agency (DCPA) Staff College for use as a student reference manual in radiological defense (RADEF) courses. It provides much of the basic technical information necessary for a proper understanding of radiological defense and summarizes RADEF planning and expected…

  9. Mobile, hybrid Compton/coded aperture imaging for detection, identification and localization of gamma-ray sources at stand-off distances

    NASA Astrophysics Data System (ADS)

    Tornga, Shawn R.

    The Stand-off Radiation Detection System (SORDS) program is an Advanced Technology Demonstration (ATD) project through the Department of Homeland Security's Domestic Nuclear Detection Office (DNDO) with the goal of detection, identification and localization of weak radiological sources in the presence of large dynamic backgrounds. The Raytheon-SORDS Tri-Modal Imager (TMI) is a mobile truck-based, hybrid gamma-ray imaging system able to quickly detect, identify and localize, radiation sources at standoff distances through improved sensitivity while minimizing the false alarm rate. Reconstruction of gamma-ray sources is performed using a combination of two imaging modalities; coded aperture and Compton scatter imaging. The TMI consists of 35 sodium iodide (NaI) crystals 5x5x2 in3 each, arranged in a random coded aperture mask array (CA), followed by 30 position sensitive NaI bars each 24x2.5x3 in3 called the detection array (DA). The CA array acts as both a coded aperture mask and scattering detector for Compton events. The large-area DA array acts as a collection detector for both Compton scattered events and coded aperture events. In this thesis, developed coded aperture, Compton and hybrid imaging algorithms will be described along with their performance. It will be shown that multiple imaging modalities can be fused to improve detection sensitivity over a broader energy range than either alone. Since the TMI is a moving system, peripheral data, such as a Global Positioning System (GPS) and Inertial Navigation System (INS) must also be incorporated. A method of adapting static imaging algorithms to a moving platform has been developed. Also, algorithms were developed in parallel with detector hardware, through the use of extensive simulations performed with the Geometry and Tracking Toolkit v4 (GEANT4). Simulations have been well validated against measured data. Results of image reconstruction algorithms at various speeds and distances will be presented as well as

  10. Identification of Tissue-Specific Protein-Coding and Noncoding Transcripts across 14 Human Tissues Using RNA-seq

    PubMed Central

    Zhu, Jinhang; Chen, Geng; Zhu, Sibo; Li, Suqing; Wen, Zhuo; Bin Li; Zheng, Yuanting; Shi, Leming

    2016-01-01

    Many diseases and adverse drug reactions exhibit tissue specificity. To better understand the tissue-specific expression characteristics of transcripts in different human tissues, we deeply sequenced RNA samples from 14 different human tissues. After filtering many lowly expressed transcripts, 24,729 protein-coding transcripts and 1,653 noncoding transcripts were identified. By analyzing highly expressed tissue-specific protein-coding transcripts (TSCTs) and noncoding transcripts (TSNTs), we found that testis expressed the highest numbers of TSCTs and TSNTs. Brain, monocytes, ovary, and heart expressed more TSCTs than the rest tissues, whereas brain, placenta, heart, and monocytes expressed more TSNTs than other tissues. Co-expression network constructed based on the TSCTs and TSNTs showed that each hub TSNT was co-expressed with several TSCTs, allowing functional annotation of TSNTs. Important biological processes and KEGG pathways highly related to the specific functions or diseases of each tissue were enriched with the corresponding TSCTs. These TSCTs and TSNTs may participate in the tissue-specific physiological or pathological processes. Our study provided a unique data set and systematic analysis of expression characteristics and functions of both TSCTs and TSNTs based on 14 distinct human tissues, and could facilitate future investigation of the mechanisms behind tissue-specific diseases and adverse drug reactions. PMID:27329541

  11. Identification of differentially expressed small non-coding RNAs in the legume endosymbiont Sinorhizobium meliloti by comparative genomics.

    PubMed

    del Val, Coral; Rivas, Elena; Torres-Quesada, Omar; Toro, Nicolás; Jiménez-Zurdo, José I

    2007-12-01

    Bacterial small non-coding RNAs (sRNAs) are being recognized as novel widespread regulators of gene expression in response to environmental signals. Here, we present the first search for sRNA-encoding genes in the nitrogen-fixing endosymbiont Sinorhizobium meliloti, performed by a genome-wide computational analysis of its intergenic regions. Comparative sequence data from eight related alpha-proteobacteria were obtained, and the interspecies pairwise alignments were scored with the programs eQRNA and RNAz as complementary predictive tools to identify conserved and stable secondary structures corresponding to putative non-coding RNAs. Northern experiments confirmed that eight of the predicted loci, selected among the original 32 candidates as most probable sRNA genes, expressed small transcripts. This result supports the combined use of eQRNA and RNAz as a robust strategy to identify novel sRNAs in bacteria. Furthermore, seven of the transcripts accumulated differentially in free-living and symbiotic conditions. Experimental mapping of the 5'-ends of the detected transcripts revealed that their encoding genes are organized in autonomous transcription units with recognizable promoter and, in most cases, termination signatures. These findings suggest novel regulatory functions for sRNAs related to the interactions of alpha-proteobacteria with their eukaryotic hosts. PMID:17971083

  12. Identification of differentially expressed small non-coding RNAs in the legume endosymbiont Sinorhizobium meliloti by comparative genomics

    PubMed Central

    del Val, Coral; Rivas, Elena; Torres-Quesada, Omar; Toro, Nicolás; Jiménez-Zurdo, José I

    2007-01-01

    Bacterial small non-coding RNAs (sRNAs) are being recognized as novel widespread regulators of gene expression in response to environmental signals. Here, we present the first search for sRNA-encoding genes in the nitrogen-fixing endosymbiont Sinorhizobium meliloti, performed by a genome-wide computational analysis of its intergenic regions. Comparative sequence data from eight related α-proteobacteria were obtained, and the interspecies pairwise alignments were scored with the programs eQRNA and RNAz as complementary predictive tools to identify conserved and stable secondary structures corresponding to putative non-coding RNAs. Northern experiments confirmed that eight of the predicted loci, selected among the original 32 candidates as most probable sRNA genes, expressed small transcripts. This result supports the combined use of eQRNA and RNAz as a robust strategy to identify novel sRNAs in bacteria. Furthermore, seven of the transcripts accumulated differentially in free-living and symbiotic conditions. Experimental mapping of the 5′-ends of the detected transcripts revealed that their encoding genes are organized in autonomous transcription units with recognizable promoter and, in most cases, termination signatures. These findings suggest novel regulatory functions for sRNAs related to the interactions of α-proteobacteria with their eukaryotic hosts. PMID:17971083

  13. Identification and analysis of the genes coding for the putative pyruvate dehydrogenase enzyme complex in Acholeplasma laidlawii.

    PubMed Central

    Wallbrandt, P; Tegman, V; Jonsson, B H; Wieslander, A

    1992-01-01

    A monospecific antibody recognizing two membrane proteins in Acholeplasma laidlawii identified a plasmid clone from a genomic library. The nucleotide sequence of the 4.6-kbp insert contained four sequential genes coding for proteins of 39 kDa (E1 alpha, N terminus not cloned), 36 kDa (E1 beta), 57 kDa (E2), and 36 kDa (E3; C terminus not cloned). The N termini of the cloned E2, E1 beta, and native A. laidlawii E2 proteins were verified by amino acid sequencing. Computer-aided searches showed that the translated DNA sequences were homologous to the four subenzymes of the pyruvate dehydrogenase complexes from gram-positive bacteria and humans. The plasmid-encoded 57-kDa (E2) protein was recognized by antibodies against the E2 subenzymes of the pyruvate and oxoglutarate dehydrogenase complexes from Bacillus subtilis. A substantial fraction of the E2 protein as well as part of the pyruvate dehydrogenase enzymatic activity was associated with the cytoplasmic membrane in A. laidlawii. In vivo complementation with three different Escherichia coli pyruvate dehydrogenase-defective mutants showed that the four plasmid-encoded proteins were able to restore pyruvate dehydrogenase enzyme activity in E. coli. Since A. laidlawii lacks oxoglutarate dehydrogenase and most likely branched-chain dehydrogenase enzyme complex activities, these results strongly suggest that the sequenced genes code for the pyruvate dehydrogenase complex. Images PMID:1735725

  14. Identification of Tissue-Specific Protein-Coding and Noncoding Transcripts across 14 Human Tissues Using RNA-seq.

    PubMed

    Zhu, Jinhang; Chen, Geng; Zhu, Sibo; Li, Suqing; Wen, Zhuo; Bin Li; Zheng, Yuanting; Shi, Leming

    2016-01-01

    Many diseases and adverse drug reactions exhibit tissue specificity. To better understand the tissue-specific expression characteristics of transcripts in different human tissues, we deeply sequenced RNA samples from 14 different human tissues. After filtering many lowly expressed transcripts, 24,729 protein-coding transcripts and 1,653 noncoding transcripts were identified. By analyzing highly expressed tissue-specific protein-coding transcripts (TSCTs) and noncoding transcripts (TSNTs), we found that testis expressed the highest numbers of TSCTs and TSNTs. Brain, monocytes, ovary, and heart expressed more TSCTs than the rest tissues, whereas brain, placenta, heart, and monocytes expressed more TSNTs than other tissues. Co-expression network constructed based on the TSCTs and TSNTs showed that each hub TSNT was co-expressed with several TSCTs, allowing functional annotation of TSNTs. Important biological processes and KEGG pathways highly related to the specific functions or diseases of each tissue were enriched with the corresponding TSCTs. These TSCTs and TSNTs may participate in the tissue-specific physiological or pathological processes. Our study provided a unique data set and systematic analysis of expression characteristics and functions of both TSCTs and TSNTs based on 14 distinct human tissues, and could facilitate future investigation of the mechanisms behind tissue-specific diseases and adverse drug reactions. PMID:27329541

  15. Identification and expression patterns of novel long non-coding RNAs in neural progenitors of the developing mammalian cortex

    PubMed Central

    Aprea, Julieta; Lesche, Mathias; Massalini, Simone; Prenninger, Silvia; Alexopoulou, Dimitra; Dahl, Andreas; Hiller, Michael; Calegari, Federico

    2015-01-01

    Long non-coding (lnc)RNAs play key roles in many biological processes. Elucidating the function of lncRNAs in cell type specification during organ development requires knowledge about their expression in individual progenitor types rather than in whole tissues. To achieve this during cortical development, we used a dual-reporter mouse line to isolate coexisting proliferating neural stem cells, differentiating neurogenic progenitors and newborn neurons and assessed the expression of lncRNAs by paired-end, high-throughput sequencing. We identified 379 genomic loci encoding novel lncRNAs and performed a comprehensive assessment of cell-specific expression patterns for all, annotated and novel, lncRNAs described to date. Our study provides a powerful new resource for studying these elusive transcripts during stem cell commitment and neurogenesis.

  16. lncRNA-MFDL: identification of human long non-coding RNAs by fusing multiple features and using deep learning.

    PubMed

    Fan, Xiao-Nan; Zhang, Shao-Wu

    2015-03-01

    Long noncoding RNAs (lncRNAs) are emerging as a novel class of noncoding RNAs and potent gene regulators, which play an important and varied role in cellular functions. lncRNAs are closely related with the occurrence and development of some diseases. High-throughput RNA-sequencing techniques combined with de novo assembly have identified a large number of novel transcripts. The discovery of large and 'hidden' transcriptomes urgently requires the development of effective computational methods that can rapidly distinguish between coding and long noncoding RNAs. In this study, we developed a powerful predictor (named as lncRNA-MFDL) to identify lncRNAs by fusing multiple features of the open reading frame, k-mer, the secondary structure and the most-like coding domain sequence and using deep learning classification algorithms. Using the same human training dataset and a 10-fold cross validation test, lncRNA-MFDL can achieve 97.1% prediction accuracy which is 5.7, 3.7, and 3.4% higher than that of CPC, CNCI and lncRNA-FMFSVM predictors, respectively. Compared with CPC and CNCI predictors in other species (e.g., anole lizard, zebrafish, chicken, gorilla, macaque, mouse, lamprey, orangutan, xenopus and C. elegans) testing datasets, the new lncRNA-MFDL predictor is also much more effective and robust. These results show that lncRNA-MFDL is a powerful tool for identifying lncRNAs. The lncRNA-MFDL software package is freely available at for academic users. PMID:25588719

  17. Perceptions of Usefulness: Using the Holland Code Theory, Multiple Intelligences Theory, and Role Model Identification to Determine a Career Niche in the Fashion Industry for First-Quarter Fashion Students

    ERIC Educational Resources Information Center

    Green, Crystal D.

    2010-01-01

    This action research study investigated the perceptions that student participants had on the development of a career exploration model and a career exploration project. The Holland code theory was the primary assessment used for this research study, in addition to the Multiple Intelligences theory and the identification of a role model for the…

  18. Experimental RNomics in Aquifex aeolicus: identification of small non-coding RNAs and the putative 6S RNA homolog

    PubMed Central

    Willkomm, Dagmar K.; Minnerup, Jens; Hüttenhofer, Alexander; Hartmann, Roland K.

    2005-01-01

    By an experimental RNomics approach, we have generated a cDNA library from small RNAs expressed from the genome of the hyperthermophilic bacterium Aquifex aeolicus. The library included RNAs that were antisense to mRNAs and tRNAs as well as RNAs encoded in intergenic regions. Substantial steady-state levels in A.aeolicus cells were confirmed for several of the cloned RNAs by northern blot analysis. The most abundant intergenic RNA of the library was identified as the 6S RNA homolog of A.aeolicus. Although shorter in size (150 nt) than its γ-proteobacterial homologs (∼185 nt), it is predicted to have the most stable structure among known 6S RNAs. As in the γ-proteobacteria, the A.aeolicus 6S RNA gene (ssrS) is located immediately upstream of the ygfA gene encoding a widely conserved 5-formyltetrahydrofolate cyclo-ligase. We identifed novel 6S RNA candidates within the γ-proteobacteria but were unable to identify reasonable 6S RNA candidates in other bacterial branches, utilizing mfold analyses of the region immediately upstream of ygfA combined with 6S RNA blastn searches. By RACE experiments, we mapped the major transcription initiation site of A.aeolicus 6S RNA primary transcripts, located within the pheT gene preceding ygfA, as well as three processing sites. PMID:15814812

  19. 32 CFR 634.25 - Installation traffic codes.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 32 National Defense 4 2013-07-01 2013-07-01 false Installation traffic codes. 634.25 Section 634.25 National Defense Department of Defense (Continued) DEPARTMENT OF THE ARMY (CONTINUED) LAW ENFORCEMENT AND CRIMINAL INVESTIGATIONS MOTOR VEHICLE TRAFFIC SUPERVISION Traffic Supervision § 634.25 Installation traffic codes. (a) Installation...

  20. 32 CFR 634.25 - Installation traffic codes.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 32 National Defense 4 2011-07-01 2011-07-01 false Installation traffic codes. 634.25 Section 634.25 National Defense Department of Defense (Continued) DEPARTMENT OF THE ARMY (CONTINUED) LAW ENFORCEMENT AND CRIMINAL INVESTIGATIONS MOTOR VEHICLE TRAFFIC SUPERVISION Traffic Supervision § 634.25 Installation traffic codes. (a) Installation...

  1. Identification of long non-coding RNAs as novel biomarker and potential therapeutic target for atrial fibrillation in old adults

    PubMed Central

    Xu, Yingjia; Huang, Ritai; Gu, Jianing; Jiang, Weifeng

    2016-01-01

    Atrial fibrillation (AF) is a highly prevalent cardiac arrhythmia disease, which widely leads to exacerbate heart failure and ischemic stroke in elder world. Recently, long non-coding RNAs (lncRNAs), a subclass of noncoding RNAs, have been reported to play critical roles in pathophysiology of cardiac heart. However, little is known of their role in cardiac arrhythmia. In the present study, we investigated the expression levels of lncRNAs of AF patients and healthy people with Agilent Human lncRNA array for the first time. 177 lncRNAs of 78243 and 153 mRNAs of 30215 tested were identified to be differentially expressed (≥ 2-fold change), indicating that the expression of many lncRNAs are upregulated or downregulated in AF. Among these, NONHSAT040387 and NONHSAT098586 were the most upregulated and downregulated lncRNAs. Real time quantitative PCR were employed to validate the microarray analysis findings, and the results confirmed the consistence. GO and KEGG pathway analysis were applied to explore the potential lncRNAs functions, some pathways including oxygen transporter activity and protein heterodimerization activity were speculated to be involved in AF pathogenesis. These results shed some light on lncRNAs' physiologic functions and provide useful information for exploring potential therapeutic treatments for heart rhythm disease. PMID:26908457

  2. Identification of a long non-coding RNA NR_026689 associated with lung carcinogenesis induced by NNK

    PubMed Central

    Xu, Yiqin; Yang, Ti; Yang, Qiaoyuan; Yang, Chengfeng; Jiang, Yiguo

    2016-01-01

    Long non-coding RNAs (lncRNA) are thought to be important epigenetic regulators involved in the development of a variety of cancers. Alterations in lncRNA expression are associated with exposure to chemical carcinogens. However, it is still unclear whether lncRNA expression during lung carcinogenesis is induced by chemical carcinogens. In this study, using NNK-induced rat lung cancer model established by our previous study, we determined the lncRNA expression profiles, and an alteration in lncRNA expression was observed in lung cancer tissues and blood in the NNK treatment group. Using quantitative reverse-transcription PCR (qRT-PCR), five differentially expressed lncRNAs were further detected and validated. We identified a novel lncRNA, NR_026689, which showed increased expression in lung cancer tissues induced by NNK and the alteration of lncRNA NR_026689 was specifically observed in lung tissue. The level of NR_026689 was determined and significantly increased in rat whole blood at the 10th and 20th week after NNK treatment to evaluate it as a potential early marker for lung cancer. Together, these findings suggest that lncRNA NR_026689 may be a potential early biomarker for lung cancer and is associated with lung carcinogenesis induced by NNK. PMID:26908441

  3. Identification of a long non-coding RNA-associated RNP complex regulating metastasis at the translational step

    PubMed Central

    Gumireddy, Kiranmai; Li, Anping; Yan, Jinchun; Setoyama, Tetsuro; Johannes, Gregg J; Ørom, Ulf A; Tchou, Julia; Liu, Qin; Zhang, Lin; Speicher, David W; Calin, George A; Huang, Qihong

    2013-01-01

    Long non-coding RNAs (lncRNAs) are a novel class of regulatory genes that play critical roles in various processes ranging from normal development to human diseases such as cancer progression. Recent studies have shown that lncRNAs regulate the gene expression by chromatin remodelling, transcription, splicing and RNA decay control, enhancer function, and epigenetic regulation. However, little is known about translation regulation by lncRNAs. We identified a translational regulatory lncRNA (treRNA) through genome-wide computational analysis. We found that treRNA is upregulated in paired clinical breast cancer primary and lymph-node metastasis samples, and that its expression stimulates tumour invasion in vitro and metastasis in vivo. Interestingly, we found that treRNA downregulates the expression of the epithelial marker E-cadherin by suppressing the translation of its mRNA. We identified a novel ribonucleoprotein (RNP) complex, consisting of RNA-binding proteins (hnRNP K, FXR1, and FXR2), PUF60 and SF3B3, that is required for this treRNA functions. Translational suppression by treRNA is dependent on the 3′UTR of the E-cadherin mRNA. Taken together, our study indicates a novel mechanism of gene regulation by lncRNAs in cancer progression. PMID:23974796

  4. 77 FR 43469 - Defense Federal Acquisition Regulation Supplement; Technical Amendments

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-07-24

    ... from the Code of Federal Regulations with the publication of DFARS Case 2011-D048 (77 FR 19128), and... DFARS Case 2012-D003 (77 FR 35879). List of Subjects in 48 CFR Part 252 Government procurement. Ynette R... Defense Acquisition Regulations System 48 CFR Part 252 Defense Federal Acquisition Regulation...

  5. 32 CFR 635.19 - Offense codes.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 32 National Defense 4 2010-07-01 2010-07-01 true Offense codes. 635.19 Section 635.19 National... INVESTIGATIONS LAW ENFORCEMENT REPORTING Offense Reporting § 635.19 Offense codes. (a) The offense code describes, as nearly as possible, the complaint or offense by using an alphanumeric code. Appendix C of AR...

  6. Technologies for Distributed Defense

    SciTech Connect

    Seiders, Barbara AB; Rybka, Anthony J.

    2002-07-01

    For Americans, the nature of warfare changed on September 11, 2001. Our national security henceforth will require distributed defense. One extreme of distributed defense is represented by fully deployed military troops responding to a threat from a hostile nation state. At the other extreme is a country of "citizen soldiers," with families and communities securing their common defense through heightened awareness, engagement as good neighbors, and local support of and cooperation with local law enforcement, emergency and health care providers. Technologies - for information exploitation, biological agent detection, health care surveillance, and security - will be critical to ensuring success in distributed defense.

  7. Environmental Fluid Dynamics Code

    EPA Science Inventory

    The Environmental Fluid Dynamics Code (EFDC)is a state-of-the-art hydrodynamic model that can be used to simulate aquatic systems in one, two, and three dimensions. It has evolved over the past two decades to become one of the most widely used and technically defensible hydrodyn...

  8. Identification of a non-coding KLF4 transcript generated from intron retention and downregulated in human hepatocellular carcinoma.

    PubMed

    Zhou, Junwei; Lai, Paul Bo-San; Tsui, Stephen Kwok-Wing

    2015-10-01

    The Krüppel-like factor 4 (KLF4) gene is related to various biological processes including stem cell reprogramming and tumorigenesis. In this study, we identified and characterized a non-coding transcript of KLF4, which was designated KLF4‑003, in human liver tissue samples. KLF4‑003 was identified in a number of cell lines by reverse transcription PCR and DNA sequencing. Its expression levels were determined in 54 pairs of human hepatocellular carcinoma (HCC) tissues and a number of HCC cell lines by real-time PCR (RT-PCR). Methylation status of KLF4‑003 CpG islands was determined by bisulfite sequencing. The regulatory effect of KLF4‑003 CpG islands hypermethylation in Hep3B cells was then validated by the 5-aza-dC demethylation treatment, followed by RT-PCR analysis. Receiver operating characteristic (ROC) curve was created to evaluate the diagnostic value for differentiating between HCC cancer and benign diseases. The association study between KLF4‑003 expression level and clinical traits of HCC patients was performed with SPSS. We found that KLF4‑003 was downregulated in 46 out of 54 HCC samples compared with their adjunct normal tissues. The reduced KLF4‑003 expression was significantly associated with HCC recurrence (P=0.045) in the follow-up of 31 HCC patients. Significant differences were detected between the methylation status of HCC specimens and their adjacent normal controls. Demethylation treatment significantly rescued the expression of KLF4‑003 in Hep3B cells. Such observation indicated that the CpG island hypermethylation was at least partially responsible for the downregulation of KLF4‑003 in HCC. The area under ROC curve for the prediction of HCC reached 0.803 (95% CI=0.719-0.886, P<0.001). Our results suggested that the expression of KLF4‑003 was epigenetically regulated by methylation status of a KLF4‑003 CpG island in HCC. The differential expression of KLF4‑003 might play an important role in HCC development and might

  9. 22 CFR 130.4 - Defense articles and defense services.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 22 Foreign Relations 1 2014-04-01 2014-04-01 false Defense articles and defense services. 130.4 Section 130.4 Foreign Relations DEPARTMENT OF STATE INTERNATIONAL TRAFFIC IN ARMS REGULATIONS POLITICAL CONTRIBUTIONS, FEES AND COMMISSIONS § 130.4 Defense articles and defense services. Defense articles and...

  10. 22 CFR 130.4 - Defense articles and defense services.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 22 Foreign Relations 1 2012-04-01 2012-04-01 false Defense articles and defense services. 130.4 Section 130.4 Foreign Relations DEPARTMENT OF STATE INTERNATIONAL TRAFFIC IN ARMS REGULATIONS POLITICAL CONTRIBUTIONS, FEES AND COMMISSIONS § 130.4 Defense articles and defense services. Defense articles and...

  11. 22 CFR 130.4 - Defense articles and defense services.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 22 Foreign Relations 1 2013-04-01 2013-04-01 false Defense articles and defense services. 130.4 Section 130.4 Foreign Relations DEPARTMENT OF STATE INTERNATIONAL TRAFFIC IN ARMS REGULATIONS POLITICAL CONTRIBUTIONS, FEES AND COMMISSIONS § 130.4 Defense articles and defense services. Defense articles and...

  12. 22 CFR 130.4 - Defense articles and defense services.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 22 Foreign Relations 1 2010-04-01 2010-04-01 false Defense articles and defense services. 130.4 Section 130.4 Foreign Relations DEPARTMENT OF STATE INTERNATIONAL TRAFFIC IN ARMS REGULATIONS POLITICAL CONTRIBUTIONS, FEES AND COMMISSIONS § 130.4 Defense articles and defense services. Defense articles and...

  13. 22 CFR 130.4 - Defense articles and defense services.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 22 Foreign Relations 1 2011-04-01 2011-04-01 false Defense articles and defense services. 130.4 Section 130.4 Foreign Relations DEPARTMENT OF STATE INTERNATIONAL TRAFFIC IN ARMS REGULATIONS POLITICAL CONTRIBUTIONS, FEES AND COMMISSIONS § 130.4 Defense articles and defense services. Defense articles and...

  14. Schools and Civil Defense.

    ERIC Educational Resources Information Center

    Office of Civil Defense (DOD), Washington, DC.

    Civil defense is a planned, coordinated action to protect the population during any emergency whether arising from thermonuclear attack or natural disaster. The Federal Government has assumed four responsibilities--(1) to keep track of the nature of the threat which the civil defense program must meet, (2) to prepare and disseminate information…

  15. Forgiveness and Defense Style

    ERIC Educational Resources Information Center

    Maltby, John; Day, Liz

    2004-01-01

    Within the literature on the psychology of forgiveness, researchers have hypothesized that the 1st stage in the process of being able to forgive is the role of psychological defense. To examine such a hypothesis, the authors explored the relationship between forgiveness and defense style. The 304 respondents (151 men, 153 women) completed measures…

  16. Defense Mechanisms: A Bibliography.

    ERIC Educational Resources Information Center

    Pedrini, D. T.; Pedrini, Bonnie C.

    This bibliography includes studies of defense mechanisms, in general, and studies of multiple mechanisms. Defense mechanisms, briefly and simply defined, are the unconscious ego defendants against unpleasure, threat, or anxiety. Sigmund Freud deserves the clinical credit for studying many mechanisms and introducing them in professional literature.…

  17. Two systems and defenses.

    PubMed

    Novick, Jack; Novick, Kerry Kelly

    2013-02-01

    The authors suggest that Freud's concept of defense differentiated psychoanalysis from other medical and psychological theories of personality development and functioning then and now. Reclaiming the concept's centrality and linking it with interdisciplinary research findings, they illustrate their extension of defense into a two-system model of self-protection and self-regulation with a clinical example. The authors suggest that the two-system model allows for the reintegration of defense into a multidimensional psychoanalytic theory and multimodal therapeutic technique. PMID:23421665

  18. 77 FR 3369 - Presidential Determination on the Eligibility of South Sudan To Receive Defense Articles and...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-24

    ... HOUSE, Washington, January 6, 2012 [FR Doc. 2012-1545 Filed 1-23-12; 8:45 am] Billing code 4710-10-P ... the Eligibility of South Sudan To Receive Defense Articles and Defense Services Under the Foreign... defense services to the Republic of South Sudan will strengthen the security of the United States...

  19. 32 CFR 321.4 - Requirements for identification.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... are maintained in a DSS system. (b) Identification. Identification of individuals is required both for... 32 National Defense 2 2012-07-01 2012-07-01 false Requirements for identification. 321.4 Section...) PRIVACY PROGRAM DEFENSE SECURITY SERVICE PRIVACY PROGRAM § 321.4 Requirements for identification....

  20. 32 CFR 321.4 - Requirements for identification.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... are maintained in a DSS system. (b) Identification. Identification of individuals is required both for... 32 National Defense 2 2011-07-01 2011-07-01 false Requirements for identification. 321.4 Section...) PRIVACY PROGRAM DEFENSE SECURITY SERVICE PRIVACY PROGRAM § 321.4 Requirements for identification....

  1. Identification and functional characterization of cDNAs coding for hydroxybenzoate/hydroxycinnamate glucosyltransferases co-expressed with genes related to proanthocyanidin biosynthesis

    PubMed Central

    Khater, F.; Fournand, D.; Vialet, S.; Meudec, E.; Cheynier, V.; Terrier, N.

    2012-01-01

    Grape proanthocyanidins (PAs) play a major role in the organoleptic properties of wine. They are accumulated mainly in grape skin and seeds during the early stages of berry development. Despite the recent progress in the identification of genes involved in PA biosynthesis, the mechanisms involved in subunit condensation, galloylation, or fine regulation of the spatio-temporal composition of grape berries in PAs are still not elucidated. Two Myb transcription factors, VvMybPA1 and VvMybPA2, controlling the PA pathway have recently been identified and ectopically over-expressed in an homologous system. In addition to already known PA genes, three genes coding for glucosyltransferases were significantly differentially expressed between hairy roots over-expressing VvMybPA1 or VvMybPA2 and control lines. The involvement of these genes in PA biosynthesis metabolism is unclear. The three glucosyltransferases display high sequence similarities with other plant glucosyltransferases able to catalyse the formation of glucose esters, which are important intermediate actors for the synthesis of different phenolic compounds. Studies of the in vitro properties of these three enzymes (Km, Vmax, substrate specificity, pH sensitivity) were performed through production of recombinant proteins in E. coli and demonstrated that they are able to catalyse the formation of 1-O-acyl-Glc esters of phenolic acids but are not active on flavonoids and stilbenes. The transcripts are expressed in the early stages of grape berry development, mainly in the berry skins and seeds. The results presented here suggest that these enzymes could be involved in vivo in PA galloylation or in the synthesis of hydroxycinnamic esters. PMID:22090445

  2. Identification of a genetic alteration in the code for bilirubin UDP-glucuronosyltransferase in the UGT1 gene complex of a Crigler-Najjar type I patient.

    PubMed Central

    Ritter, J K; Yeatman, M T; Ferreira, P; Owens, I S

    1992-01-01

    Patients with Crigler-Najjar syndrome (CN) type I inherit an autosomal recessive trait for hyperbilirubinemia, which is characterized by the total absence of bilirubin UDP-glucuronosyltransferase (transferase) activity. The recent identification of two bilirubin transferase isoforms with identical carboxyl termini (Ritter, J. K., J. M. Crawford, and I. S. Owens. 1991. J. Biol. Chem. 266:1043-1047) led to the discovery of a unique locus, UGT1, which encodes a family of UDP-glucuronosyltransferase isozymes, including the two bilirubin forms (Ritter, J. K., F. Chen, Y. Y. Sheen, H. M. Tran, S. Kimura, M. T. Yeatman, and I. S. Owens. 1992. J. Biol. Chem. 267:3257-3261). The UGT1 locus features a complex of six overlapping transcriptional units encoding transferases, each of which shares the four most 3' exons (2, 3, 4, and 5) specifying the 3' half of the transferase coding regions (condons 289-533) and the entire 3' untranslated region of each mRNA. This gene model predicts that a single critical mutation in any of these four "common" exons may inactivate the entire family of encoded transferases. In agreement with this prediction, we show here that in the first CN type I individual analyzed (patient F.B.), a 13-bp deletion has occurred in exon 2. Analysis of product generated by the polymerase chain reaction and genomic DNA demonstrated that F.B. is homozygous for the defective allele (UGT1*FB), and that the consanguineous parents are both heterozygotic at this locus. The mutation is predicted to result in the synthesis of severely truncated bilirubin transferase isozymes that are lacking a highly conserved sequence in the carboxyl-terminus and the characteristic membrane (endoplasmic reticulum)-anchoring segment of the protein molecule. Images PMID:1634606

  3. Moscow's defense intellectuals

    SciTech Connect

    Lambeth, B.S.

    1990-01-01

    This essay was originally written two decades ago as a seminar paper. A substantial portion of it addresses what were then only the first steps toward the establishment of a community of professional civilian defense analysts in the Soviet Union. Throughout most of the intervening period, that community found itself mired in immobilism as jurisdiction over such key Soviet national security inputs as military doctrine, force requirements, resource needs, and to a considerable degree, arms negotiating positions remained an exclusive prerogative of the Defense Ministry and the General Staff. Today, this former military monopoly has come to be challenged with increasing success by a host of newcomers to the Soviet defense scene, including the Foreign Ministry, the Supreme Soviet, and an ambitious cadre of civilian analysts attached to the social science research institutes of the Academy of Sciences. These individuals are making a determined bid for greater influence over Soviet defense policy, with the express encouragement of President Gorbachev and his supporters. The result has been an unprecedented infusion of pluralism into Soviet defense politics and a significant change in the content and goals of Soviet military policy.

  4. 32 CFR 1662.3 - Identification of information requested.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 32 National Defense 6 2014-07-01 2014-07-01 false Identification of information requested. 1662.3 Section 1662.3 National Defense Other Regulations Relating to National Defense SELECTIVE SERVICE SYSTEM FREEDOM OF INFORMATION ACT (FOIA) PROCEDURES § 1662.3 Identification of information requested. Any...

  5. 32 CFR 1662.3 - Identification of information requested.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 32 National Defense 6 2012-07-01 2012-07-01 false Identification of information requested. 1662.3 Section 1662.3 National Defense Other Regulations Relating to National Defense SELECTIVE SERVICE SYSTEM FREEDOM OF INFORMATION ACT (FOIA) PROCEDURES § 1662.3 Identification of information requested. Any person who requests information under...

  6. 32 CFR 1662.3 - Identification of information requested.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 32 National Defense 6 2011-07-01 2011-07-01 false Identification of information requested. 1662.3 Section 1662.3 National Defense Other Regulations Relating to National Defense SELECTIVE SERVICE SYSTEM FREEDOM OF INFORMATION ACT (FOIA) PROCEDURES § 1662.3 Identification of information requested. Any person who requests information under...

  7. 32 CFR 1662.3 - Identification of information requested.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 32 National Defense 6 2013-07-01 2013-07-01 false Identification of information requested. 1662.3 Section 1662.3 National Defense Other Regulations Relating to National Defense SELECTIVE SERVICE SYSTEM FREEDOM OF INFORMATION ACT (FOIA) PROCEDURES § 1662.3 Identification of information requested. Any person who requests information under...

  8. 32 CFR 1662.3 - Identification of information requested.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 32 National Defense 6 2010-07-01 2010-07-01 false Identification of information requested. 1662.3 Section 1662.3 National Defense Other Regulations Relating to National Defense SELECTIVE SERVICE SYSTEM FREEDOM OF INFORMATION ACT (FOIA) PROCEDURES § 1662.3 Identification of information requested. Any...

  9. The biocontrol endophytic bacterium Pseudomonas fluorescens PICF7 induces systemic defense responses in aerial tissues upon colonization of olive roots

    PubMed Central

    Gómez-Lama Cabanás, Carmen; Schilirò, Elisabetta; Valverde-Corredor, Antonio; Mercado-Blanco, Jesús

    2014-01-01

    Pseudomonas fluorescens PICF7, a native olive root endophyte and effective biocontrol agent (BCA) against Verticillium wilt of olive, is able to trigger a broad range of defense responses in root tissues of this woody plant. In order to elucidate whether strain PICF7 also induces systemic defense responses in above-ground organs, aerial tissues of olive plants grown under non-gnotobiotic conditions were collected at different time points after root bacterization with this endophytic BCA. A suppression subtractive hybridization (SSH) cDNA library, enriched in up-regulated genes, was generated. This strategy enabled the identification of 376 ESTs (99 contigs and 277 singlets), many of them related to response to different stresses. Five ESTs, involved in defense responses, were selected to carry out time-course quantitative real-time PCR (qRT-PCR) experiments aiming to: (1) validate the induction of these genes, and (2) shed light on their expression pattern along time (from 1 to 15 days). Induction of olive genes potentially coding for lipoxygenase 2, catalase, 1-aminocyclopropane-1-carboxylate oxidase, and phenylananine ammonia-lyase was thus confirmed at some time points. Computational analysis also revealed that different transcription factors were up-regulated in olive aerial tissues (i.e., JERF, bHLH, WRKY), as previously reported for roots. Results confirmed that root colonization by this endophytic bacterium does not only trigger defense responses in this organ but also mounts a wide array of systemic defense responses in distant tissues (stems, leaves). This sheds light on how olive plants respond to the “non-hostile” colonization by a bacterial endophyte and how induced defense response can contribute to the biocontrol activity of strain PICF7. PMID:25250017

  10. Value of space defenses

    SciTech Connect

    Canavan, G.H.

    1992-10-29

    This report discusses the economic value of defenses against Near-Earth Object (NEO) impacts is bounded by calculating expected losses in their absence, which illustrates the contributions from NEOs of different sizes and the sensitivity of total expected losses to impact frequencies. For typical size distributions and damage of only a few decades duration, losses are most sensitive to small NEOs, and lead to defenses worth a few $M/yr. When the persistence of damage with NEO size is taken into account, that shifts the loss to the largest NEOs and greatly increases expected loss and values.

  11. Identification of genes potentially responsible for extra-oral digestion and overcoming plant defense from salivary glands of the tarnished plant bug (Lygus lineolaris) using cDNA sequencing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Saliva is known to play a crucial role in tarnished plant bug (TPB, Lygus lineolaris) feeding. TPBs secrete saliva during feeding to facilitate the piercing into plant tissues. More importantly, the enzyme-rich saliva may be used for extra-oral digestion and for overcoming plant defense before the p...

  12. 75 FR 76423 - Defense Intelligence Agency National Defense Intelligence College Board of Visitors Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-08

    ... of the Secretary Defense Intelligence Agency National Defense Intelligence College Board of Visitors Closed Meeting AGENCY: National Defense Intelligence College, Defense Intelligence Agency, Department of... a closed meeting of the Defense Intelligence Agency National Defense Intelligence College Board...

  13. 76 FR 28960 - Defense Intelligence Agency National Defense Intelligence College Board of Visitors Closed Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-19

    ... of the Secretary Defense Intelligence Agency National Defense Intelligence College Board of Visitors Closed Meeting AGENCY: National Defense Intelligence College, Defense Intelligence Agency, Department of... a closed meeting of the Defense Intelligence Agency National Defense Intelligence College Board...

  14. 76 FR 28757 - Defense Logistics Agency Revised Regulation 1000.22, Environmental Considerations in Defense...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-18

    ... of the Secretary Defense Logistics Agency Revised Regulation 1000.22, Environmental Considerations in Defense Logistics Agency Actions AGENCY: Defense Logistics Agency, Department of Defense. ACTION: Notice of Availability (NOA) of Revised Defense Logistics Agency Regulation. SUMMARY: The Defense...

  15. Radiological Defense Manual.

    ERIC Educational Resources Information Center

    Defense Civil Preparedness Agency (DOD), Washington, DC.

    Originally prepared for use as a student textbook in Radiological Defense (RADEF) courses, this manual provides the basic technical information necessary for an understanding of RADEF. It also briefly discusses the need for RADEF planning and expected postattack emergency operations. There are 14 chapters covering these major topics: introduction…

  16. Censorship: Tactics for Defense.

    ERIC Educational Resources Information Center

    Lowery, Skip

    1998-01-01

    Book banners are generally successful because they have a wide network of support, including national coalitions with sophisticated organizational methods--such as electing certain people to school boards. School officials should get organized and devise defensive strategies, such as inviting critics to class, asking what they would like to…

  17. Defense Language Institute.

    ERIC Educational Resources Information Center

    Defense Language Inst., Washington, DC.

    Discussed in this Defense Language Institute (DLI) brochure are its intensive language programs' history, and its four schools, which are located in Monterey, California, Washington, D.C., Lackland Air Force Base, and Fort Bliss, Texas. Proficiency levels determined by the DLI and utilization of the audiolingual method are also described.…

  18. 9. BASRELIEF DECORATION, 'DEFENSE', MURAL COMMEMORATING THE DEFENSE OF FORT ...

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

    9. BAS-RELIEF DECORATION, 'DEFENSE', MURAL COMMEMORATING THE DEFENSE OF FORT DEARBORN - Chicago River Bascule Bridge, Michigan Avenue, Spanning Chicago River at North Michigan Avenue, Chicago, Cook County, IL

  19. Clinical coding. Code breakers.

    PubMed

    Mathieson, Steve

    2005-02-24

    --The advent of payment by results has seen the role of the clinical coder pushed to the fore in England. --Examinations for a clinical coding qualification began in 1999. In 2004, approximately 200 people took the qualification. --Trusts are attracting people to the role by offering training from scratch or through modern apprenticeships. PMID:15768716

  20. 22 CFR 126.16 - Exemption pursuant to the Defense Trade Cooperation Treaty between the United States and Australia.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... Explosives found at 27 CFR parts 447, 478, and 479, which are unaffected by the Defense Trade Cooperation... and USA Treaty Community//.” For example, for defense articles classified SECRET, the marking or identification shall be “//SECRET USML//REL AUS and USA Treaty Community//.” (ii) Unclassified defense...

  1. [Thoughts on "defensive" medicine].

    PubMed

    Csiba, László

    2007-03-25

    "Defensive" medicine is called medical behaviour characterized by deformation of diagnostic and therapeutic activities due to fears endangering existence and work, thus some interventions are omitted or, on the contrary, superfluous examinations are proposed on account of internal uncertainty, the patient's distrust or hostile social environment. Trust relation between patient and physician is the most gravely damaged because of aggravation and distortion of some conscienceless physicians' abuses by the media; patient-physician relations may not be degraded to contractual legal relations. Young physicians must get acquainted with the joy of success in diagnostics that enriches the personality. They shall have healthy self-esteem and be ready to take diagnostic and therapeutic challenges on themselves. All of us have to fight against social atmosphere hostile to physicians, against causes inducing and augmenting practice of defensive medicine. PMID:17444017

  2. Defense Waste Processing Facility

    SciTech Connect

    Haselow, J.S.; Wilhite, E.L.; Stieve, A.L.

    1990-05-01

    The information contained in this report is intended to supplement the original Environmental Impact Statement (EIS) for the Defense Waste Processing Facility (DWPF). Since the original EIS in 1982, alterations have been made to he conceptual process that reduce the impact to the groundwater. This reduced impact is documented in this report along with an update of the understanding of seismology and geology of the Savannah River Site. 6 refs., 2 figs., 2 tabs.

  3. Binary coding for hyperspectral imagery

    NASA Astrophysics Data System (ADS)

    Wang, Jing; Chang, Chein-I.; Chang, Chein-Chi; Lin, Chinsu

    2004-10-01

    Binary coding is one of simplest ways to characterize spectral features. One commonly used method is a binary coding-based image software system, called Spectral Analysis Manager (SPAM) for remotely sensed imagery developed by Mazer et al. For a given spectral signature, the SPAM calculates its spectral mean and inter-band spectral difference and uses them as thresholds to generate a binary code word for this particular spectral signature. Such coding scheme is generally effective and also very simple to implement. This paper revisits the SPAM and further develops three new SPAM-based binary coding methods, called equal probability partition (EPP) binary coding, halfway partition (HP) binary coding and median partition (MP) binary coding. These three binary coding methods along with the SPAM well be evaluated for spectral discrimination and identification. In doing so, a new criterion, called a posteriori discrimination probability (APDP) is also introduced for performance measure.

  4. Defense on the Move: Ant-Based Cyber Defense

    SciTech Connect

    Fink, Glenn A.; Haack, Jereme N.; McKinnon, Archibald D.; Fulp, Errin W.

    2014-04-15

    Many common cyber defenses (like firewalls and IDS) are as static as trench warfare allowing the attacker freedom to probe them at will. The concept of Moving Target Defense (MTD) adds dynamism to the defender side, but puts the systems to be defended themselves in motion, potentially at great cost to the defender. An alternative approach is a mobile resilient defense that removes attackers’ ability to rely on prior experience without requiring motion in the protected infrastructure itself. The defensive technology absorbs most of the cost of motion, is resilient to attack, and is unpredictable to attackers. The Ant-Based Cyber Defense (ABCD) is a mobile resilient defense providing a set of roaming, bio-inspired, digital-ant agents working with stationary agents in a hierarchy headed by a human supervisor. The ABCD approach provides a resilient, extensible, and flexible defense that can scale to large, multi-enterprise infrastructures like the smart electric grid.

  5. Identification and Functional Characterization of G6PC2 Coding Variants Influencing Glycemic Traits Define an Effector Transcript at the G6PC2-ABCB11 Locus

    PubMed Central

    Mahajan, Anubha; Sim, Xueling; Ng, Hui Jin; Manning, Alisa; Rivas, Manuel A.; Highland, Heather M.; Locke, Adam E.; Grarup, Niels; Im, Hae Kyung; Cingolani, Pablo; Flannick, Jason; Fontanillas, Pierre; Fuchsberger, Christian; Gaulton, Kyle J.; Teslovich, Tanya M.; Rayner, N. William; Robertson, Neil R.; Beer, Nicola L.; Rundle, Jana K.; Bork-Jensen, Jette; Ladenvall, Claes; Blancher, Christine; Buck, David; Buck, Gemma; Burtt, Noël P.; Gabriel, Stacey; Gjesing, Anette P.; Groves, Christopher J.; Hollensted, Mette; Huyghe, Jeroen R.; Jackson, Anne U.; Jun, Goo; Justesen, Johanne Marie; Mangino, Massimo; Murphy, Jacquelyn; Neville, Matt; Onofrio, Robert; Small, Kerrin S.; Stringham, Heather M.; Syvänen, Ann-Christine; Trakalo, Joseph; Abecasis, Goncalo; Bell, Graeme I.; Blangero, John; Cox, Nancy J.; Duggirala, Ravindranath; Hanis, Craig L.; Seielstad, Mark; Wilson, James G.; Christensen, Cramer; Brandslund, Ivan; Rauramaa, Rainer; Surdulescu, Gabriela L.; Doney, Alex S. F.; Lannfelt, Lars; Linneberg, Allan; Isomaa, Bo; Tuomi, Tiinamaija; Jørgensen, Marit E.; Jørgensen, Torben; Kuusisto, Johanna; Uusitupa, Matti; Salomaa, Veikko; Spector, Timothy D.; Morris, Andrew D.; Palmer, Colin N. A.; Collins, Francis S.; Mohlke, Karen L.; Bergman, Richard N.; Ingelsson, Erik; Lind, Lars; Tuomilehto, Jaakko; Hansen, Torben; Watanabe, Richard M.; Prokopenko, Inga; Dupuis, Josee; Karpe, Fredrik; Groop, Leif; Laakso, Markku; Pedersen, Oluf; Florez, Jose C.; Morris, Andrew P.; Altshuler, David; Meigs, James B.; Boehnke, Michael; McCarthy, Mark I.; Lindgren, Cecilia M.; Gloyn, Anna L.

    2015-01-01

    Genome wide association studies (GWAS) for fasting glucose (FG) and insulin (FI) have identified common variant signals which explain 4.8% and 1.2% of trait variance, respectively. It is hypothesized that low-frequency and rare variants could contribute substantially to unexplained genetic variance. To test this, we analyzed exome-array data from up to 33,231 non-diabetic individuals of European ancestry. We found exome-wide significant (P<5×10-7) evidence for two loci not previously highlighted by common variant GWAS: GLP1R (p.Ala316Thr, minor allele frequency (MAF)=1.5%) influencing FG levels, and URB2 (p.Glu594Val, MAF = 0.1%) influencing FI levels. Coding variant associations can highlight potential effector genes at (non-coding) GWAS signals. At the G6PC2/ABCB11 locus, we identified multiple coding variants in G6PC2 (p.Val219Leu, p.His177Tyr, and p.Tyr207Ser) influencing FG levels, conditionally independent of each other and the non-coding GWAS signal. In vitro assays demonstrate that these associated coding alleles result in reduced protein abundance via proteasomal degradation, establishing G6PC2 as an effector gene at this locus. Reconciliation of single-variant associations and functional effects was only possible when haplotype phase was considered. In contrast to earlier reports suggesting that, paradoxically, glucose-raising alleles at this locus are protective against type 2 diabetes (T2D), the p.Val219Leu G6PC2 variant displayed a modest but directionally consistent association with T2D risk. Coding variant associations for glycemic traits in GWAS signals highlight PCSK1, RREB1, and ZHX3 as likely effector transcripts. These coding variant association signals do not have a major impact on the trait variance explained, but they do provide valuable biological insights. PMID:25625282

  6. Identification and functional characterization of G6PC2 coding variants influencing glycemic traits define an effector transcript at the G6PC2-ABCB11 locus.

    PubMed

    Mahajan, Anubha; Sim, Xueling; Ng, Hui Jin; Manning, Alisa; Rivas, Manuel A; Highland, Heather M; Locke, Adam E; Grarup, Niels; Im, Hae Kyung; Cingolani, Pablo; Flannick, Jason; Fontanillas, Pierre; Fuchsberger, Christian; Gaulton, Kyle J; Teslovich, Tanya M; Rayner, N William; Robertson, Neil R; Beer, Nicola L; Rundle, Jana K; Bork-Jensen, Jette; Ladenvall, Claes; Blancher, Christine; Buck, David; Buck, Gemma; Burtt, Noël P; Gabriel, Stacey; Gjesing, Anette P; Groves, Christopher J; Hollensted, Mette; Huyghe, Jeroen R; Jackson, Anne U; Jun, Goo; Justesen, Johanne Marie; Mangino, Massimo; Murphy, Jacquelyn; Neville, Matt; Onofrio, Robert; Small, Kerrin S; Stringham, Heather M; Syvänen, Ann-Christine; Trakalo, Joseph; Abecasis, Goncalo; Bell, Graeme I; Blangero, John; Cox, Nancy J; Duggirala, Ravindranath; Hanis, Craig L; Seielstad, Mark; Wilson, James G; Christensen, Cramer; Brandslund, Ivan; Rauramaa, Rainer; Surdulescu, Gabriela L; Doney, Alex S F; Lannfelt, Lars; Linneberg, Allan; Isomaa, Bo; Tuomi, Tiinamaija; Jørgensen, Marit E; Jørgensen, Torben; Kuusisto, Johanna; Uusitupa, Matti; Salomaa, Veikko; Spector, Timothy D; Morris, Andrew D; Palmer, Colin N A; Collins, Francis S; Mohlke, Karen L; Bergman, Richard N; Ingelsson, Erik; Lind, Lars; Tuomilehto, Jaakko; Hansen, Torben; Watanabe, Richard M; Prokopenko, Inga; Dupuis, Josee; Karpe, Fredrik; Groop, Leif; Laakso, Markku; Pedersen, Oluf; Florez, Jose C; Morris, Andrew P; Altshuler, David; Meigs, James B; Boehnke, Michael; McCarthy, Mark I; Lindgren, Cecilia M; Gloyn, Anna L

    2015-01-01

    Genome wide association studies (GWAS) for fasting glucose (FG) and insulin (FI) have identified common variant signals which explain 4.8% and 1.2% of trait variance, respectively. It is hypothesized that low-frequency and rare variants could contribute substantially to unexplained genetic variance. To test this, we analyzed exome-array data from up to 33,231 non-diabetic individuals of European ancestry. We found exome-wide significant (P<5×10-7) evidence for two loci not previously highlighted by common variant GWAS: GLP1R (p.Ala316Thr, minor allele frequency (MAF)=1.5%) influencing FG levels, and URB2 (p.Glu594Val, MAF = 0.1%) influencing FI levels. Coding variant associations can highlight potential effector genes at (non-coding) GWAS signals. At the G6PC2/ABCB11 locus, we identified multiple coding variants in G6PC2 (p.Val219Leu, p.His177Tyr, and p.Tyr207Ser) influencing FG levels, conditionally independent of each other and the non-coding GWAS signal. In vitro assays demonstrate that these associated coding alleles result in reduced protein abundance via proteasomal degradation, establishing G6PC2 as an effector gene at this locus. Reconciliation of single-variant associations and functional effects was only possible when haplotype phase was considered. In contrast to earlier reports suggesting that, paradoxically, glucose-raising alleles at this locus are protective against type 2 diabetes (T2D), the p.Val219Leu G6PC2 variant displayed a modest but directionally consistent association with T2D risk. Coding variant associations for glycemic traits in GWAS signals highlight PCSK1, RREB1, and ZHX3 as likely effector transcripts. These coding variant association signals do not have a major impact on the trait variance explained, but they do provide valuable biological insights. PMID:25625282

  7. Plant Defense against Insect Herbivores

    PubMed Central

    Fürstenberg-Hägg, Joel; Zagrobelny, Mika; Bak, Søren

    2013-01-01

    Plants have been interacting with insects for several hundred million years, leading to complex defense approaches against various insect feeding strategies. Some defenses are constitutive while others are induced, although the insecticidal defense compound or protein classes are often similar. Insect herbivory induce several internal signals from the wounded tissues, including calcium ion fluxes, phosphorylation cascades and systemic- and jasmonate signaling. These are perceived in undamaged tissues, which thereafter reinforce their defense by producing different, mostly low molecular weight, defense compounds. These bioactive specialized plant defense compounds may repel or intoxicate insects, while defense proteins often interfere with their digestion. Volatiles are released upon herbivory to repel herbivores, attract predators or for communication between leaves or plants, and to induce defense responses. Plants also apply morphological features like waxes, trichomes and latices to make the feeding more difficult for the insects. Extrafloral nectar, food bodies and nesting or refuge sites are produced to accommodate and feed the predators of the herbivores. Meanwhile, herbivorous insects have adapted to resist plant defenses, and in some cases even sequester the compounds and reuse them in their own defense. Both plant defense and insect adaptation involve metabolic costs, so most plant-insect interactions reach a stand-off, where both host and herbivore survive although their development is suboptimal. PMID:23681010

  8. 32 CFR 634.21 - Department of Defense Form 2220.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... Department of Defense Form 2220. (a) Use. DD Form 2220 will be used to identify registered POVs on Army, Navy...). (ii) Alphanumeric individual form identification number. (iii) DOD seal. (2) Name of the installation... guided by state or host nation laws will specify the exact placement of DD Form 2220. (5) For Navy...

  9. 32 CFR 634.21 - Department of Defense Form 2220.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... Department of Defense Form 2220. (a) Use. DD Form 2220 will be used to identify registered POVs on Army, Navy...). (ii) Alphanumeric individual form identification number. (iii) DOD seal. (2) Name of the installation... guided by state or host nation laws will specify the exact placement of DD Form 2220. (5) For Navy...

  10. 32 CFR 634.21 - Department of Defense Form 2220.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... Department of Defense Form 2220. (a) Use. DD Form 2220 will be used to identify registered POVs on Army, Navy...). (ii) Alphanumeric individual form identification number. (iii) DOD seal. (2) Name of the installation... guided by state or host nation laws will specify the exact placement of DD Form 2220. (5) For Navy...

  11. 32 CFR 634.21 - Department of Defense Form 2220.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Department of Defense Form 2220. (a) Use. DD Form 2220 will be used to identify registered POVs on Army, Navy...). (ii) Alphanumeric individual form identification number. (iii) DOD seal. (2) Name of the installation... guided by state or host nation laws will specify the exact placement of DD Form 2220. (5) For Navy...

  12. Identification of a Novel Small Cysteine-Rich Protein in the Fraction from the Biocontrol Fusarium oxysporum Strain CS-20 that Mitigates Fusarium Wilt Symptoms and Triggers Defense Responses in Tomato

    PubMed Central

    Shcherbakova, Larisa A.; Odintsova, Tatyana I.; Stakheev, Alexander A.; Fravel, Deborah R.; Zavriev, Sergey K.

    2016-01-01

    The biocontrol effect of the non-pathogenic Fusarium oxysporum strain CS-20 against the tomato wilt pathogen F. oxysporum f. sp. lycopersici (FOL) has been previously reported to be primarily plant-mediated. This study shows that CS-20 produces proteins, which elicit defense responses in tomato plants. Three protein-containing fractions were isolated from CS-20 biomass using size exclusion chromatography. Exposure of seedling roots to one of these fractions prior to inoculation with pathogenic FOL strains significantly reduced wilt severity. This fraction initiated an ion exchange response in cultured tomato cells resulting in a reversible alteration of extracellular pH; increased tomato chitinase activity, and induced systemic resistance by enhancing PR-1 expression in tomato leaves. Two other protein fractions were inactive in seedling protection. The main polypeptide (designated CS20EP), which was specifically present in the defense-inducing fraction and was not detected in inactive protein fractions, was identified. The nucleotide sequence encoding this protein was determined, and its complete amino acid sequence was deduced from direct Edman degradation (25 N-terminal amino acid residues) and DNA sequencing. The CS20EP was found to be a small basic cysteine-rich protein with a pI of 9.87 and 23.43% of hydrophobic amino acid residues. BLAST search in the NCBI database showed that the protein is new; however, it displays 48% sequence similarity with a hypothetical protein FGSG_10784 from F. graminearum strain PH-1. The contribution of CS20EP to elicitation of tomato defense responses resulting in wilt mitigating is discussed. PMID:26779237

  13. Phonological coding during reading

    PubMed Central

    Leinenger, Mallorie

    2014-01-01

    The exact role that phonological coding (the recoding of written, orthographic information into a sound based code) plays during silent reading has been extensively studied for more than a century. Despite the large body of research surrounding the topic, varying theories as to the time course and function of this recoding still exist. The present review synthesizes this body of research, addressing the topics of time course and function in tandem. The varying theories surrounding the function of phonological coding (e.g., that phonological codes aid lexical access, that phonological codes aid comprehension and bolster short-term memory, or that phonological codes are largely epiphenomenal in skilled readers) are first outlined, and the time courses that each maps onto (e.g., that phonological codes come online early (pre-lexical) or that phonological codes come online late (post-lexical)) are discussed. Next the research relevant to each of these proposed functions is reviewed, discussing the varying methodologies that have been used to investigate phonological coding (e.g., response time methods, reading while eyetracking or recording EEG and MEG, concurrent articulation) and highlighting the advantages and limitations of each with respect to the study of phonological coding. In response to the view that phonological coding is largely epiphenomenal in skilled readers, research on the use of phonological codes in prelingually, profoundly deaf readers is reviewed. Finally, implications for current models of word identification (activation-verification model (Van Order, 1987), dual-route model (e.g., Coltheart, Rastle, Perry, Langdon, & Ziegler, 2001), parallel distributed processing model (Seidenberg & McClelland, 1989)) are discussed. PMID:25150679

  14. Phonological coding during reading.

    PubMed

    Leinenger, Mallorie

    2014-11-01

    The exact role that phonological coding (the recoding of written, orthographic information into a sound based code) plays during silent reading has been extensively studied for more than a century. Despite the large body of research surrounding the topic, varying theories as to the time course and function of this recoding still exist. The present review synthesizes this body of research, addressing the topics of time course and function in tandem. The varying theories surrounding the function of phonological coding (e.g., that phonological codes aid lexical access, that phonological codes aid comprehension and bolster short-term memory, or that phonological codes are largely epiphenomenal in skilled readers) are first outlined, and the time courses that each maps onto (e.g., that phonological codes come online early [prelexical] or that phonological codes come online late [postlexical]) are discussed. Next the research relevant to each of these proposed functions is reviewed, discussing the varying methodologies that have been used to investigate phonological coding (e.g., response time methods, reading while eye-tracking or recording EEG and MEG, concurrent articulation) and highlighting the advantages and limitations of each with respect to the study of phonological coding. In response to the view that phonological coding is largely epiphenomenal in skilled readers, research on the use of phonological codes in prelingually, profoundly deaf readers is reviewed. Finally, implications for current models of word identification (activation-verification model, Van Orden, 1987; dual-route model, e.g., M. Coltheart, Rastle, Perry, Langdon, & Ziegler, 2001; parallel distributed processing model, Seidenberg & McClelland, 1989) are discussed. PMID:25150679

  15. Synthetic plant defense elicitors

    PubMed Central

    Bektas, Yasemin; Eulgem, Thomas

    2015-01-01

    To defend themselves against invading pathogens plants utilize a complex regulatory network that coordinates extensive transcriptional and metabolic reprogramming. Although many of the key players of this immunity-associated network are known, the details of its topology and dynamics are still poorly understood. As an alternative to forward and reverse genetic studies, chemical genetics-related approaches based on bioactive small molecules have gained substantial popularity in the analysis of biological pathways and networks. Use of such molecular probes can allow researchers to access biological space that was previously inaccessible to genetic analyses due to gene redundancy or lethality of mutations. Synthetic elicitors are small drug-like molecules that induce plant defense responses, but are distinct from known natural elicitors of plant immunity. While the discovery of some synthetic elicitors had already been reported in the 1970s, recent breakthroughs in combinatorial chemical synthesis now allow for inexpensive high-throughput screens for bioactive plant defense-inducing compounds. Along with powerful reverse genetics tools and resources available for model plants and crop systems, comprehensive collections of new synthetic elicitors will likely allow plant scientists to study the intricacies of plant defense signaling pathways and networks in an unparalleled fashion. As synthetic elicitors can protect crops from diseases, without the need to be directly toxic for pathogenic organisms, they may also serve as promising alternatives to conventional biocidal pesticides, which often are harmful for the environment, farmers and consumers. Here we are discussing various types of synthetic elicitors that have been used for studies on the plant immune system, their modes-of-action as well as their application in crop protection. PMID:25674095

  16. Nanomaterials for Defense Applications

    NASA Astrophysics Data System (ADS)

    Turaga, Uday; Singh, Vinitkumar; Lalagiri, Muralidhar; Kiekens, Paul; Ramkumar, Seshadri S.

    Nanotechnology has found a number of applications in electronics and healthcare. Within the textile field, applications of nanotechnology have been limited to filters, protective liners for chemical and biological clothing and nanocoatings. This chapter presents an overview of the applications of nanomaterials such as nanofibers and nanoparticles that are of use to military and industrial sectors. An effort has been made to categorize nanofibers based on the method of production. This chapter particularly focuses on a few latest developments that have taken place with regard to the application of nanomaterials such as metal oxides in the defense arena.

  17. Identification of a xyloglucan-specific endo-(1-4)-beta-D-glucanase inhibitor protein from apple (Malus × domestica Borkh.) as a potential defense gene against Botryosphaeria dothidea.

    PubMed

    Bai, Suhua; Dong, Chaohua; Zhu, Jun; Zhang, Yugang; Dai, Hongyi

    2015-02-01

    Botryosphaeria dothidea is the causal agent of apple ring rot which is a highly destructive apple disease in China. Here, a putative xyloglucan-specific endo-(1-4)-beta-d-glucanase inhibitor protein from Malus×domestica (designated as MdXEGIP1) was found to be involved in defense against B. dothidea infection. MdXEGIP1 shares high amino acid sequence identity with other apple XEGIPs, but exhibited significantly different responses to B. dothidea infection. Quantitative real-time PCR revealed that MdXEGIP1 expression was significantly induced in shoot bark of apple plant by B. dothidea and showed different expression pattern in resistant and susceptible apple cultivars. In resistant cultivar, MdXEGIP1 expression was elevated with larger amplitude than that in susceptible cultivar after B. dothidea infection. MdXEGIP1 expression was also significantly enhanced by treatment with exogenous methyl jasmonate and salicylic acid in apple plantlets. Further investigation revealed that recombinant MdXEGIP1 has significant inhibitor activity to XEGs from family 12 and 74 of glycoside hydrolase. More importantly, recombinant MdXEGIP1 inhibited crude enzyme solution of XEG from B. dothidea, suggesting that MdXEGIP1 might protect apple plant from B. dothidea infection by inhibiting XEG activity. Taken together, the results indicated that MdXEGIP1 is a potential defense gene against B. dothidea in apple. PMID:25575987

  18. 32 CFR 536.125 - Statutory authority for Uniform Code of Military Justice (UCMJ) Claims.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Justice (UCMJ) Claims. 536.125 Section 536.125 National Defense Department of Defense (Continued... 139, Uniform Code of Military Justice § 536.125 Statutory authority for Uniform Code of Military Justice (UCMJ) Claims. The authority for this subpart is Article 139, Uniform Code of Military...

  19. Immune defense mechanisms of the dental pulp.

    PubMed

    Jontell, M; Okiji, T; Dahlgren, U; Bergenholtz, G

    1998-01-01

    Defense reactions of the dentin/pulp complex involve a variety of biological systems, in which the immune system plays a pivotal role. The knowledge of the organization and function of pulpal immunocompetent cells has been sparse, but in recent years a significant body of information of immune mechanisms in general has provided a footing for substantial new knowledge of the immune mechanisms of the dental pulp. The identification of pulpal dendritic cells (DCs) has generated research activities which have led to a concept of how an antigenic challenge may evoke a pulpal inflammatory response. Although DCs are not able to identify foreign antigens specifically, they provide necessary signals to activate T-lymphocytes which in turn will orchestrate other immunocompetent cells to mount the local immune defense of the dental pulp. The purpose of this review is to accent the organization and function of pulpal DCs and other tissue and cellular components and to provide a basis for how they may interact to instigate pulpal defense mechanisms. PMID:9603235

  20. Light regulation of plant defense.

    PubMed

    Ballaré, Carlos L

    2014-01-01

    Precise allocation of limited resources between growth and defense is critical for plant survival. In shade-intolerant species, perception of competition signals by informational photoreceptors activates shade-avoidance responses and reduces the expression of defenses against pathogens and insects. The main mechanism underlying defense suppression is the simultaneous downregulation of jasmonate and salicylic acid signaling by low ratios of red:far-red radiation. Inactivation of phytochrome B by low red:far-red ratios appears to suppress jasmonate responses by altering the balance between DELLA and JASMONATE ZIM DOMAIN (JAZ) proteins in favor of the latter. Solar UVB radiation is a positive modulator of plant defense, signaling through jasmonate-dependent and jasmonate-independent pathways. Light, perceived by phytochrome B and presumably other photoreceptors, helps plants concentrate their defensive arsenals in photosynthetically valuable leaves. The discovery of connections between photoreceptors and defense signaling is revealing novel mechanisms that control key resource allocation decisions in plant canopies. PMID:24471835

  1. 75 FR 3178 - Defense Federal Acquisition Regulation Supplement; Lead System Integrators

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-01-20

    ... an interim rule at 73 FR 1823 on January 10, 2008, to implement Section 807 of the National ] Defense... 74 FR 34268 on July 15, 2009, is adopted as a final rule without change. BILLING CODE 5001-08-P ... Acquisition Regulation Supplement; Lead System Integrators AGENCY: Department of Defense (DoD). ACTION:...

  2. 76 FR 71465 - Defense Federal Acquisition Regulation Supplement: Management of Manufacturing Risk in Major...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-11-18

    ... interim rule in the Federal Register at 76 FR 38050 on June 29, 2011, to amend Defense Federal Acquisition... at 76 FR 38050 on June 29, 2011, is adopted as a final rule without change. BILLING CODE 5001-06-P ... Regulation Supplement: Management of Manufacturing Risk in Major Defense Acquisition Programs (DFARS...

  3. 75 FR 32087 - Designating the Chairperson of the Defense Production Act Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-07

    ..., 2010 [FR Doc. 2010-13659 Filed 6-4-10; 8:45 am] Billing code 4410-10-P ...#0;#0; ] Memorandum of May 19, 2010 Designating the Chairperson of the Defense Production Act... authority vested in me by section 722(b)(2) of the Defense Production Act of 1950, as amended (section 11...

  4. 48 CFR 211.275 - Radio frequency identification.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 3 2010-10-01 2010-10-01 false Radio frequency identification. 211.275 Section 211.275 Federal Acquisition Regulations System DEFENSE ACQUISITION REGULATIONS... Requirements Documents 211.275 Radio frequency identification....

  5. Codes and Standards Technical Team Roadmap

    SciTech Connect

    2013-06-01

    The Hydrogen Codes and Standards Tech Team (CSTT) mission is to enable and facilitate the appropriate research, development, & demonstration (RD&D) for the development of safe, performance-based defensible technical codes and standards that support the technology readiness and are appropriate for widespread consumer use of fuel cells and hydrogen-based technologies with commercialization by 2020. Therefore, it is important that the necessary codes and standards be in place no later than 2015.

  6. Speech coding

    NASA Astrophysics Data System (ADS)

    Gersho, Allen

    1990-05-01

    Recent advances in algorithms and techniques for speech coding now permit high quality voice reproduction at remarkably low bit rates. The advent of powerful single-ship signal processors has made it cost effective to implement these new and sophisticated speech coding algorithms for many important applications in voice communication and storage. Some of the main ideas underlying the algorithms of major interest today are reviewed. The concept of removing redundancy by linear prediction is reviewed, first in the context of predictive quantization or DPCM. Then linear predictive coding, adaptive predictive coding, and vector quantization are discussed. The concepts of excitation coding via analysis-by-synthesis, vector sum excitation codebooks, and adaptive postfiltering are explained. The main idea of vector excitation coding (VXC) or code excited linear prediction (CELP) are presented. Finally low-delay VXC coding and phonetic segmentation for VXC are described.

  7. Improvement of genome assembly completeness and identification of novel full-length protein-coding genes by RNA-seq in the giant panda genome.

    PubMed

    Chen, Meili; Hu, Yibo; Liu, Jingxing; Wu, Qi; Zhang, Chenglin; Yu, Jun; Xiao, Jingfa; Wei, Fuwen; Wu, Jiayan

    2015-01-01

    High-quality and complete gene models are the basis of whole genome analyses. The giant panda (Ailuropoda melanoleuca) genome was the first genome sequenced on the basis of solely short reads, but the genome annotation had lacked the support of transcriptomic evidence. In this study, we applied RNA-seq to globally improve the genome assembly completeness and to detect novel expressed transcripts in 12 tissues from giant pandas, by using a transcriptome reconstruction strategy that combined reference-based and de novo methods. Several aspects of genome assembly completeness in the transcribed regions were effectively improved by the de novo assembled transcripts, including genome scaffolding, the detection of small-size assembly errors, the extension of scaffold/contig boundaries, and gap closure. Through expression and homology validation, we detected three groups of novel full-length protein-coding genes. A total of 12.62% of the novel protein-coding genes were validated by proteomic data. GO annotation analysis showed that some of the novel protein-coding genes were involved in pigmentation, anatomical structure formation and reproduction, which might be related to the development and evolution of the black-white pelage, pseudo-thumb and delayed embryonic implantation of giant pandas. The updated genome annotation will help further giant panda studies from both structural and functional perspectives. PMID:26658305

  8. Improvement of genome assembly completeness and identification of novel full-length protein-coding genes by RNA-seq in the giant panda genome

    PubMed Central

    Chen, Meili; Hu, Yibo; Liu, Jingxing; Wu, Qi; Zhang, Chenglin; Yu, Jun; Xiao, Jingfa; Wei, Fuwen; Wu, Jiayan

    2015-01-01

    High-quality and complete gene models are the basis of whole genome analyses. The giant panda (Ailuropoda melanoleuca) genome was the first genome sequenced on the basis of solely short reads, but the genome annotation had lacked the support of transcriptomic evidence. In this study, we applied RNA-seq to globally improve the genome assembly completeness and to detect novel expressed transcripts in 12 tissues from giant pandas, by using a transcriptome reconstruction strategy that combined reference-based and de novo methods. Several aspects of genome assembly completeness in the transcribed regions were effectively improved by the de novo assembled transcripts, including genome scaffolding, the detection of small-size assembly errors, the extension of scaffold/contig boundaries, and gap closure. Through expression and homology validation, we detected three groups of novel full-length protein-coding genes. A total of 12.62% of the novel protein-coding genes were validated by proteomic data. GO annotation analysis showed that some of the novel protein-coding genes were involved in pigmentation, anatomical structure formation and reproduction, which might be related to the development and evolution of the black-white pelage, pseudo-thumb and delayed embryonic implantation of giant pandas. The updated genome annotation will help further giant panda studies from both structural and functional perspectives. PMID:26658305

  9. Antipredator defenses predict diversification rates

    PubMed Central

    Arbuckle, Kevin; Speed, Michael P.

    2015-01-01

    The “escape-and-radiate” hypothesis predicts that antipredator defenses facilitate adaptive radiations by enabling escape from constraints of predation, diversified habitat use, and subsequently speciation. Animals have evolved diverse strategies to reduce the direct costs of predation, including cryptic coloration and behavior, chemical defenses, mimicry, and advertisement of unprofitability (conspicuous warning coloration). Whereas the survival consequences of these alternative defenses for individuals are well-studied, little attention has been given to the macroevolutionary consequences of alternative forms of defense. Here we show, using amphibians as the first, to our knowledge, large-scale empirical test in animals, that there are important macroevolutionary consequences of alternative defenses. However, the escape-and-radiate hypothesis does not adequately describe them, due to its exclusive focus on speciation. We examined how rates of speciation and extinction vary across defensive traits throughout amphibians. Lineages that use chemical defenses show higher rates of speciation as predicted by escape-and-radiate but also show higher rates of extinction compared with those without chemical defense. The effect of chemical defense is a net reduction in diversification compared with lineages without chemical defense. In contrast, acquisition of conspicuous coloration (often used as warning signals or in mimicry) is associated with heightened speciation rates but unchanged extinction rates. We conclude that predictions based on the escape-and-radiate hypothesis must incorporate the effect of traits on both speciation and extinction, which is rarely considered in such studies. Our results also suggest that knowledge of defensive traits could have a bearing on the predictability of extinction, perhaps especially important in globally threatened taxa such as amphibians. PMID:26483488

  10. Antipredator defenses predict diversification rates.

    PubMed

    Arbuckle, Kevin; Speed, Michael P

    2015-11-01

    The "escape-and-radiate" hypothesis predicts that antipredator defenses facilitate adaptive radiations by enabling escape from constraints of predation, diversified habitat use, and subsequently speciation. Animals have evolved diverse strategies to reduce the direct costs of predation, including cryptic coloration and behavior, chemical defenses, mimicry, and advertisement of unprofitability (conspicuous warning coloration). Whereas the survival consequences of these alternative defenses for individuals are well-studied, little attention has been given to the macroevolutionary consequences of alternative forms of defense. Here we show, using amphibians as the first, to our knowledge, large-scale empirical test in animals, that there are important macroevolutionary consequences of alternative defenses. However, the escape-and-radiate hypothesis does not adequately describe them, due to its exclusive focus on speciation. We examined how rates of speciation and extinction vary across defensive traits throughout amphibians. Lineages that use chemical defenses show higher rates of speciation as predicted by escape-and-radiate but also show higher rates of extinction compared with those without chemical defense. The effect of chemical defense is a net reduction in diversification compared with lineages without chemical defense. In contrast, acquisition of conspicuous coloration (often used as warning signals or in mimicry) is associated with heightened speciation rates but unchanged extinction rates. We conclude that predictions based on the escape-and-radiate hypothesis must incorporate the effect of traits on both speciation and extinction, which is rarely considered in such studies. Our results also suggest that knowledge of defensive traits could have a bearing on the predictability of extinction, perhaps especially important in globally threatened taxa such as amphibians. PMID:26483488

  11. Uplink Coding

    NASA Technical Reports Server (NTRS)

    Pollara, Fabrizio; Hamkins, Jon; Dolinar, Sam; Andrews, Ken; Divsalar, Dariush

    2006-01-01

    This viewgraph presentation reviews uplink coding. The purpose and goals of the briefing are (1) Show a plan for using uplink coding and describe benefits (2) Define possible solutions and their applicability to different types of uplink, including emergency uplink (3) Concur with our conclusions so we can embark on a plan to use proposed uplink system (4) Identify the need for the development of appropriate technology and infusion in the DSN (5) Gain advocacy to implement uplink coding in flight projects Action Item EMB04-1-14 -- Show a plan for using uplink coding, including showing where it is useful or not (include discussion of emergency uplink coding).

  12. Self-Defense for Teens

    ERIC Educational Resources Information Center

    Givler, Jill I.

    2005-01-01

    Resources for self-defense training programs have become more popular and available over the last few years. Introducing a self-defense unit as part of a school physical education program is a wonderful way to address a number of psychosocial issues that prevail among teenagers today. The physical skills learned in this type of program allow…

  13. 32 CFR 634.25 - Installation traffic codes.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 32 National Defense 4 2010-07-01 2010-07-01 true Installation traffic codes. 634.25 Section 634.25... CRIMINAL INVESTIGATIONS MOTOR VEHICLE TRAFFIC SUPERVISION Traffic Supervision § 634.25 Installation traffic codes. (a) Installation or activity commanders will establish a traffic code for operation of...

  14. 32 CFR 634.25 - Installation traffic codes.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 32 National Defense 4 2014-07-01 2013-07-01 true Installation traffic codes. 634.25 Section 634.25... CRIMINAL INVESTIGATIONS MOTOR VEHICLE TRAFFIC SUPERVISION Traffic Supervision § 634.25 Installation traffic codes. (a) Installation or activity commanders will establish a traffic code for operation of...

  15. 32 CFR 634.25 - Installation traffic codes.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 32 National Defense 4 2012-07-01 2011-07-01 true Installation traffic codes. 634.25 Section 634.25... CRIMINAL INVESTIGATIONS MOTOR VEHICLE TRAFFIC SUPERVISION Traffic Supervision § 634.25 Installation traffic codes. (a) Installation or activity commanders will establish a traffic code for operation of...

  16. 32 CFR 1907.13 - Identification of material at issue.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 32 National Defense 6 2012-07-01 2012-07-01 false Identification of material at issue. 1907.13 Section 1907.13 National Defense Other Regulations Relating to National Defense CENTRAL INTELLIGENCE AGENCY CHALLENGES TO CLASSIFICATION OF DOCUMENTS BY AUTHORIZED HOLDERS PURSUANT TO SEC. 1.8 OF...

  17. 32 CFR 1907.13 - Identification of material at issue.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 32 National Defense 6 2014-07-01 2014-07-01 false Identification of material at issue. 1907.13 Section 1907.13 National Defense Other Regulations Relating to National Defense CENTRAL INTELLIGENCE AGENCY CHALLENGES TO CLASSIFICATION OF DOCUMENTS BY AUTHORIZED HOLDERS PURSUANT TO SEC. 1.8 OF...

  18. 32 CFR 1907.13 - Identification of material at issue.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 32 National Defense 6 2013-07-01 2013-07-01 false Identification of material at issue. 1907.13 Section 1907.13 National Defense Other Regulations Relating to National Defense CENTRAL INTELLIGENCE AGENCY CHALLENGES TO CLASSIFICATION OF DOCUMENTS BY AUTHORIZED HOLDERS PURSUANT TO SEC. 1.8 OF...

  19. 32 CFR 1802.13 - Identification of material at issue.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 32 National Defense 6 2010-07-01 2010-07-01 false Identification of material at issue. 1802.13 Section 1802.13 National Defense Other Regulations Relating to National Defense NATIONAL COUNTERINTELLIGENCE CENTER CHALLENGES TO CLASSIFICATION OF DOCUMENTS BY AUTHORIZED HOLDERS PURSUANT TO SECTION 1.9...

  20. 32 CFR 1802.13 - Identification of material at issue.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 32 National Defense 6 2012-07-01 2012-07-01 false Identification of material at issue. 1802.13 Section 1802.13 National Defense Other Regulations Relating to National Defense NATIONAL COUNTERINTELLIGENCE CENTER CHALLENGES TO CLASSIFICATION OF DOCUMENTS BY AUTHORIZED HOLDERS PURSUANT TO SECTION 1.9...

  1. 32 CFR 1802.13 - Identification of material at issue.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 32 National Defense 6 2011-07-01 2011-07-01 false Identification of material at issue. 1802.13 Section 1802.13 National Defense Other Regulations Relating to National Defense NATIONAL COUNTERINTELLIGENCE CENTER CHALLENGES TO CLASSIFICATION OF DOCUMENTS BY AUTHORIZED HOLDERS PURSUANT TO SECTION 1.9...

  2. 32 CFR 1802.13 - Identification of material at issue.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 32 National Defense 6 2014-07-01 2014-07-01 false Identification of material at issue. 1802.13 Section 1802.13 National Defense Other Regulations Relating to National Defense NATIONAL COUNTERINTELLIGENCE CENTER CHALLENGES TO CLASSIFICATION OF DOCUMENTS BY AUTHORIZED HOLDERS PURSUANT TO SECTION 1.9...

  3. 32 CFR 1802.13 - Identification of material at issue.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 32 National Defense 6 2013-07-01 2013-07-01 false Identification of material at issue. 1802.13 Section 1802.13 National Defense Other Regulations Relating to National Defense NATIONAL COUNTERINTELLIGENCE CENTER CHALLENGES TO CLASSIFICATION OF DOCUMENTS BY AUTHORIZED HOLDERS PURSUANT TO SECTION 1.9...

  4. 32 CFR 2400.12 - Identification and markings.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 32 National Defense 6 2013-07-01 2013-07-01 false Identification and markings. 2400.12 Section 2400.12 National Defense Other Regulations Relating to National Defense OFFICE OF SCIENCE AND TECHNOLOGY POLICY REGULATIONS TO IMPLEMENT E.O. 12356; OFFICE OF SCIENCE AND TECHNOLOGY POLICY...

  5. 32 CFR 2400.12 - Identification and markings.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 32 National Defense 6 2014-07-01 2014-07-01 false Identification and markings. 2400.12 Section 2400.12 National Defense Other Regulations Relating to National Defense OFFICE OF SCIENCE AND TECHNOLOGY POLICY REGULATIONS TO IMPLEMENT E.O. 12356; OFFICE OF SCIENCE AND TECHNOLOGY POLICY...

  6. 32 CFR 2400.12 - Identification and markings.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 32 National Defense 6 2012-07-01 2012-07-01 false Identification and markings. 2400.12 Section 2400.12 National Defense Other Regulations Relating to National Defense OFFICE OF SCIENCE AND TECHNOLOGY POLICY REGULATIONS TO IMPLEMENT E.O. 12356; OFFICE OF SCIENCE AND TECHNOLOGY POLICY...

  7. 32 CFR 2400.12 - Identification and markings.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 32 National Defense 6 2011-07-01 2011-07-01 false Identification and markings. 2400.12 Section 2400.12 National Defense Other Regulations Relating to National Defense OFFICE OF SCIENCE AND TECHNOLOGY POLICY REGULATIONS TO IMPLEMENT E.O. 12356; OFFICE OF SCIENCE AND TECHNOLOGY POLICY...

  8. 32 CFR 1907.13 - Identification of material at issue.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 32 National Defense 6 2011-07-01 2011-07-01 false Identification of material at issue. 1907.13 Section 1907.13 National Defense Other Regulations Relating to National Defense CENTRAL INTELLIGENCE AGENCY CHALLENGES TO CLASSIFICATION OF DOCUMENTS BY AUTHORIZED HOLDERS PURSUANT TO § 1.9 OF...

  9. 32 CFR 1907.13 - Identification of material at issue.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 32 National Defense 6 2010-07-01 2010-07-01 false Identification of material at issue. 1907.13 Section 1907.13 National Defense Other Regulations Relating to National Defense CENTRAL INTELLIGENCE AGENCY CHALLENGES TO CLASSIFICATION OF DOCUMENTS BY AUTHORIZED HOLDERS PURSUANT TO § 1.9 OF...

  10. 78 FR 20624 - Information Collection Requirement; Defense Federal Acquisition Regulation Supplement (DFARS...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-05

    ... Regulation Supplement (DFARS); Radio Frequency Identification Advance Shipment Notices AGENCY: Defense... Supplement (DFARS), Part 211 and related clause at 252.211; Radio Frequency Identification Advance Shipment.... Annual Burden Hours: 31,556. Frequency: On occasion. Summary of Information Collection The clause...