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Sample records for ago2 immunoprecipitation identifies

  1. Ago2 immunoprecipitation identifies predicted microRNAs in human embryonic stem cells and neural precursors.

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    Loyal A Goff

    Full Text Available BACKGROUND: MicroRNAs are required for maintenance of pluripotency as well as differentiation, but since more microRNAs have been computationally predicted in genome than have been found, there are likely to be undiscovered microRNAs expressed early in stem cell differentiation. METHODOLOGY/PRINCIPAL FINDINGS: SOLiD ultra-deep sequencing identified >10(7 unique small RNAs from human embryonic stem cells (hESC and neural-restricted precursors that were fit to a model of microRNA biogenesis to computationally predict 818 new microRNA genes. These predicted genomic loci are associated with chromatin patterns of modified histones that are predictive of regulated gene expression. 146 of the predicted microRNAs were enriched in Ago2-containing complexes along with 609 known microRNAs, demonstrating association with a functional RISC complex. This Ago2 IP-selected subset was consistently expressed in four independent hESC lines and exhibited complex patterns of regulation over development similar to previously-known microRNAs, including pluripotency-specific expression in both hESC and iPS cells. More than 30% of the Ago2 IP-enriched predicted microRNAs are new members of existing families since they share seed sequences with known microRNAs. CONCLUSIONS/SIGNIFICANCE: Extending the classic definition of microRNAs, this large number of new microRNA genes, the majority of which are less conserved than their canonical counterparts, likely represent evolutionarily recent regulators of early differentiation. The enrichment in Ago2 containing complexes, the presence of chromatin marks indicative of regulated gene expression, and differential expression over development all support the identification of 146 new microRNAs active during early hESC differentiation.

  2. KRAS Engages AGO2 to Enhance Cellular Transformation

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    Sunita Shankar

    2016-02-01

    Full Text Available Oncogenic mutations in RAS provide a compelling yet intractable therapeutic target. Using co-immunoprecipitation mass spectrometry, we uncovered an interaction between RAS and Argonaute 2 (AGO2. Endogenously, RAS and AGO2 co-sediment and co-localize in the endoplasmic reticulum. The AGO2 N-terminal domain directly binds the Switch II region of KRAS, agnostic of nucleotide (GDP/GTP binding. Functionally, AGO2 knockdown attenuates cell proliferation in mutant KRAS-dependent cells and AGO2 overexpression enhances KRASG12V-mediated transformation. Using AGO2−/− cells, we demonstrate that the RAS-AGO2 interaction is required for maximal mutant KRAS expression and cellular transformation. Mechanistically, oncogenic KRAS attenuates AGO2-mediated gene silencing. Overall, the functional interaction with AGO2 extends KRAS function beyond its canonical role in signaling.

  3. Chromatin Immunoprecipitation.

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    Wiehle, Laura; Breiling, Achim

    2016-01-01

    Chromatin immunoprecipitation (ChIP) is a valuable method to investigate protein-DNA interactions in vivo. Since its discovery it has been indispensable to identify binding sites and patterns of a variety of DNA-interacting proteins, such as transcription factors and regulators, modified histones, and epigenetic modifiers. The Polycomb repressors were the first proteins that have been mapped using this technique, which provided the mechanistic basis for the understanding of their biological function. Cross-linked (XChIP) or native (NChIP) chromatin from tissues or cultured cells is fragmented and the protein of interest is immunoprecipitated using a specific antibody. The co-precipitated DNA is then purified and subjected to analysis by region-specific PCR, DNA microarray (ChIP-on-chip), or next-generation sequencing (ChIP-seq). The assay can therefore produce information about the localization of the analyzed protein at specific candidate loci or throughout the entire genome. In this chapter, we provide a detailed protocol of the basic standard ChIP assay and some remarks about variations. PMID:27659971

  4. Analysis list: AGO2 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available AGO2 Blood,Prostate + hg19 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/target/AGO2.1.tsv http:...//dbarchive.biosciencedbc.jp/kyushu-u/hg19/target/AGO2.5.tsv http://dbarchive.biosciencedbc.j...p/kyushu-u/hg19/target/AGO2.10.tsv http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/colo/AGO2.Blood.tsv,http:...//dbarchive.biosciencedbc.jp/kyushu-u/hg19/colo/AGO2.Prostate.tsv http://dbarchiv...e.biosciencedbc.jp/kyushu-u/hg19/colo/Blood.gml,http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/colo/Prostate.gml ...

  5. KRAS-MEK Signaling Controls Ago2 Sorting into Exosomes

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    Andrew J. McKenzie; Daisuke Hoshino; Nan Hyung Hong; Diana J. Cha; Jeffrey L. Franklin; Robert J. Coffey; James G. Patton; Alissa M. Weaver

    2016-01-01

    Secretion of RNAs in extracellular vesicles is a newly recognized form of intercellular communication. A potential regulatory protein for microRNA (miRNA) secretion is the critical RNA-induced silencing complex (RISC) component Argonaute 2 (Ago2). Here, we use isogenic colon cancer cell lines to show that overactivity of KRAS due to mutation inhibits localization of Ago2 to multivesicular endosomes (MVEs) and decreases Ago2 secretion in exosomes. Mechanistically, inhibition of mitogen-activat...

  6. KRAS-MEK Signaling Controls Ago2 Sorting into Exosomes

    OpenAIRE

    McKenzie, Andrew J.; Hoshino, Daisuke; Hong, Nan Hyung; Diana J Cha; Franklin, Jeffrey L.; Coffey, Robert J.; Patton, James G.; Weaver, Alissa M.

    2016-01-01

    Summary Secretion of RNAs in extracellular vesicles is a newly recognized form of intercellular communication. A potential regulatory protein for microRNA (miRNA) secretion is the critical RNA-induced silencing complex (RISC) component Argonaute 2 (Ago2). Here, we use isogenic colon cancer cell lines to show that overactivity of KRAS due to mutation inhibits localization of Ago2 to multivesicular endosomes (MVEs) and decreases Ago2 secretion in exosomes. Mechanistically, inhibition of mitogen...

  7. Chromatin immunoprecipitation and multiplex sequencing (ChIP-Seq) to identify global transcription factor binding sites in the nematode Caenorhabditis elegans.

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    Brdlik, Cathleen M; Niu, Wei; Snyder, Michael

    2014-01-01

    The global identification of transcription factor (TF) binding sites is a critical step in the elucidation of the functional elements of the genome. Several methods have been developed that map TF binding in human cells, yeast, and other model organisms. These methods make use of chromatin immunoprecipitation, or ChIP, and take advantage of the fact that formaldehyde fixation of living cells can be used to cross-link DNA sequences to the TFs that bind them in vivo. In ChIP, the cross-linked TF-DNA complexes are sheared by sonication, size fractionated, and incubated with antibody specific to the TF of interest to generate a library of TF-bound DNA sequences. ChIP-chip was the first technology developed to globally identify TF-bound DNA sequences and involves subsequent hybridization of the ChIP DNA to oligonucleotide microarrays. However, ChIP-chip proved to be costly, labor-intensive, and limited by the fixed number of probes available on the microarray chip. ChIP-Seq combines ChIP with massively parallel high-throughput sequencing (see Explanatory Chapter: Next Generation Sequencing) and has demonstrated vast improvement over ChIP-chip with respect to time and cost, signal-to-noise ratio, and resolution. In particular, multiplex sequencing can be used to achieve a higher throughput in ChIP-Seq analyses involving organisms with genomes of lower complexity than that of human (Lefrançois et al., 2009) and thereby reduce the cost and amount of time needed for each result. The multiplex ChIP-Seq method described in this section has been developed for Caenorhabditis elegans, but is easily adaptable for other organisms.

  8. An antiviral defense role of AGO2 in plants.

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    Jagger J W Harvey

    Full Text Available BACKGROUND: Argonaute (AGO proteins bind to small-interfering (siRNAs and micro (miRNAs to target RNA silencing against viruses, transgenes and in regulation of mRNAs. Plants encode multiple AGO proteins but, in Arabidopsis, only AGO1 is known to have an antiviral role. METHODOLOGY/PRINCIPAL FINDINGS: To uncover the roles of specific AGOs in limiting virus accumulation we inoculated turnip crinkle virus (TCV to Arabidopsis plants that were mutant for each of the ten AGO genes. The viral symptoms on most of the plants were the same as on wild type plants although the ago2 mutants were markedly hyper-susceptible to this virus. ago2 plants were also hyper-susceptible to cucumber mosaic virus (CMV, confirming that the antiviral role of AGO2 is not specific to a single virus. For both viruses, this phenotype was associated with transient increase in virus accumulation. In wild type plants the AGO2 protein was induced by TCV and CMV infection. CONCLUSIONS/SIGNIFICANCE: Based on these results we propose that there are multiple layers to RNA-mediated defense and counter-defense in the interactions between plants and their viruses. AGO1 represents a first layer. With some viruses, including TCV and CMV, this layer is overcome by viral suppressors of silencing that can target AGO1 and a second layer involving AGO2 limits virus accumulation. The second layer is activated when the first layer is suppressed because AGO2 is repressed by AGO1 via miR403. The activation of the second layer is therefore a direct consequence of the loss of the first layer of defense.

  9. Identification of Associated Proteins by Immunoprecipitation and Mass Spectrometry Analysis.

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    Cao, Xiumei; Yan, Jianshe

    2016-01-01

    Protein-protein interactions play central roles in intercellular and intracellular signal transduction. Impairment of protein-protein interactions causes many diseases such as cancer, cardiomyopathies, diabetes, microbial infections, and genetic and neurodegenerative disorders. Immunoprecipitation is a technique in which a target protein of interest bound by an antibody is used to pull down the protein complex out of cell lysates, which can be identified by mass spectrometry. Here, we describe the protocol to immunoprecipitate and identify the components of the protein complexes of ElmoE in Dictyostelium discoideum cells. PMID:27271899

  10. Ago2 facilitates Rad51 recruitment and DNA double-strand break repair by homologous recombination

    DEFF Research Database (Denmark)

    Gao, Min; Wei, Wei; Li, Ming Hua;

    2014-01-01

    (Ago) proteins and play an important role in DSB repair, though the mechanism through which they act remains unclear. Here, we report that the role of diRNAs in DSB repair is restricted to repair by homologous recombination (HR) and that it specifically relies on the effector protein Ago2 in mammalian...... to facilitate repair by HR....

  11. eIF1A augments Ago2-mediated Dicer-independent miRNA biogenesis and RNA interference

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    Yi, Tingfang; Arthanari, Haribabu; Akabayov, Barak; Song, Huaidong; Papadopoulos, Evangelos; Qi, Hank H.; Jedrychowski, Mark; Güttler, Thomas; Guo, Cuicui; Luna, Rafael E.; Gygi, Steven P.; Huang, Stephen A.; Wagner, Gerhard

    2015-05-01

    MicroRNA (miRNA) biogenesis and miRNA-guided RNA interference (RNAi) are essential for gene expression in eukaryotes. Here we report that translation initiation factor eIF1A directly interacts with Ago2 and promotes Ago2 activities in RNAi and miR-451 biogenesis. Biochemical and NMR analyses demonstrate that eIF1A binds to the MID domain of Ago2 and this interaction does not impair translation initiation. Alanine mutation of the Ago2-facing Lys56 in eIF1A impairs RNAi activities in human cells and zebrafish. The eIF1A-Ago2 assembly facilitates Dicer-independent biogenesis of miR-451, which mediates erythrocyte maturation. Human eIF1A (heIF1A), but not heIF1A(K56A), rescues the erythrocyte maturation delay in eif1axb knockdown zebrafish. Consistently, miR-451 partly compensates erythrocyte maturation defects in zebrafish with eif1axb knockdown and eIF1A(K56A) expression, supporting a role of eIF1A in miRNA-451 biogenesis in this model. Our results suggest that eIF1A is a novel component of the Ago2-centred RNA-induced silencing complexes (RISCs) and augments Ago2-dependent RNAi and miRNA biogenesis.

  12. Hypomethylation of intragenic LINE-1 represses transcription in cancer cells through AGO2.

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    Chatchawit Aporntewan

    Full Text Available In human cancers, the methylation of long interspersed nuclear element -1 (LINE-1 or L1 retrotransposons is reduced. This occurs within the context of genome wide hypomethylation, and although it is common, its role is poorly understood. L1s are widely distributed both inside and outside of genes, intragenic and intergenic, respectively. Interestingly, the insertion of active full-length L1 sequences into host gene introns disrupts gene expression. Here, we evaluated if intragenic L1 hypomethylation influences their host gene expression in cancer. First, we extracted data from L1base (http://l1base.molgen.mpg.de, a database containing putatively active L1 insertions, and compared intragenic and intergenic L1 characters. We found that intragenic L1 sequences have been conserved across evolutionary time with respect to transcriptional activity and CpG dinucleotide sites for mammalian DNA methylation. Then, we compared regulated mRNA levels of cells from two different experiments available from Gene Expression Omnibus (GEO, a database repository of high throughput gene expression data, (http://www.ncbi.nlm.nih.gov/geo by chi-square. The odds ratio of down-regulated genes between demethylated normal bronchial epithelium and lung cancer was high (p<1E(-27; OR = 3.14; 95% CI = 2.54-3.88, suggesting cancer genome wide hypomethylation down-regulating gene expression. Comprehensive analysis between L1 locations and gene expression showed that expression of genes containing L1s had a significantly higher likelihood to be repressed in cancer and hypomethylated normal cells. In contrast, many mRNAs derived from genes containing L1s are elevated in Argonaute 2 (AGO2 or EIF2C2-depleted cells. Hypomethylated L1s increase L1 mRNA levels. Finally, we found that AGO2 targets intronic L1 pre-mRNA complexes and represses cancer genes. These findings represent one of the mechanisms of cancer genome wide hypomethylation altering gene expression

  13. HuR and Ago2 Bind the Internal Ribosome Entry Site of Enterovirus 71 and Promote Virus Translation and Replication.

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    Jing-Yi Lin

    Full Text Available EV71 (enterovirus 71 RNA contains an internal ribosomal entry site (IRES that directs cap-independent initiation of translation. IRES-dependent translation requires the host's translation initiation factors and IRES-associated trans-acting factors (ITAFs. We reported recently that mRNA decay factor AUF1 is a negative-acting ITAF that binds IRES stem-loop II. We also reported that the small RNA-processing enzyme Dicer produces at least four small RNAs (vsRNAs from the EV71 IRES. One of these, vsRNA1, derived from IRES stem-loop II, reduces IRES activity and virus replication. Since its mechanism of action is unknown, we hypothesized that it might control association of ITAFs with the IRES. Here, we identified the mRNA stability factor HuR and the RISC subunit Argonaute 2 (Ago2 as two ITAFs that bind stem-loop II. In contrast to AUF1, HuR and Ago2 promote EV71 IRES activity and virus replication. In vitro RNA-binding assays revealed that vsRNA1 can alter association of Ago2, HuR, and AUF1 with stem-loop II. This presents a possible mechanism by which vsRNA1 could control viral translation and replication.

  14. TP53 regulates miRNA association with AGO2 to remodel the miRNA-mRNA interaction network.

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    Krell, Jonathan; Stebbing, Justin; Carissimi, Claudia; Dabrowska, Aleksandra F; de Giorgio, Alexander; Frampton, Adam E; Harding, Victoria; Fulci, Valerio; Macino, Giuseppe; Colombo, Teresa; Castellano, Leandro

    2016-03-01

    DNA damage activates TP53-regulated surveillance mechanisms that are crucial in suppressing tumorigenesis. TP53 orchestrates these responses directly by transcriptionally modulating genes, including microRNAs (miRNAs), and by regulating miRNA biogenesis through interacting with the DROSHA complex. However, whether the association between miRNAs and AGO2 is regulated following DNA damage is not yet known. Here, we show that, following DNA damage, TP53 interacts with AGO2 to induce or reduce AGO2's association of a subset of miRNAs, including multiple let-7 family members. Furthermore, we show that specific mutations in TP53 decrease rather than increase the association of let-7 family miRNAs, reducing their activity without preventing TP53 from interacting with AGO2. This is consistent with the oncogenic properties of these mutants. Using AGO2 RIP-seq and PAR-CLIP-seq, we show that the DNA damage-induced increase in binding of let-7 family members to the RISC complex is functional. We unambiguously determine the global miRNA-mRNA interaction networks involved in the DNA damage response, validating them through the identification of miRNA-target chimeras formed by endogenous ligation reactions. We find that the target complementary region of the let-7 seed tends to have highly fixed positions and more variable ones. Additionally, we observe that miRNAs, whose cellular abundance or differential association with AGO2 is regulated by TP53, are involved in an intricate network of regulatory feedback and feedforward circuits. TP53-mediated regulation of AGO2-miRNA interaction represents a new mechanism of miRNA regulation in carcinogenesis. PMID:26701625

  15. The human Ago2 MC region does not contain an eIF4E-like mRNA cap binding motif

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    Grishin Nick V

    2009-01-01

    Full Text Available Abstract Background Argonaute (Ago proteins interact with small regulatory RNAs to mediate gene regulatory pathways. A recent report by Kiriakidou et al. 1 describes an MC sequence region identified in Ago2 that displays similarity to the cap-binding motif in translation initiation factor 4E (eIF4E. In a cap-bound eIF4E structure, two important aromatic residues of the motif stack on either side of a 7-methylguanosine 5'-triphosphate (m7Gppp base. The corresponding Ago2 aromatic residues (F450 and F505 were hypothesized to perform the same cap-binding function. However, the detected similarity between the MC sequence and the eIF4E cap-binding motif was questionable. Results A number of sequence-based and structure-based bioinformatics methods reveal the reported similarity between the Ago2 MC sequence region and the eIF4E cap-binding motif to be spurious. Alternatively, the MC sequence region is confidently assigned to the N-terminus of the Ago piwi module, within the mid domain of experimentally determined prokaryotic Ago structures. Confident mapping of the Ago2 MC sequence region to the piwi mid domain results in a homology-based structure model that positions the identified aromatic residues over 20 Å apart, with one of the aromatic side chains (F450 contributing instead to the hydrophobic core of the domain. Conclusion Correct functional prediction based on weak sequence similarity requires substantial evolutionary and structural support. The evolutionary context of the Ago mid domain suggested by multiple sequence alignment is limited to a conserved hydrophobicity profile required for the fold and a motif following the MC region that binds guide RNA. Mapping of the MC sequence to the mid domain structure reveals Ago2 aromatics that are incompatible with eIF4E-like mRNA cap-binding, yet display some limited local structure similarities that cause the chance sequence match to eIF4E. Reviewers This article was reviewed by Arcady Mushegian

  16. Bioenergetics and gene silencing approaches for unraveling nucleotide recognition by the human EIF2C2/Ago2 PAZ domain.

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    Mahmoud Kandeel

    Full Text Available Gene silencing and RNA interference are major cellular processes that control gene expression via the cleavage of target mRNA. Eukaryotic translation initiation factor 2C2 (EIF2C2, Argonaute protein 2, Ago2 is considered to be the major player of RNAi as it is the core component of RISC complexes. While a considerable amount of research has focused on RNA interference and its associated mechanisms, the nature and mechanisms of nucleotide recognition by the PAZ domain of EIF2C2/Ago2 have not yet been characterized. Here, we demonstrate that the EIF2C2/Ago2 PAZ domain has an inherent lack of binding to adenine nucleotides, a feature that highlights the poor binding of 3'-adenylated RNAs with the PAZ domain as well as the selective high trimming of the 3'-ends of miRNA containing adenine nucleotides. We further show that the PAZ domain selectively binds all ribonucleotides (except adenosine, whereas it poorly recognizes deoxyribonucleotides. In this context, the modification of dTMP to its ribonucleotide analogue gave a drastic improvement of binding enthalpy and, hence, binding affinity. Additionally, higher in vivo gene silencing efficacy was correlated with the stronger PAZ domain binders. These findings provide new insights into the nature of the interactions of the EIF2C2/Ago2 PAZ domain.

  17. Immunoprecipitation of membrane proteins of cultured human sarcoma cells.

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    Grófová, M; Forchhammer, J; Lizonová, A; Popovic, M

    1981-01-01

    Human sarcoma associated antigens (HSAA) have previously been identified by indirect immune fluorescence in human sarcoma cells in culture using sera from patients bearing different types of sarcoma. To further characterize these HSAA, surface proteins of cultured cells were labeled with 125Iodine, [3H]-glucosamine and [35S]-methionine and solubilized. After immunoprecipitation labeled proteins were detected in immune complexes by SDS polyacrylamide gel electrophoresis and autoradiography, which allowed comparison with antigens described by other groups. A surface protein (Mr 96 000) was precipitated with sera from sarcoma bearing patients, and two glycoproteins (Mr 115 000 and 85 000) were preferentially precipitated with antisera from rabbits immunized with membranes from two human sarcoma cell lines. At least two of these proteins were found in each of five human sarcoma cell lines studied (U-4SS, U-3930S, U-20S, B-5GT and B-6FS). None of the proteins were precipitated with three human control sera, and only occasionally a faint band was observed in immunoprecipitates from control cells (B-25F, B-41B, B-42FC, U-2S, and U-393S with the immune sera. These proteins are probably some of the antigens responsible for the immune fluorescence observed in determination of HSAA. However, purification of the proteins and competition experiments are needed before this can be finally established.

  18. Identification of an archaeal mercury regulon by chromatin immunoprecipitation.

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    Rudrappa, Deepak; Yao, Andrew I; White, Derrick; Pavlik, Benjamin J; Singh, Raghuveer; Facciotti, Marc T; Blum, Paul

    2015-12-01

    Mercury is a heavy metal and toxic to all forms of life. Metal exposure can invoke a response to improve survival. In archaea, several components of a mercury response system have been identified, but it is not known whether metal transport is a member of this system. To identify such missing components, a peptide-tagged MerR transcription factor was used to localize enriched chromosome regions by chromosome immunoprecipitation combined with DNA sequence analysis. Such regions could serve as secondary regulatory binding sites to control the expression of additional genes associated with mercury detoxification. Among the 31 highly enriched loci, a subset of five was pursued as potential candidates based on their current annotations. Quantitative reverse transcription-PCR analysis of these regions with and without mercury treatment in WT and mutant strains lacking merR indicated significant regulatory responses under these conditions. Of these, a Family 5 extracellular solute-binding protein and the MarR transcription factor shown previously to control responses to oxidation were most strongly affected. Inactivation of the solute-binding protein by gene disruption increased the resistance of mutant cells to mercury challenge. Inductively coupled plasma-MS analysis of the mutant cell line following metal challenge indicated there was less intracellular mercury compared with the isogenic WT strain. Together, these regulated genes comprise new members of the archaeal MerR regulon and reveal a cascade of transcriptional control not previously demonstrated in this model organism.

  19. Inferring protein inverted question markprotein interaction complexes from immunoprecipitation data

    NARCIS (Netherlands)

    J. Kutzera; H.C.J. Hoefsloot; A. Malovannaya; A.B. Smit; I. van Mechelen; A.K. Smilde

    2013-01-01

    BACKGROUND: Protein inverted question markprotein interactions in cells are widely explored using small inverted question markscale experiments. However, the search for protein complexes and their interactions in data from high throughput experiments such as immunoprecipitation is still a challenge.

  20. Genome-Wide Methylated DNA Immunoprecipitation Analysis of Patients with Polycystic Ovary Syndrome

    OpenAIRE

    Shen, Hao-ran; Qiu, Li-Hua; Zhang, Zhi-Qing; Qin, Yuan-Yuan; Cao, Cong; DI, WEN

    2013-01-01

    Polycystic ovary syndrome (PCOS) is a complex, heterogeneous disorder of uncertain etiology. Recent studies suggested that insulin resistance (IR) plays an important role in the development of PCOS. In the current study, we aimed to investigate the molecular mechanism of IR in PCOS. We employed genome-wide methylated DNA immunoprecipitation (MeDIP) analysis to characterize genes that are differentially methylated in PCOS patients vs. healthy controls. Besides, we also identified the different...

  1. Identification of the immunoproteome of the meningococcus by cell surface immunoprecipitation and MS.

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    Newcombe, Jane; Mendum, Tom A; Ren, Chuan-peng; McFadden, Johnjoe

    2014-02-01

    Most healthy adults are protected from meningococcal disease by the presence of naturally acquired anti-meningococcal antibodies; however, the identity of the target antigens of this protective immunity remains unclear, particularly for protection against serogroup B disease. To identify the protein targets of natural protective immunity we developed an immunoprecipitation and proteomics approach to define the immunoproteome of the meningococcus. Sera from 10 healthy individuals showing serum bactericidal activity against both a meningococcal C strain (L91543) and the B strain MC58, together with commercially available pooled human sera, were used as probe antisera. Immunoprecipitation was performed with each serum sample and live cells from both meningococcal strains. Immunoprecipitated proteins were identified by MS. Analysis of the immunoproteome from each serum demonstrated both pan-reactive antigens that were recognized by most sera as well as subject-specific antigens. Most antigens were found in both meningococcal strains, but a few were strain-specific. Many of the immunoprecipitated proteins have been characterized previously as surface antigens, including adhesins and proteases, several of which have been recognized as vaccine candidate antigens, e.g. factor H-binding protein, NadA and neisserial heparin-binding antigen. The data demonstrate clearly the presence of meningococcal antibodies in healthy individuals with no history of meningococcal infection and a wide diversity of immune responses. The identification of the immunoreactive proteins of the meningococcus provides a basis for understanding the role of each antigen in the natural immunity associated with carriage and may help to design vaccination strategies. PMID:24275101

  2. Methylated DNA Immunoprecipitation Analysis of Mammalian Endogenous Retroviruses.

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    Rebollo, Rita; Mager, Dixie L

    2016-01-01

    Endogenous retroviruses are repetitive sequences found abundantly in mammalian genomes which are capable of modulating host gene expression. Nevertheless, most endogenous retrovirus copies are under tight epigenetic control via histone-repressive modifications and DNA methylation. Here we describe a common method used in our laboratory to detect, quantify, and compare mammalian endogenous retrovirus DNA methylation. More specifically we describe methylated DNA immunoprecipitation (MeDIP) followed by quantitative PCR. PMID:26895065

  3. Isolation of proteins and protein complexes by immunoprecipitation.

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    Kaboord, Barbara; Perr, Maria

    2008-01-01

    Immunoprecipitation (IP) uses the specificity of antibodies to isolate target proteins (antigens) out of complex sample mixtures. Three different approaches for performing IP will be discussed; traditional (classical) method, oriented affinity method and direct affinity method. The traditional method of incubating the IP antibody with the sample and sequentially binding to Protein A or G agarose beads (resin) facilitates the most efficient target antigen recovery. However, this approach results in the target protein becoming contaminated with the IP antibody that can interfere with downstream analyses. The orientated affinity method uses Protein A or G beads to serve as an anchor to which the IP antibody is crosslinked thereby preventing the antibody from co-eluting with the target protein. Similarly, the direct affinity method also immobilizes the IP antibody except in this case it is directly attached to a chemically activated support. Both methods prevent co-elution of the IP antibody enabling reuse of the immunomatrix. All three approaches have unique advantages and can also be used for co-immunoprecipitation to study protein:protein interactions and investigate the functional proteome.

  4. Nanodisc-based Co-immunoprecipitation for Mass Spectrometric Identification of Membrane-interacting Proteins

    DEFF Research Database (Denmark)

    Borch-Jensen, Jonas; Roepstorff, Peter; Møller-Jensen, Jakob

    2011-01-01

    interaction partners of the glycolipid ganglioside GM1 harbored by nanodiscs. Highly specific binding activity for nanodisc-GM1 immobilized on sensorchips was observed by surface plasmon resonance in culture media from enterotoxigenic Escherischia coli. To isolate the interaction partner(s) from...... enterotoxigenic Escherischia coli, GM1-nanodiscs were employed for co-immunoprecipitation. The B subunit of heat labile enterotoxin was identified as a specific interaction partner by mass spectrometry, thus demonstrating that nanodisc technology is useful for highly specific detection and identification of...

  5. Chromatin immunoprecipitation from fixed clinical tissues reveals tumor-specific enhancer profiles.

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    Cejas, Paloma; Li, Lewyn; O'Neill, Nicholas K; Duarte, Melissa; Rao, Prakash; Bowden, Michaela; Zhou, Chensheng W; Mendiola, Marta; Burgos, Emilio; Feliu, Jaime; Moreno-Rubio, Juan; Guadalajara, Héctor; Moreno, Víctor; García-Olmo, Damián; Bellmunt, Joaquim; Mullane, Stephanie; Hirsch, Michelle; Sweeney, Christopher J; Richardson, Andrea; Liu, X Shirley; Brown, Myles; Shivdasani, Ramesh A; Long, Henry W

    2016-06-01

    Extensive cross-linking introduced during routine tissue fixation of clinical pathology specimens severely hampers chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) analysis from archived tissue samples. This limits the ability to study the epigenomes of valuable, clinically annotated tissue resources. Here we describe fixed-tissue chromatin immunoprecipitation sequencing (FiT-seq), a method that enables reliable extraction of soluble chromatin from formalin-fixed paraffin-embedded (FFPE) tissue samples for accurate detection of histone marks. We demonstrate that FiT-seq data from FFPE specimens are concordant with ChIP-seq data from fresh-frozen samples of the same tumors. By using multiple histone marks, we generate chromatin-state maps and identify cis-regulatory elements in clinical samples from various tumor types that can readily allow us to distinguish between cancers by the tissue of origin. Tumor-specific enhancers and superenhancers that are elucidated by FiT-seq analysis correlate with known oncogenic drivers in different tissues and can assist in the understanding of how chromatin states affect gene regulation.

  6. A chromatin immunoprecipitation (ChIP) protocol for use in whole human adipose tissue.

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    Haim, Yulia; Tarnovscki, Tanya; Bashari, Dana; Rudich, Assaf

    2013-11-01

    Chromatin immunoprecipitation (ChIP) has become a central method when studying in vivo protein-DNA interactions, with the major challenge being the hope to capture "authentic" interactions. While ChIP protocols have been optimized for use with specific cell types and tissues including adipose tissue-derived cells, a working ChIP protocol addressing the challenges imposed by fresh whole human adipose tissue has not been described. Utilizing human paired omental and subcutaneous adipose tissue obtained during elective abdominal surgeries, we have carefully identified and optimized individual steps in the ChIP protocol employed directly on fresh tissue fragments. We describe a complete working protocol for using ChIP on whole adipose tissue fragments. Specific steps required adaptation of the ChIP protocol to human whole adipose tissue. In particular, a cross-linking step was performed directly on fresh small tissue fragments. Nuclei were isolated before releasing chromatin, allowing better management of fat content; a sonication protocol to obtain fragmented chromatin was optimized. We also demonstrate the high sensitivity of immunoprecipitated chromatin from adipose tissue to freezing. In conclusion, we describe the development of a ChIP protocol optimized for use in studying whole human adipose tissue, providing solutions for the unique challenges imposed by this tissue. Unraveling protein-DNA interaction in whole human adipose tissue will likely contribute to elucidating molecular pathways contributing to common human diseases such as obesity and type 2 diabetes.

  7. Chromatin immunoprecipitation from fixed clinical tissues reveals tumor-specific enhancer profiles.

    Science.gov (United States)

    Cejas, Paloma; Li, Lewyn; O'Neill, Nicholas K; Duarte, Melissa; Rao, Prakash; Bowden, Michaela; Zhou, Chensheng W; Mendiola, Marta; Burgos, Emilio; Feliu, Jaime; Moreno-Rubio, Juan; Guadalajara, Héctor; Moreno, Víctor; García-Olmo, Damián; Bellmunt, Joaquim; Mullane, Stephanie; Hirsch, Michelle; Sweeney, Christopher J; Richardson, Andrea; Liu, X Shirley; Brown, Myles; Shivdasani, Ramesh A; Long, Henry W

    2016-06-01

    Extensive cross-linking introduced during routine tissue fixation of clinical pathology specimens severely hampers chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) analysis from archived tissue samples. This limits the ability to study the epigenomes of valuable, clinically annotated tissue resources. Here we describe fixed-tissue chromatin immunoprecipitation sequencing (FiT-seq), a method that enables reliable extraction of soluble chromatin from formalin-fixed paraffin-embedded (FFPE) tissue samples for accurate detection of histone marks. We demonstrate that FiT-seq data from FFPE specimens are concordant with ChIP-seq data from fresh-frozen samples of the same tumors. By using multiple histone marks, we generate chromatin-state maps and identify cis-regulatory elements in clinical samples from various tumor types that can readily allow us to distinguish between cancers by the tissue of origin. Tumor-specific enhancers and superenhancers that are elucidated by FiT-seq analysis correlate with known oncogenic drivers in different tissues and can assist in the understanding of how chromatin states affect gene regulation. PMID:27111282

  8. Identification of Transcribed Enhancers by Genome-Wide Chromatin Immunoprecipitation Sequencing.

    Science.gov (United States)

    Blinka, Steven; Reimer, Michael H; Pulakanti, Kirthi; Pinello, Luca; Yuan, Guo-Cheng; Rao, Sridhar

    2017-01-01

    Recent work has shown that RNA polymerase II-mediated transcription at distal cis-regulatory elements serves as a mark of highly active enhancers. Production of noncoding RNAs at enhancers, termed eRNAs, correlates with higher expression of genes that the enhancer interacts with; hence, eRNAs provide a new tool to model gene activity in normal and disease tissues. Moreover, this unique class of noncoding RNA has diverse roles in transcriptional regulation. Transcribed enhancers can be identified by a common signature of epigenetic marks by overlaying a series of genome-wide chromatin immunoprecipitation and RNA sequencing datasets. A computational approach to filter non-enhancer elements and other classes of noncoding RNAs is essential to not cloud downstream analysis. Here we present a protocol that combines wet and dry bench methods to accurately identify transcribed enhancers genome-wide as well as an experimental procedure to validate these datasets. PMID:27662872

  9. 白纹伊蚊AGO2和Dcr-2基因片段克隆及各发育期转录水平分析%Cloning of AGO2 and Dcr-2 Gene Fragments and Analysis of Their Transcription Level in Different Developmental Stages of Aedes albopictus

    Institute of Scientific and Technical Information of China (English)

    蔡燕丽; 郑学礼

    2012-01-01

    Objective To perform molecular cloning of the ACO2 and Dcr-2 gene fragments associated with RNA interference pathway of Aedes albopictus and characterize the transcription level of the two genes across all life stages of the mosquito. Methods The degenerate primers were designed based on the conserved regions of AGO2 and Dcr-2 amino acid sequences, and the AGO2 and Dcr-2 cDNA fragments were amplified from total RNA of a female mosquito by RT-PCR. The PCR products were cloned into pMD18-T vector and transformed into E. Coli DH5α strain, and the positive clones were selected and sequenced, with the results for homology analysis by Blastx. The specific primers were designed according to the sequences of ACO2 and Dcr-2 from Ae. Albopictus, which were used to investigate the transcription levels of these two genes from eggs, Ⅰ and Ⅱ instars larvae, Ⅲ and IV instars larvae, pupa, male and female mosquitoes by semi-quantitative RT-PCR. Results The AGO2 and Dcr-2 cDNA fragments obtained were 326 bp and 491 bp in length, with the Accession number of JQ764670 and JQ764671, respectively. The Blastx analysis showed that the AC02 and Dcr-2 amino acid sequences shared 91% similarity to AGO2 of Ae. Aegypti and 98% to Dcr-2 of Ae. Albopictus. The transcription of ACO2 and Dcr-2 genes was detected in all life stages of Ae. Albopictus, with the highest level of mRNA in female mosquitoes, which was 3.1 times and 15.5 times higher for AGO2 and Dcr-2 than in male mosquitoes, respectively, and significantly higher than other developmental stages (P<0.05). Conclusion The AGO2 and Dcr-2 cDNA sequences have been partially obtained and the hightest transcription level found in female Ae. Albopictus, suggesting that AGO2 and Dcr-2 are the key genes of RNA interference in female mosquitoes.%目的 克隆白纹伊蚊(Aedes albopictus )RNA干扰通路相关AGO2和Dcr-2基因片段,并分析该蚊种不同发育阶段这2个基因片段的转录水平.方法

  10. Tagging of MADS domain proteins for chromatin immunoprecipitation

    Directory of Open Access Journals (Sweden)

    van Zuijlen Lisette GC

    2007-09-01

    Full Text Available Abstract Background Most transcription factors fulfill their role in complexes and regulate their target genes upon binding to DNA motifs located in upstream regions or introns. To date, knowledge about transcription factor target genes and their corresponding transcription factor binding sites are still very limited. Two related methods that allow in vivo identification of transcription factor binding sites are chromatin immunoprecipitation (ChIP and chromatin affinity purification (ChAP. For ChAP, the protein of interest is tagged with a peptide or protein, which can be used for affinity purification of the protein-DNA complex and hence, the identification of the target gene. Results Here, we present the results of experiments aiming at the development of a generic tagging approach for the Arabidopsis MADS domain proteins AGAMOUS, SEPALLATA3, and FRUITFULL. For this, Arabidopsis wild type plants were transformed with constructs containing a MADS-box gene fused to either a double Strep-tag® II-FLAG-tag, a triple HA-tag, or an eGFP-tag, all under the control of the constitutive double 35S Cauliflower Mosaic Virus (CaMV promoter. Strikingly, in all cases, the number of transformants with loss-of-function phenotypes was much larger than those with an overexpression phenotype. Using endogenous promoters in stead of the 35S CaMV resulted in a dramatic reduction in the frequency of loss-of-function phenotypes. Furthermore, pleiotropic defects occasionally caused by an overexpression strategy can be overcome by using the native promoter of the gene. Finally, a ChAP result is presented using GFP antibody on plants carrying a genomic fragment of a MADS-box gene fused to GFP. Conclusion This study revealed that MADS-box proteins are very sensitive to fusions with small peptide tags and GFP tags. Furthermore, for the expression of chimeric versions of MADS-box genes it is favorable to use the entire genomic region in frame to the tag of choice

  11. Proteomics Analysis of Cellular Proteins Co-Immunoprecipitated with Nucleoprotein of Influenza A Virus (H7N9

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    Ningning Sun

    2015-10-01

    Full Text Available Avian influenza A viruses are serious veterinary pathogens that normally circulate among avian populations, causing substantial economic impacts. Some strains of avian influenza A viruses, such as H5N1, H9N2, and recently reported H7N9, have been occasionally found to adapt to humans from other species. In order to replicate efficiently in the new host, influenza viruses have to interact with a variety of host factors. In the present study, H7N9 nucleoprotein was transfected into human HEK293T cells, followed by immunoprecipitated and analyzed by proteomics approaches. A series of host proteins co-immunoprecipitated were identified with high confidence, some of which were found to be acetylated at their lysine residues. Bioinformatics analysis revealed that spliceosome might be the most relevant pathway involved in host response to nucleoprotein expression, increasing our emerging knowledge of host proteins that might be involved in influenza virus replication activities.

  12. Genome-Wide Chromatin Immunoprecipitation in Candida albicans and Other Yeasts

    Science.gov (United States)

    Lohse, Matthew B.; Kongsomboonvech, Pisiwat; Madrigal, Maria; Hernday, Aaron D.; Nobile, Clarissa J.

    2016-01-01

    Chromatin immunoprecipitation experiments are critical to investigating the interactions between DNA and a wide range of nuclear proteins within a cell or biological sample. In this chapter we outline an optimized protocol for genome-wide chromatin immunoprecipitation that has been used successfully for several distinct morphological forms of numerous yeast species, and include an optimized method for amplification of chromatin immunoprecipitated DNA samples and hybridization to a high-density oligonucleotide tiling microarray. We also provide detailed suggestions on how to analyze the complex data obtained from these experiments. PMID:26483022

  13. A DNA immunoprecipitation assay used in quantitative detection of in vitro DNA-protein complex binding.

    Science.gov (United States)

    Kim, Min Young; Chae, Ji Hyung; Oh, Chang-Ho; Kim, Chul Geun

    2013-10-15

    To begin gene transcription, several transcription factors must bind to specific DNA sequences to form a complex via DNA-protein interactions. We established an in vitro method for specific and sensitive analyses of DNA-protein interactions based on a DNA immunoprecipitation (DIP) method. We verified the accuracy and efficiency of the DIP assay in quantitatively measuring DNA-protein binding using transcription factor CP2c as a model. With our DIP assay, we could detect specific interactions within a DNA-CP2c complex, with reproducible and quantitative binding values. In addition, we were able to effectively measure the changes in DNA-CP2c binding by the addition of a small molecule, FQI1 (factor quinolinone inhibitor 1), previously identified as a specific inhibitor of this binding. To identify a new regulator of DNA-CP2c binding, we analyzed several CP2c binding peptides and found that only one class of peptide severely inhibits DNA-CP2c binding. These data show that our DIP assay is very useful in quantitatively detecting the binding dynamics of DNA-protein complex. Because DNA-protein interaction is very dynamic in different cellular environments, our assay can be applied to the detection of active transcription factors, including promoter occupancy in normal and disease conditions. Moreover, it may be used to develop a targeted regulator of specific DNA-protein interaction.

  14. Sequential chromatin immunoprecipitation protocol for global analysis through massive parallel sequencing (reChIP-seq)

    OpenAIRE

    sprotocols

    2015-01-01

    Authors: Marco Antonio Mendoza-Parra, Shankaranarayanan Pattabhiraman & Hinrich Gronemeyer ### Abstract Chromatin immunoprecipitation combined with massive parallel sequencing (ChIP-seq) is increasingly used to study protein-chromatin interactions or local epigenetic modifications at genome-wide scale. ChIP-seq can be performed directly with several ng of immunoprecipitated DNA, which is generally obtained from a several million cells, depending on the quality of the antibody. ChI...

  15. Identification of potential target genes for the tomato fruit-ripening regulator RIN by chromatin immunoprecipitation

    Directory of Open Access Journals (Sweden)

    Nakano Toshitsugu

    2011-01-01

    Full Text Available Abstract Background During ripening, climacteric fruits increase their ethylene level and subsequently undergo various physiological changes, such as softening, pigmentation and development of aroma and flavor. These changes occur simultaneously and are caused by the highly synchronized expression of numerous genes at the onset of ripening. In tomatoes, the MADS-box transcription factor RIN has been regarded as a key regulator responsible for the onset of ripening by acting upstream of both ethylene- and non-ethylene-mediated controls. However, except for LeACS2, direct targets of RIN have not been clarified, and little is known about the transcriptional cascade for ripening. Results Using immunoprecipitated (IPed DNA fragments recovered by chromatin immunoprecipitation (ChIP with anti-RIN antibody from ripening tomato fruit, we analyzed potential binding sites for RIN (CArG-box sites in the promoters of representative ripening-induced genes by quantitative PCR. Results revealed nearly a 5- to 20-fold enrichment of CArG boxes in the promoters of LeACS2, LeACS4, PG, TBG4, LeEXP1, and LeMAN4 and of RIN itself, indicating direct interaction of RIN with their promoters in vivo. Moreover, sequence analysis and genome mapping of 51 cloned IPed DNAs revealed potential RIN binding sites. Quantitative PCR revealed that four of the potential binding sites were enriched 4- to 17-fold in the IPed DNA pools compared with the controls, indicating direct interaction of RIN with these sites in vivo. Near one of the four CArG boxes we found a gene encoding a protein similar to thioredoxin y1. An increase in the transcript level of this gene was observed with ripening in normal fruit but not in the rin mutant, suggesting that RIN possibly induces its expression. Conclusions The presented results suggest that RIN controls fruit softening and ethylene production by the direct transcriptional regulation of cell-wall-modifying genes and ethylene biosynthesis genes

  16. Immunoprecipitation techniques and Elisa in the detection of anti-Fonsecaea pedrosoi antibodies in chromoblastomycosis

    Directory of Open Access Journals (Sweden)

    Vidal Mônica Scarpelli Martinelli

    2003-01-01

    Full Text Available Chromoblastomycosis (CBM is a chronic subcutaneous infection caused by several dematiaceous fungi. The most commonly etiological agent found in Brazil is Fonsecaea pedrosoi, which appears as thick walled, brownish colored cells with transverse and longitudinal division in the lesions, called "muriform cells". This disease is found worldwide but countries like Madagascar and Brazil have highest incidence. Diagnosis is made by clinical, direct and histopathologic examination and culture of specimens. Serological tests have been used to identify specific antibodies against Fonsecaea pedrosoi antigens, as well as immunotechniques have been used for CBM serological identification and diagnosis. In the present study double immunodiffusion (DID, counterimmunoelectrophoresis (CIE and immunoenzymatic test (ELISA have been used to evaluate humoral immune response in patients with CBM caused by F. pedrosoi. Metabolic antigen was used for immunoprecipitation tests (DID and CIE while somatic antigen for ELISA. Our results demonstrated 53% sensitivity and 96% specificity for DID, while CIE presented 68% sensitivity and 90.5% specificity. ELISA demonstrated 78% sensibility and 83% specificity. Serological tests can be a useful tool to study different aspects of CBM, such as helping differential diagnosis, when culture of the pathogenic agent is impossible.

  17. Protocol: fine-tuning of a Chromatin Immunoprecipitation (ChIP protocol in tomato

    Directory of Open Access Journals (Sweden)

    Iusem Norberto D

    2010-04-01

    Full Text Available Abstract Background Searching thoroughly for plant cis-elements corresponding to transcription factors is worthwhile to reveal novel gene activation cascades. At the same time, a great deal of research is currently focused on epigenetic events in plants. A widely used method serving both purposes is chromatin immunoprecipitation, which was developed for Arabidopsis and other plants but is not yet operational for tomato (Solanum lycopersicum, a model plant species for a group of economically important crops. Results We developed a chromatin immunoprecipitation protocol suitable for tomato by adjusting the parameters to optimise in vivo crosslinking, purification of nuclei, chromatin extraction, DNA shearing and precipitate analysis using real-time PCR. Results were obtained with two different antibodies, five control loci and two normalisation criteria. Conclusion Here we provide a chromatin immunoprecipitation procedure for tomato leaves that could be combined with high-throughput sequencing to generate a detailed map of epigenetic modifications or genome-wide nucleosome positioning data.

  18. Characterizing RNA-protein interaction using cross-linking and metabolite supplemented nuclear RNA-immunoprecipitation.

    Science.gov (United States)

    Au, Phil Chi Khang; Helliwell, Chris; Wang, Ming-Bo

    2014-05-01

    RNA-immunoprecipitation (RNA-IP) is a method used to isolate and identify RNA molecules specifically associated with an RNA-binding protein. Non-coding RNAs are emerging as key regulators of many biological and developmental pathways and RNA-IP has become an important tool in studying their function(s). While RNA-IP is successfully used to determine protein-RNA interaction, specific details regarding the level of this association and the metabolic requirement of this interaction which can influence the success of RNA-IP remain unclear. Here, we investigate the conditions required for efficient nuclear RNA-IP using Arabidopsis AGO4 (Argonaute 4) and siRNA binding as the study model. We showed that formaldehyde cross-linking, but not UV cross-linking, allowed for efficient pull-down of 24-nt siRNAs, suggesting that AGO4-siRNA interaction involves other protein(s). We also showed that, while formaldehyde cross-linking could also be performed on purified nuclei, ATP supplementation to the nuclei isolation buffer was needed to efficiently pull down 24-nt siRNAs. This result indicates that ATP is required for efficient siRNA loading onto AGO4. As most of the known RNA-mediated regulatory processes occur in the nucleus, our findings on cross-linking conditions and metabolite requirement for successful AGO4 nuclear RNA-IP provide a valuable insight and future consideration when studying the function of protein-RNA interactions in plants.

  19. Genomic response to Wnt signalling is highly context-dependent - Evidence from DNA microarray and chromatin immunoprecipitation screens of Wnt/TCF targets

    Energy Technology Data Exchange (ETDEWEB)

    Railo, Antti [Oulu Centre for Cell Matrix Research, Biocenter Oulu, Laboratory of Developmental Biology and Department of Medical Biochemistry and Molecular Biology, FIN-90014, University of Oulu, P. O. Box 5000 (Finland); Pajunen, Antti [Department of Biochemistry, University of Oulu (Finland); Itaeranta, Petri; Naillat, Florence; Vuoristo, Jussi; Kilpelaeinen, Pekka [Oulu Centre for Cell Matrix Research, Biocenter Oulu, Laboratory of Developmental Biology and Department of Medical Biochemistry and Molecular Biology, FIN-90014, University of Oulu, P. O. Box 5000 (Finland); Vainio, Seppo, E-mail: Seppo.Vainio@oulu.fi [Oulu Centre for Cell Matrix Research, Biocenter Oulu, Laboratory of Developmental Biology and Department of Medical Biochemistry and Molecular Biology, FIN-90014, University of Oulu, P. O. Box 5000 (Finland)

    2009-10-01

    Wnt proteins are important regulators of embryonic development, and dysregulated Wnt signalling is involved in the oncogenesis of several human cancers. Our knowledge of the downstream target genes is limited, however. We used a chromatin immunoprecipitation-based assay to isolate and characterize the actual gene segments through which Wnt-activatable transcription factors, TCFs, regulate transcription and an Affymetrix microarray analysis to study the global transcriptional response to the Wnt3a ligand. The anti-{beta}-catenin immunoprecipitation of DNA-protein complexes from mouse NIH3T3 fibroblasts expressing a fusion protein of {beta}-catenin and TCF7 resulted in the identification of 92 genes as putative TCF targets. GeneChip assays of gene expression performed on NIH3T3 cells and the rat pheochromocytoma cell line PC12 revealed 355 genes in NIH3T3 and 129 genes in the PC12 cells with marked changes in expression after Wnt3a stimulus. Only 2 Wnt-regulated genes were shared by both cell lines. Surprisingly, Disabled-2 was the only gene identified by the chromatin immunoprecipitation approach that displayed a marked change in expression in the GeneChip assay. Taken together, our approaches give an insight into the complex context-dependent nature of Wnt pathway transcriptional responses and identify Disabled-2 as a potential new direct target for Wnt signalling.

  20. Accounting for immunoprecipitation efficiencies in the statistical analysis of ChIP-seq data

    OpenAIRE

    Bao, Yanchun; Vinciotti, Veronica; Wit, Ernst; ’t Hoen, Peter AC

    2013-01-01

    Background: ImmunoPrecipitation (IP) efficiencies may vary largely between different antibodies and between repeated experiments with the same antibody. These differences have a large impact on the quality of ChIP-seq data: a more efficient experiment will necessarily lead to a higher signal to background ratio, and therefore to an apparent larger number of enriched regions, compared to a less efficient experiment. In this paper, we show how IP efficiencies can be explicitly accounted for in ...

  1. Protocol: methodology for chromatin immunoprecipitation (ChIP) in Chlamydomonas reinhardtii

    OpenAIRE

    Strenkert Daniela; Schmollinger Stefan; Schroda Michael

    2011-01-01

    Abstract We report on a detailed chromatin immunoprecipitation (ChIP) protocol for the unicellular green alga Chlamydomonas reinhardtii. The protocol is suitable for the analysis of nucleosome occupancy, histone modifications and transcription factor binding sites at the level of mononucleosomes for targeted and genome-wide studies. We describe the optimization of conditions for crosslinking, chromatin fragmentation and antibody titer determination and provide recommendations and an example f...

  2. High throughput automated chromatin immunoprecipitation as a platform for drug screening and antibody validation†,‡

    OpenAIRE

    Wu, Angela R.; Tiara L A Kawahara; Rapicavoli, Nicole A; van Riggelen, Jan; Shroff, Emelyn H.; Xu, Liwen; Felsher, Dean W.; Chang, Howard Y.; Quake, Stephen R.

    2012-01-01

    Chromatin immunoprecipitation (ChIP) is an assay for interrogating protein–DNA interactions that is increasingly being used for drug target discovery and screening applications. Currently the complexity of the protocol and the amount of hands-on time required for this assay limits its use to low throughput applications; furthermore, variability in antibody quality poses an additional obstacle in scaling up ChIP for large scale screening purposes. To address these challenges, we report HTChIP,...

  3. A Microfluidic Device with Integrated Sonication and Immunoprecipitation for Sensitive Epigenetic Assays.

    Science.gov (United States)

    Cao, Zhenning; Lu, Chang

    2016-02-01

    Epigenetic studies increasingly require analysis of a small number of cells that are of one specific type and derived from patients or animals. In this report, we demonstrate a simple microfluidic device that integrates sonication and immunoprecipitation (IP) for epigenetic assays, such as chromatin immunoprecipitation (ChIP) and methylated DNA immunoprecipitation (MeDIP). By incorporating an ultrasonic transducer with a microfluidic chamber, we implemented microscale sonication for both shearing chromatin/DNA and mixing/washing of IP beads. Such integration allowed highly sensitive tests starting with 100 cross-linked cells for ChIP or 500 pg of genomic DNA for MeDIP (compared to 10(6)-10(7) cells for ChIP and 1-10 μg of DNA for MeDIP in conventional assays). The entire on-chip process of sonication and IP took only 1 h. Our tool will be useful for highly sensitive epigenetic studies based on a small quantity of sample.

  4. Protocol: methodology for chromatin immunoprecipitation (ChIP in Chlamydomonas reinhardtii

    Directory of Open Access Journals (Sweden)

    Strenkert Daniela

    2011-11-01

    Full Text Available Abstract We report on a detailed chromatin immunoprecipitation (ChIP protocol for the unicellular green alga Chlamydomonas reinhardtii. The protocol is suitable for the analysis of nucleosome occupancy, histone modifications and transcription factor binding sites at the level of mononucleosomes for targeted and genome-wide studies. We describe the optimization of conditions for crosslinking, chromatin fragmentation and antibody titer determination and provide recommendations and an example for the normalization of ChIP results as determined by real-time PCR.

  5. Autoantibodies to IA-2 in insulin-dependent diabetes mellitus. Measurements with a new immunoprecipitation assay.

    Science.gov (United States)

    Masuda, M; Powell, M; Chen, S; Beer, C; Fichna, P; Rees Smith, B; Furmaniak, J

    2000-01-20

    An immunoprecipitation assay for autoantibodies (Abs) to the human islet cell antigen IA-2 has been developed using 125I-labelled recombinant IA-2 expressed in E. coli. With this assay IA-2 Abs were detected in 103/217 (47%) of IDDM patients of different ages and with different disease duration. IA-2 Ab prevalence was higher in younger patients (at the age of 15 years or below) with the recent onset IDDM (64/113; 57%) compared to patients above the age of 15 years (11/25; 44%). One of 40 (2.5%) Graves' disease patients and five of 204 (2.5%) of NIDDM patients were also positive. IA-2 Abs were not detected in sera from patients with Hashimoto's thyroiditis (n=32), myasthenia gravis (n=20) or systemic lupus erythematosus (n=10). IA-2 Ab measurements based on 125I-labelled IA-2 showed a good correlation with the results of an immunoprecipitation assay based on 35S-labelled IA-2 produced in the in vitro transcription/translation system (r=0.78; n=113; pAb testing in IDDM. Overall, the IA-2 Ab assay based on 125I-labelled recombinant IA-2 showed good sensitivity, precision and specificity which, combined with an easy and convenient protocol, makes it attractive for routine use.

  6. Probing flagellar promoter occupancy in wild-type and mutant Caulobacter crescentus by chromatin immunoprecipitation.

    Science.gov (United States)

    Davis, Nicole J; Viollier, Patrick H

    2011-06-01

    In the asymmetric predivisional cell of Caulobacter crescentus, TipF and TipN mark the cellular pole for future flagellar development. TipF is essential for motility and contains a cyclic-di-GMP phosphodiesterase-like (EAL) domain that is necessary for proper function. TipN is localized to the flagellar pole before TipF and is essential for the proper placement of the flagellum in C. crescentus. Using β-galactosidase promoter-probe assays and quantitative chromatin immunoprecipitation, we investigated the influence of the C. crescentus flagellar assembly regulator TipF on flagellar gene transcription. We compared the transcriptional activity of class II-fliF-lacZ, class III-flgE-lacZ, and class IV-fljL-lacZ fusions in a ΔtipF mutant with that of other flagellar mutants and the wild-type strain. We subsequently verified the in vivo occupancy of the fliF, flgE, and fljL flagellar promoters by the flagellar regulators CtrA, FlbD, and FliX in addition to RNA polymerase. We deduce that TipF contributes to proper expression of flagellar genes in C. crescentus by acting both within and outside of the canonical flagellar gene expression hierarchy.

  7. Chromatin analyses of Zymoseptoria tritici: Methods for chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq).

    Science.gov (United States)

    Soyer, Jessica L; Möller, Mareike; Schotanus, Klaas; Connolly, Lanelle R; Galazka, Jonathan M; Freitag, Michael; Stukenbrock, Eva H

    2015-06-01

    The presence or absence of specific transcription factors, chromatin remodeling machineries, chromatin modification enzymes, post-translational histone modifications and histone variants all play crucial roles in the regulation of pathogenicity genes. Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) provides an important tool to study genome-wide protein-DNA interactions to help understand gene regulation in the context of native chromatin. ChIP-seq is a convenient in vivo technique to identify, map and characterize occupancy of specific DNA fragments with proteins against which specific antibodies exist or which can be epitope-tagged in vivo. We optimized existing ChIP protocols for use in the wheat pathogen Zymoseptoria tritici and closely related sister species. Here, we provide a detailed method, underscoring which aspects of the technique are organism-specific. Library preparation for Illumina sequencing is described, as this is currently the most widely used ChIP-seq method. One approach for the analysis and visualization of representative sequence is described; improved tools for these analyses are constantly being developed. Using ChIP-seq with antibodies against H3K4me2, which is considered a mark for euchromatin or H3K9me3 and H3K27me3, which are considered marks for heterochromatin, the overall distribution of euchromatin and heterochromatin in the genome of Z. tritici can be determined. Our ChIP-seq protocol was also successfully applied to Z. tritici strains with high levels of melanization or aberrant colony morphology, and to different species of the genus (Z. ardabiliae and Z. pseudotritici), suggesting that our technique is robust. The methods described here provide a powerful framework to study new aspects of chromatin biology and gene regulation in this prominent wheat pathogen.

  8. Identification of oxidised proteins in the matrix of rice leaf mitochondria by immunoprecipitation and two-dimensional liquid chromatography-tandem mass spectrometry

    DEFF Research Database (Denmark)

    Kristensen, B.K.; Askerlund, P.; Bykova, N.V.;

    2004-01-01

    blots showed that neither the isolation of mitochondria, nor their subfractionation introduced carbonyl groups. We therefore conclude that a number of proteins are oxidised in the matrix of rice leaf mitochondria in vivo and further identify a group of proteins that are particularly susceptible to mild......Highly purified mitochondria were isolated from green 7-day-old rice leaves. The mitochondria were sonicated and the matrix fraction isolated as the 100,000g supernatant. Part of the matrix fraction was left untreated while the other part was subjected to a mild oxidative treatment (0.5 mM H2O2 + 0.......2 mM CuSO4 for 10 min at room temperature). The oxidised proteins in both samples were tagged with dinitrophenylhydrazine (DNP), which forms a covalent bond with carbonyl groups. The DNP-tagged proteins were immunoprecipitated using anti-DNP antibodies and digested with trypsin. The mixture of...

  9. Microplate-based platform for combined chromatin and DNA methylation immunoprecipitation assays

    Directory of Open Access Journals (Sweden)

    Yu Jingjing

    2011-11-01

    Full Text Available Abstract Background The processes that compose expression of a given gene are far more complex than previously thought presenting unprecedented conceptual and mechanistic challenges that require development of new tools. Chromatin structure, which is regulated by DNA methylation and histone modification, is at the center of gene regulation. Immunoprecipitations of chromatin (ChIP and methylated DNA (MeDIP represent a major achievement in this area that allow researchers to probe chromatin modifications as well as specific protein-DNA interactions in vivo and to estimate the density of proteins at specific sites genome-wide. Although a critical component of chromatin structure, DNA methylation has often been studied independently of other chromatin events and transcription. Results To allow simultaneous measurements of DNA methylation with other genomic processes, we developed and validated a simple and easy-to-use high throughput microplate-based platform for analysis of DNA methylation. Compared to the traditional beads-based MeDIP the microplate MeDIP was more sensitive and had lower non-specific binding. We integrated the MeDIP method with a microplate ChIP assay which allows measurements of both DNA methylation and histone marks at the same time, Matrix ChIP-MeDIP platform. We illustrated several applications of this platform to relate DNA methylation, with chromatin and transcription events at selected genes in cultured cells, human cancer and in a model of diabetic kidney disease. Conclusion The high throughput capacity of Matrix ChIP-MeDIP to profile tens and potentially hundreds of different genomic events at the same time as DNA methylation represents a powerful platform to explore complex genomic mechanism at selected genes in cultured cells and in whole tissues. In this regard, Matrix ChIP-MeDIP should be useful to complement genome-wide studies where the rich chromatin and transcription database resources provide fruitful foundation

  10. Quantitative Evaluation of His-Tag Purification and Immunoprecipitation of Tristetraprolin and Its Mutant Proteins from Transfected Human Cells

    OpenAIRE

    Cao, Heping; Lin, Rui

    2009-01-01

    Histidine (His)-tag is widely used for affinity purification of recombinant proteins, but the yield and purity of expressed proteins are quite different. Little information is available about quantitative evaluation of this procedure. The objective of current study was to evaluate His-tag procedure quantitatively and to compare it with immunoprecipitation using radiolabeled tristetraprolin (TTP), a zinc finger protein with anti-inflammatory property. Human embryonic kidney 293 cells were tran...

  11. Quantitative determination of intracellular, ferritin-associated radioactive iron by high-performance liquid chromatography and immunoprecipitation

    International Nuclear Information System (INIS)

    Antibodies raised against ferritin preparations of diverse origin provide an uncertain reagent for quantitation of the ferritin present in specific cell lysates. Utilizing K562 cells, a human leukemic cell line, techniques are described to resolve and to quantitate the ferritin-bound cytosolic iron. Processing the cell lysates by HPLC employing an anion-exchange or hydrophobic interaction column resulted in recovery of a single, ferritin-containing radioactive peak widely separated from the bulk of the non-ferritin-bound iron. Comparison of the yield obtained by chromatography with that by immunoprecipitation confirmed both the specificity and the quantitation of the antibody technique

  12. RNA profiling and chromatin immunoprecipitation-sequencing reveal that PTF1a stabilizes pancreas progenitor identity via the control of MNX1/HLXB9 and a network of other transcription factors

    DEFF Research Database (Denmark)

    Thompson, Nancy; Gésina, Emilie; Scheinert, Peter;

    2012-01-01

    those factors, PTF1a, a basic helix-loop-helix (bHLH) transcription factor which controls pancreas exocrine cell differentiation, maintenance, and functionality, is also needed for the early specification of pancreas progenitors. We used RNA profiling and chromatin immunoprecipitation (ChIP) sequencing...... promoted by PTF1a. These proteins, most of which were previously shown to be necessary for pancreas bud maintenance or formation, form a transcription factor network that allows the maintenance of pancreas progenitors. In addition, we identify Bmp7, Nr5a2, RhoV, and P2rx1 as new targets of PTF1a in...

  13. Inference of RNA polymerase II transcription dynamics from chromatin immunoprecipitation time course data.

    Directory of Open Access Journals (Sweden)

    Ciira wa Maina

    2014-05-01

    Full Text Available Gene transcription mediated by RNA polymerase II (pol-II is a key step in gene expression. The dynamics of pol-II moving along the transcribed region influence the rate and timing of gene expression. In this work, we present a probabilistic model of transcription dynamics which is fitted to pol-II occupancy time course data measured using ChIP-Seq. The model can be used to estimate transcription speed and to infer the temporal pol-II activity profile at the gene promoter. Model parameters are estimated using either maximum likelihood estimation or via Bayesian inference using Markov chain Monte Carlo sampling. The Bayesian approach provides confidence intervals for parameter estimates and allows the use of priors that capture domain knowledge, e.g. the expected range of transcription speeds, based on previous experiments. The model describes the movement of pol-II down the gene body and can be used to identify the time of induction for transcriptionally engaged genes. By clustering the inferred promoter activity time profiles, we are able to determine which genes respond quickly to stimuli and group genes that share activity profiles and may therefore be co-regulated. We apply our methodology to biological data obtained using ChIP-seq to measure pol-II occupancy genome-wide when MCF-7 human breast cancer cells are treated with estradiol (E2. The transcription speeds we obtain agree with those obtained previously for smaller numbers of genes with the advantage that our approach can be applied genome-wide. We validate the biological significance of the pol-II promoter activity clusters by investigating cluster-specific transcription factor binding patterns and determining canonical pathway enrichment. We find that rapidly induced genes are enriched for both estrogen receptor alpha (ERα and FOXA1 binding in their proximal promoter regions.

  14. DNA immunoprecipitation semiconductor sequencing (DIP-SC-seq) as a rapid method to generate genome wide epigenetic signatures.

    Science.gov (United States)

    Thomson, John P; Fawkes, Angie; Ottaviano, Raffaele; Hunter, Jennifer M; Shukla, Ruchi; Mjoseng, Heidi K; Clark, Richard; Coutts, Audrey; Murphy, Lee; Meehan, Richard R

    2015-05-14

    Modification of DNA resulting in 5-methylcytosine (5 mC) or 5-hydroxymethylcytosine (5hmC) has been shown to influence the local chromatin environment and affect transcription. Although recent advances in next generation sequencing technology allow researchers to map epigenetic modifications across the genome, such experiments are often time-consuming and cost prohibitive. Here we present a rapid and cost effective method of generating genome wide DNA modification maps utilising commercially available semiconductor based technology (DNA immunoprecipitation semiconductor sequencing; "DIP-SC-seq") on the Ion Proton sequencer. Focussing on the 5hmC mark we demonstrate, by directly comparing with alternative sequencing strategies, that this platform can successfully generate genome wide 5hmC patterns from as little as 500 ng of genomic DNA in less than 4 days. Such a method can therefore facilitate the rapid generation of multiple genome wide epigenetic datasets.

  15. Specific detection of peste des petits ruminants virus antibodies in sheep and goat sera by the luciferase immunoprecipitation system.

    Science.gov (United States)

    Berguido, Francisco J; Bodjo, Sanne Charles; Loitsch, Angelika; Diallo, Adama

    2016-01-01

    Peste des petits ruminants (PPR) is a contagious and often fatal transboundary animal disease affecting mostly sheep, goats and wild small ruminants. This disease is endemic in most of Africa, the Middle, Near East, and large parts of Asia. The causal agent is peste des petits ruminants virus (PPRV), which belongs to the genus Morbillivirus in the family Paramyxoviridae. This genus also includes measles virus (MV), canine distemper virus (CDV) and rinderpest virus (RPV). All are closely related viruses with serological cross reactivity. In this study, we have developed a Luciferase Immunoprecipitation System (LIPS) for the rapid detection of antibodies against PPRV in serum samples and for specific differentiation from antibodies against RPV. PPR and rinderpest (RP) serum samples were assayed by PPR-LIPS and two commercially available PPR cELISA tests. The PPR-LIPS showed high sensitivity and specificity for the samples tested and showed no cross reactivity with RPV unlike the commercial PPR cELISA tests which did cross react with RPV. Based on the results shown in this study, PPR-LIPS is presented as a good candidate for the specific serosurveillance of PPR. PMID:26506137

  16. MOBE-ChIP: a large-scale chromatin immunoprecipitation assay for cell type-specific studies.

    Science.gov (United States)

    Lau, On Sun; Bergmann, Dominique C

    2015-10-01

    Cell type-specific transcriptional regulators play critical roles in the generation and maintenance of multicellularity. As they are often expressed at low levels, in vivo DNA-binding studies of these regulators by standard chromatin immunoprecipitation (ChIP) assays are technically challenging. We describe here an optimized ChIP protocol termed Maximized Objects for Better Enrichment (MOBE)-ChIP, which enhances the sensitivity of ChIP assays for detecting cell type-specific signals. The protocol, which is based on the disproportional increase of target signals over background at higher scales, uses substantially greater volume of starting materials than conventional ChIPs to achieve high signal enrichment. This technique can capture weak binding events that are ambiguous in standard ChIP assays, and is useful both in gene-specific and whole-genome analysis. This protocol has been optimized for Arabidopsis, but should be applicable to other model systems with minor modifications. The full procedure can be completed within 3 days.

  17. Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP)

    NARCIS (Netherlands)

    Kaufmann, K.; Muiño, J.M.; Østerås, M.; Farinelli, L.; Krajewski, P.; Angenent, G.C.

    2010-01-01

    Chromatin immunoprecipitation (ChIP) is a powerful technique to study interactions between transcription factors (TFs) and DNA in vivo. For genome-wide de novo discovery of TF-binding sites, the DNA that is obtained in ChIP experiments needs to be processed for sequence identification. The sequences

  18. Functional analysis of neuronal microRNAs in Caenorhabditis elegans dauer formation by combinational genetics and Neuronal miRISC immunoprecipitation.

    Directory of Open Access Journals (Sweden)

    Minh T Than

    2013-06-01

    Full Text Available Identifying the physiological functions of microRNAs (miRNAs is often challenging because miRNAs commonly impact gene expression under specific physiological conditions through complex miRNA::mRNA interaction networks and in coordination with other means of gene regulation, such as transcriptional regulation and protein degradation. Such complexity creates difficulties in dissecting miRNA functions through traditional genetic methods using individual miRNA mutations. To investigate the physiological functions of miRNAs in neurons, we combined a genetic "enhancer" approach complemented by biochemical analysis of neuronal miRNA-induced silencing complexes (miRISCs in C. elegans. Total miRNA function can be compromised by mutating one of the two GW182 proteins (AIN-1, an important component of miRISC. We found that combining an ain-1 mutation with a mutation in unc-3, a neuronal transcription factor, resulted in an inappropriate entrance into the stress-induced, alternative larval stage known as dauer, indicating a role of miRNAs in preventing aberrant dauer formation. Analysis of this genetic interaction suggests that neuronal miRNAs perform such a role partly by regulating endogenous cyclic guanosine monophosphate (cGMP signaling, potentially influencing two other dauer-regulating pathways. Through tissue-specific immunoprecipitations of miRISC, we identified miRNAs and their likely target mRNAs within neuronal tissue. We verified the biological relevance of several of these miRNAs and found that many miRNAs likely regulate dauer formation through multiple dauer-related targets. Further analysis of target mRNAs suggests potential miRNA involvement in various neuronal processes, but the importance of these miRNA::mRNA interactions remains unclear. Finally, we found that neuronal genes may be more highly regulated by miRNAs than intestinal genes. Overall, our study identifies miRNAs and their targets, and a physiological function of these miRNAs in

  19. Assessing the efficiency and significance of Methylated DNA Immunoprecipitation (MeDIP assays in using in vitro methylated genomic DNA

    Directory of Open Access Journals (Sweden)

    Jia Jinsong

    2010-09-01

    Full Text Available Abstract Background DNA methylation contributes to the regulation of gene expression during development and cellular differentiation. The recently developed Methylated DNA ImmunoPrecipitation (MeDIP assay allows a comprehensive analysis of this epigenetic mark at the genomic level in normal and disease-derived cells. However, estimating the efficiency of the MeDIP technique is difficult without previous knowledge of the methylation status of a given cell population. Attempts to circumvent this problem have involved the use of in vitro methylated DNA in parallel to the investigated samples. Taking advantage of this stratagem, we sought to improve the sensitivity of the approach and to assess potential biases resulting from DNA amplification and hybridization procedures using MeDIP samples. Findings We performed MeDIP assays using in vitro methylated DNA, with or without previous DNA amplification, and hybridization to a human promoter array. We observed that CpG content at gene promoters indeed correlates strongly with the MeDIP signal obtained using in vitro methylated DNA, even when lowering significantly the amount of starting material. In analyzing MeDIP products that were subjected to whole genome amplification (WGA, we also revealed a strong bias against CpG-rich promoters during this amplification procedure, which may potentially affect the significance of the resulting data. Conclusion We illustrate the use of in vitro methylated DNA to assess the efficiency and accuracy of MeDIP procedures. We report that efficient and reproducible genome-wide data can be obtained via MeDIP experiments using relatively low amount of starting genomic DNA; and emphasize for the precaution that must be taken in data analysis when an additional DNA amplification step is required.

  20. Identification of Pou5f1, Sox2, and Nanog downstream target genes with statistical confidence by applying a novel algorithm to time course microarray and genome-wide chromatin immunoprecipitation data

    Directory of Open Access Journals (Sweden)

    Xin Li

    2008-06-01

    Full Text Available Abstract Background Target genes of a transcription factor (TF Pou5f1 (Oct3/4 or Oct4, which is essential for pluripotency maintenance and self-renewal of embryonic stem (ES cells, have previously been identified based on their response to Pou5f1 manipulation and occurrence of Chromatin-immunoprecipitation (ChIP-binding sites in promoters. However, many responding genes with binding sites may not be direct targets because response may be mediated by other genes and ChIP-binding site may not be functional in terms of transcription regulation. Results To reduce the number of false positives, we propose to separate responding genes into groups according to direction, magnitude, and time of response, and to apply the false discovery rate (FDR criterion to each group individually. Using this novel algorithm with stringent statistical criteria (FDR Pou5f1 suppression and published ChIP data, we identified 420 tentative target genes (TTGs for Pou5f1. The majority of TTGs (372 were down-regulated after Pou5f1 suppression, indicating that the Pou5f1 functions as an activator of gene expression when it binds to promoters. Interestingly, many activated genes are potent suppressors of transcription, which include polycomb genes, zinc finger TFs, chromatin remodeling factors, and suppressors of signaling. Similar analysis showed that Sox2 and Nanog also function mostly as transcription activators in cooperation with Pou5f1. Conclusion We have identified the most reliable sets of direct target genes for key pluripotency genes – Pou5f1, Sox2, and Nanog, and found that they predominantly function as activators of downstream gene expression. Thus, most genes related to cell differentiation are suppressed indirectly.

  1. Genome-wide mapping of the distribution of CarD, RNAP σA, and RNAP β on the Mycobacterium smegmatis chromosome using chromatin immunoprecipitation sequencing

    Science.gov (United States)

    Landick, Robert; Krek, Azra; Glickman, Michael S.; Socci, Nicholas D.; Stallings, Christina L.

    2014-01-01

    CarD is an essential mycobacterial protein that binds the RNA polymerase (RNAP) and affects the transcriptional profile of Mycobacterium smegmatis and Mycobacterium tuberculosis [6]. We predicted that CarD was directly regulating RNAP function but our prior experiments had not determined at what stage of transcription CarD was functioning and at which genes CarD interacted with the RNAP. To begin to address these open questions, we performed chromatin immunoprecipitation sequencing (ChIP-seq) to survey the distribution of CarD throughout the M. smegmatis chromosome. The distribution of RNAP subunits β and σA were also profiled. We expected that RNAP β would be present throughout transcribed regions and RNAP σA would be predominantly enriched at promoters based on work in Escherichia coli [3], however this had yet to be determined in mycobacteria. The ChIP-seq analyses revealed that CarD was never present on the genome in the absence of RNAP, was primarily associated with promoter regions, and was highly correlated with the distribution of RNAP σA. The colocalization of σA and CarD led us to propose that in vivo, CarD associates with RNAP initiation complexes at most promoters and is therefore a global regulator of transcription initiation. Here we describe in detail the data from the ChIP-seq experiments associated with the study published by Srivastava and colleagues in the Proceedings of the National Academy of Science in 2013 [5] as well as discuss the findings from this dataset in relation to both CarD and mycobacterial transcription as a whole. The ChIP-seq data have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. GSE48164). PMID:25089258

  2. Dataset of integrin-linked kinase protein: Protein interactions in cardiomyocytes identified by mass spectrometry.

    Science.gov (United States)

    Traister, Alexandra; Lu, Mingliang; Coles, John G; Maynes, Jason T

    2016-06-01

    Using hearts from mice overexpressing integrin linked kinase (ILK) behind the cardiac specific promoter αMHC, we have performed immunoprecipitation and mass spectrometry to identify novel ILK protein:protein interactions that regulate cardiomyocyte activity and calcium flux. Integrin linked kinase complexes were captured from mouse heart lysates using a commercial antibody, with subsequent liquid chromatography tandem mass spectral analysis. Interacting partners were identified using the MASCOT server, and important interactions verified using reverse immunoprecipitation and mass spectrometry. All ILK interacting proteins were identified in a non-biased manner, and are stored in the ProteomeXchange Consortium via the PRIDE partner repository (reference ID PRIDE: PXD001053). The functional role of identified ILK interactions in cardiomyocyte function and arrhythmia were subsequently confirmed in human iPSC-cardiomyocytes. PMID:27408918

  3. Human lung tumor-associated antigen identified as an extracellular matrix adhesion molecule

    OpenAIRE

    1991-01-01

    A single chain glycoprotein with an estimated molecular mass of 160 kD (gp160) was previously identified as a human lung tumor-associated antigen. This tumor marker is shown here to be associated noncovalently with a second 130-kD protein. Sequential immunoprecipitation studies of surface iodinated lung tumor cell lysates reveal that this heterodimeric complex is indistinguishable serologically and structurally from the integrin VLA-2, found originally on activated T lymphocytes and platelets...

  4. 染色质免疫沉淀技术分析HePG2细胞TCF7L2蛋白与IDE基因转录启动子的结合%Detection of TCF7L2 Binding to IDE Gene Promoters by Chromatin Immunoprecipitation

    Institute of Scientific and Technical Information of China (English)

    许丹; 任伟; 郑晓雅; 毕健琨

    2012-01-01

    TCF7L2 is the key transcriptional factor regulating glucose metabolism through the Wnt signaling pathway. Insulin-degrading enzyme (IDE) plays a key role in insulin degradation in celluar level and is closely related to hyperglycemia, insulin resistance as well as hyperinsulinemia in patients with Type 2 diabetes mellitus (T2DM). To identify the region in IDE gene promoter where the transcriptional factor TCF7L2 can bind in HePG2 cells. Chromatin immunoprecipitation and PCR were performed using the antibody specific for TCF7L2 to verify the binding of TCF7L2 to IDE promoter. Results indicated that IDE gene specific fragments were detected in the DNA fragments immunoprecipitated by antibody specific for TCF7L2. Thus it proved that TCF7L2 protein could bind to the promoter regions of IDE gene in HePG2 cells and may involved in regulation of IDE gene expression.%TCF7L2是一种重要的转录因子,通过Wnt信号途径,调节葡萄糖代谢.胰岛素降解酶(IDE)是细胞水平催化胰岛素降解的最关键的酶,与2型糖尿病(T2DM)高血糖、胰岛素抵抗、高胰岛素血症密切相关.为了检测HePG2细胞内转录因子TCF7L2与IDE基因启动子区的结合情况,采用染色质免疫沉淀技术结合PCR技术检测IDE基因启动子序列.结果表明,在特异性TCF7L2抗体免疫沉淀的DNA片段中扩增出IDE基因启动子序列,因此证实在HePG2细胞内,TCF7L2蛋白可与IDE基因转录启动子的特异区域结合,进而可能参与IDE基因的表达调控.

  5. Novel association of APC with intermediate filaments identified using a new versatile APC antibody

    Directory of Open Access Journals (Sweden)

    Coffey Robert J

    2009-10-01

    Full Text Available Abstract Background As a key player in suppression of colon tumorigenesis, Adenomatous Polyposis Coli (APC has been widely studied to determine its cellular functions. However, inconsistencies of commercially available APC antibodies have limited the exploration of APC function. APC is implicated in spindle formation by direct interactions with tubulin and microtubule-binding protein EB1. APC also interacts with the actin cytoskeleton to regulate cell polarity. Until now, interaction of APC with the third cytoskeletal element, intermediate filaments, has remained unexamined. Results We generated an APC antibody (APC-M2 pAb raised against the 15 amino acid repeat region, and verified its reliability in applications including immunoprecipitation, immunoblotting, and immunofluorescence in cultured cells and tissue. Utilizing this APC-M2 pAb, we immunoprecipitated endogenous APC and its binding proteins from colon epithelial cells expressing wild-type APC. Using Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS, we identified 42 proteins in complex with APC, including β-catenin and intermediate filament (IF proteins lamin B1 and keratin 81. Association of lamin B1 with APC in cultured cells and human colonic tissue was verified by co-immunoprecipitation and colocalization. APC also colocalized with keratins and remained associated with IF proteins throughout a sequential extraction procedure. Conclusion We introduce a versatile APC antibody that is useful for cell/tissue immunostaining, immunoblotting and immunoprecipitation. We also present evidence for interactions between APC and IFs, independent of actin filaments and microtubules. Our results suggest that APC associates with all three major components of the cytoskeleton, thus expanding potential roles for APC in the regulation of cytoskeletal integrity.

  6. Isolation of Specific Genomic Regions and Identification of Their Associated Molecules by Engineered DNA-Binding Molecule-Mediated Chromatin Immunoprecipitation (enChIP) Using the CRISPR System and TAL Proteins.

    Science.gov (United States)

    Fujii, Hodaka; Fujita, Toshitsugu

    2015-09-09

    Comprehensive understanding of genome functions requires identification of molecules (proteins, RNAs, genomic regions, etc.) bound to specific genomic regions of interest in vivo. To perform biochemical and molecular biological analysis of specific genomic regions, we developed engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) to purify genomic regions of interest. In enChIP, specific genomic regions are tagged for biochemical purification using engineered DNA-binding molecules, such as transcription activator-like (TAL) proteins and a catalytically inactive form of the clustered regularly interspaced short palindromic repeats (CRISPR) system. enChIP is a comprehensive approach that emphasizes non-biased search using next-generation sequencing (NGS), microarrays, mass spectrometry (MS), and other methods. Moreover, this approach is not restricted to cultured cell lines and can be easily extended to organisms. In this review, we discuss applications of enChIP to elucidating the molecular mechanisms underlying genome functions.

  7. Identifiability in stochastic models

    CERN Document Server

    1992-01-01

    The problem of identifiability is basic to all statistical methods and data analysis, occurring in such diverse areas as Reliability Theory, Survival Analysis, and Econometrics, where stochastic modeling is widely used. Mathematics dealing with identifiability per se is closely related to the so-called branch of ""characterization problems"" in Probability Theory. This book brings together relevant material on identifiability as it occurs in these diverse fields.

  8. Quantitative Characterization of E-selectin Interaction with Native CD44 and P-selectin Glycoprotein Ligand-1 (PSGL-1) Using a Real Time Immunoprecipitation-based Binding Assay

    KAUST Repository

    Abu Samra, Dina Bashir Kamil

    2015-06-29

    Selectins (E-, P-, and L-selectins) interact with glycoprotein ligands to mediate the essential tethering/rolling step in cell transport and delivery that captures migrating cells from the circulating flow. In this work, we developed a real time immunoprecipitation assay on a surface plasmon resonance chip that captures native glycoforms of two well known E-selectin ligands (CD44/hematopoietic cell E-/L-selectin ligand and P-selectin glycoprotein ligand-1) from hematopoietic cell extracts. Here we present a comprehensive characterization of their binding to E-selectin. We show that both ligands bind recombinant monomeric E-selectin transiently with fast on- and fast off-rates, whereas they bind dimeric E-selectin with remarkably slow onand off-rates. This binding requires the sialyl Lewis x sugar moiety to be placed on both O- and N-glycans, and its association, but not dissociation, is sensitive to the salt concentration. Our results suggest a mechanism through which monomeric selectins mediate initial fast on and fast off kinetics to help capture cells out of the circulating shear flow; subsequently, tight binding by dimeric/oligomeric selectins is enabled to significantly slow rolling. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  9. Identifying Unknown Proteins

    OpenAIRE

    Barker, Winona C.; Dayhoff, Margaret O.

    1983-01-01

    In this paper we discuss ways to identify a protein, both when its amino acid sequence is known and, particularly, prior to the determination of the complete sequence. If a similar sequence is in the Protein Sequence Database, an unknown may be identified on the basis of partial or ambiguous sequence data, or on the basis of amino acid composition. Identification in the early stages of structural determination can save time and scarce resources by preventing duplicate effort or by suggesting ...

  10. Genome-Wide Chromatin Immunoprecipitation Sequencing Analysis Shows that WhiB Is a Transcription Factor That Cocontrols Its Regulon with WhiA To Initiate Developmental Cell Division in Streptomyces

    Directory of Open Access Journals (Sweden)

    Matthew J. Bush

    2016-04-01

    Full Text Available WhiB is the founding member of a family of proteins (the WhiB-like [Wbl] family that carry a [4Fe-4S] iron-sulfur cluster and play key roles in diverse aspects of the biology of actinomycetes, including pathogenesis, antibiotic resistance, and the control of development. In Streptomyces, WhiB is essential for the process of developmentally controlled cell division that leads to sporulation. The biochemical function of Wbl proteins has been controversial; here, we set out to determine unambiguously if WhiB functions as a transcription factor using chromatin immunoprecipitation sequencing (ChIP-seq in Streptomyces venezuelae. In the first demonstration of in vivo genome-wide Wbl binding, we showed that WhiB regulates the expression of key genes required for sporulation by binding upstream of ~240 transcription units. Strikingly, the WhiB regulon is identical to the previously characterized WhiA regulon, providing an explanation for the identical phenotypes of whiA and whiB mutants. Using ChIP-seq, we demonstrated that in vivo DNA binding by WhiA depends on WhiB and vice versa, showing that WhiA and WhiB function cooperatively to control expression of a common set of WhiAB target genes. Finally, we show that mutation of the cysteine residues that coordinate the [4Fe-4S] cluster in WhiB prevents DNA binding by both WhiB and WhiA in vivo.

  11. Identifying Knowledge and Communication

    Directory of Open Access Journals (Sweden)

    Eduardo Coutinho Lourenço de Lima

    2006-12-01

    Full Text Available In this paper, I discuss how the principle of identifying knowledge which Strawson advances in ‘Singular Terms and Predication’ (1961, and in ‘Identifying Reference and Truth-Values’ (1964 turns out to constrain communication. The principle states that a speaker’s use of a referring expression should invoke identifying knowledge on the part of the hearer, if the hearer is to understand what the speaker is saying, and also that, in so referring, speakers are attentive to hearers’ epistemic states. In contrasting it with Russell’s Principle (Evans 1982, as well as with the principle of identifying descriptions (Donnellan 1970, I try to show that the principle of identifying knowledge, ultimately a condition for understanding, makes sense only in a situation of conversation. This allows me to conclude that the cooperative feature of communication (Grice 1975 and reference (Clark andWilkes-Gibbs 1986 holds also at the understanding level. Finally, I discuss where Strawson’s views seem to be unsatisfactory, and suggest how they might be improved.

  12. Metal alloy identifier

    Science.gov (United States)

    Riley, William D.; Brown, Jr., Robert D.

    1987-01-01

    To identify the composition of a metal alloy, sparks generated from the alloy are optically observed and spectrographically analyzed. The spectrographic data, in the form of a full-spectrum plot of intensity versus wavelength, provide the "signature" of the metal alloy. This signature can be compared with similar plots for alloys of known composition to establish the unknown composition by a positive match with a known alloy. An alternative method is to form intensity ratios for pairs of predetermined wavelengths within the observed spectrum and to then compare the values of such ratios with similar values for known alloy compositions, thereby to positively identify the unknown alloy composition.

  13. Identifying Fiscal Inflation

    OpenAIRE

    De Graeve, Ferre; Queijo von Heideken, Virginia

    2013-01-01

    Fiscal theorists warn about the risk of future inflation as a consequence of current fiscal imbalances in the US. Because actual inflation remains historically low and data on inflation expectations do not corroborate such risks, warnings for fiscal inflation are often ignored in policy and academic circles. This paper shows that a canonical NK- DSGE model enables identifying an anticipated component of inflation expectations that is closely related to fiscal policy. Estimation results sugges...

  14. Strategies to identify long noncoding RNAs involved in gene regulation

    Directory of Open Access Journals (Sweden)

    Lee Catherine

    2012-11-01

    Full Text Available Abstract Long noncoding RNAs (lncRNAs have been detected in nearly every cell type and found to be fundamentally involved in many biological processes. The characterization of lncRNAs has immense potential to advance our comprehensive understanding of cellular processes and gene regulation, along with implications for the treatment of human disease. The recent ENCODE (Encyclopedia of DNA Elements study reported 9,640 lncRNA loci in the human genome, which corresponds to around half the number of protein-coding genes. Because of this sheer number and their functional diversity, it is crucial to identify a pool of potentially relevant lncRNAs early on in a given study. In this review, we evaluate the methods for isolating lncRNAs by immunoprecipitation and review the advantages, disadvantages, and applications of three widely used approaches – microarray, tiling array, and RNA-seq – for identifying lncRNAs involved in gene regulation. We also look at ways in which data from publicly available databases such as ENCODE can support the study of lncRNAs.

  15. Random Cell Identifiers Assignment

    Directory of Open Access Journals (Sweden)

    Robert Bestak

    2012-01-01

    Full Text Available Despite integration of advanced functions that enable Femto Access Points (FAPs to be deployed in a plug-and-play manner, the femtocell concept still cause several opened issues to be resolved. One of them represents an assignment of Physical Cell Identifiers (PCIs to FAPs. This paper analyses a random based assignment algorithm in LTE systems operating in diverse femtocell scenarios. The performance of the algorithm is evaluated by comparing the number of confusions for various femtocell densities, PCI ranges and knowledge of vicinity. Simulation results show that better knowledge of vicinity can significantly reduce the number of confusions events.

  16. Digital Identifier Systems: Comparative Evaluation

    OpenAIRE

    Hamid Reza Khedmatgozar; Mehdi Alipour-Hafezi; Payam Hanafizadeh

    2015-01-01

    Identifier is one of the main elements in identifying an object in digital environment. Digital identifier systems were developed followed by a lot of problems such as violation of persistency and uniqueness of physical identifiers and URL in digital environment. These identifiers try to guarantee uniqueness and persistency of hostnames by using indirect names for Domain Name System (DNS). The main objective of this research is to identify qualified digital identifier system among other syste...

  17. Blood pressure loci identified with a gene-centric array.

    Science.gov (United States)

    Johnson, Toby; Gaunt, Tom R; Newhouse, Stephen J; Padmanabhan, Sandosh; Tomaszewski, Maciej; Kumari, Meena; Morris, Richard W; Tzoulaki, Ioanna; O'Brien, Eoin T; Poulter, Neil R; Sever, Peter; Shields, Denis C; Thom, Simon; Wannamethee, Sasiwarang G; Whincup, Peter H; Brown, Morris J; Connell, John M; Dobson, Richard J; Howard, Philip J; Mein, Charles A; Onipinla, Abiodun; Shaw-Hawkins, Sue; Zhang, Yun; Davey Smith, George; Day, Ian N M; Lawlor, Debbie A; Goodall, Alison H; Fowkes, F Gerald; Abecasis, Gonçalo R; Elliott, Paul; Gateva, Vesela; Braund, Peter S; Burton, Paul R; Nelson, Christopher P; Tobin, Martin D; van der Harst, Pim; Glorioso, Nicola; Neuvrith, Hani; Salvi, Erika; Staessen, Jan A; Stucchi, Andrea; Devos, Nabila; Jeunemaitre, Xavier; Plouin, Pierre-François; Tichet, Jean; Juhanson, Peeter; Org, Elin; Putku, Margus; Sõber, Siim; Veldre, Gudrun; Viigimaa, Margus; Levinsson, Anna; Rosengren, Annika; Thelle, Dag S; Hastie, Claire E; Hedner, Thomas; Lee, Wai K; Melander, Olle; Wahlstrand, Björn; Hardy, Rebecca; Wong, Andrew; Cooper, Jackie A; Palmen, Jutta; Chen, Li; Stewart, Alexandre F R; Wells, George A; Westra, Harm-Jan; Wolfs, Marcel G M; Clarke, Robert; Franzosi, Maria Grazia; Goel, Anuj; Hamsten, Anders; Lathrop, Mark; Peden, John F; Seedorf, Udo; Watkins, Hugh; Ouwehand, Willem H; Sambrook, Jennifer; Stephens, Jonathan; Casas, Juan-Pablo; Drenos, Fotios; Holmes, Michael V; Kivimaki, Mika; Shah, Sonia; Shah, Tina; Talmud, Philippa J; Whittaker, John; Wallace, Chris; Delles, Christian; Laan, Maris; Kuh, Diana; Humphries, Steve E; Nyberg, Fredrik; Cusi, Daniele; Roberts, Robert; Newton-Cheh, Christopher; Franke, Lude; Stanton, Alice V; Dominiczak, Anna F; Farrall, Martin; Hingorani, Aroon D; Samani, Nilesh J; Caulfield, Mark J; Munroe, Patricia B

    2011-12-01

    Raised blood pressure (BP) is a major risk factor for cardiovascular disease. Previous studies have identified 47 distinct genetic variants robustly associated with BP, but collectively these explain only a few percent of the heritability for BP phenotypes. To find additional BP loci, we used a bespoke gene-centric array to genotype an independent discovery sample of 25,118 individuals that combined hypertensive case-control and general population samples. We followed up four SNPs associated with BP at our p < 8.56 × 10(-7) study-specific significance threshold and six suggestively associated SNPs in a further 59,349 individuals. We identified and replicated a SNP at LSP1/TNNT3, a SNP at MTHFR-NPPB independent (r(2) = 0.33) of previous reports, and replicated SNPs at AGT and ATP2B1 reported previously. An analysis of combined discovery and follow-up data identified SNPs significantly associated with BP at p < 8.56 × 10(-7) at four further loci (NPR3, HFE, NOS3, and SOX6). The high number of discoveries made with modest genotyping effort can be attributed to using a large-scale yet targeted genotyping array and to the development of a weighting scheme that maximized power when meta-analyzing results from samples ascertained with extreme phenotypes, in combination with results from nonascertained or population samples. Chromatin immunoprecipitation and transcript expression data highlight potential gene regulatory mechanisms at the MTHFR and NOS3 loci. These results provide candidates for further study to help dissect mechanisms affecting BP and highlight the utility of studying SNPs and samples that are independent of those studied previously even when the sample size is smaller than that in previous studies. PMID:22100073

  18. Argonaute 2 complexes selectively protect the circulating microRNAs in cell-secreted microvesicles.

    Directory of Open Access Journals (Sweden)

    Limin Li

    Full Text Available Cell-secreted miRNAs are highly stable and can serve as biomarkers for various diseases and signaling molecules in intercellular communication. The mechanism underlying the stability of circulating miRNAs, however, remains incompletely understood. Here we show that Argonaute 2 (Ago2 complexes and microvesicles (MVs provide specific and non-specific protection for miRNA in cell-secreted MVs, respectively. First, the resistance of MV-encapsulated miRNAs to RNaseA was both depended on intact vesicular structure of MVs and protease-sensitive. Second, an immunoprecipitation assay using a probe complementary to human miR-16, a miRNA primarily located in the MVs and showed a strong, protease-sensitive resistance to RNaseA, identified Ago2 as a major miR-16-associated protein. Compared with protein-free miR-16, Ago2-associated miR-16 was resistant to RNaseA in a dose- and time-dependent fashion. Third, when the miR-16/Ago2 complex was disrupted by trypaflavine, the resistance of miR-16 to RNaseA was decreased. In contrast, when the association of miR-16 with the Ago2 complexes was increased during cell apoptosis, although the total amount of miR-16 and Ago2 remained unchanged, the resistance of miR-16 to RNaseA in the MVs was enhanced. A similar correlation between the increase of miR-223/Ago2 association and the resistance of miR-223 against RNaseA was observed during all trans retinoic acid (ATRA-induced cell differentiation of promyelocytic HL60 cells. In conclusion, the association of miRNAs with Ago2 complexes, an event that is linked to cell functional status, plays a critical role in stabilizing the circulating miRNAs in cell-secreted MVs.

  19. Epigenetic Library Screen Identifies Abexinostat as Novel Regulator of Adipocytic and Osteoblastic Differentiation of Human Skeletal (Mesenchymal) Stem Cells

    DEFF Research Database (Denmark)

    Ali; Hamam; Alfayez;

    2016-01-01

    The epigenetic mechanisms promoting lineage-specific commitment of human skeletal (mesenchymal or stromal) stem cells (hMSCs) into adipocytes or osteoblasts are still not fully understood. Herein, we performed an epigenetic library functional screen and identified several novel compounds, including...... abexinostat, which promoted adipocytic and osteoblastic differentiation of hMSCs. Using gene expression microarrays, chromatin immunoprecipitation for H3K9Ac combined with high-throughput DNA sequencing (ChIP-seq), and bioinformatics, we identified several key genes involved in regulating stem cell...... or stromal) stem cells (hMSCs). These data provide new insight into the understanding of the relationship between the epigenetic effect of histone deacetylase inhibitors, transcription factors, and differentiation pathways controlling adipocyte and osteoblast differentiation of hMSCs. Manipulating...

  20. New Criteria to Identify Spectrum

    Indian Academy of Sciences (India)

    A Jensen; M Krishna

    2005-05-01

    In this paper we give some new criteria for identifying the components of a probability measure, in its Lebesgue decomposition. This enables us to give new criteria to identify spectral types of self-adjoint operators on Hilbert spaces, especially those of interest.

  1. New criteria to identify spectrum

    DEFF Research Database (Denmark)

    Jensen, Arne; Krishna, M.

    2005-01-01

    In this paper we give some new criteria for identifying the components of a probability measure, in its Lebesgue decomposition. This enables us to give new criteria to identify spectral types of self-adjoint operators on Hilbert spaces, especially those of interest....

  2. Author Identifiers in Scholarly Repositories

    CERN Document Server

    Warner, Simeon

    2010-01-01

    Bibliometric and usage-based analyses and tools highlight the value of information about scholarship contained within the network of authors, articles and usage data. Less progress has been made on populating and using the author side of this network than the article side, in part because of the difficulty of unambiguously identifying authors. I briefly review a sample of author identifier schemes, and consider use in scholarly repositories. I then describe preliminary work at arXiv to implement public author identifiers, services based on them, and plans to make this information useful beyond the boundaries of arXiv.

  3. Identifying Occupationally Specific Affective Behaviors.

    Science.gov (United States)

    Pucel, David J.

    1993-01-01

    Data from two groups of cosmetology instructors (n=15) and two groups of machinist instructors (n=17) validated the Occupational Affective Behavior Analysis instrument as capable of identifying affective behaviors viewed as important to success in a given occupation. (SK)

  4. Algorithms to identify failure pattern

    OpenAIRE

    Poudel, Bhuwan Krishna Som

    2013-01-01

    This project report was written for ?Algorithms to Identify Failure Pattern? at NTNU (Norwegian University of Science and Technology), IME (Faculty of Information Technology, Mathematics and Electrical Engineering) and IDI (Department of Computer Science).In software application, there are three types of failure pattern: point pattern, block pattern and stripe pattern. The purpose of the report is to prepare an algorithm that identifies the pattern in a software application. Only theoretical ...

  5. Individual Identifiability Predicts Population Identifiability in Forensic Microsatellite Markers.

    Science.gov (United States)

    Algee-Hewitt, Bridget F B; Edge, Michael D; Kim, Jaehee; Li, Jun Z; Rosenberg, Noah A

    2016-04-01

    Highly polymorphic genetic markers with significant potential for distinguishing individual identity are used as a standard tool in forensic testing [1, 2]. At the same time, population-genetic studies have suggested that genetically diverse markers with high individual identifiability also confer information about genetic ancestry [3-6]. The dual influence of polymorphism levels on ancestry inference and forensic desirability suggests that forensically useful marker sets with high levels of individual identifiability might also possess substantial ancestry information. We study a standard forensic marker set-the 13 CODIS loci used in the United States and elsewhere [2, 7-9]-together with 779 additional microsatellites [10], using direct population structure inference to test whether markers with substantial individual identifiability also produce considerable information about ancestry. Despite having been selected for individual identification and not for ancestry inference [11], the CODIS markers generate nontrivial model-based clustering patterns similar to those of other sets of 13 tetranucleotide microsatellites. Although the CODIS markers have relatively low values of the F(ST) divergence statistic, their high heterozygosities produce greater ancestry inference potential than is possessed by less heterozygous marker sets. More generally, we observe that marker sets with greater individual identifiability also tend toward greater population identifiability. We conclude that population identifiability regularly follows as a byproduct of the use of highly polymorphic forensic markers. Our findings have implications for the design of new forensic marker sets and for evaluations of the extent to which individual characteristics beyond identification might be predicted from current and future forensic data.

  6. Regulatory O-GlcNAcylation sites on FoxO1 are yet to be identified

    Energy Technology Data Exchange (ETDEWEB)

    Fardini, Yann [INSERM, U1016, Institut Cochin, Paris (France); CNRS, UMR8104, Paris (France); Université Paris Descartes, Sorbonne Paris Cité, Paris (France); Perez-Cervera, Yobana [Structural and Functional Glycobiology Unit, Lille 1 University, CNRS (UMR 8576), IFR 117, Villeneuve d' Ascq (France); Facultad de Odontología, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca (Mexico); Camoin, Luc [INSERM, U1068, CRCM, Marseille Protéomique IBiSA, Marseille, F-13009 (France); Institut Paoli-Calmettes Team, Cell Polarity, Cell Signaling and Cancer, Marseille, F-13009 (France); Aix-Marseille Université, F-13284, Marseille (France); CNRS, UMR7258, CRCM, Marseille, F-13009 (France); Pagesy, Patrick [INSERM, U1016, Institut Cochin, Paris (France); CNRS, UMR8104, Paris (France); Université Paris Descartes, Sorbonne Paris Cité, Paris (France); Lefebvre, Tony [Structural and Functional Glycobiology Unit, Lille 1 University, CNRS (UMR 8576), IFR 117, Villeneuve d' Ascq (France); Issad, Tarik, E-mail: tarik.issad@inserm.fr [INSERM, U1016, Institut Cochin, Paris (France); CNRS, UMR8104, Paris (France); Université Paris Descartes, Sorbonne Paris Cité, Paris (France)

    2015-06-26

    O-GlcNAcylation is a reversible post-translational modification that regulates cytosolic and nuclear proteins. We and others previously demonstrated that FoxO1 is O-GlcNAcylated in different cell types, resulting in an increase in its transcriptional activity. Four O-GlcNAcylation sites were identified in human FOXO1 but directed mutagenesis of each site individually had modest (T317) or no effect (S550, T648, S654) on its O-GlcNAcylation status and transcriptional activity. Moreover, the consequences of mutating all four sites had not been investigated. In the present work, we mutated these sites in the mouse Foxo1 and found that mutation of all four sites did not decrease Foxo1 O-GlcNAcylation status and transcriptional activity, and would even tend to increase them. In an attempt to identify other O-GlcNAcylation sites, we immunoprecipitated wild-type O-GlcNAcylated Foxo1 and analysed the tryptic digest peptides by mass spectrometry using High-energy Collisional Dissociation. We identified T646 as a new O-GlcNAcylation site on Foxo1. However, site directed mutagenesis of this site individually or together with all four previously identified residues did not impair Foxo1 O-GlcNAcylation and transcriptional activity. These results suggest that residues important for the control of Foxo1 activity by O-GlcNAcylation still remain to be identified. - Highlights: • We mutate four previously identified O-GlcNAcylation sites on Foxo1. • Unexpectedly, these mutations do not reduce Foxo1 O-GlcNAcylation. • These mutation do not reduce Foxo1 transcriptional activity. • We identify a new O-GlcNAcylation site on Foxo1 by mass spectrometry. • Mutation of this site increases Foxo1 transcriptional activity.

  7. Sparse Linear Identifiable Multivariate Modeling

    DEFF Research Database (Denmark)

    Henao, Ricardo; Winther, Ole

    2011-01-01

    In this paper we consider sparse and identifiable linear latent variable (factor) and linear Bayesian network models for parsimonious analysis of multivariate data. We propose a computationally efficient method for joint parameter and model inference, and model comparison. It consists of a fully...... Bayesian hierarchy for sparse models using slab and spike priors (two-component δ-function and continuous mixtures), non-Gaussian latent factors and a stochastic search over the ordering of the variables. The framework, which we call SLIM (Sparse Linear Identifiable Multivariate modeling), is validated...... computational complexity. We attribute this mainly to the stochastic search strategy used, and to parsimony (sparsity and identifiability), which is an explicit part of the model. We propose two extensions to the basic i.i.d. linear framework: non-linear dependence on observed variables, called SNIM (Sparse Non-linear...

  8. Football refereeing: Identifying innovative methods

    Directory of Open Access Journals (Sweden)

    Reza MohammadKazemi

    2014-08-01

    Full Text Available The aim of the present study is to identify the potentials innovation in football industry. Data were collected from 10 national and international referees, assistant referees and referees’ supervisors in Iran. In this study, technological innovations are identified that assist better refereeing performances. The analysis revealed a significant relationship between using new technologies and referees ‘performance. The results indicate that elite referees, assistant referees and supervisors agreed to use new technological innovations during the game. According to their comments, this kind of technology causes the referees’ performance development.

  9. Identifying the Gifted Child Humorist.

    Science.gov (United States)

    Fern, Tami L.

    1991-01-01

    This study attempted to identify gifted child humorists among 1,204 children in grades 3-6. Final identification of 13 gifted child humorists was determined through application of such criteria as funniness, originality, and exemplary performance or product. The influence of intelligence, development, social factors, sex differences, family…

  10. Identifying Two-Sided Markets

    NARCIS (Netherlands)

    Filistrucchi, L.; Geradin, D.A.A.G.; van Damme, E.E.C.

    2012-01-01

    Abstract: We review the burgeoning literature on two-sided markets focusing on the different definitions that have been proposed. In particular, we show that the well-known definition given by Evans is a particular case of the more general definition proposed by Rochet and Tirole. We then identify t

  11. Identifying high-risk medication

    DEFF Research Database (Denmark)

    Sædder, Eva; Brock, Birgitte; Nielsen, Lars Peter;

    2014-01-01

    salicylic acid, and beta-blockers; 30 drugs or drug classes caused 82 % of all serious MEs. The top ten drugs involved in fatal events accounted for 73 % of all drugs identified. CONCLUSION: Increasing focus on seven drugs/drug classes can potentially reduce hospitalizations, extended hospitalizations...

  12. Identifying Emotion from Natural Walking

    OpenAIRE

    Cui, Liqing; Li, Shun; Zhang, Wan; Zhang, Zhan; Zhu, Tingshao

    2015-01-01

    Emotion identification from gait aims to automatically determine persons affective state, it has attracted a great deal of interests and offered immense potential value in action tendency, health care, psychological detection and human-computer(robot) interaction.In this paper, we propose a new method of identifying emotion from natural walking, and analyze the relevance between the traits of walking and affective states. After obtaining the pure acceleration data of wrist and ankle, we set a...

  13. Identifying High Performance ERP Projects

    OpenAIRE

    Stensrud, Erik; Myrtveit, Ingunn

    2002-01-01

    Learning from high performance projects is crucial for software process improvement. Therefore, we need to identify outstanding projects that may serve as role models. It is common to measure productivity as an indicator of performance. It is vital that productivity measurements deal correctly with variable returns to scale and multivariate data. Software projects generally exhibit variable returns to scale, and the output from ERP projects is multivariate. We propose to use Data Envelopment ...

  14. Chromatin Immunoprecipitation of Replication Factors Moving with the Replication Fork

    OpenAIRE

    Rapp, Jordan B.; Ansbach, Alison B.; Noguchi, Chiaki; Noguchi, Eishi

    2009-01-01

    Replication of chromosomes involves a variety of replication proteins including DNA polymerases, DNA helicases, and other accessory factors. Many of these proteins are known to localize at replication forks and travel with them as components of the replisome complex. Other proteins do not move with replication forks but still play an essential role in DNA replication. Therefore, in order to understand the mechanisms of DNA replication and its controls, it is important to examine localization ...

  15. Studying RNA-protein interactions in vivo by RNA immunoprecipitation

    DEFF Research Database (Denmark)

    Selth, Luke A; Close, Pierre; Svejstrup, Jesper Q

    2011-01-01

    The crucial roles played by RNA-binding proteins in all aspects of RNA metabolism, particularly in the regulation of transcription, have become increasingly evident. Moreover, other factors that do not directly interact with RNA molecules can nevertheless function proximally to RNA polymerases an...

  16. Immunoprecipitation of bisphenol A by antibody–mesoporous silica composites

    Directory of Open Access Journals (Sweden)

    Toru Orita

    2014-09-01

    Full Text Available Bisphenol A (BPA is of global concern because of its disruption of endocrine systems and ubiquity in aquatic environment. In this study, BPA antibody was successfully immobilised on novel mesoporous silica (MPS carriers that display unique properties such as high surface area, highly uniform pore distribution and high adsorption capacity. Mobil Crystalline Material MCM-41 (2.7 nm, Santa Barbara Amorphous SBA-15-1 (12.3 nm and SBA-15-2 (24.0 nm materials were used as supports for these antibodies. On these carriers, the BPA antibody immobilisation reached 40 μg mg−1. For each MPS, 15 ng of BPA antigen was adsorbed on 1 mg of MPS–antibody composite, which resulted in an antibody activity of 30%. The highest recovery rate of BPA antigen was observed for 80% acetonitrile in 10 mM phosphate buffer (pH 7. After six repeated runs, BPA antibodies immobilised on SBA-15-1 and SBA-15-2 retained about 30% of their initial activity. In contrast, these antibodies showed 13% lower residual activity on MCM-41 than on SBA-15-1 and SBA-15-2. This result indicated that entire antibody molecules were adsorbed inside SBA-15-1 and SBA-15-2 pores, stabilising their structural conformation.

  17. Can tests identify creative people?

    Science.gov (United States)

    Bell, Peter M.

    It is always a popular pursuit by academic administrators to assess the creativity or innovative qualities of scientists in order to evaluate their research capabilities. Of course, traditionally such evaluations have been fraught with subjectivity (i.e., innovative scientists are commonly thought to be weird, under 40 years old, independent, risk-taking, etc.), and thus such evaluations have not been highly valued. In recent years, through testing, the American Chemical Society (ACS) has attempted to give respectability to the art of predicting the creativity of a scientist. ACS, which draws its members from both industrial and academic laboratories, held a symposium on the subject of evaluating the creativity of scientists. The proceedings were published by ACS as ‘Innovation and U.S. Research: Problems and Recommendations’ (W. N. Smith and C.F. Larson, eds., 1980). In the proceedings, as reported in the July 1982 Chemtec (all quotes here are from the Chemtec article), A. Nisson was able to identify only the following two-part characteristic of an innovative person: (1) a low threshold to ‘a state of discomfort with some aspect of the order of things, the status quo,’ and (2) ‘an extraordinarily high level of mental stamina enabling him or her to persist until the state of discomfort is removed.’

  18. Identifying barriers to billing compliance.

    Science.gov (United States)

    Lorence, Daniel P; Ibrahim, Ibrahim Awad

    2003-01-01

    Programs designed toward the control of health care fraud are leading to increasingly aggressive enforcement and prosecutorial efforts by federal regulators, related to over-reimbursement for service providers. Greater penalties for fraudulent practices have been touted as an effective deterrent to practices that encourage, or fail to prevent, incorrect claims for reimbursement. In such a context, this study sought to examine the extent of compliance management barriers through a national survey of all accredited US health information managers, examining likely barriers to payment of health care claims. Using data from a series of surveys on the stated compliance actions of more than 16,000 health care managers, we find that the publication and dissemination of compliance enforcement regulations had a significant effect on the reduction of fraud. Results further suggest that significant non-adoption of proper billing compliance measures continues to occur, despite the existence of counter-fraud prosecution risk designed to enforce proper compliance. Finally, we identify benchmarks of compliance management and show how they vary across demographic, practice setting, and market characteristics. We find significant variation in influence across practice settings and managed care markets. While greater publicity related to proper billing procedures generally leads to greater compliance awareness, this trend may have created pockets of "institutional non-compliance," which result in an increase in the prevalence of non-compliant management actions. As a more general proposition, we find that it is not sufficient to consider compliance actions independent of institutional or industry-wide influences. PMID:12967244

  19. DNA Microarrays for Identifying Fishes

    Science.gov (United States)

    Nölte, M.; Weber, H.; Silkenbeumer, N.; Hjörleifsdottir, S.; Hreggvidsson, G. O.; Marteinsson, V.; Kappel, K.; Planes, S.; Tinti, F.; Magoulas, A.; Garcia Vazquez, E.; Turan, C.; Hervet, C.; Campo Falgueras, D.; Antoniou, A.; Landi, M.; Blohm, D.

    2008-01-01

    In many cases marine organisms and especially their diverse developmental stages are difficult to identify by morphological characters. DNA-based identification methods offer an analytically powerful addition or even an alternative. In this study, a DNA microarray has been developed to be able to investigate its potential as a tool for the identification of fish species from European seas based on mitochondrial 16S rDNA sequences. Eleven commercially important fish species were selected for a first prototype. Oligonucleotide probes were designed based on the 16S rDNA sequences obtained from 230 individuals of 27 fish species. In addition, more than 1200 sequences of 380 species served as sequence background against which the specificity of the probes was tested in silico. Single target hybridisations with Cy5-labelled, PCR-amplified 16S rDNA fragments from each of the 11 species on microarrays containing the complete set of probes confirmed their suitability. True-positive, fluorescence signals obtained were at least one order of magnitude stronger than false-positive cross-hybridisations. Single nontarget hybridisations resulted in cross-hybridisation signals at approximately 27% of the cases tested, but all of them were at least one order of magnitude lower than true-positive signals. This study demonstrates that the 16S rDNA gene is suitable for designing oligonucleotide probes, which can be used to differentiate 11 fish species. These data are a solid basis for the second step to create a “Fish Chip” for approximately 50 fish species relevant in marine environmental and fisheries research, as well as control of fisheries products. PMID:18270778

  20. A novel single cell method to identify the genetic composition at a single nuclear body

    Science.gov (United States)

    Anchel, David; Ching, Reagan W.; Cotton, Rachel; Li, Ren; Bazett-Jones, David P.

    2016-01-01

    Gene loci make specific associations with compartments of the nucleus (e.g. the nuclear envelope, nucleolus, and transcription factories) and this association may determine or reflect a mechanism of genetic control. With current methods, it is not possible to identify sets of genes that converge to form a “gene hub” as there is a reliance on loci-specific probes, or immunoprecipitation of a particular protein from bulk cells. We introduce a method that will allow for the identification of loci contained within the vicinity of a single nuclear body in a single cell. For the first time, we demonstrate that the DNA sequences originating from a single sub-nuclear structure in a single cell targeted by two-photon irradiation can be determined, and mapped to a particular locus. Its application to single PML nuclear bodies reveals ontologically related loci that frequently associate with each other and with PML bodies in a population of cells, and a possible nuclear body targeting role for specific transcription factor binding sites. PMID:27389808

  1. Genome-wide analysis of p63 binding sites identifies AP-2 factors as co-regulators of epidermal differentiation

    Science.gov (United States)

    McDade, Simon S.; Henry, Alexandra E.; Pivato, Geraldine P.; Kozarewa, Iwanka; Mitsopoulos, Constantinos; Fenwick, Kerry; Assiotis, Ioannis; Hakas, Jarle; Zvelebil, Marketa; Orr, Nicholas; Lord, Christopher J.; Patel, Daksha; Ashworth, Alan; McCance, Dennis J.

    2012-01-01

    The p63 transcription factor (TP63) is critical in development, growth and differentiation of stratifying epithelia. This is highlighted by the severity of congenital abnormalities caused by TP63 mutations in humans, the dramatic phenotypes in knockout mice and de-regulation of TP63 expression in neoplasia altering the tumour suppressive roles of the TP53 family. In order to define the normal role played by TP63 and provide the basis for better understanding how this network is perturbed in disease, we used chromatin immunoprecipitation combined with massively parallel sequencing (ChIP-seq) to identify >7500 high-confidence TP63-binding regions across the entire genome, in primary human neonatal foreskin keratinocytes (HFKs). Using integrative strategies, we demonstrate that only a subset of these sites are bound by TP53 in response to DNA damage. We identify a role for TP63 in transcriptional regulation of multiple genes genetically linked to cleft palate and identify AP-2alpha (TFAP2A) as a co-regulator of a subset of these genes. We further demonstrate that AP-2gamma (TFAP2C) can bind a subset of these regions and that acute depletion of either TFAP2A or TFAP2C alone is sufficient to reduce terminal differentiation of organotypic epidermal skin equivalents, indicating overlapping physiological functions with TP63. PMID:22573176

  2. Direct and heterologous approaches to identify the LET-756/FGF interactome

    Directory of Open Access Journals (Sweden)

    Birnbaum Daniel

    2006-05-01

    Full Text Available Abstract Background Fibroblast growth factors (FGFs are multifunctional proteins that play important roles in cell communication, proliferation and differentiation. However, many aspects of their activities are not well defined. LET-756, one of the two C. elegans FGFs, is expressed throughout development and is essential for worm development. It is both expressed in the nucleus and secreted. Results To identify nuclear factors associated with LET-756, we used three approaches. First, we screened a two-hybrid cDNA library derived from mixed stages worms and from a normalized library, using LET-756 as bait. This direct approach allowed the identification of several binding partners that play various roles in the nucleus/nucleolus, such as PAL-1, a transcription regulator, or RPS-16, a component of the small ribosomal subunit. The interactions were validated by co-immunoprecipitation and determination of their site of occurrence in mammalian cells. Second, because patterns of protein interactions may be conserved throughout species, we searched for orthologs of known mammalian interactors and measured binary interaction with these predicted candidates. We found KIN-3 and KIN-10, the orthologs of CK2α and CK2β, as new partners of LET-756. Third, following the assumption that recognition motifs mediating protein interaction may be conserved between species, we screened a two-hybrid cDNA human library using LET-756 as bait. Among the few FGF partners detected was 14-3-3β. In support of this interaction we showed that the two 14-3-3β orthologous proteins, FTT-1 and FTT-2/PAR-5, interacted with LET-756. Conclusion We have conducted the first extensive search for LET-756 interactors using a multi-directional approach and established the first interaction map of LET-756/FGF with other FGF binding proteins from other species. The interactors identified play various roles in developmental process or basic biochemical events such as ribosome biogenesis.

  3. Approach for Identifying Human Leukocyte Antigen (HLA)-DR Bound Peptides from Scarce Clinical Samples.

    Science.gov (United States)

    Heyder, Tina; Kohler, Maxie; Tarasova, Nataliya K; Haag, Sabrina; Rutishauser, Dorothea; Rivera, Natalia V; Sandin, Charlotta; Mia, Sohel; Malmström, Vivianne; Wheelock, Åsa M; Wahlström, Jan; Holmdahl, Rikard; Eklund, Anders; Zubarev, Roman A; Grunewald, Johan; Ytterberg, A Jimmy

    2016-09-01

    Immune-mediated diseases strongly associating with human leukocyte antigen (HLA) alleles are likely linked to specific antigens. These antigens are presented to T cells in the form of peptides bound to HLA molecules on antigen presenting cells, e.g. dendritic cells, macrophages or B cells. The identification of HLA-DR-bound peptides presents a valuable tool to investigate the human immunopeptidome. The lung is likely a key player in the activation of potentially auto-aggressive T cells prior to entering target tissues and inducing autoimmune disease. This makes the lung of exceptional interest and presents an ideal paradigm to study the human immunopeptidome and to identify antigenic peptides.Our previous investigation of HLA-DR peptide presentation in the lung required high numbers of cells (800 × 10(6) bronchoalveolar lavage (BAL) cells). Because BAL from healthy nonsmokers typically contains 10-15 × 10(6) cells, there is a need for a highly sensitive approach to study immunopeptides in the lungs of individual patients and controls.In this work, we analyzed the HLA-DR immunopeptidome in the lung by an optimized methodology to identify HLA-DR-bound peptides from low cell numbers. We used an Epstein-Barr Virus (EBV) immortalized B cell line and bronchoalveolar lavage (BAL) cells obtained from patients with sarcoidosis, an inflammatory T cell driven disease mainly occurring in the lung. Specifically, membrane complexes were isolated prior to immunoprecipitation, eluted peptides were identified by nanoLC-MS/MS and processed using the in-house developed ClusterMHCII software. With the optimized procedure we were able to identify peptides from 10 × 10(6) cells, which on average correspond to 10.9 peptides/million cells in EBV-B cells and 9.4 peptides/million cells in BAL cells. This work presents an optimized approach designed to identify HLA-DR-bound peptides from low numbers of cells, enabling the investigation of the BAL immunopeptidome from individual patients

  4. Novel Human Embryonic Stem Cell Regulators Identified by Conserved and Distinct CpG Island Methylation State.

    Directory of Open Access Journals (Sweden)

    Steve Pells

    Full Text Available Human embryonic stem cells (hESCs undergo epigenetic changes in vitro which may compromise function, so an epigenetic pluripotency "signature" would be invaluable for line validation. We assessed Cytosine-phosphate-Guanine Island (CGI methylation in hESCs by genomic DNA hybridisation to a CGI array, and saw substantial variation in CGI methylation between lines. Comparison of hESC CGI methylation profiles to corresponding somatic tissue data and hESC mRNA expression profiles identified a conserved hESC-specific methylation pattern associated with expressed genes. Transcriptional repressors and activators were over-represented amongst genes whose associated CGIs were methylated or unmethylated specifically in hESCs, respectively. Knockdown of candidate transcriptional regulators (HMGA1, GLIS2, PFDN5 induced differentiation in hESCs, whereas ectopic expression in fibroblasts modulated iPSC colony formation. Chromatin immunoprecipitation confirmed interaction between the candidates and the core pluripotency transcription factor network. We thus identify novel pluripotency genes on the basis of a conserved and distinct epigenetic configuration in human stem cells.

  5. Bacterial beta-lactamase fragmentation complementation strategy can be used as a method for identifying interacting protein pairs.

    Science.gov (United States)

    Park, Jong-Hwa; Back, Jung Ho; Hahm, Soo Hyun; Shim, Hye-Young; Park, Min Ju; Ko, Sung Il; Han, Ye Sun

    2007-10-01

    We investigated the applicability of the TEM-1 beta- lactamase fragment complementation (BFC) system to develop a strategy for the screening of protein-protein interactions in bacteria. A BFC system containing a human Fas-associated death domain (hFADD) and human Fas death domain (hFasDD) was generated. The hFADD-hFasDD interaction was verified by cell survivability in ampicillin-containing medium and the colorimetric change of nitrocefin. It was also confirmed by His pull-down assay using cell lysates obtained in selection steps. A coiled-coil helix coiled-coil domain-containing protein 5 (CHCH5) was identified as an interacting protein of human uracil DNA glycosylase (hUNG) from the bacterial BFC cDNA library strategy. The interaction between hUNG and CHCH5 was further confirmed with immunoprecipitation using a mammalian expression system. CHCH5 enhanced the DNA glycosylase activity of hUNG to remove uracil from DNA duplexes containing a U/G mismatch pair. These results suggest that the bacterial BFC cDNA library strategy can be effectively used to identify interacting protein pairs.

  6. A synthetic interaction screen identifies factors selectively required for proliferation and TERT transcription in p53-deficient human cancer cells.

    Directory of Open Access Journals (Sweden)

    Li Xie

    Full Text Available Numerous genetic and epigenetic alterations render cancer cells selectively dependent on specific genes and regulatory pathways, and represent potential vulnerabilities that can be therapeutically exploited. Here we describe an RNA interference (RNAi-based synthetic interaction screen to identify genes preferentially required for proliferation of p53-deficient (p53- human cancer cells. We find that compared to p53-competent (p53+ human cancer cell lines, diverse p53- human cancer cell lines are preferentially sensitive to loss of the transcription factor ETV1 and the DNA damage kinase ATR. In p53- cells, RNAi-mediated knockdown of ETV1 or ATR results in decreased expression of the telomerase catalytic subunit TERT leading to growth arrest, which can be reversed by ectopic TERT expression. Chromatin immunoprecipitation analysis reveals that ETV1 binds to a region downstream of the TERT transcriptional start-site in p53- but not p53+ cells. We find that the role of ATR is to phosphorylate and thereby stabilize ETV1. Our collective results identify a regulatory pathway involving ETV1, ATR, and TERT that is preferentially important for proliferation of diverse p53- cancer cells.

  7. Affinity purification-mass spectrometry analysis of bcl-2 interactome identified SLIRP as a novel interacting protein.

    Science.gov (United States)

    Trisciuoglio, D; Desideri, M; Farini, V; De Luca, T; Di Martile, M; Tupone, M G; Urbani, A; D'Aguanno, S; Del Bufalo, D

    2016-01-01

    Members of the bcl-2 protein family share regions of sequence similarity, the bcl-2 homology (BH) domains. Bcl-2, the most studied member of this family, has four BH domains, BH1-4, and has a critical role in resistance to antineoplastic drugs by regulating the mitochondrial apoptotic pathway. Moreover, it is also involved in other relevant cellular processes such as tumor progression, angiogenesis and autophagy. Deciphering the network of bcl-2-interacting factors should provide a critical advance in understanding the different functions of bcl-2. Here, we characterized bcl-2 interactome by mass spectrometry in human lung adenocarcinoma cells. In silico functional analysis associated most part of the identified proteins to mitochondrial functions. Among them we identified SRA stem-loop interacting RNA-binding protein, SLIRP, a mitochondrial protein with a relevant role in regulating mitochondrial messenger RNA (mRNA) homeostasis. We validated bcl-2/SLIRP interaction by immunoprecipitation and immunofluorescence experiments in cancer cell lines from different histotypes. We showed that, although SLIRP is not involved in mediating bcl-2 ability to protect from apoptosis and oxidative damage, bcl-2 binds and stabilizes SLIRP protein and regulates mitochondrial mRNA levels. Moreover, we demonstrated that the BH4 domain of bcl-2 has a role in maintaining this binding. PMID:26866271

  8. NIH Researchers Identify OCD Risk Gene

    Science.gov (United States)

    ... News From NIH NIH Researchers Identify OCD Risk Gene Past Issues / Summer 2006 Table of Contents For ... and Alcoholism (NIAAA) have identified a previously unknown gene variant that doubles an individual's risk for obsessive- ...

  9. Psychosocial counselling of identifiable sperm donors

    NARCIS (Netherlands)

    M. Visser; M.H. Mochtar; A.A. de Melker; F. van der Veen; S. Repping; T. Gerrits

    2016-01-01

    STUDY QUESTION: What do identifiable sperm donors feel about psychosocial counselling? SUMMARY ANSWER: Identifiable sperm donors found it important that psychosocial counselling focused on emotional consequences and on rules and regulations and they expected to have access to psychosocial counsellin

  10. Identifying Causal Effects with Computer Algebra

    CERN Document Server

    García-Puente, Luis David; Sullivant, Seth

    2010-01-01

    The long-standing identification problem for causal effects in graphical models has many partial results but lacks a systematic study. We show how computer algebra can be used to either prove that a causal effect can be identified, generically identified, or show that the effect is not generically identifiable. We report on the results of our computations for linear structural equation models, where we determine precisely which causal effects are generically identifiable for all graphs on three and four vertices.

  11. Ability of Slovakian Pupils to Identify Birds

    Science.gov (United States)

    Prokop, Pavol; Rodak, Rastislav

    2009-01-01

    A pupil's ability to identify common organisms is necessary for acquiring further knowledge of biology. We investigated how pupils were able to identify 25 bird species following their song, growth habits, or both features presented simultaneously. Just about 19% of birds were successfully identified by song, about 39% by growth habit, and 45% of…

  12. 29 CFR 4010.7 - Identifying information.

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 9 2010-07-01 2010-07-01 false Identifying information. 4010.7 Section 4010.7 Labor... DISCLOSURE REQUIREMENTS ANNUAL FINANCIAL AND ACTUARIAL INFORMATION REPORTING § 4010.7 Identifying information..., http://www.pbgc.gov, the following identifying information with respect to each member of the...

  13. 47 CFR 2.926 - FCC identifier.

    Science.gov (United States)

    2010-10-01

    ... 47 Telecommunication 1 2010-10-01 2010-10-01 false FCC identifier. 2.926 Section 2.926... Authorizations § 2.926 FCC identifier. (a) A grant of equipment authorization issued by the Commission will list the validated FCC Identifier consisting of the grantee code assigned by the FCC pursuant to...

  14. De-identifying an EHR Database

    DEFF Research Database (Denmark)

    Lauesen, Søren; Pantazos, Kostas; Lippert, Søren

    2011-01-01

    Abstract. Electronic health records (EHR) contain a large amount of structured data and free text. Exploring and sharing clinical data can improve healthcare and facilitate the development of medical software. However, revealing confidential information is against ethical principles and laws. We de...... lists of identifiers from the database and external resources, define a replacement for each identifier, and replace identifiers in structured data and free text. Some patient records could not be safely de-identified, so the de-identified database has 323,122 patient records with an acceptable degree...

  15. IVOA Identifiers Version 2.0

    CERN Document Server

    Demleitner, Markus; Linde, Tony; Williams, Roy; Noddle, Keith

    2016-01-01

    An IVOA Identifier is a globally unique name for a resource within the Virtual Observatory. This name can be used to retrieve a unique description of the resource from an IVOA-compliant registry or to identify an entity like a dataset or a protocol without dereferencing the identifier. This document describes the syntax for IVOA Identifiers as well as how they are created. The syntax has been defined to encourage global-uniqueness naturally and to maximize the freedom of resource providers to control the character content of an identifier.

  16. Identifying shortage occupations in the UK

    OpenAIRE

    Anna Downs

    2009-01-01

    This article describes the top-down methodology used by the Migration Advisory Committee (MAC) to identify shortage occupations. Identifying shortage occupations is difficult and few countries have attempted to do this in a systematic way. The methodology developed by the MAC to identify shortage occupations is the first to use a comprehensive range of indicators. The methodology dovetails national level top-down data with bottom-up micro-level data and qualitative information from stakeholde...

  17. Determination of set-membership identifiability sets

    OpenAIRE

    Ravanbod-Hosseini, Laleh; Verdière, Nathalie; Jauberthie, Carine

    2014-01-01

    This paper concerns the concept of set-membership identifiability introduced in \\cite{jauberthie}. Given a model, a set-membership identifiable set is a connected set in the parameter domain of the model such that its corresponding trajectories are distinct to trajectories arising from its complementary. For obtaining the so-called set-membership identifiable sets, we propose an algorithm based on interval analysis tools. The proposed algorithm is decomposed into three parts namely {\\it minci...

  18. Identifying Information Focuses in Listening Comprehension

    Science.gov (United States)

    Zhang, Hong-yan

    2011-01-01

    The study explains the process of learners' listening comprehension within Halliday's information theory in functional grammar, including the skills of identifying focuses while listening in college English teaching. Identifying information focuses in listening is proved to improve the students' communicative listening ability by the means of a…

  19. Moving Beyond Weak Identifiers for Proxemic Interaction

    DEFF Research Database (Denmark)

    Sørensen, Henrik; Kjeldskov, Jesper

    2013-01-01

    significantly closer than what is actually the case. This makes the smartphone a weak identifier for applications that need to track persons. With a focus on feasible interaction design, we present a concept and prototype of a platform, which seek to support proxemic interaction beyond weak identifiers. The...... limitations that need to be addressed....

  20. Healthcare Identifiers legislation: a whiff of fourberie.

    Science.gov (United States)

    Mendelson, Danuta

    2010-05-01

    The Healthcare Identifiers Bill 2010 (Cth), which will establish "the national e-health Healthcare Identifiers Service to provide that patients, healthcare providers and provider organisations can be consistently identified", is in the process of being enacted by the Australian Federal Parliament. The legislation will enable the government to assign to each "healthcare recipient" a 26-digit electronic "Healthcare Identifier", which will be accessible, with or without the recipient's consent, to a broad range of health care service providers as well as other entities. The individual Healthcare Identifier file will initially contain such identifying information as, where applicable, the Medicare number and/or the Veterans' Affairs number; name; address; gender; date of birth; and "the date of birth accuracy indicator" presumably birth certificate. However, since each "service" provided by a health care provider to a health care recipient will be automatically recorded on each individual's Healthcare Identifier file, in time these electronic files should contain a full record of such services or contacts. Moreover, the Healthcare Identifiers are considered a "key" to, or a "foundation stone" for, the implementation of the shared electronic health records scheme, because they will enable linkage with and retrieval of each patient's clinical records throughout the health care service system. However, there has been virtually no discussion about the legal, ethical and social implications of this legislation. PMID:20552931

  1. EZID: Long term identifiers made easy (Invited)

    Science.gov (United States)

    Starr, J.

    2013-12-01

    Scholarly research is producing ever increasing amounts of digital research data, and this data should be managed throughout the research life cycle both as part of good scientific practice, but also to comply with funder mandates, such as the 2013 OSTP Public Access Memo (http://www.whitehouse.gov/sites/default/files/microsites/ostp/ostp_public_access_memo_2013.pdf). By assigning unique and persistent identifiers to data objects, data managers can gain control and flexibility over what can be a daunting task. This is due to the fact that the objects can be moved to new locations without disruption to links, as long as the identifier target is maintained. EZID is a tool that makes assigning and maintaining unique, persistent identifiers easy. It was designed and built by California Digital Library (CDL) and has both a user interface and a RESTful API. EZID currently offers services for two globally unique, persistent identifier schemes: Digital Object Identifiers (DOIs) and Archival Resource Keys (ARKs). DOIs are identifiers originating from the publishing world and are in widespread use for journal articles. CDL is able to offer DOIs because of being a founding member of DataCite (http://www.datacite.org/), an international consortium established to provide easier access to scientific research data on the Internet. ARKs are identifiers originating from the library, archive and museum community. Like DOIs, they become persistent when the objects and identifier forwarding information is maintained. DOIs and ARKs have a key role in data management and, therefore, in data management plans. DOIs are the recommended identifier for use in data citation, and ARKs provide the maximum flexibility needed for data documentation and management throughout the early phases of a project. The two identifier schemes are able to be used together, and EZID is made to work with both. EZID clients, coming from education, research, government, and the private sector, are utilizing the

  2. Researchers Identify Early Sign of Pancreatic Cancer

    Science.gov (United States)

    ... of pancreatic cancer Researchers identify early sign of pancreatic cancer September 28, 2014 Tags: PancreaticCancer Brian Wolpin, MD ... discovered a sign of the early development of pancreatic cancer – an upsurge in certain amino acids that occurs ...

  3. Identifiable Data Files - Health Outcomes Survey (HOS)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Medicare Health Outcomes Survey (HOS) identifiable data files are comprised of the entire national sample for a given 2-year cohort (including both respondents...

  4. Identifying motivational factors within a multinational company

    OpenAIRE

    Daniela Bradutanu

    2011-01-01

    The aim of the study is to identify the main motivational factors within a multinational company. The first objective is to identify work functions, formulated on Abraham Maslow’s pyramid, following the identification of the key characteristics that motivate an employee at the work place and last, but not least, the type of motivation that employees focus, intrinsic or extrinsic. The research method targeted a questionnaire based survey, including various company employees and an interv...

  5. ORCID Author Identifiers: A Primer for Librarians.

    Science.gov (United States)

    Akers, Katherine G; Sarkozy, Alexandra; Wu, Wendy; Slyman, Alison

    2016-01-01

    The ORCID (Open Researcher and Contributor ID) registry helps disambiguate authors and streamline research workflows by assigning unique 16-digit author identifiers that enable automatic linkages between researchers and their scholarly activities. This article describes how ORCID works, the benefits of using ORCID, and how librarians can promote ORCID at their institutions by raising awareness of ORCID, helping researchers create and populate ORCID profiles, and integrating ORCID identifiers into institutional repositories and other university research information systems. PMID:27054531

  6. ORCID Author Identifiers: A Primer for Librarians.

    Science.gov (United States)

    Akers, Katherine G; Sarkozy, Alexandra; Wu, Wendy; Slyman, Alison

    2016-01-01

    The ORCID (Open Researcher and Contributor ID) registry helps disambiguate authors and streamline research workflows by assigning unique 16-digit author identifiers that enable automatic linkages between researchers and their scholarly activities. This article describes how ORCID works, the benefits of using ORCID, and how librarians can promote ORCID at their institutions by raising awareness of ORCID, helping researchers create and populate ORCID profiles, and integrating ORCID identifiers into institutional repositories and other university research information systems.

  7. Identifying Domestic and Imported Core Inflation

    OpenAIRE

    Bjørnland, Hilde C.

    2000-01-01

    This paper estimates core inflation in Norway, identified as that component of inflation that has no long-run effect on GDP. The model distinguishes explicitly between domestic and imported core inflation. The results show that (domestic) core inflation is the main component of CPI inflation. CPI inflation, however, misrepresents core inflation in some periods. The differences are well explained by the other shocks identified in the model, in particular the oil price shocks of the 1970s when ...

  8. Newly identified YSO candidates towards LDN 1188

    Science.gov (United States)

    Marton , G.; Verebélyi, E.; Kiss, Cs.; Smidla, J.

    2013-11-01

    We present an analysis of young stellar object (YSO) candidates towards the LDN 1188 molecular cloud. The YSO candidates were selected from the WISE all-sky catalogue, based on a statistical method. We found 601 candidates in the region, and classified them as Class I, Flat, and Class II YSOs. Groups were identified and described with the Minimal Spanning Tree (MST) method. Previously identified molecular cores show evidence of ongoing star formation at different stages throughout the cloud complex.

  9. Identifying knowledge in decision-making processes

    DEFF Research Database (Denmark)

    Jensen, Anna Rose Vagn; Ahmed-Kristensen, Saeema

    2010-01-01

    Managing knowledge reflects the innovation capability of a company. Mapping decision processes and links to knowledge is a way to learn more in structuring knowledge in innovation processes. Through an empirical study the paper aims to identify knowledge......Managing knowledge reflects the innovation capability of a company. Mapping decision processes and links to knowledge is a way to learn more in structuring knowledge in innovation processes. Through an empirical study the paper aims to identify knowledge...

  10. Identifying glass compositions in fly ash

    Science.gov (United States)

    Aughenbaugh, Katherine; Stutzman, Paul; Juenger, Maria

    2016-01-01

    In this study, four Class F fly ashes were studied with a scanning electron microscope; the glassy phases were identified and their compositions quantified using point compositional analysis with k-means clustering and multispectral image analysis. The results showed that while the bulk oxide contents of the fly ashes were different, the four fly ashes had somewhat similar glassy phase compositions. Aluminosilicate glasses (AS), calcium aluminosilicate glasses (CAS), a mixed glass, and, in one case, a high iron glass were identified in the fly ashes. Quartz and iron crystalline phases were identified in each fly ash as well. The compositions of the three main glasses identified, AS, CAS, and mixed glass, were relatively similar in each ash. The amounts of each glass were varied by fly ash, with the highest calcium fly ash containing the most of calcium-containing glass. Some of the glasses were identified as intermixed in individual particles, particularly the calcium-containing glasses. Finally, the smallest particles in the fly ashes, with the most surface area available to react in alkaline solution, such as when mixed with portland cement or in alkali-activated fly ash, were not different in composition than the large particles, with each of the glasses represented. The method used in the study may be applied to a fly ash of interest for use as a cementing material in order to understand its potential for reactivity.

  11. Identifying glass compositions in fly ash

    Directory of Open Access Journals (Sweden)

    Katherine eAughenbaugh

    2016-01-01

    Full Text Available In this study, four Class F fly ashes were studied with a scanning electron microscope; the glassy phases were identified and their compositions quantified using point compositional analysis with k-means clustering and multispectral image analysis. The results showed that while the bulk oxide contents of the fly ashes were different, the four fly ashes had somewhat similar glassy phase compositions. Aluminosilicate glasses (AS, calcium aluminosilicate glasses (CAS, a mixed glass, and, in one case, a high iron glass were identified in the fly ashes. Quartz and iron crystalline phases were identified in each fly ash as well. The compositions of the three main glasses identified, AS, CAS, and mixed glass, were relatively similar in each ash. The amounts of each glass were varied by fly ash, with the highest calcium fly ash containing the most of calcium-containing glass. Some of the glasses were identified as intermixed in individual particles, particularly the calcium-containing glasses. Finally, the smallest particles in the fly ashes, with the most surface area available to react in alkaline solution, such as when mixed with portland cement or in alkali-activated fly ash, were not different in composition than the large particles, with each of the glasses represented. The method used in the study may be applied to a fly ash of interest for use as a cementing material in order to understand its potential for reactivity.

  12. Identifying Turbulent Structures through Topological Segmentation

    Energy Technology Data Exchange (ETDEWEB)

    Bremer, Peer-Timo; Gruber, Andrea; Bennett, Janine C.; Gyulassy, Attila; Kolla, Hemanth; Chen, Jacqueline H.; Grout, Ray W.

    2016-01-01

    A new method of extracting vortical structures from a turbulent flow is proposed whereby topological segmentation of an indicator function scalar field is used to identify the regions of influence of the individual vortices. This addresses a long-standing challenge in vector field topological analysis: indicator functions commonly used produce a scalar field based on the local velocity vector field; reconstructing regions of influence for a particular structure requires selecting a threshold to define vortex extent. In practice, the same threshold is rarely meaningful throughout a given flow. By also considering the topology of the indicator field function, the characteristics of vortex strength and extent can be separated and the ambiguity in the choice of the threshold reduced. The proposed approach is able to identify several types of vortices observed in a jet in cross-flow configuration simultaneously where no single threshold value for a selection of common indicator functions appears able to identify all of these vortex types.

  13. Identifying Geographic Clusters: A Network Analytic Approach

    CERN Document Server

    Catini, Roberto; Penner, Orion; Riccaboni, Massimo

    2015-01-01

    In recent years there has been a growing interest in the role of networks and clusters in the global economy. Despite being a popular research topic in economics, sociology and urban studies, geographical clustering of human activity has often studied been by means of predetermined geographical units such as administrative divisions and metropolitan areas. This approach is intrinsically time invariant and it does not allow one to differentiate between different activities. Our goal in this paper is to present a new methodology for identifying clusters, that can be applied to different empirical settings. We use a graph approach based on k-shell decomposition to analyze world biomedical research clusters based on PubMed scientific publications. We identify research institutions and locate their activities in geographical clusters. Leading areas of scientific production and their top performing research institutions are consistently identified at different geographic scales.

  14. Coherence method of identifying signal noise model

    International Nuclear Information System (INIS)

    The noise analysis method is discussed in identifying perturbance models and their parameters by a stochastic analysis of the noise model of variables measured on a reactor. The analysis of correlations is made in the frequency region using coherence analysis methods. In identifying an actual specific perturbance, its model should be determined and recognized in a compound model of the perturbance system using the results of observation. The determination of the optimum estimate of the perturbance system model is based on estimates of related spectral densities which are determined from the spectral density matrix of the measured variables. Partial and multiple coherence, partial transfers, the power spectral densities of the input and output variables of the noise model are determined from the related spectral densities. The possibilities of applying the coherence identification methods were tested on a simple case of a simulated stochastic system. Good agreement was found of the initial analytic frequency filters and the transfers identified. (B.S.)

  15. Identifying motivational factors within a multinational company

    Directory of Open Access Journals (Sweden)

    Daniela Bradutanu

    2011-08-01

    Full Text Available The aim of the study is to identify the main motivational factors within a multinational company. The first objective is to identify work functions, formulated on Abraham Maslow’s pyramid, following the identification of the key characteristics that motivate an employee at the work place and last, but not least, the type of motivation that employees focus, intrinsic or extrinsic. The research method targeted a questionnaire based survey, including various company employees and an interview with the manager. The results confirmed that in Romania, employees put great emphasis on extrinsic motivation, a certain income and job security being primary. These results have implications for managers that in order to effectively motivate staff, first, must know their needs and expectations. To identify the main needs and motivational factors we had as a starting point Maslow's pyramid.

  16. Scientometric methods for identifying emerging technologies

    Science.gov (United States)

    Abercrombie, Robert K; Schlicher, Bob G; Sheldon, Frederick T

    2015-11-03

    Provided is a method of generating a scientometric model that tracks the emergence of an identified technology from initial discovery (via original scientific and conference literature), through critical discoveries (via original scientific, conference literature and patents), transitioning through Technology Readiness Levels (TRLs) and ultimately on to commercial application. During the period of innovation and technology transfer, the impact of scholarly works, patents and on-line web news sources are identified. As trends develop, currency of citations, collaboration indicators, and on-line news patterns are identified. The combinations of four distinct and separate searchable on-line networked sources (i.e., scholarly publications and citation, worldwide patents, news archives, and on-line mapping networks) are assembled to become one collective network (a dataset for analysis of relations). This established network becomes the basis from which to quickly analyze the temporal flow of activity (searchable events) for the example subject domain.

  17. Identifying Discourse Markers in Spoken Dialog

    CERN Document Server

    Heeman, P A; Allen, J F; Heeman, Peter A.; Byron, Donna; Allen, James F.

    1998-01-01

    In this paper, we present a method for identifying discourse marker usage in spontaneous speech based on machine learning. Discourse markers are denoted by special POS tags, and thus the process of POS tagging can be used to identify discourse markers. By incorporating POS tagging into language modeling, discourse markers can be identified during speech recognition, in which the timeliness of the information can be used to help predict the following words. We contrast this approach with an alternative machine learning approach proposed by Litman (1996). This paper also argues that discourse markers can be used to help the hearer predict the role that the upcoming utterance plays in the dialog. Thus discourse markers should provide valuable evidence for automatic dialog act prediction.

  18. Photoacoustic tomography to identify inflammatory arthritis

    Science.gov (United States)

    Rajian, Justin Rajesh; Girish, Gandikota; Wang, Xueding

    2012-09-01

    Identifying neovascularity (angiogenesis) as an early feature of inflammatory arthritis can help in early accurate diagnosis and treatment monitoring of this disease. Photoacoustic tomography (PAT) is a hybrid imaging modality which relies on intrinsic differences in the optical absorption among the tissues being imaged. Since blood has highly absorbing chromophores including both oxygenated and deoxygenated hemoglobin, PAT holds potential in identifying early angiogenesis associated with inflammatory joint diseases. PAT is used to identify changes in the development of inflammatory arthritis in a rat model. Imaging at two different wavelengths, 1064 nm and 532 nm, on rats revealed that there is a significant signal enhancement in the ankle joints of the arthritis affected rats when compared to the normal control group. Histology images obtained from both the normal and the arthritis affected rats correlated well with the PAT findings. Results support the fact that the emerging PAT could become a new tool for clinical management of inflammatory arthritis.

  19. Identifying Adverse Drug Events by Relational Learning.

    Science.gov (United States)

    Page, David; Costa, Vítor Santos; Natarajan, Sriraam; Barnard, Aubrey; Peissig, Peggy; Caldwell, Michael

    2012-07-01

    The pharmaceutical industry, consumer protection groups, users of medications and government oversight agencies are all strongly interested in identifying adverse reactions to drugs. While a clinical trial of a drug may use only a thousand patients, once a drug is released on the market it may be taken by millions of patients. As a result, in many cases adverse drug events (ADEs) are observed in the broader population that were not identified during clinical trials. Therefore, there is a need for continued, post-marketing surveillance of drugs to identify previously-unanticipated ADEs. This paper casts this problem as a reverse machine learning task, related to relational subgroup discovery and provides an initial evaluation of this approach based on experiments with an actual EMR/EHR and known adverse drug events. PMID:24955289

  20. Identifiability of surface sources from Cauchy data

    International Nuclear Information System (INIS)

    We explore the reconstruction of surface sources from single Cauchy data on the potential. Identifiability is first proven when the location of these sources is known and their density is to be sought. We also investigate the ill-posedness degree to establish that the problem is severely ill-posed, and exhibit the necessary orthogonality conditions fulfilled by exact Cauchy data, for which the process of recovering the density function of the sources succeeds. We later turn to the more difficult reconstruction of the location, the shape and the density function of the sources. Identifiability cannot be obtained for general geometries. Nevertheless, under some acceptable assumptions on the size and the location of these sources, we are able to state identifiability results

  1. Identifying, analysing and solving problems in practice.

    Science.gov (United States)

    Hewitt-Taylor, Jaqui

    When a problem is identified in practice, it is important to clarify exactly what it is and establish the cause before seeking a solution. This solution-seeking process should include input from those directly involved in the problematic situation, to enable individuals to contribute their perspective, appreciate why any change in practice is necessary and what will be achieved by the change. This article describes some approaches to identifying and analysing problems in practice so that effective solutions can be devised. It includes a case study and examples of how the Five Whys analysis, fishbone diagram, problem tree analysis, and Seven-S Model can be used to analyse a problem.

  2. Molecular Fingerprints to Identify Candida Species

    Directory of Open Access Journals (Sweden)

    Claudia Spampinato

    2013-01-01

    Full Text Available A wide range of molecular techniques have been developed for genotyping Candida species. Among them, multilocus sequence typing (MLST and microsatellite length polymorphisms (MLP analysis have recently emerged. MLST relies on DNA sequences of internal regions of various independent housekeeping genes, while MLP identifies microsatellite instability. Both methods generate unambiguous and highly reproducible data. Here, we review the results achieved by using these two techniques and also provide a brief overview of a new method based on high-resolution DNA melting (HRM. This method identifies sequence differences by subtle deviations in sample melting profiles in the presence of saturating fluorescent DNA binding dyes.

  3. Factors identifying pigs predisposed to tail biting

    OpenAIRE

    Beattie, V. E.; Breuer, K.; O Connell, N. E.; Sneddon, I. A.; Mercer, J. T.; Rance, K. A.; Sutcliffe, M. E. M.; Edwards, S A

    2005-01-01

    Approximately 5% of pigs slaughtered in the UK have been tail-bitten, leading to welfare and production issues. Tail biting is sporadic and not all pigs tail bite. The aim of this study was to identify factors that are common in pigs that perform tail-biting behaviour, and that might be used in a predictive way to identify such animals. The behaviour of 159 pigs was observed in the post-weaning period. Pigs were weaned at 4 weeks of age. In the week prior to weaning and at 6 weeks of age each...

  4. Minimal covariant observables identifying all pure states

    Energy Technology Data Exchange (ETDEWEB)

    Carmeli, Claudio, E-mail: claudio.carmeli@gmail.com [D.I.M.E., Università di Genova, Via Cadorna 2, I-17100 Savona (Italy); I.N.F.N., Sezione di Genova, Via Dodecaneso 33, I-16146 Genova (Italy); Heinosaari, Teiko, E-mail: teiko.heinosaari@utu.fi [Turku Centre for Quantum Physics, Department of Physics and Astronomy, University of Turku (Finland); Toigo, Alessandro, E-mail: alessandro.toigo@polimi.it [Dipartimento di Matematica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano (Italy); I.N.F.N., Sezione di Milano, Via Celoria 16, I-20133 Milano (Italy)

    2013-09-02

    It has been recently shown by Heinosaari, Mazzarella and Wolf (2013) [1] that an observable that identifies all pure states of a d-dimensional quantum system has minimally 4d−4 outcomes or slightly less (the exact number depending on d). However, no simple construction of this type of minimal observable is known. We investigate covariant observables that identify all pure states and have minimal number of outcomes. It is shown that the existence of this kind of observables depends on the dimension of the Hilbert space.

  5. Methods of Identifying and Preventing SQL Attacks

    Directory of Open Access Journals (Sweden)

    Bojken Shehu

    2012-11-01

    Full Text Available The paper begins by identifying the organizations which are vulnerable to the SQL attack referred to as an SQL injection attack. The term SQL injection attack is defined and a diagram is used to illustrate the way that attack occurs. In another section, the paper identifies the methods used to detect an attack to SQL, whereby the techniques are discussed extensively using relevant diagrams for illustration. The other sections cover the preventive methods, where the methods are also discussed with an illustration using diagrams.

  6. Systematic Determination of Human Cyclin Dependent Kinase (CDK)-9 Interactome Identifies Novel Functions in RNA Splicing Mediated by the DEAD Box (DDX)-5/17 RNA Helicases.

    Science.gov (United States)

    Yang, Jun; Zhao, Yingxin; Kalita, Mridul; Li, Xueling; Jamaluddin, Mohammad; Tian, Bing; Edeh, Chukwudi B; Wiktorowicz, John E; Kudlicki, Andrzej; Brasier, Allan R

    2015-10-01

    Inducible transcriptional elongation is a rapid, stereotypic mechanism for activating immediate early immune defense genes by the epithelium in response to viral pathogens. Here, the recruitment of a multifunctional complex containing the cyclin dependent kinase 9 (CDK9) triggers the process of transcriptional elongation activating resting RNA polymerase engaged with innate immune response (IIR) genes. To identify additional functional activity of the CDK9 complex, we conducted immunoprecipitation (IP) enrichment-stable isotope labeling LC-MS/MS of the CDK9 complex in unstimulated cells and from cells activated by a synthetic dsRNA, polyinosinic/polycytidylic acid [poly (I:C)]. 245 CDK9 interacting proteins were identified with high confidence in the basal state and 20 proteins in four functional classes were validated by IP-SRM-MS. These data identified that CDK9 interacts with DDX 5/17, a family of ATP-dependent RNA helicases, important in alternative RNA splicing of NFAT5, and mH2A1 mRNA two proteins controlling redox signaling. A direct comparison of the basal versus activated state was performed using stable isotope labeling and validated by IP-SRM-MS. Recruited into the CDK9 interactome in response to poly(I:C) stimulation are HSPB1, DNA dependent kinases, and cytoskeletal myosin proteins that exchange with 60S ribosomal structural proteins. An integrated human CDK9 interactome map was developed containing all known human CDK9- interacting proteins. These data were used to develop a probabilistic global map of CDK9-dependent target genes that predicted two functional states controlling distinct cellular functions, one important in immune and stress responses. The CDK9-DDX5/17 complex was shown to be functionally important by shRNA-mediated knockdown, where differential accumulation of alternatively spliced NFAT5 and mH2A1 transcripts and alterations in downstream redox signaling were seen. The requirement of CDK9 for DDX5 recruitment to NFAT5 and mH2A1

  7. Neoplasms identified in free-flying birds

    Science.gov (United States)

    Siegfried, L.M.

    1983-01-01

    Nine neoplasms were identified in carcasses of free-flying wild birds received at the National Wildlife Health Laboratory; gross and microscopic descriptions are reported herein. The prevalence of neoplasia in captive and free-flying birds is discussed, and lesions in the present cases are compared with those previously described in mammals and birds.

  8. Identifying the Multiple Intelligences of Your Students

    Science.gov (United States)

    McClellan, Joyce A.; Conti, Gary J.

    2008-01-01

    One way of addressing individual differences among adult learners is to identify the Multiple Intelligences of the learner. Multiple Intelligences refers to the concept developed by Howard Gardner that challenges the traditional view of intelligence and explains the presence of nine different Multiple Intelligences. The purpose of this study was…

  9. Identifying Ethical Hypernorms for Accounting Educators

    Science.gov (United States)

    Siegel, Philip H.; Mintz, Steven; Naser-Tavakolian, Mohsen; O'Shaughnessy, John

    2012-01-01

    Accounting educators have a unique role in academe because students learn about codes of ethics that will guide their actions as professionals. We identify hypernorms related to internal auditing educators that reflect unethical behaviors believed to be universally unacceptable by that community. We then compare the results to a prior survey of…

  10. Identifying Sexual Harassment: A Classroom Activity

    Science.gov (United States)

    Madson, Laura; Shoda, Jennifer

    2002-01-01

    We created a classroom activity to illustrate the complexity involved in identifying sexual harassment. In the activity, students decided whether 6 fictional scenarios constituted sexual harassment. The activity stimulates animated discussion, and evaluation data indicate that it received positive feedback from students and refined students'…

  11. DOI: A New Identifier for Digital Content.

    Science.gov (United States)

    Berinstein, Paula

    1998-01-01

    Previews Digital Object Identifiers (DOIs), a potential unifying classification system for the Web and the Internet developed by the Association of American Publishers and the Corporation for National Research Initiatives. Discusses issues and problems surrounding DOI implementation and usage and how DOI would affect publishers, users,…

  12. Non identified emissions in natural radioactivities

    International Nuclear Information System (INIS)

    Six-branched stars (including one short branch) have been observed in nuclear emulsions impregnated with chemical fractions of monazite. Also low-energy α-particle groups not corresponding to known emitters have been seen in Si spectra of monazite and hematite. An experiment in which magnetic mass separation was performed showed a non-identified α-radioactivity at mass 239

  13. 34 CFR 300.32 - Personally identifiable.

    Science.gov (United States)

    2010-07-01

    ... 34 Education 2 2010-07-01 2010-07-01 false Personally identifiable. 300.32 Section 300.32 Education Regulations of the Offices of the Department of Education (Continued) OFFICE OF SPECIAL EDUCATION AND REHABILITATIVE SERVICES, DEPARTMENT OF EDUCATION ASSISTANCE TO STATES FOR THE EDUCATION...

  14. The external muon identifier (EMI) for BEBC

    CERN Multimedia

    1977-01-01

    This detector identifies muons produced in neutrino interactions in BEBC. Whereas hadrons are absorbed in the iron shield around BEBC, muons penetrate and are detected in a 150 m2 layer of proportional chambers, each equipped with three sensitive planes, i.e. two anode wire and one cathode plane.

  15. Problems Identifying Independent and Dependent Variables

    Science.gov (United States)

    Leatham, Keith R.

    2012-01-01

    This paper discusses one step from the scientific method--that of identifying independent and dependent variables--from both scientific and mathematical perspectives. It begins by analyzing an episode from a middle school mathematics classroom that illustrates the need for students and teachers alike to develop a robust understanding of…

  16. Teaching science students to identify entrepreneurial opportunities

    NARCIS (Netherlands)

    Nab, J.

    2015-01-01

    This dissertation describes a research project on teaching science students to identify entrepreneurial opportunities, which is a core competence for entrepreneurs that should be emphasized in education. This research consists of four studies. The first case study aims at finding design strategies f

  17. Identifying Benefit Segments among College Students.

    Science.gov (United States)

    Brown, Joseph D.

    1991-01-01

    Using concept of market segmentation (dividing market into distinct groups requiring different product benefits), surveyed 398 college students to determine benefit segments among students selecting a college to attend and factors describing each benefit segment. Identified one major segment of students (classroomers) plus three minor segments…

  18. Automatically identifying periodic social events from Twitter

    NARCIS (Netherlands)

    Kunneman, F.A.; Bosch, A.P.J. van den

    2015-01-01

    Many events referred to on Twitter are of a periodic nature, characterized by roughly constant time intervals in between occurrences. Examples are annual music festivals, weekly television programs, and the full moon cycle. We propose a system that can automatically identify periodic events from Twi

  19. Identify Your Brand, Before You Market.

    Science.gov (United States)

    Claggett, Laura

    2002-01-01

    Discusses marketing in special libraries and suggests that librarians need to identify library services that set them apart from others. Highlights include the competitive environment and alternatives for the consumer; value that the library offers; targeting consumers; return on investment; and determining why consumers choose your services. (LRW)

  20. A Young Gene Specific to Man Identified

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    @@ ACAS-Max Planck Junior Research Group headed by WANG Wen, vice director of the CAS Kunming Institute of Zoology (KIZ), recently identified a young gene specific to man clorf37-dup. Their work was published on the June 1 issue of Human Molecular Genetics.

  1. Radio Frequency Identifiers: What are the Possibilities?

    CERN Document Server

    Elmorshidy, Ahmed

    2010-01-01

    This paper defines the components of radio frequency identifiers (RFID). It also explores the different areas and sectors where RFID can be beneficial. The paper discusses the uses and advantages of RFID in deference, consumer packaged goods (CPG), healthcare, logistics, manufacturing, and retail.

  2. Identifying systematic DFT errors in catalytic reactions

    DEFF Research Database (Denmark)

    Christensen, Rune; Hansen, Heine Anton; Vegge, Tejs

    2015-01-01

    Using CO2 reduction reactions as examples, we present a widely applicable method for identifying the main source of errors in density functional theory (DFT) calculations. The method has broad applications for error correction in DFT calculations in general, as it relies on the dependence...

  3. Where to look when identifying roadkilled amphibians?

    Directory of Open Access Journals (Sweden)

    Marc Franch

    2015-12-01

    Full Text Available Roads have multiple effects on wildlife; amphibians are one of the groups more intensely affected by roadkills. Monitoring roadkills is expensive and time consuming. Automated mapping systems for detecting roadkills, based on robotic computer vision techniques, are largely necessary. Amphibians can be recognised by a set of features as shape, size, colouration, habitat and location. This species identification by using multiple features at the same time is known as “jizz”. In a similar way to human vision, computer vision algorithms must incorporate a prioritisation process when analysing the objects in an image. Our main goal here was to give a numerical priority sequence of particular characteristics of roadkilled amphibians to improve the computing and learning process of algorithms. We asked hundred and five amateur and professional herpetologists to answer a simple test of five sets with ten images each of roadkilled amphibians, in order to determine which body parts or characteristics (body form, colour, and other patterns are used to identify correctly the species. Anura was the group most easily identified when it was roadkilled and Caudata was the most difficult. The lower the taxonomic level of amphibian, the higher the difficulty of identifying them, both in Anura and Caudata. Roadkilled amphibians in general and Anura group were mostly identified by the Form, by the combination of Form and Colour, and finally by Colour. Caudata was identified mainly on Form and Colour and on Colour. Computer vision algorithms must incorporate these combinations of features, avoiding to work exclusively in one specific feature.

  4. Data Identifiers and Citations Enable Reproducible Science

    Science.gov (United States)

    Tilmes, C.

    2011-12-01

    Modern science often involves data processing with tremendous volumes of data. Keeping track of that data has been a growing challenge for data center. Researchers who access and use that data don't always reference and cite their data sources adequately for consumers of their research to follow their methodology or reproduce their analyses or experiments. Recent research has led to recommendations for good identifiers and citations that can help address this problem. This paper will describe some of the best practices in data identifiers, reference and citation. Using a simplified example scenario based on a long term remote sensing satellite mission, it will explore issues in identifying dynamic data sets and the importance of good data citations for reproducibility. It will describe the difference between granule and collection level identifiers, using UUIDs and DOIs to illustrate some recommendations for developing identifiers and assigning them during data processing. As data processors create data products, the provenance of the input products and precise steps that led to their creation are recorded and published for users of the data to see. As researchers access the data from an archive, they can use the provenance to help understand the genesis of the data, which could have effects on their usage of the data. By citing the data on publishing their research, others can retrieve the precise data used in their research and reproduce the analyses and experiments to confirm the results. Describing the experiment to a sufficient extent to reproduce the research enforces a formal approach that lends credibility to the results, and ultimately, to the policies of decision makers depending on that research.

  5. Identifying a novel locus for psoriatic arthritis.

    Science.gov (United States)

    Budu-Aggrey, Ashley; Bowes, John; Barton, Anne

    2016-01-01

    A number of studies have identified genetic risk loci for PsA, the majority of which also confer risk for psoriasis. The stronger heritability of PsA in comparison with psoriasis suggests that there should be risk loci that are specific for PsA. Identifying such loci could potentially inform therapy development to provide more effective treatments for PsA patients, especially with a considerable proportion being non-responsive to current therapies. Evidence of a PsA-specific locus has been previously found at HLA-B27 within the MHC region. A recent study has provided evidence of non-HLA risk loci that are specific for PsA at IL23R, PTPN22 and on chromosome 5q31. Functional characterization of these loci will provide further understanding of the pathways underlying PsA, and enable us to apply genetic findings for patient benefit. PMID:26255310

  6. Identifying, analysing and solving problems in practice.

    Science.gov (United States)

    Hewitt-Taylor, Jaqui

    When a problem is identified in practice, it is important to clarify exactly what it is and establish the cause before seeking a solution. This solution-seeking process should include input from those directly involved in the problematic situation, to enable individuals to contribute their perspective, appreciate why any change in practice is necessary and what will be achieved by the change. This article describes some approaches to identifying and analysing problems in practice so that effective solutions can be devised. It includes a case study and examples of how the Five Whys analysis, fishbone diagram, problem tree analysis, and Seven-S Model can be used to analyse a problem. PMID:22848969

  7. Machine learning for identifying botnet network traffic

    DEFF Research Database (Denmark)

    Stevanovic, Matija; Pedersen, Jens Myrup

    2013-01-01

    . Due to promise of non-invasive and resilient detection, botnet detection based on network traffic analysis has drawn a special attention of the research community. Furthermore, many authors have turned their attention to the use of machine learning algorithms as the mean of inferring botnet......-related knowledge from the monitored traffic. This paper presents a review of contemporary botnet detection methods that use machine learning as a tool of identifying botnet-related traffic. The main goal of the paper is to provide a comprehensive overview on the field by summarizing current scientific efforts...... of using machine learning for identifying botnet traffic and outlines possibilities for the future development of machine learning-based botnet detection systems....

  8. Wham: Identifying Structural Variants of Biological Consequence.

    Science.gov (United States)

    Kronenberg, Zev N; Osborne, Edward J; Cone, Kelsey R; Kennedy, Brett J; Domyan, Eric T; Shapiro, Michael D; Elde, Nels C; Yandell, Mark

    2015-12-01

    Existing methods for identifying structural variants (SVs) from short read datasets are inaccurate. This complicates disease-gene identification and efforts to understand the consequences of genetic variation. In response, we have created Wham (Whole-genome Alignment Metrics) to provide a single, integrated framework for both structural variant calling and association testing, thereby bypassing many of the difficulties that currently frustrate attempts to employ SVs in association testing. Here we describe Wham, benchmark it against three other widely used SV identification tools-Lumpy, Delly and SoftSearch-and demonstrate Wham's ability to identify and associate SVs with phenotypes using data from humans, domestic pigeons, and vaccinia virus. Wham and all associated software are covered under the MIT License and can be freely downloaded from github (https://github.com/zeeev/wham), with documentation on a wiki (http://zeeev.github.io/wham/). For community support please post questions to https://www.biostars.org/.

  9. Trustworthy persistent identifier systems of the future

    Science.gov (United States)

    Golodoniuc, Pavel; Klump, Jens; Car, Nicholas

    2016-04-01

    Over the last two decades, persistent identifier (PID) systems have seen some significant changes in their governance policies, system capabilities, and technology. The development of most systems was driven by two main application areas, namely archives and libraries. Guidelines and criteria for trustworthy PID systems have been clearly devised (Bütikofer, 2009) and many PID system implementations for the identification of static digital objects have been built (e.g., PURL). However systems delivering persistent identifiers for dynamic datasets are not yet mature. There has been a rapid proliferation of different PID systems caused by the specific technical or organisational requirements of various communities that could not be met by existing systems such as DOI, ISBN, and EAN. Many of these different systems were limited by their inability to provide native means of persistent identifier resolution. This has prompted a decoupling of PID-associated data from the resolution service and this is where the Handle system has played a significant role. The Handle allowed to build a distributed system of independently managed resolver services. A trustworthy PID system must be designed to outlive the objects it provides persistent identifiers for, which may cease to exist or otherwise be deprecated, and the technology used to implement it, which will certainly need to change with time. We propose that such a system should rest on four pillars of agreements - (i) definitions, (ii) policies, (iii) services, and (iv) data services, to ensure longevity. While we believe all four pillars are equally important, we intentionally leave regulating aspects of issuing of identifiers and their registration out of the scope of this paper and focus on the agreements that have to be established between PID resolver services and the data sources indicated by the persistent identifiers. We propose an approach to development of PID systems that combines the use of (a) the Handle system

  10. Identifying pelagic ecosystem indicators for management

    DEFF Research Database (Denmark)

    Trenkel, Verena; Hintzen, Niels; Rindorf, Anna;

    2013-01-01

    to pelagic fisheries to further explore the setting of management objectives. The objectives were identified through a participatory process including industry, management, scientist and NGO representatives. These objectives were used to identify appropriate driver, pressure and state indicators. The links......When exploiting fish populations under the ecosystem approach, aiming for MSY is not necessarily sufficient to ensure wider ecosystem sustainability. All of the large stocks of pelagic fish are managed through harvest control rules based on an MSY approach. Ensuring good environmental status...... will probably require further constraints to be imposed by management. Most of the current paradigm with regards to GES for fisheries has been based on demersal fish. Pelagic fisheries and fish are operationally and biologically respectively different. We use the example of applying the ecosystem approach...

  11. Wham: Identifying Structural Variants of Biological Consequence.

    Directory of Open Access Journals (Sweden)

    Zev N Kronenberg

    2015-12-01

    Full Text Available Existing methods for identifying structural variants (SVs from short read datasets are inaccurate. This complicates disease-gene identification and efforts to understand the consequences of genetic variation. In response, we have created Wham (Whole-genome Alignment Metrics to provide a single, integrated framework for both structural variant calling and association testing, thereby bypassing many of the difficulties that currently frustrate attempts to employ SVs in association testing. Here we describe Wham, benchmark it against three other widely used SV identification tools-Lumpy, Delly and SoftSearch-and demonstrate Wham's ability to identify and associate SVs with phenotypes using data from humans, domestic pigeons, and vaccinia virus. Wham and all associated software are covered under the MIT License and can be freely downloaded from github (https://github.com/zeeev/wham, with documentation on a wiki (http://zeeev.github.io/wham/. For community support please post questions to https://www.biostars.org/.

  12. Identifying the borders of mathematical knowledge

    International Nuclear Information System (INIS)

    Based on a divide and conquer approach, knowledge about nature has been organized into a set of interrelated facts, allowing a natural representation in terms of graphs: each 'chunk' of knowledge corresponds to a node, while relationships between such chunks are expressed as edges. This organization becomes particularly clear in the case of mathematical theorems, with their intense cross-implications and relationships. We have derived a web of mathematical theorems from Wikipedia and, thanks to the powerful concept of entropy, identified its more central and frontier elements. Our results also suggest that the central nodes are the oldest theorems, while the frontier nodes are those recently added to the network. The network communities have also been identified, allowing further insights about the organization of this network, such as its highly modular structure.

  13. Persistent Identifiers for Dutch cultural heritage institutions

    Science.gov (United States)

    Ras, Marcel; Kruithof, Gijsbert

    2016-04-01

    Over the past years, more and more collections belonging to archives, libraries, media, museums, and knowledge institutes are being digitised and made available online. These are exciting times for ALM institutions. They are realising that, in the information society, their collections are goldmines. Unfortunately most heritage institutions in the Netherlands do not yet meet the basic preconditions for long-term availability of their collections. The digital objects often have no long lasting fixed reference yet. URL's and web addresses change. Some digital objects that were referenced in Europeana and other portals can no longer be found. References in scientific articles have a very short life span, which is damaging for scholarly research. In 2015, the Dutch Digital Heritage Network (NDE) has started a two-year work program to co-ordinate existing initiatives in order to improve the (long-term) accessibility of the Dutch digital heritage for a wide range of users, anytime, anyplace. The Digital Heritage Network is a partnership established on the initiative of the Ministry of Education, Culture and Science. The members of the NDE are large, national institutions that strive to professionally preserve and manage digital data, e.g. the National Library, The Netherlands Institute for Sound and Vision, the Netherlands Cultural Heritage Agency, the Royal Netherlands Academy of Arts and Sciences, the National Archive of the Netherlands and the DEN Foundation, and a growing number of associations and individuals both within and outside the heritage sector. By means of three work programmes the goals of the Network should be accomplished and improve the visibility, the usability and the sustainability of digital heritage. Each programme contains of a set of projects. Within the sustainability program a project on creating a model for persistent identifiers is taking place. The main goals of the project are (1) raise awareness among cultural heritage institutions on the

  14. Identifying influential spreaders in complex networks

    CERN Document Server

    Kitsak, Maksim; Havlin, Shlomo; Liljeros, Fredrik; Muchnik, Lev; Stanley, H Eugene; Makse, Hernan A

    2010-01-01

    Networks portray a multitude of interactions through which people meet, ideas are spread, and infectious diseases propagate within a society. Identifying the most efficient "spreaders" in a network is an important step to optimize the use of available resources and ensure the more efficient spread of information. Here we show that, in contrast to common belief, the most influential spreaders in a social network do not correspond to the best connected people or to the most central people (high betweenness centrality). Instead, we find: (i) The most efficient spreaders are those located within the core of the network as identified by the k-shell decomposition analysis. (ii) When multiple spreaders are considered simultaneously, the distance between them becomes the crucial parameter that determines the extend of the spreading. Furthermore, we find that-- in the case of infections that do not confer immunity on recovered individuals-- the infection persists in the high k-shell layers of the network under conditi...

  15. Identifying Groundwater Recharge in Arid Regions

    Science.gov (United States)

    Thomas, B. F.; Famiglietti, J. S.

    2015-12-01

    Recharge epodicity in arid regions provides a method to estimate annual groundwater recharge given a relationship expressed as the recharge to precipitation ratio. Traditionally, in-situ observations are required to identify aquifer recharge events, while more advanced approaches such as the water-table fluctuation method or the episodic master recession method are necessary to delineate the recharge event. Our study uses the Gravity Recovery and Climate Experiment (GRACE) observations to estimate monthly changes in groundwater storage which are attributed to the combination of groundwater abstraction and episodic recharge in the arid southwestern United States. Our results illustrate the ability of remote sensing technologies to identify episodic groundwater recharge in arid regions which can be used within sustainable groundwater management frameworks to effectively manage groundwater resources.

  16. An Xpert screen to identify carbapenemases

    Directory of Open Access Journals (Sweden)

    Mubin Kazi

    2016-01-01

    Full Text Available To prevent the spread of carbapenemases-producing Enterobacteriaceae (CPE active surveillance, contact isolation and cohorting infected patients should be practiced. Rectal swabs for the Xpert MDRO-assay of 32 patients were included. 71.85% were positive for targets incorporated into the MDRO-assay; whereas 28% were phenotypically not CRE and Xpert negative (9.37% had different mechanism [bla OXA]. The assay identified 59.3%, 9.37% and 3.1% as bla NDM, bla NDM+VIM and bla VIM, respectively. The assay is a screening test that identifies CPE harbouring organism within an hour and can be installed at tertiary-care facilities to screen colonized patients.

  17. Guidelines for identifying suspect/counterfeit material

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-09-01

    These guidelines are intended to assist users of products in identifying: substandard, misrepresented, or fraudulently marked items. The guidelines provide information about such topics as: precautions, inspection and testing, dispositioning identified items, installed inspection and reporting suspect/counterfeit materials. These guidelines apply to users who are developing procurement documents, product acceptance/verification methods, company procedures, work instructions, etc. The intent of these SM guidelines in relation to the Quality Assurance Program Description (QAPD) and implementing company Management Control Procedures is not to substitute or replace existing requirements, as defined in either the QAPD or company implementing instructions (Management Control Procedures). Instead, the guidelines are intended to provide a consolidated source of information addressing the issue of Suspect/Counterfeit materials. These guidelines provide an extensive suspect component listing and suspect indications listing. Users can quickly check their suspect items against the list of manufacturers products (i.e., type, LD. number, and nameplate information) by consulting either of these listings.

  18. Identifying Genetic Variation for Alcohol Dependence

    OpenAIRE

    Agrawal, Arpana; Bierut, Laura J.

    2012-01-01

    Researchers are using various strategies to identify the genes that may be associated with alcoholism. The initial efforts primarily relied on candidate gene and linkage studies; more recently, however, modern advances in genotyping have resulted in widespread use of genome-wide association studies for alcohol dependence. The key findings of the earlier studies were that variations (i.e., polymorphisms) in the DNA sequences of the genes encoding alcohol dehydrogenase 1B (i.e., the ADH1B gene)...

  19. The Complexity of Identifying Large Equivalence Classes

    DEFF Research Database (Denmark)

    Skyum, Sven; Frandsen, Gudmund Skovbjerg; Miltersen, Peter Bro;

    1999-01-01

    We prove that at least 3k−4/k(2k−3)(n/2) – O(k)equivalence tests and no more than 2/k (n/2) + O(n) equivalence tests are needed in the worst case to identify the equivalence classes with at least k members in set of n elements. The upper bound is an improvement by a factor 2 compared to known res...

  20. Identifying learning techniques among high achievers

    OpenAIRE

    Shanmukananda P; L. Padma

    2013-01-01

    Background: In every college, it is noticed that in spite of being exposed to the same teaching modalities and adopting seemingly similar strategies, some students perform much better than their peers. This can be evaluated in the form of better academic performance in the internal assessments they undertake. This project is an endeavor to identify the learning techniques among high achievers which they employ to outperform others. We can also suggest the same to the medium and low achievers ...

  1. Asteroid secular dynamics: Ceres' fingerprint identified

    OpenAIRE

    Novaković, Bojan; Maurel, Clara; Tsirvoulis, Georgios; Knezević, Zoran

    2015-01-01

    Here we report on the significant role of a so far overlooked dynamical aspect, namely a secular resonance between the dwarf planet Ceres and other asteroids. We demonstrate that this type of secular resonance can be the dominant dynamical factor in certain regions of the main asteroid belt. Specifically, we performed a dynamical analysis of the asteroids belonging to the (1726) Hoffmeister family. To identify which dynamical mechanisms are actually at work in this part of the main asteroid b...

  2. Identifying nanotechnological linkages in the Finnish economy

    OpenAIRE

    Nikulainen, Tuomo

    2007-01-01

    Nanotechnology, as an emerging science-based technology, is seen to have great potential both in scientific as well as economic terms. In this paper the focus is on identifying the technological linkages between the Finnish nanotechnology community and the industrial incumbents. These technological link-ages are first observed at a broader level in comparison with the technological strengths of the Finnish industries, and then in greater detail at the level of companies. In addition, the abso...

  3. Identifying innovation in higher education elearning strategies

    OpenAIRE

    Aczel, James; Continat, Olivier; Hardy, Pascale; Iggulden, Helen; Komáromi, Laszlo; Maillet, Katherine; Medina, Sara; Meiszner, Andreas; Obermueller, Eva; SPINOGLIO Mark; Staniland, Karen

    2006-01-01

    There are many case studies of individual Higher Education Institutions (HEIs) devising distinctive eLearning strategies, reported by the HEI itself, journalists, or research observatories. An extraordinarily wide range of university-level eLearning programmes are rapidly becoming available from large numbers of HEIs across Europe, and there are strong attempts being made to identify and disseminate case studies of innovative eLearning practices (e.g. MENON, 2006). However, the vital research...

  4. Identifying spatial priorities for protecting ecosystem services.

    Science.gov (United States)

    Luck, Gary W; Chan, Kai Ma; Klien, Carissa J

    2012-01-01

    Priorities for protecting ecosystem services must be identified to ensure future human well-being. Approaches to broad-scale spatial prioritization of ecosystem services are becoming increasingly popular and are a vital precursor to identifying locations where further detailed analyses of the management of ecosystem services is required (e.g., examining trade-offs among management actions). Prioritization approaches often examine the spatial congruence between priorities for protecting ecosystem services and priorities for protecting biodiversity; therefore, the spatial prioritization method used is crucial because it will influence the alignment of service protection and conservation goals. While spatial prioritization of ecosystem services and prioritization for conservation share similarities, such as the need to document threats and costs, the former differs substantially from the latter owing to the requirement to measure the following components: supply of services; availability of human-derived alternatives to service provision; capacity to meet beneficiary demand; and site dependency in and scale of service delivery. We review studies that identify broad-scale spatial priorities for managing ecosystem services and demonstrate that researchers have used different approaches and included various measures for identifying priorities, and most studies do not consider all of the components listed above. We describe a conceptual framework for integrating each of these components into spatial prioritization of ecosystem services and illustrate our approach using a worked example for water provision. A fuller characterization of the biophysical and social context for ecosystem services that we call for should improve future prioritization and the identification of locations where ecosystem-service management is especially important or cost effective. PMID:24555017

  5. Identifying the Universal part of TMDs

    CERN Document Server

    Van der Veken, F F

    2016-01-01

    We attempt to identify a path layout in the definition of transverse-momentum-dependent T-odd parton distribution functions (TMD)s which combines features of both, initial- and final-state interactions, so that it remains universal despite the fact that the Wilson lines entering such TMDs change their orientation. The generic structure of the quark correlator for this path layout is calculated.

  6. Teaching science students to identify entrepreneurial opportunities

    OpenAIRE

    Nab, J.

    2015-01-01

    This dissertation describes a research project on teaching science students to identify entrepreneurial opportunities, which is a core competence for entrepreneurs that should be emphasized in education. This research consists of four studies. The first case study aims at finding design strategies for entrepreneurship education that is successful in generating new start-ups. This study resulted in five design strategies for a learning environment that includes those elements of entrepreneursh...

  7. Identifying Topics in Microblogs Using Wikipedia.

    Science.gov (United States)

    Yıldırım, Ahmet; Üsküdarlı, Suzan; Özgür, Arzucan

    2016-01-01

    Twitter is an extremely high volume platform for user generated contributions regarding any topic. The wealth of content created at real-time in massive quantities calls for automated approaches to identify the topics of the contributions. Such topics can be utilized in numerous ways, such as public opinion mining, marketing, entertainment, and disaster management. Towards this end, approaches to relate single or partial posts to knowledge base items have been proposed. However, in microblogging systems like Twitter, topics emerge from the culmination of a large number of contributions. Therefore, identifying topics based on collections of posts, where individual posts contribute to some aspect of the greater topic is necessary. Models, such as Latent Dirichlet Allocation (LDA), propose algorithms for relating collections of posts to sets of keywords that represent underlying topics. In these approaches, figuring out what the specific topic(s) the keyword sets represent remains as a separate task. Another issue in topic detection is the scope, which is often limited to specific domain, such as health. This work proposes an approach for identifying domain-independent specific topics related to sets of posts. In this approach, individual posts are processed and then aggregated to identify key tokens, which are then mapped to specific topics. Wikipedia article titles are selected to represent topics, since they are up to date, user-generated, sophisticated articles that span topics of human interest. This paper describes the proposed approach, a prototype implementation, and a case study based on data gathered during the heavily contributed periods corresponding to the four US election debates in 2012. The manually evaluated results (0.96 precision) and other observations from the study are discussed in detail. PMID:26991442

  8. Confirming congenital hypothyroidism identified from neonatal screening.

    OpenAIRE

    Foo, A.; Leslie, H.; Carson, D. J.

    2002-01-01

    All patients identified in the neonatal screening programme for congenital hypothyroidism in Northern Ireland between 1983 and 1993 were reviewed. 131 infants were recalled because of TSH elevation of whom 85 proved to have true permanent congenital hypothyroidism, while 44 had transient TSH elevation and 2 cases died before the diagnosis could be confirmed. TSH elevation at presentation was milder in the transient group and these infants were more likely to be unwell and/or suffering from co...

  9. Identifying Topics in Microblogs Using Wikipedia.

    Directory of Open Access Journals (Sweden)

    Ahmet Yıldırım

    Full Text Available Twitter is an extremely high volume platform for user generated contributions regarding any topic. The wealth of content created at real-time in massive quantities calls for automated approaches to identify the topics of the contributions. Such topics can be utilized in numerous ways, such as public opinion mining, marketing, entertainment, and disaster management. Towards this end, approaches to relate single or partial posts to knowledge base items have been proposed. However, in microblogging systems like Twitter, topics emerge from the culmination of a large number of contributions. Therefore, identifying topics based on collections of posts, where individual posts contribute to some aspect of the greater topic is necessary. Models, such as Latent Dirichlet Allocation (LDA, propose algorithms for relating collections of posts to sets of keywords that represent underlying topics. In these approaches, figuring out what the specific topic(s the keyword sets represent remains as a separate task. Another issue in topic detection is the scope, which is often limited to specific domain, such as health. This work proposes an approach for identifying domain-independent specific topics related to sets of posts. In this approach, individual posts are processed and then aggregated to identify key tokens, which are then mapped to specific topics. Wikipedia article titles are selected to represent topics, since they are up to date, user-generated, sophisticated articles that span topics of human interest. This paper describes the proposed approach, a prototype implementation, and a case study based on data gathered during the heavily contributed periods corresponding to the four US election debates in 2012. The manually evaluated results (0.96 precision and other observations from the study are discussed in detail.

  10. Using compression to identify acronyms in text

    OpenAIRE

    Yeates, Stuart; Bainbridge, David; Witten, Ian H

    2000-01-01

    Text mining is about looking for patterns in natural language text, and may be defined as the process of analyzing text to extract information from it for particular purposes. In previous work, we claimed that compression is a key technology for text mining, and backed this up with a study that showed how particular kinds of lexical tokens---names, dates, locations, etc.---can be identified and located in running text, using compression models to provide the leverage necessary to distinguish ...

  11. Identifying the Universal Part of TMDs

    Science.gov (United States)

    Van der Veken, F. F.; Stefanis, N. G.

    2016-08-01

    We attempt to identify a path layout in the definition of transverse-momentum-dependent T-odd parton distribution functions (TMD)s which combines features of both, initial- and final-state interactions, so that it remains universal despite the fact that the Wilson lines entering such TMDs change their orientation. The generic structure of the quark correlator for this path layout is calculated.

  12. Identifying Topics in Microblogs Using Wikipedia

    Science.gov (United States)

    Yıldırım, Ahmet; Üsküdarlı, Suzan; Özgür, Arzucan

    2016-01-01

    Twitter is an extremely high volume platform for user generated contributions regarding any topic. The wealth of content created at real-time in massive quantities calls for automated approaches to identify the topics of the contributions. Such topics can be utilized in numerous ways, such as public opinion mining, marketing, entertainment, and disaster management. Towards this end, approaches to relate single or partial posts to knowledge base items have been proposed. However, in microblogging systems like Twitter, topics emerge from the culmination of a large number of contributions. Therefore, identifying topics based on collections of posts, where individual posts contribute to some aspect of the greater topic is necessary. Models, such as Latent Dirichlet Allocation (LDA), propose algorithms for relating collections of posts to sets of keywords that represent underlying topics. In these approaches, figuring out what the specific topic(s) the keyword sets represent remains as a separate task. Another issue in topic detection is the scope, which is often limited to specific domain, such as health. This work proposes an approach for identifying domain-independent specific topics related to sets of posts. In this approach, individual posts are processed and then aggregated to identify key tokens, which are then mapped to specific topics. Wikipedia article titles are selected to represent topics, since they are up to date, user-generated, sophisticated articles that span topics of human interest. This paper describes the proposed approach, a prototype implementation, and a case study based on data gathered during the heavily contributed periods corresponding to the four US election debates in 2012. The manually evaluated results (0.96 precision) and other observations from the study are discussed in detail. PMID:26991442

  13. Identifying the learning needs of senior nurses.

    Science.gov (United States)

    Cerinus, Marie

    There has been a drive to encourage nurses into positions of leadership but, despite the importance of considering how the senior nurse role should be developed and the needs of senior nurses, little literature exists on the subject. To explore senior nurse development, one health. board in Scotland invited senior nurses to participate in a "development conversation". Key points were noted during each conversation and themed. This article outlines the needs identified and explores how they could be addressed. PMID:27386709

  14. Preclinical Assays for Identifying Cancer Chemopreventive Phytochemicals

    OpenAIRE

    Oyama, Takeru; Yasui, Yumiko; Sugie, Shigeyuki; Tanaka, Takuji

    2009-01-01

    Dietary factors influence carcinogenesis in a variety of tissues. The consumption of fruits and vegetables is associated with a decreased risk of several types of epithelial malignancies. In addition, there are interrelationships between diet, environmental factors, and genetics that can affect cancer risk. Potential chemopreventive agents against cancer development can be found among nutritive and/or nonnutritive compounds in inedible and edible plants. To identify potential cancer chemoprev...

  15. Identifying mechanistic similarities in drug responses

    KAUST Repository

    Zhao, C.

    2012-05-15

    Motivation: In early drug development, it would be beneficial to be able to identify those dynamic patterns of gene response that indicate that drugs targeting a particular gene will be likely or not to elicit the desired response. One approach would be to quantitate the degree of similarity between the responses that cells show when exposed to drugs, so that consistencies in the regulation of cellular response processes that produce success or failure can be more readily identified.Results: We track drug response using fluorescent proteins as transcription activity reporters. Our basic assumption is that drugs inducing very similar alteration in transcriptional regulation will produce similar temporal trajectories on many of the reporter proteins and hence be identified as having similarities in their mechanisms of action (MOA). The main body of this work is devoted to characterizing similarity in temporal trajectories/signals. To do so, we must first identify the key points that determine mechanistic similarity between two drug responses. Directly comparing points on the two signals is unrealistic, as it cannot handle delays and speed variations on the time axis. Hence, to capture the similarities between reporter responses, we develop an alignment algorithm that is robust to noise, time delays and is able to find all the contiguous parts of signals centered about a core alignment (reflecting a core mechanism in drug response). Applying the proposed algorithm to a range of real drug experiments shows that the result agrees well with the prior drug MOA knowledge. © The Author 2012. Published by Oxford University Press. All rights reserved.

  16. A novel motif identified in dependence receptors.

    Directory of Open Access Journals (Sweden)

    Gabriel del Rio

    Full Text Available Programmed cell death signaling is a critical feature of development, cellular turnover, oncogenesis, and neurodegeneration, among other processes. Such signaling may be transduced via specific receptors, either following ligand binding-to death receptors-or following the withdrawal of trophic ligands-from dependence receptors. Although dependence receptors display functional similarities, no common structural domains have been identified. Therefore, we employed the Multiple Expectation Maximization for Motif Elicitation and the Motif Alignment and Search Tool software programs to identify a novel transmembrane motif, dubbed dependence-associated receptor transmembrane (DART motif, that is common to all described dependence receptors. Of 3,465 human transmembrane proteins, 25 (0.7% display the DART motif. The predicted secondary structure features an alpha helical structure, with an unusually high percentage of valine residues. At least four of the proteins undergo regulated intramembrane proteolysis. To date, we have not identified a function for this putative domain. We speculate that the DART motif may be involved in protein processing, interaction with other proteins or lipids, or homomultimerization.

  17. Identifying web usage behavior of bank customers

    Science.gov (United States)

    Araya, Sandro; Silva, Mariano; Weber, Richard

    2002-03-01

    The bank Banco Credito e Inversiones (BCI) started its virtual bank in 1996 and its registered customers perform currently more than 10,000 Internet transactions daily, which typically cause les than 10% of traditional transaction costs. Since most of the customers are still not registered for online banking, one of the goals of the virtual bank is to increase then umber of registered customers. Objective of the presented work was to identify customers who are likely to perform online banking but still do not use this medium for their transactions. This objective has been reached by determining profiles of registered customers who perform many transactions online. Based on these profiles the bank's Data Warehouse is explored for twins of these heavy users that are still not registered for online banking. We applied clustering in order to group the registered customers into five classes. One of these classes contained almost 30% of all registered customers and could clearly be identified as class of heavy users. Next a neural network assigned online customers to the previously found five classes. Applying the network trained on online customers to all the bank customers identified twins of heavy users that, however had not performed online transactions so far. A mailing to these candidates informing about the advantages of online banking doubled the number of registrations compared to previous campaigns.

  18. Identifying differentially regulated subnetworks from phosphoproteomic data

    Directory of Open Access Journals (Sweden)

    Tebbe Andreas

    2010-06-01

    Full Text Available Abstract Background Various high throughput methods are available for detecting regulations at the level of transcription, translation or posttranslation (e.g. phosphorylation. Integrating these data with protein networks should make it possible to identify subnetworks that are significantly regulated. Furthermore, such integration can support identification of regulated entities from often noisy high throughput data. In particular, processing mass spectrometry-based phosphoproteomic data in this manner may expose signal transduction pathways and, in the case of experiments with drug-treated cells, reveal the drug's mode of action. Results Here, we introduce SubExtractor, an algorithm that combines phosphoproteomic data with protein network information from STRING to identify differentially regulated subnetworks and individual proteins. The method is based on a Bayesian probabilistic model combined with a genetic algorithm and rigorous significance testing. The Bayesian model accounts for information about both differential regulation and network topology. The method was tested with artificial data and subsequently applied to a comprehensive phosphoproteomics study investigating the mode of action of sorafenib, a small molecule kinase inhibitor. Conclusions SubExtractor reliably identifies differentially regulated subnetworks from phosphoproteomic data by integrating protein networks. The method can also be applied to gene or protein expression data.

  19. Identifiability of large phylogenetic mixture models.

    Science.gov (United States)

    Rhodes, John A; Sullivant, Seth

    2012-01-01

    Phylogenetic mixture models are statistical models of character evolution allowing for heterogeneity. Each of the classes in some unknown partition of the characters may evolve by different processes, or even along different trees. Such models are of increasing interest for data analysis, as they can capture the variety of evolutionary processes that may be occurring across long sequences of DNA or proteins. The fundamental question of whether parameters of such a model are identifiable is difficult to address, due to the complexity of the parameterization. Identifiability is, however, essential to their use for statistical inference.We analyze mixture models on large trees, with many mixture components, showing that both numerical and tree parameters are indeed identifiable in these models when all trees are the same. This provides a theoretical justification for some current empirical studies, and indicates that extensions to even more mixture components should be theoretically well behaved. We also extend our results to certain mixtures on different trees, using the same algebraic techniques.

  20. Integration of TP53, DREAM, MMB-FOXM1 and RB-E2F target gene analyses identifies cell cycle gene regulatory networks.

    Science.gov (United States)

    Fischer, Martin; Grossmann, Patrick; Padi, Megha; DeCaprio, James A

    2016-07-27

    Cell cycle (CC) and TP53 regulatory networks are frequently deregulated in cancer. While numerous genome-wide studies of TP53 and CC-regulated genes have been performed, significant variation between studies has made it difficult to assess regulation of any given gene of interest. To overcome the limitation of individual studies, we developed a meta-analysis approach to identify high confidence target genes that reflect their frequency of identification in independent datasets. Gene regulatory networks were generated by comparing differential expression of TP53 and CC-regulated genes with chromatin immunoprecipitation studies for TP53, RB1, E2F, DREAM, B-MYB, FOXM1 and MuvB. RNA-seq data from p21-null cells revealed that gene downregulation by TP53 generally requires p21 (CDKN1A). Genes downregulated by TP53 were also identified as CC genes bound by the DREAM complex. The transcription factors RB, E2F1 and E2F7 bind to a subset of DREAM target genes that function in G1/S of the CC while B-MYB, FOXM1 and MuvB control G2/M gene expression. Our approach yields high confidence ranked target gene maps for TP53, DREAM, MMB-FOXM1 and RB-E2F and enables prediction and distinction of CC regulation. A web-based atlas at www.targetgenereg.org enables assessing the regulation of any human gene of interest. PMID:27280975

  1. Revisiting the concept of identifiable neurons.

    Science.gov (United States)

    Bullock, T H

    2000-05-01

    Although eutely in nematodes was known, giant neurons in several taxa and unique motor neurons to leg muscles in decapod crustaceans, the idea that many animals have many identifiable neurons with relatively consistent dynamical properties and connections was only slowly established in the late 1960s and early 1970s. This has to be one of the important quiet revolutions in neurobiology. It stimulated a vast acquisition of specific information and led to some euphoria in the degree and pace of understanding activity of nervous systems and consequent behavior in terms of neuronal connections and properties. Some implications, problems and opportunities for new discovery are developed. The distribution of identifiable neurons among taxa and parts of the nervous system is not yet satisfactorily known. Their evolution may have been a case of several independent inventions. The degree of consistency has been quantified only in a few examples and the plasticity is little known. Identified neurons imply identifiable circuits but whether this extends to discrete systems, functionally definable, seems likely to have several answers in different animals or sites. Very limited attempts have been made to extend the concept to cases of two or ten or a hundred fully equivalent neurons, on all kinds of criteria. These attempts suggest a much smaller redundancy and vaster number of types of neurons than hitherto believed. Theory as well as empirical information has not yet interpreted the range of systems from those with small sets of relatively reliable neurons to those with large numbers of parallel, partially redundant units. The now classical notion of local circuits has to be extended to take account of and find roles for the plethora of integrative variables, of evidence for neural processing independent of spikes and classical synapses, of spatial configurations of terminal arbors and dendritic geometry, of modulators and transmitters, degrees of rhythmicity (regularity

  2. Persistent Identifiers, Discoverability and Open Science (Communication)

    Science.gov (United States)

    Murphy, Fiona; Lehnert, Kerstin; Hanson, Brooks

    2016-04-01

    Early in 2016, the American Geophysical Union announced it was incorporating ORCIDs into its submission workflows. This was accompanied by a strong statement supporting the use of other persistent identifiers - such as IGSNs, and the CrossRef open registry 'funding data'. This was partly in response to funders' desire to track and manage their outputs. However the more compelling argument, and the reason why the AGU has also signed up to the Center for Open Science's Transparency and Openness Promotion (TOP) Guidelines (http://cos.io/top), is that ultimately science and scientists will be the richer for these initiatives due to increased opportunities for interoperability, reproduceability and accreditation. The AGU has appealed to the wider community to engage with these initiatives, recognising that - unlike the introduction of Digital Object Identifiers (DOIs) for articles by CrossRef - full, enriched use of persistent identifiers throughout the scientific process requires buy-in from a range of scholarly communications stakeholders. At the same time, across the general research landscape, initiatives such as Project CRediT (contributor roles taxonomy), Publons (reviewer acknowledgements) and the forthcoming CrossRef DOI Event Tracker are contributing to our understanding and accreditation of contributions and impact. More specifically for earth science and scientists, the cross-functional Coalition for Publishing Data in the Earth and Space Sciences (COPDESS) was formed in October 2014 and is working to 'provide an organizational framework for Earth and space science publishers and data facilities to jointly implement and promote common policies and procedures for the publication and citation of data across Earth Science journals'. Clearly, the judicious integration of standards, registries and persistent identifiers such as ORCIDs and International Geo Sample Numbers (IGSNs) to the research and research output processes is key to the success of this venture

  3. Body linear traits for identifying prolific goats

    Directory of Open Access Journals (Sweden)

    Avijit Haldar

    2014-12-01

    Full Text Available Aim: The present study was conducted on prolific goat breed to identify body linear type traits that might be associated with prolificacy trait in goats. Materials and Methods: Two-stage stratified random sample survey based data were collected from 1427 non-pregnant goats with the history of single, twin and triplet litter sizes (LZ between January 2008 to February 2011 for 3 years in 68 villages located in East and North East India. Data on sixteen body linear traits were analyzed using logistic regression model to do the step-wise selection for identifying the body linear traits that could determine LZ. An average value for each identified body linear trait was determined for classifying the goats into three categories: Goats having the history of single LZ, goats having the history of twin LZ and goats having the history of triplet LZ. Results: The LZ proportions for single, twin and triplet, were 29.50, 59.14 and 11.36%, respectively, with the prolificacy rate of 181.85% in Indian Black Bengal goats. A total of eight body linear traits that could determine LZ in prolific goats were identified. Heart girth (HG measurement (>60.90 cm, paunch girth (PG (>70.22 cm, wither height (WH (>49.75 cm, neck length (>21.45 cm, ear length (>12.80 cm and distance between trochanter major (DTM bones (>12.28 cm, pelvic triangle area (PTA (>572.25 cm2 and clearance at udder (CU (>23.16 cm showed an increase likelihood of multiple LZ when compared to single LZ. Further, HG measurement (>62.29 cm, WH (>50.54 cm, PG (>71.85 cm and ear length (>13.00 cm, neck length (>22.01 cm, PTA (>589.64 cm2, CU (>23.20 cm and DTM bones (>12.47 cm were associated with increased likelihood of triplet LZ, when compared with that of twin LZ. Conclusion: HG measurement was the best discriminating factor, while PG, neck length, DTM bones, CU, PTA, WH and ear length measurements were other important factors that could be used for identifying prolific goats to achieve economic

  4. Characterization of novel MSX1 mutations identified in Japanese patients with nonsyndromic tooth agenesis.

    Directory of Open Access Journals (Sweden)

    Seishi Yamaguchi

    Full Text Available Since MSX1 and PAX9 are linked to the pathogenesis of nonsyndromic tooth agenesis, we performed detailed mutational analysis of these two genes sampled from Japanese patients. We identified two novel MSX1 variants with an amino acid substitution within the homeodomain; Thr174Ile (T174I from a sporadic hypodontia case and Leu205Arg (L205R from a familial oligodontia case. Both the Thr174 and Leu205 residues in the MSX1 homeodomain are highly conserved among different species. To define possible roles of mutations at these amino acids in the pathogenesis of nonsyndromic tooth agenesis, we performed several functional analyses. It has been demonstrated that MSX1 plays a pivotal role in hard tissue development as a suppressor for mesenchymal cell differentiation. To evaluate the suppression activity of the variants in mesenchymal cells, we used the myoD-promoter, which is one of convenient reporter assay system for MSX1. Although the gene products of these MSX1 variants are stable and capable of normal nuclear localization, they do not suppress myoD-promoter activity in differentiated C2C12 cells. To clarify the molecular mechanisms underlying our results, we performed further analyses including electrophoretic mobility shift assays, and co-immunoprecipitation assays to survey the molecular interactions between the mutant MSX1 proteins and the oligonucleotide DNA with MSX1 consensus binding motif or EZH2 methyltransferase. Since EZH2 is reported to interact with MSX1 and regulate MSX1 mediated gene suppression, we hypothesized that the T174I and L205R substitutions would impair this interaction. We conclude from the results of our experiments that the DNA binding ability of MSX1 is abolished by these two amino acid substitutions. This illustrates a causative role of the T174I and L205R MSX1 homeodomain mutations in tooth agenesis, and suggests that they may influence cell proliferation and differentiation resulting in lesser tooth germ formation in

  5. Identifying predictive factors in melanoma progression.

    Science.gov (United States)

    Dabrowska, D M; Elashoff, R M; Ho, W; Morton, D L

    1998-01-01

    Identification of risk factors is a fundamental goal of melanoma studies. The current understanding of melanoma progression is based primarily on two-stage modeling. A multistate Markov chain process combined with Cox proportional hazard regression is used to model the melanoma progression. The model is applied to 3,434 patients initially diagnosed as AJCC stage I or stage II. Parameter estimates are obtained using Cox regression and supplemented by plots of survival probabilities. Age is associated with increased risk of progression from stage I, II to stage III and from stage III to stage IV. Males experienced an increased risk of stage I, II to stage III progression. Primary tumor located on extremities decreased the risk of all transitions. Clark's level of invasion >III and Breslow's depth >1 mm increased the risk of progression from stage I, II to stage III and stage IV. The following interactions among the prognostic factors were identified for the first time in this research: interaction of age and gender in progression from stage I, II to stage III; interactions of level and depth and site by gender were found in the progression from stage I, II to stage III; interaction of site and gender in progression from stage III to stage IV and stage IV to death. Also we identified primary site as a new prognostic factor for the progression from stage IV to death. The study employed a multistate model in order to identify prognostic factors relevant for disease progression. The unique feature is the modeling of interactions among the prognostic factors and their identification. PMID:9538154

  6. Identifying single copy orthologs in Metazoa.

    Directory of Open Access Journals (Sweden)

    Christopher J Creevey

    2011-12-01

    Full Text Available The identification of single copy (1-to-1 orthologs in any group of organisms is important for functional classification and phylogenetic studies. The Metazoa are no exception, but only recently has there been a wide-enough distribution of taxa with sufficiently high quality sequenced genomes to gain confidence in the wide-spread single copy status of a gene.Here, we present a phylogenetic approach for identifying overlooked single copy orthologs from multigene families and apply it to the Metazoa. Using 18 sequenced metazoan genomes of high quality we identified a robust set of 1,126 orthologous groups that have been retained in single copy since the last common ancestor of Metazoa. We found that the use of the phylogenetic procedure increased the number of single copy orthologs found by over a third more than standard taxon-count approaches. The orthologs represented a wide range of functional categories, expression profiles and levels of divergence.To demonstrate the value of our set of single copy orthologs, we used them to assess the completeness of 24 currently published metazoan genomes and 62 EST datasets. We found that the annotated genes in published genomes vary in coverage from 79% (Ciona intestinalis to 99.8% (human with an average of 92%, suggesting a value for the underlying error rate in genome annotation, and a strategy for identifying single copy orthologs in larger datasets. In contrast, the vast majority of EST datasets with no corresponding genome sequence available are largely under-sampled and probably do not accurately represent the actual genomic complement of the organisms from which they are derived.

  7. Identifying novel drug indications through automated reasoning.

    Directory of Open Access Journals (Sweden)

    Luis Tari

    Full Text Available BACKGROUND: With the large amount of pharmacological and biological knowledge available in literature, finding novel drug indications for existing drugs using in silico approaches has become increasingly feasible. Typical literature-based approaches generate new hypotheses in the form of protein-protein interactions networks by means of linking concepts based on their cooccurrences within abstracts. However, this kind of approaches tends to generate too many hypotheses, and identifying new drug indications from large networks can be a time-consuming process. METHODOLOGY: In this work, we developed a method that acquires the necessary facts from literature and knowledge bases, and identifies new drug indications through automated reasoning. This is achieved by encoding the molecular effects caused by drug-target interactions and links to various diseases and drug mechanism as domain knowledge in AnsProlog, a declarative language that is useful for automated reasoning, including reasoning with incomplete information. Unlike other literature-based approaches, our approach is more fine-grained, especially in identifying indirect relationships for drug indications. CONCLUSION/SIGNIFICANCE: To evaluate the capability of our approach in inferring novel drug indications, we applied our method to 943 drugs from DrugBank and asked if any of these drugs have potential anti-cancer activities based on information on their targets and molecular interaction types alone. A total of 507 drugs were found to have the potential to be used for cancer treatments. Among the potential anti-cancer drugs, 67 out of 81 drugs (a recall of 82.7% are indeed known cancer drugs. In addition, 144 out of 289 drugs (a recall of 49.8% are non-cancer drugs that are currently tested in clinical trials for cancer treatments. These results suggest that our method is able to infer drug indications (original or alternative based on their molecular targets and interactions alone and has

  8. Identified nerve cells and insect behavior.

    Science.gov (United States)

    Comer, C M; Robertson, R M

    2001-03-01

    Studies of insect identified neurons over the past 25 years have provided some of the very best data on sensorimotor integration; tracing information flow from sensory to motor networks. General principles have emerged that have increased the sophistication with which we now understand both sensory processing and motor control. Two overarching themes have emerged from studies of identified sensory interneurons. First, within a species, there are profound differences in neuronal organization associated with both the sex and the social experience of the individual. Second, single neurons exhibit some surprisingly rich examples of computational sophistication in terms of (a) temporal dynamics (coding superimposed upon circadian and shorter-term rhythms), and also (b) what Kenneth Roeder called "neural parsimony": that optimal information can be encoded, and complex acts of sensorimotor coordination can be mediated, by small ensembles of cells. Insect motor systems have proven to be relatively complex, and so studies of their organization typically have not yielded completely defined circuits as are known from some other invertebrates. However, several important findings have emerged. Analysis of neuronal oscillators for rhythmic behavior have delineated a profound influence of sensory feedback on interneuronal circuits: they are not only modulated by feedback, but may be substantially reconfigured. Additionally, insect motor circuits provide potent examples of neuronal restructuring during an organism's lifetime, as well as insights on how circuits have been modified across evolutionary time. Several areas where future advances seem likely to occur include: molecular genetic analyses, neuroecological syntheses, and neuroinformatics--the use of digital resources to organize databases with information on identified nerve cells and behavior. PMID:11163685

  9. Identifying learning techniques among high achievers

    Directory of Open Access Journals (Sweden)

    Shanmukananda P

    2013-04-01

    Full Text Available Background: In every college, it is noticed that in spite of being exposed to the same teaching modalities and adopting seemingly similar strategies, some students perform much better than their peers. This can be evaluated in the form of better academic performance in the internal assessments they undertake. This project is an endeavor to identify the learning techniques among high achievers which they employ to outperform others. We can also suggest the same to the medium and low achievers so that they can improve their academic performance. This study was conducted to identify different learning techniques adopted by high achievers and suggesting the same to medium and low achievers. Methods: After obtaining clearance from the institutional ethics committee, the high achievers were identified by selecting the upper third of the students in the ascending order of marks obtained in the consecutive three internal assessments in three consecutive batches. The identity of the students was not revealed. They were then administered an open ended questionnaire which addressed relevant issues. The most common and feasible techniques will be suggested to the medium and low achievers. Results: The respondents’ (n=101 replies were analyzed by calculating the percentages of responses, and assessing based on that, which were the most frequently adapted techniques by these high achievers Conclusions: High-achievers have a diligent study pattern; they not only study regularly, but also involve in group discussions and approach their teachers when in doubt. Additionally, they refer to other sources of information like the internet, demonstrating a proactive attitude towards studies. [Int J Basic Clin Pharmacol 2013; 2(2.000: 203-207

  10. Newly Identified Rydberg Emission Lines in Novae

    Science.gov (United States)

    Lynch, David K.; Rudy, R. J.; Bernstein, L. S.

    2008-09-01

    Newly Identified Rydberg Emission Lines in Novae David K. Lynch, Richard. J. Rudy (The Aerospace Corporation) & Lawrence S. Bernstein (Spectral Sciences, Inc.) Novae spectra in the near infrared frequently show a set of six emission lines that have not been positively identified (Williams, Longmore, & Geballe 1996, MNRAS, 279, 804; Lynch et al. 2001, AJ, 122, 2013; Rudy et al. 2002 ApJ, 573, 794; Lynch et al. 2004 Astron. J. 127, 1089-1097). These lines are at 0.8926, 1.1114, 1.1901, 1.5545, 2.0996 and 2.425 µm ± 0.005 µm. Krautter et al. (1984 A&A 137, 304) suggested that three of the lines were due to rydberg (hydrogenic) transitions in an unspecified atomic species that was in the 4th or 5th ionization stage (core charge = 4 & 5). We believe that Krautter et al.'s explanation is correct based on 4 additional lines that we have identified in the visible and near infrared spectrum of V723 Cassiopeiae. The observed Rydberg lines appear to originate from high angular momentum states with negligible quantum defects. The species cannot be determined with any certainty because in rydberg states, the outer electron sees a nucleus shielded by the inner electrons and together the inner atom appears to have a charge of +1, like hydrogen. As a result, the atom looks hydrogenic and species such as CV, NV, OV, MgV, SiV, etc. have their rydberg transitions at very similar wavelengths. All the lines represent permitted transitions, most likely formed by recombination. Atoms with core charges 4, 5 & 6 are rarely seen in the astrophysical environment because an extremely hot radiation field is necessary to ionize them. Thermonuclear runaways on the surface of a white dwarf can reach millions of degrees K, and thus there are enough X-ray photons available to achieve the necessary high ionization levels.

  11. Identifying biomass fuel shortages in Sri Lanka

    Energy Technology Data Exchange (ETDEWEB)

    Howes, Michael (Sussex Univ., Brighton (UK). Inst. of Development Studies)

    1989-01-01

    This paper analyses data from the Sri Lankan Forestry Master Plan and other sources, to explore the causes of biomass shortages, and to identify the areas where interventions are likely to have most impact. Five districts, concentrated in the wet lowland and hill country zones, are found to be in overall biomass fuel deficit whilst in a further five, which include dry zone locations, fuelwood consumption exceeds potential supply, Within the area of overall deficit, poorer urban groups and rural families with no home gardens - who together comprise 15% of all households nationally - are affected most severely. Another 10% of households are likely to suffer to a lesser extent. (author).

  12. Cheater identifiable visual secret sharing scheme

    Institute of Scientific and Technical Information of China (English)

    Gan Zhi; Chen Kefei

    2005-01-01

    The visual secret sharing scheme proposed by Naor and Shamir provides a way to encrypt a secret black-white image into shares. A qualified group of participants can recover the secret message without using any cryptographic computation. But the original scheme can easily be corrupted by malicious participant. We propose an extension of VSS(visual secret sharing) to identify cheaters before the secret is recovered. Without the need for any additional information and cryptographic computation, every participant can verify the validity of shares of other participants, thus the security of VSS is enhanced.

  13. Identifying Nuclear Materials Using Tagged Muons

    CERN Document Server

    Morris, C L; Borodzin, K; Durham, J M; Fabritius, J M; Guardincerri, E; Hecht, A; Milner, E C; Miyadera, H; Perry, J O; Poulson, D

    2014-01-01

    Experimental results from a new technique that uses neutrons generated by stopped cosmic-ray muons to identify nuclear materials are described. The neutrons are used to tag muon-induced fission events in actinides and laminography is used to form images of the stopping material. This technique allows the imaging of uranium objects tagged using muon tracking detectors located above or to the side of the objects. The specificity of the technique to significant quantities of nuclear material along with its insensitivity to spatial details may provide a new method for the task of warhead verification for future arms reduction treaties.

  14. Identifying and managing malnutrition in the community.

    Science.gov (United States)

    McEvilly, Aimee

    2016-01-01

    Malnutrition affects more than 3 million people in the UK, most of whom live in the community. Malnutrition is both a cause and consequence of disease and can lead to increased mortality and morbidity, delayed recovery from illness and impaired body function which can make carrying out activities of daily living difficult. Managing malnutrition in the community involves identifying malnutrition using a universally validated screening tool and implementing appropriate care plans according to the degree of malnutrition. Regional and local guidance can be used to assist healthcare professionals to prescribe appropriate oral nutritional supplements and monitor nutritional aims and goals. PMID:27396860

  15. Identifying Phase Space Boundaries with Voronoi Tessellations

    CERN Document Server

    Debnath, Dipsikha; Kilic, Can; Kim, Doojin; Matchev, Konstantin T; Yang, Yuan-Pao

    2016-01-01

    Determining the masses of new physics particles appearing in decay chains is an important and longstanding problem in high energy phenomenology. Recently it has been shown that these mass measurements can be improved by utilizing the boundary of the allowed region in the fully differentiable phase space in its full dimensionality. Here we show that the practical challenge of identifying this boundary can be solved using techniques based on the geometric properties of the cells resulting from Voronoi tessellations of the relevant data. The robust detection of such phase space boundaries in the data could also be used to corroborate a new physics discovery based on a cut-and-count analysis.

  16. Can Chameleon Field be identified with Quintessence ?

    OpenAIRE

    A. N. Ivanov; Wellenzohn, M.

    2016-01-01

    We analyse the Friedmann-Einstein equations for the Universe evolution with the expansion parameter $a$ dependent on time only in the Einstein gravity with the chameleon field, changing its mass in dependence of a density of its environment. We show that the chameleon field can be identified with quintessence (a canonical scalar field responsible for the late-time acceleration of the Universe expansion and dark energy dynamics) if and only if the radiation rho_r(a) and matter rho_m(a) (dark a...

  17. Identifying PHM market and network opportunities.

    Science.gov (United States)

    Grube, Mark E; Krishnaswamy, Anand; Poziemski, John; York, Robert W

    2015-11-01

    Two key processes for healthcare organizations seeking to assume a financially sustainable role in population health management (PHM), after laying the groundwork for the effort, are to identify potential PHM market opportunities and determine the scope of the PHM network. Key variables organizations should consider with respect to market opportunities include the patient population, the overall insurance/employer market, and available types of insurance products. Regarding the network's scope, organizations should consider both traditional strategic criteria for a viable network and at least five additional criteria: network essentiality and PHM care continuum, network adequacy, service distribution right-sizing, network growth strategy, and organizational agility.

  18. Factor analysis identifies subgroups of constipation

    Institute of Scientific and Technical Information of China (English)

    Philip G Dinning; Mike Jones; Linda Hunt; Sergio E Fuentealba; Jamshid Kalanter; Denis W King; David Z Lubowski; Nicholas J Talley; Ian J Cook

    2011-01-01

    AIM: To determine whether distinct symptom groupings exist in a constipated population and whether such grouping might correlate with quantifiable pathophysiological measures of colonic dysfunction. METHODS: One hundred and ninety-one patients presenting to a Gastroenterology clinic with constipation and 32 constipated patients responding to a newspaper advertisement completed a 53-item, wide-ranging selfreport questionnaire. One hundred of these patients had colonic transit measured scintigraphically. Factor analysis determined whether constipation-related symptoms grouped into distinct aspects of symptomatology. Cluster analysis was used to determine whether individual patients naturally group into distinct subtypes. RESULTS: Cluster analysis yielded a 4 cluster solution with the presence or absence of pain and laxative unresponsiveness providing the main descriptors. Amongst all clusters there was a considerable proportion of patients with demonstrable delayed colon transit, irritable bowel syndrome positive criteria and regular stool frequency. The majority of patients with these characteristics also reported regular laxative use. CONCLUSION: Factor analysis identified four constipation subgroups, based on severity and laxative unresponsiveness, in a constipated population. However, clear stratification into clinically identifiable groups remains imprecise.

  19. Identifying Synonymous Regulatory Elements in Vertebrate Genomes

    Energy Technology Data Exchange (ETDEWEB)

    Ovcharenko, I; Nobrega, M A

    2005-02-07

    Synonymous gene regulation, defined as driving shared temporal and/or spatial expression of groups of genes, is likely predicated on genomic elements that contain similar modules of certain transcription factor binding sites (TFBS). We have developed a method to scan vertebrate genomes for evolutionary conserved modules of TFBS in a predefined configuration, and created a tool, named SynoR that identify synonymous regulatory elements (SREs) in vertebrate genomes. SynoR performs de novo identification of SREs utilizing known patterns of TFBS in active regulatory elements (REs) as seeds for genome scans. Layers of multiple-species conservation allow the use of differential phylogenetic sequence conservation filters in the search of SREs and the results are displayed as to provide an extensive annotation of genes containing detected REs. Gene Ontology categories are utilized to further functionally classify the identified genes, and integrated GNF Expression Atlas 2 data allow the cataloging of tissue-specificities of the predicted SREs. We illustrate how this new tool can be used to establish a linkage between human diseases and noncoding genomic content. SynoR is publicly available at http://synor.dcode.org.

  20. Identifying MMORPG Bots: A Traffic Analysis Approach

    Directory of Open Access Journals (Sweden)

    Wen-Chin Chen

    2008-11-01

    Full Text Available Massively multiplayer online role playing games (MMORPGs have become extremely popular among network gamers. Despite their success, one of MMORPG's greatest challenges is the increasing use of game bots, that is, autoplaying game clients. The use of game bots is considered unsportsmanlike and is therefore forbidden. To keep games in order, game police, played by actual human players, often patrol game zones and question suspicious players. This practice, however, is labor-intensive and ineffective. To address this problem, we analyze the traffic generated by human players versus game bots and propose general solutions to identify game bots. Taking Ragnarok Online as our subject, we study the traffic generated by human players and game bots. We find that their traffic is distinguishable by 1 the regularity in the release time of client commands, 2 the trend and magnitude of traffic burstiness in multiple time scales, and 3 the sensitivity to different network conditions. Based on these findings, we propose four strategies and two ensemble schemes to identify bots. Finally, we discuss the robustness of the proposed methods against countermeasures of bot developers, and consider a number of possible ways to manage the increasingly serious bot problem.

  1. Identifying dependability requirements for space software systems

    Directory of Open Access Journals (Sweden)

    Edgar Toshiro Yano

    2010-09-01

    Full Text Available Computer systems are increasingly used in space, whether in launch vehicles, satellites, ground support and payload systems. Software applications used in these systems have become more complex, mainly due to the high number of features to be met, thus contributing to a greater probability of hazards related to software faults. Therefore, it is fundamental that the specification activity of requirements have a decisive role in the effort of obtaining systems with high quality and safety standards. In critical systems like the embedded software of the Brazilian Satellite Launcher, ambiguity, non-completeness, and lack of good requirements can cause serious accidents with economic, material and human losses. One way to assure quality with safety, reliability and other dependability attributes may be the use of safety analysis techniques during the initial phases of the project in order to identify the most adequate dependability requirements to minimize possible fault or failure occurrences during the subsequent phases. This paper presents a structured software dependability requirements analysis process that uses system software requirement specifications and traditional safety analysis techniques. The main goal of the process is to help to identify a set of essential software dependability requirements which can be added to the software requirement previously specified for the system. The final results are more complete, consistent, and reliable specifications.

  2. ABCB5 Identifies Immunoregulatory Dermal Cells

    Directory of Open Access Journals (Sweden)

    Tobias Schatton

    2015-09-01

    Full Text Available Cell-based strategies represent a new frontier in the treatment of immune-mediated disorders. However, the paucity of markers for isolation of molecularly defined immunomodulatory cell populations poses a barrier to this field. Here, we show that ATP-binding cassette member B5 (ABCB5 identifies dermal immunoregulatory cells (DIRCs capable of exerting therapeutic immunoregulatory functions through engagement of programmed cell death 1 (PD-1. Purified Abcb5+ DIRCs suppressed T cell proliferation, evaded immune rejection, homed to recipient immune tissues, and induced Tregs in vivo. In fully major-histocompatibility-complex-mismatched cardiac allotransplantation models, allogeneic DIRCs significantly prolonged allograft survival. Blockade of DIRC-expressed PD-1 reversed the inhibitory effects of DIRCs on T cell activation, inhibited DIRC-dependent Treg induction, and attenuated DIRC-induced prolongation of cardiac allograft survival, indicating that DIRC immunoregulatory function is mediated, at least in part, through PD-1. Our results identify ABCB5+ DIRCs as a distinct immunoregulatory cell population and suggest promising roles of this expandable cell subset in cellular immunotherapy.

  3. Identifying MMORPG Bots: A Traffic Analysis Approach

    Science.gov (United States)

    Chen, Kuan-Ta; Jiang, Jhih-Wei; Huang, Polly; Chu, Hao-Hua; Lei, Chin-Laung; Chen, Wen-Chin

    2008-12-01

    Massively multiplayer online role playing games (MMORPGs) have become extremely popular among network gamers. Despite their success, one of MMORPG's greatest challenges is the increasing use of game bots, that is, autoplaying game clients. The use of game bots is considered unsportsmanlike and is therefore forbidden. To keep games in order, game police, played by actual human players, often patrol game zones and question suspicious players. This practice, however, is labor-intensive and ineffective. To address this problem, we analyze the traffic generated by human players versus game bots and propose general solutions to identify game bots. Taking Ragnarok Online as our subject, we study the traffic generated by human players and game bots. We find that their traffic is distinguishable by 1) the regularity in the release time of client commands, 2) the trend and magnitude of traffic burstiness in multiple time scales, and 3) the sensitivity to different network conditions. Based on these findings, we propose four strategies and two ensemble schemes to identify bots. Finally, we discuss the robustness of the proposed methods against countermeasures of bot developers, and consider a number of possible ways to manage the increasingly serious bot problem.

  4. Identifying, meeting, and assessing customer expectations

    International Nuclear Information System (INIS)

    Maintaining proficiency in carrying out mission goals is fundamental to the success of any organization. The definitive mission of the Waste Management and Remedial Action Division (WMRAD) of Oak Ridge National Laboratory (ORNL) is open-quotes to conduct waste management activities in a compliant, publicly acceptable, technically sound, and cost-efficient mannerclose quotes. In order to effectively fulfill this mission, must meet or exceed several standards in respect to our customers. These include: (1) identifying current and future customer expectations; (2) managing our relationships with our customers; (3) ensuring our commitment to our customers; and (4) measuring our success m customer satisfaction. Our customers have a great variety of requirements and expectations. Many of these are in the form of local, state, and federal regulations and environmental standards. Others are brought to our attention through inquires made to the Department of Energy (DOE).Consumer surveys have proven to be effective tools which have been used to make improvements, enhance certain program elements, and identify beneficial areas in already existing programs. In addition, national working groups, technology transfer meetings, and manager/contractor's meeting offer excellent opportunities to assess our activities

  5. Identifying Bitcoin users by transaction behavior

    Science.gov (United States)

    Monaco, John V.

    2015-05-01

    Digital currencies, such as Bitcoin, offer convenience and security to criminals operating in the black marketplace. Some Bitcoin marketplaces, such as Silk Road, even claim anonymity. This claim contradicts the findings in this work, where long term transactional behavior is used to identify and verify account holders. Transaction timestamps and network properties observed over time contribute to this finding. The timestamp of each transaction is the result of many factors: the desire purchase an item, daily schedule and activities, as well as hardware and network latency. Dynamic network properties of the transaction, such as coin flow and the number of edge outputs and inputs, contribute further to reveal account identity. In this paper, we propose a novel methodology for identifying and verifying Bitcoin users based on the observation of Bitcoin transactions over time. The behavior we attempt to quantify roughly occurs in the social band of Newell's time scale. A subset of the Blockchain 230686 is taken, selecting users that initiated between 100 and 1000 unique transactions per month for at least 6 different months. This dataset shows evidence of being nonrandom and nonlinear, thus a dynamical systems approach is taken. Classification and authentication accuracies are obtained under various representations of the monthly Bitcoin samples: outgoing transactions, as well as both outgoing and incoming transactions are considered, along with the timing and dynamic network properties of transaction sequences. The most appropriate representations of monthly Bitcoin samples are proposed. Results show an inherent lack of anonymity by exploiting patterns in long-term transactional behavior.

  6. Process Architecture for Managing Digital Object Identifiers

    Science.gov (United States)

    Wanchoo, L.; James, N.; Stolte, E.

    2014-12-01

    In 2010, NASA's Earth Science Data and Information System (ESDIS) Project implemented a process for registering Digital Object Identifiers (DOIs) for data products distributed by Earth Observing System Data and Information System (EOSDIS). For the first 3 years, ESDIS evolved the process involving the data provider community in the development of processes for creating and assigning DOIs, and guidelines for the landing page. To accomplish this, ESDIS established two DOI User Working Groups: one for reviewing the DOI process whose recommendations were submitted to ESDIS in February 2014; and the other recently tasked to review and further develop DOI landing page guidelines for ESDIS approval by end of 2014. ESDIS has recently upgraded the DOI system from a manually-driven system to one that largely automates the DOI process. The new automated feature include: a) reviewing the DOI metadata, b) assigning of opaque DOI name if data provider chooses, and c) reserving, registering, and updating the DOIs. The flexibility of reserving the DOI allows data providers to embed and test the DOI in the data product metadata before formally registering with EZID. The DOI update process allows the changing of any DOI metadata except the DOI name unless the name has not been registered. Currently, ESDIS has processed a total of 557 DOIs of which 379 DOIs are registered with EZID and 178 are reserved with ESDIS. The DOI incorporates several metadata elements that effectively identify the data product and the source of availability. Of these elements, the Uniform Resource Locator (URL) attribute has the very important function of identifying the landing page which describes the data product. ESDIS in consultation with data providers in the Earth Science community is currently developing landing page guidelines that specify the key data product descriptive elements to be included on each data product's landing page. This poster will describe in detail the unique automated process and

  7. Identifying seasonal stars in Kaurna astronomical traditions

    Science.gov (United States)

    Hamacher, Duane W.

    2015-03-01

    Early ethnographers and missionaries recorded Aboriginal languages and oral traditions across Australia. Their general lack of astronomical training resulted in misidentifications, transcription errors and omissions in these records. In western Victoria and southeast South Australia many astronomical traditions were recorded but, cur- iously, some of the brightest stars in the sky were omitted. Scholars claimed these stars did not feature in Aboriginal traditions. This continues to be repeated in the literature, but current research shows that these stars may in fact feature in Aboriginal traditions and could be seasonal calendar markers. This paper uses established techniques to identify seasonal stars in the traditions of the Kaurna Aboriginal people of the Adelaide Plains, South Australia.

  8. Identifying financial crises in real time

    Science.gov (United States)

    da Fonseca, Eder Lucio; Ferreira, Fernando F.; Muruganandam, Paulsamy; Cerdeira, Hilda A.

    2013-03-01

    Following the thermodynamic formulation of a multifractal measure that was shown to enable the detection of large fluctuations at an early stage, here we propose a new index which permits us to distinguish events like financial crises in real time. We calculate the partition function from which we can obtain thermodynamic quantities analogous to the free energy and specific heat. The index is defined as the normalized energy variation and it can be used to study the behavior of stochastic time series, such as financial market daily data. Famous financial market crashes-Black Thursday (1929), Black Monday (1987) and the subprime crisis (2008)-are identified with clear and robust results. The method is also applied to the market fluctuations of 2011. From these results it appears as if the apparent crisis of 2011 is of a different nature to the other three. We also show that the analysis has forecasting capabilities.

  9. Identifying Community Structures in Dynamic Networks

    CERN Document Server

    Alvari, Hamidreza; Sukthankar, Gita; Lakkaraju, Kiran

    2016-01-01

    Most real-world social networks are inherently dynamic, composed of communities that are constantly changing in membership. To track these evolving communities, we need dynamic community detection techniques. This article evaluates the performance of a set of game theoretic approaches for identifying communities in dynamic networks. Our method, D-GT (Dynamic Game Theoretic community detection), models each network node as a rational agent who periodically plays a community membership game with its neighbors. During game play, nodes seek to maximize their local utility by joining or leaving the communities of network neighbors. The community structure emerges after the game reaches a Nash equilibrium. Compared to the benchmark community detection methods, D-GT more accurately predicts the number of communities and finds community assignments with a higher normalized mutual information, while retaining a good modularity.

  10. Identifying driver mutations in sequenced cancer genomes

    DEFF Research Database (Denmark)

    Raphael, Benjamin J; Dobson, Jason R; Oesper, Layla;

    2014-01-01

    High-throughput DNA sequencing is revolutionizing the study of cancer and enabling the measurement of the somatic mutations that drive cancer development. However, the resulting sequencing datasets are large and complex, obscuring the clinically important mutations in a background of errors, noise......, and random mutations. Here, we review computational approaches to identify somatic mutations in cancer genome sequences and to distinguish the driver mutations that are responsible for cancer from random, passenger mutations. First, we describe approaches to detect somatic mutations from high-throughput DNA...... sequencing data, particularly for tumor samples that comprise heterogeneous populations of cells. Next, we review computational approaches that aim to predict driver mutations according to their frequency of occurrence in a cohort of samples, or according to their predicted functional impact on protein...

  11. Bacterial spoilage profiles to identify irradiated fish

    International Nuclear Information System (INIS)

    Effects of low dose gamma-irradiation of fish product on spoilage potentials of bacteria (Aeromonas hydrophila, Salmonella typhimurium, Bacillus megaterium, and Pseudomonas marinoglutinosa) and mixed flora were examined for ability to proliferate in radurized fish and produce volatile acids (TVA) and bases (TVBN). Bacteria proliferated well in unirradiated and irradiated fish, but formation of VA and VB were lower in irradiated than unirradiated counterparts. This was found in Bombay duck, Indian mackerel, white pomfret, seer and shrimp gamma-irradiated at 0 to 5 kGy under ice. TVA and TVBN produced by the organisms or mixed flora from fish were only 30-50% those of controls. A method for identifying radiation-processed fish could evolve based on lower susceptibility of irradiated fish to bacterial spoilage

  12. Identifying important characteristics of municipal carbon footprints

    Energy Technology Data Exchange (ETDEWEB)

    Larsen, Hogne N.; Hertwich, Edgar G. [Industrial Ecology Programme and Department of Energy and Process Engineering, Norwegian University of Science and Technology (NTNU), Realfagbygget E1, NO-7491 Trondheim (Norway)

    2010-11-15

    Local climate action has been identified as a vital contributor to global mitigation of greenhouse gas (GHG) emissions. This paper focuses on the GHG emissions resulting from the provision of local public services, illustrated through the Carbon Footprint (CF) indicator. The CF of all 429 Norwegian municipalities is calculated and compared to variables of interest. Results show that the CF changes significantly depending on size and wealth. Small and/or wealthy municipalities tend to have a much higher CF per capita compared to more populated and/or less wealthy cities. While wealth and CF relate very well linearly, increased population is only beneficial up to a certain size. Results indicate that the CF per capita increases in municipalities with more than {proportional_to}50,000 inhabitants, thus indicating a possible ideal size of municipalities to achieve the optimal municipal CF. (author)

  13. Identifying States of a Financial Market

    Science.gov (United States)

    Münnix, Michael C.; Shimada, Takashi; Schäfer, Rudi; Leyvraz, Francois; Seligman, Thomas H.; Guhr, Thomas; Stanley, H. Eugene

    2012-09-01

    The understanding of complex systems has become a central issue because such systems exist in a wide range of scientific disciplines. We here focus on financial markets as an example of a complex system. In particular we analyze financial data from the S&P 500 stocks in the 19-year period 1992-2010. We propose a definition of state for a financial market and use it to identify points of drastic change in the correlation structure. These points are mapped to occurrences of financial crises. We find that a wide variety of characteristic correlation structure patterns exist in the observation time window, and that these characteristic correlation structure patterns can be classified into several typical ``market states''. Using this classification we recognize transitions between different market states. A similarity measure we develop thus affords means of understanding changes in states and of recognizing developments not previously seen.

  14. Identifying Relevant Studies in Software Engineering

    DEFF Research Database (Denmark)

    Zhang, He; Ali Babar, Muhammad; Tell, Paolo

    2011-01-01

    Context: Systematic literature review (SLR) has become an important research methodology in software engineering since the introduction of evidence-based software engineering (EBSE) in 2004. One critical step in applying this methodology is to design and execute appropriate and effective search...... strategy. This is a time-consuming and error-prone step, which needs to be carefully planned and implemented. There is an apparent need for a systematic approach to designing, executing, and evaluating a suitable search strategy for optimally retrieving the target literature from digital libraries....... Objective: The main objective of the research reported in this paper is to improve the search step of undertaking SLRs in software engineering (SE) by devising and evaluating systematic and practical approaches to identifying relevant studies in SE. Method: We have systematically selected and analytically...

  15. Identifying the seasonal origins of human campylobacteriosis.

    Science.gov (United States)

    Strachan, N J C; Rotariu, O; Smith-Palmer, A; Cowden, J; Sheppard, S K; O'Brien, S J; Maiden, M C J; Macrae, M; Bessell, P R; Matthews, L; Reid, S W J; Innocent, G T; Ogden, I D; Forbes, K J

    2013-06-01

    Human campylobacteriosis exhibits a distinctive seasonality in temperate regions. This paper aims to identify the origins of this seasonality. Clinical isolates [typed by multi-locus sequence typing (MLST)] and epidemiological data were collected from Scotland. Young rural children were found to have an increased burden of disease in the late spring due to strains of non-chicken origin (e.g. ruminant and wild bird strains from environmental sources). In contrast the adult population had an extended summer peak associated with chicken strains. Travel abroad and UK mainland travel were associated with up to 17% and 18% of cases, respectively. International strains were associated with chicken, had a higher diversity than indigenous strains and a different spectrum of MLST types representative of these countries. Integrating empirical epidemiology and molecular subtyping can successfully elucidate the seasonal components of human campylobacteriosis. The findings will enable public health officials to focus strategies to reduce the disease burden.

  16. Identifying states of a financial market.

    Science.gov (United States)

    Münnix, Michael C; Shimada, Takashi; Schäfer, Rudi; Leyvraz, Francois; Seligman, Thomas H; Guhr, Thomas; Stanley, H Eugene

    2012-01-01

    The understanding of complex systems has become a central issue because such systems exist in a wide range of scientific disciplines. We here focus on financial markets as an example of a complex system. In particular we analyze financial data from the S&P 500 stocks in the 19-year period 1992-2010. We propose a definition of state for a financial market and use it to identify points of drastic change in the correlation structure. These points are mapped to occurrences of financial crises. We find that a wide variety of characteristic correlation structure patterns exist in the observation time window, and that these characteristic correlation structure patterns can be classified into several typical "market states". Using this classification we recognize transitions between different market states. A similarity measure we develop thus affords means of understanding changes in states and of recognizing developments not previously seen.

  17. Can Chameleon Field be identified with Quintessence ?

    CERN Document Server

    Ivanov, A N

    2016-01-01

    We analyse the Friedmann-Einstein equations for the Universe evolution with the expansion parameter $a$ dependent on time only in the Einstein gravity with the chameleon field, changing its mass in dependence of a density of its environment. We show that the chameleon field can be identified with quintessence (a canonical scalar field responsible for the late-time acceleration of the Universe expansion and dark energy dynamics) if and only if the radiation rho_r(a) and matter rho_m(a) (dark and baryon matter) densities in the Universe evolution differ from their standard dependence on the expansion parameter a, i.e. rho_r(a) ~ a^{-4} and rho_m ~ a^{-3}, respectively, and these deviations are caused by the conformal factor, relating the Einstein and Jordan frames and defining the interaction of the chameleon field with its environment.

  18. Identifying the structural discontinuities of human interactions

    CERN Document Server

    Grauwin, Sebastian; Sobolevsky, Stanislav; Hövel, Philipp; Simini, Filippo; Vanhoof, Maarten; Smoreda, Zbigniew; Barabasi, Albert-Laszlo; Ratti, Carlo

    2015-01-01

    The idea of a hierarchical spatial organization of society lies at the core of seminal theories in human geography that have strongly influenced our understanding of social organization. In the same line, the recent availability of large-scale human mobility and communication data has offered novel quantitative insights hinting at a strong geographical confinement of human interactions within neighboring regions, extending to local levels within countries. However, models of human interaction largely ignore this effect. Here, we analyze several country-wide networks of telephone calls and uncover a systematic decrease of communication induced by borders which we identify as the missing variable in state-of-the-art models. Using this empirical evidence, we propose an alternative modeling framework that naturally stylize the damping effect of borders. We show that this new notion substantially improves the predictive power of widely used interaction models, thus increasing our ability to predict social activiti...

  19. Identifying seasonal stars in Kaurna astronomical traditions

    CERN Document Server

    Hamacher, Duane W

    2015-01-01

    Early ethnographers and missionaries recorded Aboriginal languages and oral traditions across Australia. Their general lack of astronomical training resulted in misidentifications, transcription errors, and omissions in these records. Additionally, many of these early records are fragmented. In western Victoria and southeast South Australia, many astronomical traditions were recorded, but curiously, some of the brightest stars in the sky were omitted. Scholars claimed these stars did not feature in Aboriginal traditions. This under-representation continues to be repeated in the literature, but current research shows that some of these stars may in fact feature in Aboriginal traditions and could be seasonal calendar markers. This paper uses established techniques in cultural astronomy to identify seasonal stars in the traditions of the Kaurna Aboriginal people of the Adelaide Plains, South Australia.

  20. Identifying crucial parameter correlations maintaining bursting activity.

    Directory of Open Access Journals (Sweden)

    Anca Doloc-Mihu

    2014-06-01

    Full Text Available Recent experimental and computational studies suggest that linearly correlated sets of parameters (intrinsic and synaptic properties of neurons allow central pattern-generating networks to produce and maintain their rhythmic activity regardless of changing internal and external conditions. To determine the role of correlated conductances in the robust maintenance of functional bursting activity, we used our existing database of half-center oscillator (HCO model instances of the leech heartbeat CPG. From the database, we identified functional activity groups of burster (isolated neuron and half-center oscillator model instances and realistic subgroups of each that showed burst characteristics (principally period and spike frequency similar to the animal. To find linear correlations among the conductance parameters maintaining functional leech bursting activity, we applied Principal Component Analysis (PCA to each of these four groups. PCA identified a set of three maximal conductances (leak current, [Formula: see text]Leak; a persistent K current, [Formula: see text]K2; and of a persistent Na+ current, [Formula: see text]P that correlate linearly for the two groups of burster instances but not for the HCO groups. Visualizations of HCO instances in a reduced space suggested that there might be non-linear relationships between these parameters for these instances. Experimental studies have shown that period is a key attribute influenced by modulatory inputs and temperature variations in heart interneurons. Thus, we explored the sensitivity of period to changes in maximal conductances of [Formula: see text]Leak, [Formula: see text]K2, and [Formula: see text]P, and we found that for our realistic bursters the effect of these parameters on period could not be assessed because when varied individually bursting activity was not maintained.

  1. Identifying sites for elk restoration in Arkansas

    Science.gov (United States)

    Telesco, R.L.; Van Manen, F.T.; Clark, J.D.; Cartwright, Michael E.

    2007-01-01

    We used spatial data to identify potential areas for elk (Cervus elaphus) restoration in Arkansas. To assess habitat, we used locations of 239 elk groups collected from helicopter surveys in the Buffalo National River area of northwestern Arkansas, USA, from 1992 to 2002. We calculated the Mahalanobis distance (D2) statistic based on the relationship between those elk-group locations and a suite of 9 landscape variables to evaluate winter habitat in Arkansas. We tested model performance in the Buffalo National River area by comparing the D2 values of pixels representing areas with and without elk pellets along 19 fixed-width transects surveyed in March 2002. Pixels with elk scat had lower D2 values than pixels in which we found no pellets (logistic regression: Wald χ2 = 24.37, P cover, gently sloping ridge tops and valleys, low human population density, and low road densities. To assess the potential for elk–human conflicts in Arkansas, we used the analytical hierarchy process to rank the importance of 8 criteria based on expert opinion from biologists involved in elk management. The biologists ranked availability of forage on public lands as having the strongest influence on the potential for elk–human conflict (33%), followed by human population growth rate (22%) and the amount of private land in row crops (18%). We then applied those rankings in a weighted linear summation to map the relative potential for elk–human conflict. Finally, we used white-tailed deer (Odocoileus virginianus) densities to identify areas where success of elk restoration may be hampered due to meningeal worm (Parelaphostrongylus tenuis) transmission. By combining results of the 3 spatial data layers (i.e., habitat model, elk–human conflict model, deer density), our model indicated that restoration sites located in west-central and north-central Arkansas were most favorable for reintroduction.

  2. Vulnerability of critical infrastructures : identifying critical nodes.

    Energy Technology Data Exchange (ETDEWEB)

    Cox, Roger Gary; Robinson, David Gerald

    2004-06-01

    The objective of this research was the development of tools and techniques for the identification of critical nodes within critical infrastructures. These are nodes that, if disrupted through natural events or terrorist action, would cause the most widespread, immediate damage. This research focuses on one particular element of the national infrastructure: the bulk power system. Through the identification of critical elements and the quantification of the consequences of their failure, site-specific vulnerability analyses can be focused at those locations where additional security measures could be effectively implemented. In particular, with appropriate sizing and placement within the grid, distributed generation in the form of regional power parks may reduce or even prevent the impact of widespread network power outages. Even without additional security measures, increased awareness of sensitive power grid locations can provide a basis for more effective national, state and local emergency planning. A number of methods for identifying critical nodes were investigated: small-world (or network theory), polyhedral dynamics, and an artificial intelligence-based search method - particle swarm optimization. PSO was found to be the only viable approach and was applied to a variety of industry accepted test networks to validate the ability of the approach to identify sets of critical nodes. The approach was coded in a software package called Buzzard and integrated with a traditional power flow code. A number of industry accepted test networks were employed to validate the approach. The techniques (and software) are not unique to power grid network, but could be applied to a variety of complex, interacting infrastructures.

  3. Identifying environmental correlates of intraspecific genetic variation.

    Science.gov (United States)

    Harrisson, K A; Yen, J D L; Pavlova, A; Rourke, M L; Gilligan, D; Ingram, B A; Lyon, J; Tonkin, Z; Sunnucks, P

    2016-09-01

    Genetic variation is critical to the persistence of populations and their capacity to adapt to environmental change. The distribution of genetic variation across a species' range can reveal critical information that is not necessarily represented in species occurrence or abundance patterns. We identified environmental factors associated with the amount of intraspecific, individual-based genetic variation across the range of a widespread freshwater fish species, the Murray cod Maccullochella peelii. We used two different approaches to statistically quantify the relative importance of predictor variables, allowing for nonlinear relationships: a random forest model and a Bayesian approach. The latter also accounted for population history. Both approaches identified associations between homozygosity by locus and both disturbance to the natural flow regime and mean annual flow. Homozygosity by locus was negatively associated with disturbance to the natural flow regime, suggesting that river reaches with more disturbed flow regimes may support larger, more genetically diverse populations. Our findings are consistent with the hypothesis that artificially induced perennial flows in regulated channels may provide greater and more consistent habitat and reduce the frequency of population bottlenecks that can occur frequently under the highly variable and unpredictable natural flow regime of the system. Although extensive river regulation across eastern Australia has not had an overall positive effect on Murray cod numbers over the past century, regulation may not represent the primary threat to Murray cod survival. Instead, pressures other than flow regulation may be more critical to the persistence of Murray cod (for example, reduced frequency of large floods, overfishing and chemical pollution). PMID:27273322

  4. Using BAC transgenesis in zebrafish to identify regulatory sequences of the amyloid precursor protein gene in humans

    Directory of Open Access Journals (Sweden)

    Shakes Leighcraft A

    2012-09-01

    Full Text Available Abstract Background Non-coding DNA in and around the human Amyloid Precursor Protein (APP gene that is central to Alzheimer’s disease (AD shares little sequence similarity with that of appb in zebrafish. Identifying DNA domains regulating expression of the gene in such situations becomes a challenge. Taking advantage of the zebrafish system that allows rapid functional analyses of gene regulatory sequences, we previously showed that two discontinuous DNA domains in zebrafish appb are important for expression of the gene in neurons: an enhancer in intron 1 and sequences 28–31 kb upstream of the gene. Here we identify the putative transcription factor binding sites responsible for this distal cis-acting regulation, and use that information to identify a regulatory region of the human APP gene. Results Functional analyses of intron 1 enhancer mutations in enhancer-trap BACs expressed as transgenes in zebrafish identified putative binding sites of two known transcription factor proteins, E4BP4/ NFIL3 and Forkhead, to be required for expression of appb. A cluster of three E4BP4 sites at −31 kb is also shown to be essential for neuron-specific expression, suggesting that the dependence of expression on upstream sequences is mediated by these E4BP4 sites. E4BP4/ NFIL3 and XFD1 sites in the intron enhancer and E4BP4/ NFIL3 sites at −31 kb specifically and efficiently bind the corresponding zebrafish proteins in vitro. These sites are statistically over-represented in both the zebrafish appb and the human APP genes, although their locations are different. Remarkably, a cluster of four E4BP4 sites in intron 4 of human APP exists in actively transcribing chromatin in a human neuroblastoma cell-line, SHSY5Y, expressing APP as shown using chromatin immunoprecipitation (ChIP experiments. Thus although the two genes share little sequence conservation, they appear to share the same regulatory logic and are regulated by a similar set of transcription

  5. Can we identify source lithology of basalt?

    Science.gov (United States)

    Yang, Zong-Feng; Zhou, Jun-Hong

    2013-01-01

    The nature of source rocks of basaltic magmas plays a fundamental role in understanding the composition, structure and evolution of the solid earth. However, identification of source lithology of basalts remains uncertainty. Using a parameterization of multi-decadal melting experiments on a variety of peridotite and pyroxenite, we show here that a parameter called FC3MS value (FeO/CaO-3*MgO/SiO2, all in wt%) can identify most pyroxenite-derived basalts. The continental oceanic island basalt-like volcanic rocks (MgO>7.5%) (C-OIB) in eastern China and Mongolia are too high in the FC3MS value to be derived from peridotite source. The majority of the C-OIB in phase diagrams are equilibrium with garnet and clinopyroxene, indicating that garnet pyroxenite is the dominant source lithology. Our results demonstrate that many reputed evolved low magnesian C-OIBs in fact represent primary pyroxenite melts, suggesting that many previous geological and petrological interpretations of basalts based on the single peridotite model need to be reconsidered.

  6. Asteroid secular dynamics: Ceres' fingerprint identified

    CERN Document Server

    Novaković, Bojan; Tsirvoulis, Georgios; Knezević, Zoran

    2015-01-01

    Here we report on the significant role of a so far overlooked dynamical aspect, namely a secular resonance between the dwarf planet Ceres and other asteroids. We demonstrate that this type of secular resonance can be the dominant dynamical factor in certain regions of the main asteroid belt. Specifically, we performed a dynamical analysis of the asteroids belonging to the (1726) Hoffmeister family. To identify which dynamical mechanisms are actually at work in this part of the main asteroid belt, i.e. to isolate the main perturber(s), we study the evolution of this family in time. The study is accomplished using numerical integrations of test particles performed within different dynamical models. The obtained results reveal that the post-impact evolution of the Hoffmeister asteroid family is a direct consequence of the nodal secular resonance with Ceres. This leads us to the conclusion that similar effects must exist in other parts of the asteroid belt. In this respect, the obtained results shed light on an i...

  7. A New Observable for Identifying Dijet Resonances

    CERN Document Server

    Izaguirre, Eder; Yavin, Itay

    2014-01-01

    The development of techniques for identifying hadronic signals from the overwhelming multi-jet backgrounds is an important part of the Large Hadron Collider (LHC) program. Of prime importance are resonances decaying into a pair of partons, such as the Higgs and $\\rm W$/$\\rm Z$ bosons, as well as hypothetical new particles. We present a simple observable to help discriminate a dijet resonance from background that is effective even when the decaying resonance is not strongly boosted. We find consistent performance of the observable over a variety of processes and degree of boosts, and show that it leads to a reduction of the background by a factor of $3-5$ relative to signal at the price of $10-20\\%$ signal efficiency. This approach represents a significant increase in sensitivity for Standard Model (SM) measurements and searches for new physics that are dominated by systematic uncertainties, which is true of many analyses involving jets - particularly in the high-luminosity running of the LHC.

  8. Identifying Middlewares for Mashup Personal Learning Environments

    Directory of Open Access Journals (Sweden)

    Jinan Fiaidhi

    2009-08-01

    Full Text Available The common understanding of e-learning has shifted over the last decade from the traditional learning objects portals to learning paradigms that enforces constructivism, discovery learning and social collaboration. Such type of learning takes place outside the formal academic settings (e.g., seminars or lectures where a learning environment is created by using some kind of web application mashup tools. The use of these mashup tools moves the learning environment further away from being a monolithic platform towards providing an open set of learning tools, an unrestricted number of actors, and an open corpus of artifacts, either pre-existing or created by the learning process – freely combinable and utilizable by learners within their learning activities. However, collaboration, mashup and contextualization can only be supported through services, which can be created and modified dynamically based on middlewares to suit the current needs and situations of learners. This article identifies middlewares suitable for creating effective personal learning environment based on Web 2.0 mashup tools. This article also proposed a general framework for constructing such personal learning environments based on Ambient Learning realized by learning agents and the use of Enterprise Mashup servers.

  9. Ebola Virus Infection Modelling and Identifiability Problems

    Directory of Open Access Journals (Sweden)

    Van-Kinh eNguyen

    2015-04-01

    Full Text Available The recent outbreaks of Ebola virus (EBOV infections have underlined the impact of the virus as a major threat for human health. Due to the high biosafety classification of EBOV (level 4, basic research is very limited. Therefore, the development of new avenues of thinking to advance quantitative comprehension of the virus and its interaction with the host cells is urgently neededto tackle this lethal disease. Mathematical modelling of the EBOV dynamics can be instrumental to interpret Ebola infection kinetics on quantitative grounds. To the best of our knowledge, a mathematical modelling approach to unravel the interaction between EBOV and the host cells isstill missing. In this paper, a mathematical model based on differential equations is used to represent the basic interactions between EBOV and wild-type Vero cells in vitro. Parameter sets that represent infectivity of pathogens are estimated for EBOV infection and compared with influenza virus infection kinetics. The average infecting time of wild-type Vero cells in EBOV is slower than in influenza infection. Simulation results suggest that the slow infecting time of EBOV could be compensated by its efficient replication. This study reveals several identifiability problems and what kind of experiments are necessary to advance the quantification of EBOV infection. A first mathematical approach of EBOV dynamics and the estimation of standard parametersin viral infections kinetics is the key contribution of this work, paving the way for future modelling work on EBOV infection.

  10. Analytical methods to identify irradiated food

    International Nuclear Information System (INIS)

    During the last years, three promising techniques for the identification of irradiated food were developed: - Studies of luminescence, mainly thermoluminescence measurements, of food containing mineral impurities like spices, dried vegetables: and fresh fuit and vegetables. This technique can probably be applied also to food with crystalline components like shells or bones. - Gaschromatographic/mass-spectrometric investigation of radiation-induced lipid changes. - Electron-spin-resonance measurements of dried products or of products containing dry components like bones, fish bones, shells or seeds. The thermoluminescence technique has been routinely applied for more than one year by several German Food Inspection Laboratories. The results suggest that there are scarcely any irradiated spices and dried vegetables in the German market. Gaschromatography/mass spectrometry of lipid components and electron-spin-resonance spectroscopy will be established in routine food inspections in Germany in the next two years. Further possibilities to identify irradiated food are the analysis of specific changes in amino acids, DNA and carbohydrates. Radiation-induced viscosity changes, and changes in electric properties (impedance) may be helpful in identifiying at least some irradiated products. Also microbiological and biological techniques as e.g. microbial flora shift or embryo development tests in citrus fruit have been considered. All activities concerning the development of identification techniques are now coordinated by the European Communities and by IAEA. (orig.)

  11. Indexing molecules with chemical graph identifiers.

    Science.gov (United States)

    Gregori-Puigjané, Elisabet; Garriga-Sust, Rut; Mestres, Jordi

    2011-09-01

    Fast and robust algorithms for indexing molecules have been historically considered strategic tools for the management and storage of large chemical libraries. This work introduces a modified and further extended version of the molecular equivalence number naming adaptation of the Morgan algorithm (J Chem Inf Comput Sci 2001, 41, 181-185) for the generation of a chemical graph identifier (CGI). This new version corrects for the collisions recognized in the original adaptation and includes the ability to deal with graph canonicalization, ensembles (salts), and isomerism (tautomerism, regioisomerism, optical isomerism, and geometrical isomerism) in a flexible manner. Validation of the current CGI implementation was performed on the open NCI database and the drug-like subset of the ZINC database containing 260,071 and 5,348,089 structures, respectively. The results were compared with those obtained with some of the most widely used indexing codes, such as the CACTVS hash code and the new InChIKey. The analyses emphasize the fact that compound management activities, like duplicate analysis of chemical libraries, are sensitive to the exact definition of compound uniqueness and thus still depend, to a minor extent, on the type and flexibility of the molecular index being used.

  12. Identifying electrons and positrons with AMS-02

    Energy Technology Data Exchange (ETDEWEB)

    Zimmermann, Nikolas [RWTH Aachen University (Germany)

    2015-07-01

    The AMS-02 experiment is a multi-purpose detector for cosmic ray particles mounted on the International Space Station. It recorded over 40 billion events since its installation in 2011. The bulk of these events are protons, which are most abundant in cosmic rays. Electrons are 100 times and positrons 1000 times less abundant. Measuring the positrons as function of energy is especially interesting, as an excess over the expected astrophysical background may hint at an additional source of positrons in the galaxy or a new phenomena responsible for the excess, e.g. dark-matter annihilation. In order to measure positrons accurately with a small uncertainty, a large proton rejection of 10{sup 6} is needed. AMS-02 offers a transition radiation detector to separate positrons from protons and an electromagnetic calorimeter allowing a precise measurement of the kinetic energy of an incoming lepton. This talk covers the general strategy of identifying electrons/positrons with AMS-02 and presents the so-obtained electron/positron fluxes that were recently published.

  13. Recognizing and identifying people: A neuropsychological review.

    Science.gov (United States)

    Barton, Jason J S; Corrow, Sherryse L

    2016-02-01

    Recognizing people is a classic example of a cognitive function that involves multiple processing stages and parallel routes of information. Neuropsychological data have provided important evidence for models of this process, particularly from case reports; however, the quality and extent of the data varies widely between studies. In this review we first discuss the requirements and logical basis of the types of neuropsychological evidence to support conclusions about the modules in this process. We then survey the adequacy of the current body of reports to address two key issues. First is the question of which cognitive operation generates a sense of familiarity: the current debate revolves around whether familiarity arises in modality-specific recognition units or later amodal processes. Key evidence on this point comes from the search for dissociations between familiarity for faces, voices and names. The second question is whether lesions can differentially affect the abilities to link diverse sources of person information (e.g., face, voice, name, biographic data). Dissociations of these linkages may favor a 'distributed-only' model of the organization of semantic knowledge, whereas a 'person-hub' model would predict uniform impairments of all linkages. While we conclude that there is reasonable evidence for dissociations in name, voice and face familiarity in regards to the first question, the evidence for or against dissociated linkages between information stores in regards to the second question is tenuous at best. We identify deficiencies in the current literature that should motivate and inform the design of future studies. PMID:26773237

  14. Identifying and Evaluating of Oil Reservoir

    Institute of Scientific and Technical Information of China (English)

    Yang Haixia

    2002-01-01

    The identification and evaluation of oil reservoir with logging data are one of most important ways in geologic logging services. For the last decades, with the further development of the oil & gas exploration, great advances have been achieved in techniques on the acquisition, processing and interpretative evaluation of logging data. How to identify fluid characteristics and evaluate the productivity in light oil reservoir (the crude density being between 0.74g/cm3 and 0.82g/cm3)has become one of the difficulties.With the establishment of the regional interpretation criterion of the study blocks, the optimized logging parameters that reflect the reservoir characteristics have been used to establish the chart for the interpretation of oil-water reservoir combining with well logging parameters. Then, to begin with geologic reserves of crude in single well, we establish evaluation criterion for productivity in oil reservoir with determining lower limit value of the reservoir and applying the relationship between chart parameters. The techniques are verified in production and get better effect.On the basis of the reservoir characteristics analysis of both basin A and B, We established the evaluation method of static productivity on light oil reservoir with getting quantitative evaluation parameters after quantitatively evaluating the date of core, pyrolysis chromatogram and gas chromatogram. It provides new technique 7 for new well interpretation and old well review, as well as evidence for project.design of well testing.

  15. Identifying electrons and positrons with AMS-02

    International Nuclear Information System (INIS)

    The AMS-02 experiment is a multi-purpose detector for cosmic ray particles mounted on the International Space Station. It recorded over 40 billion events since its installation in 2011. The bulk of these events are protons, which are most abundant in cosmic rays. Electrons are 100 times and positrons 1000 times less abundant. Measuring the positrons as function of energy is especially interesting, as an excess over the expected astrophysical background may hint at an additional source of positrons in the galaxy or a new phenomena responsible for the excess, e.g. dark-matter annihilation. In order to measure positrons accurately with a small uncertainty, a large proton rejection of 106 is needed. AMS-02 offers a transition radiation detector to separate positrons from protons and an electromagnetic calorimeter allowing a precise measurement of the kinetic energy of an incoming lepton. This talk covers the general strategy of identifying electrons/positrons with AMS-02 and presents the so-obtained electron/positron fluxes that were recently published.

  16. From Slovene into English: Identifying Definiteness

    Directory of Open Access Journals (Sweden)

    Frančiška Lipovšek

    2008-06-01

    Full Text Available The paper addresses some typical instances of the translator’s failure to recognize definite reference in Slovene, which, in turn, results in an inappropriate determiner selection in English. It is argued that errors of this kind are ascribable not solely to the fact that the Slovene determiner system lacks an overt non-selective determiner parallel to the definite article, but to the relatively scarce use of overt determiners in general. Since definiteness is typically signalled by an anaphoric relation, some factors are explored that may help identify textual co-reference despite the absence of explicit anaphoric markers. Besides the translator’s inability to recognize the given phrase as anaphoric, two other major causes of inappropriate determiner selection are discussed: the misconception that the absence of an anaphoric relation entails indefiniteness and the translator’s misinterpreting an anaphoric expression as an ascriptive, non-referential entity. The second part of the paper focuses on the difference in use between the selective demonstrative pronoun and the non-selective definite article.

  17. The Protein Identifier Cross-Referencing (PICR service: reconciling protein identifiers across multiple source databases

    Directory of Open Access Journals (Sweden)

    Leinonen Rasko

    2007-10-01

    Full Text Available Abstract Background Each major protein database uses its own conventions when assigning protein identifiers. Resolving the various, potentially unstable, identifiers that refer to identical proteins is a major challenge. This is a common problem when attempting to unify datasets that have been annotated with proteins from multiple data sources or querying data providers with one flavour of protein identifiers when the source database uses another. Partial solutions for protein identifier mapping exist but they are limited to specific species or techniques and to a very small number of databases. As a result, we have not found a solution that is generic enough and broad enough in mapping scope to suit our needs. Results We have created the Protein Identifier Cross-Reference (PICR service, a web application that provides interactive and programmatic (SOAP and REST access to a mapping algorithm that uses the UniProt Archive (UniParc as a data warehouse to offer protein cross-references based on 100% sequence identity to proteins from over 70 distinct source databases loaded into UniParc. Mappings can be limited by source database, taxonomic ID and activity status in the source database. Users can copy/paste or upload files containing protein identifiers or sequences in FASTA format to obtain mappings using the interactive interface. Search results can be viewed in simple or detailed HTML tables or downloaded as comma-separated values (CSV or Microsoft Excel (XLS files suitable for use in a local database or a spreadsheet. Alternatively, a SOAP interface is available to integrate PICR functionality in other applications, as is a lightweight REST interface. Conclusion We offer a publicly available service that can interactively map protein identifiers and protein sequences to the majority of commonly used protein databases. Programmatic access is available through a standards-compliant SOAP interface or a lightweight REST interface. The PICR

  18. Identifying Hendra virus diversity in pteropid bats.

    Directory of Open Access Journals (Sweden)

    Ina Smith

    Full Text Available Hendra virus (HeV causes a zoonotic disease with high mortality that is transmitted to humans from bats of the genus Pteropus (flying foxes via an intermediary equine host. Factors promoting spillover from bats to horses are uncertain at this time, but plausibly encompass host and/or agent and/or environmental factors. There is a lack of HeV sequence information derived from the natural bat host, as previously sequences have only been obtained from horses or humans following spillover events. In order to obtain an insight into possible variants of HeV circulating in flying foxes, collection of urine was undertaken in multiple flying fox roosts in Queensland, Australia. HeV was found to be geographically widespread in flying foxes with a number of HeV variants circulating at the one time at multiple locations, while at times the same variant was found circulating at disparate locations. Sequence diversity within variants allowed differentiation on the basis of nucleotide changes, and hypervariable regions in the genome were identified that could be used to differentiate circulating variants. Further, during the study, HeV was isolated from the urine of flying foxes on four occasions from three different locations. The data indicates that spillover events do not correlate with particular HeV isolates, suggesting that host and/or environmental factors are the primary determinants of bat-horse spillover. Thus future spillover events are likely to occur, and there is an on-going need for effective risk management strategies for both human and animal health.

  19. An approach to identify urban groundwater recharge

    Directory of Open Access Journals (Sweden)

    E. Vázquez-Suñé

    2010-10-01

    Full Text Available Evaluating the proportion in which waters from different origins are mixed in a given water sample is relevant for many hydrogeological problems, such as quantifying total recharge, assessing groundwater pollution risks, or managing water resources. Our work is motivated by urban hydrogeology, where waters with different chemical signature can be identified (losses from water supply and sewage networks, infiltration from surface runoff and other water bodies, lateral aquifers inflows, .... The relative contribution of different sources to total recharge can be quantified by means of solute mass balances, but application is hindered by the large number of potential origins. Hence, the need to incorporate data from a large number of conservative species, the uncertainty in sources concentrations and measurement errors. We present a methodology to compute mixing ratios and end-members composition, which consists of (i Identification of potential recharge sources, (ii Selection of tracers, (iii Characterization of the hydrochemical composition of potential recharge sources and mixed water samples, and (iv Computation of mixing ratios and reevaluation of end-members. The analysis performed in a data set from samples of the Barcelona city aquifers suggests that the main contributors to total recharge are the water supply network losses (22%, the sewage network losses (30%, rainfall, concentrated in the non-urbanized areas (17%, from runoff infiltration (20%, and the Besòs River (11%. Regarding species, halogens (chloride, fluoride and bromide, sulfate, total nitrogen, and stable isotopes (18O, 2H, and 34S behaved quite conservatively. Boron, residual alkalinity, EDTA and Zn did not. Yet, including these species in the computations did not affect significantly the proportion estimations.

  20. An approach to identify urban groundwater recharge

    Directory of Open Access Journals (Sweden)

    E. Vázquez-Suñé

    2010-04-01

    Full Text Available Evaluating the proportion in which waters from different origins are mixed in a given water sample is relevant for many hydrogeological problems, such as quantifying total recharge, assessing groundwater pollution risks, or managing water resources. Our work is motivated by urban hydrogeology, where waters with different chemical signature can be identified (losses from water supply and sewage networks, infiltration from surface runoff and other water bodies, lateral aquifers inflows, .... The relative contribution of different sources to total recharge can be quantified by means of solute mass balances, but application is hindered by the large number of potential origins. Hence, the need to incorporate data from a large number of conservative species, the uncertainty in sources concentrations and measurement errors. We present a methodology to compute mixing ratios and end-members composition, which consists of (i Identification of potential recharge sources, (ii Selection of tracers, (iii Characterization of the hydrochemical composition of potential recharge sources and mixed water samples, and (iv Computation of mixing ratios and reevaluation of end-members. The analysis performed in a data set from samples of the Barcelona city aquifers suggests that the main contributors to total recharge are the water supply network losses (22%, the sewage network losses (30%, rainfall, concentrated in the non-urbanized areas (17%, from runoff infiltration (20%, and the Besòs River (11%. Regarding species, halogens (chloride, fluoride and bromide, sulfate, total nitrogen, and stable isotopes (18O2H, and 34S behaved quite conservatively. Boron, residual alkalinity, EDTA and Zn did not. Yet, including these species in the computations did not affect significantly the proportion estimations.

  1. Identifying enabling management practices for employee engagement

    Directory of Open Access Journals (Sweden)

    Marius Joubert

    2011-12-01

    Full Text Available Orientation: A currently emerging viewpoint is that today's management practices no longer add value to organisations. The focus of this article is to conduct a systematic review of the scholarly literature on management practices that could be related to employee engagement. Research purpose: This study searched for evidence in support of the notion of a management value chain, and enabling management practices within each value chain component that could relate to employee engagement. Motivation for the study: An alternative management value chain model could contribute towards a better understanding of which management practices may potentially impact employee engagement. Research design, approach, and method: This is a non-empirical (theoretical study, based on a systematic, in-depth literature review to identify the key management components and enabling practices within this proposed management value chain. Scholarly research databases were sourced for relevant peer reviewed research conducted since 1990, not excluding important contributions prior to 1990. The literature was systematically searched, selected, studied, and contextualized within this study. Main findings: Support was found for the notion of a management value chain, for enabling management practices within each proposed management value chain component, and it was also established these management practices indeed have an impact on employee engagement. Practical/managerial/implications: The possibility that management work can be presented as a generic management value chain allows managers to approach engaging management practices more systematically. Contribution/value-add: This study highlights the importance of some management practices that have never been seen as part of management work.

  2. Identifying Fishes through DNA Barcodes and Microarrays

    Science.gov (United States)

    Kochzius, Marc; Seidel, Christian; Antoniou, Aglaia; Botla, Sandeep Kumar; Campo, Daniel; Cariani, Alessia; Vazquez, Eva Garcia; Hauschild, Janet; Hervet, Caroline; Hjörleifsdottir, Sigridur; Hreggvidsson, Gudmundur; Kappel, Kristina; Landi, Monica; Magoulas, Antonios; Marteinsson, Viggo; Nölte, Manfred; Planes, Serge; Tinti, Fausto; Turan, Cemal; Venugopal, Moleyur N.; Weber, Hannes; Blohm, Dietmar

    2010-01-01

    Background International fish trade reached an import value of 62.8 billion Euro in 2006, of which 44.6% are covered by the European Union. Species identification is a key problem throughout the life cycle of fishes: from eggs and larvae to adults in fisheries research and control, as well as processed fish products in consumer protection. Methodology/Principal Findings This study aims to evaluate the applicability of the three mitochondrial genes 16S rRNA (16S), cytochrome b (cyt b), and cytochrome oxidase subunit I (COI) for the identification of 50 European marine fish species by combining techniques of “DNA barcoding” and microarrays. In a DNA barcoding approach, neighbour Joining (NJ) phylogenetic trees of 369 16S, 212 cyt b, and 447 COI sequences indicated that cyt b and COI are suitable for unambiguous identification, whereas 16S failed to discriminate closely related flatfish and gurnard species. In course of probe design for DNA microarray development, each of the markers yielded a high number of potentially species-specific probes in silico, although many of them were rejected based on microarray hybridisation experiments. None of the markers provided probes to discriminate the sibling flatfish and gurnard species. However, since 16S-probes were less negatively influenced by the “position of label” effect and showed the lowest rejection rate and the highest mean signal intensity, 16S is more suitable for DNA microarray probe design than cty b and COI. The large portion of rejected COI-probes after hybridisation experiments (>90%) renders the DNA barcoding marker as rather unsuitable for this high-throughput technology. Conclusions/Significance Based on these data, a DNA microarray containing 64 functional oligonucleotide probes for the identification of 30 out of the 50 fish species investigated was developed. It represents the next step towards an automated and easy-to-handle method to identify fish, ichthyoplankton, and fish products. PMID

  3. Identifying Fishes through DNA Barcodes and Microarrays.

    Directory of Open Access Journals (Sweden)

    Marc Kochzius

    Full Text Available BACKGROUND: International fish trade reached an import value of 62.8 billion Euro in 2006, of which 44.6% are covered by the European Union. Species identification is a key problem throughout the life cycle of fishes: from eggs and larvae to adults in fisheries research and control, as well as processed fish products in consumer protection. METHODOLOGY/PRINCIPAL FINDINGS: This study aims to evaluate the applicability of the three mitochondrial genes 16S rRNA (16S, cytochrome b (cyt b, and cytochrome oxidase subunit I (COI for the identification of 50 European marine fish species by combining techniques of "DNA barcoding" and microarrays. In a DNA barcoding approach, neighbour Joining (NJ phylogenetic trees of 369 16S, 212 cyt b, and 447 COI sequences indicated that cyt b and COI are suitable for unambiguous identification, whereas 16S failed to discriminate closely related flatfish and gurnard species. In course of probe design for DNA microarray development, each of the markers yielded a high number of potentially species-specific probes in silico, although many of them were rejected based on microarray hybridisation experiments. None of the markers provided probes to discriminate the sibling flatfish and gurnard species. However, since 16S-probes were less negatively influenced by the "position of label" effect and showed the lowest rejection rate and the highest mean signal intensity, 16S is more suitable for DNA microarray probe design than cty b and COI. The large portion of rejected COI-probes after hybridisation experiments (>90% renders the DNA barcoding marker as rather unsuitable for this high-throughput technology. CONCLUSIONS/SIGNIFICANCE: Based on these data, a DNA microarray containing 64 functional oligonucleotide probes for the identification of 30 out of the 50 fish species investigated was developed. It represents the next step towards an automated and easy-to-handle method to identify fish, ichthyoplankton, and fish products.

  4. Integrated cistromic and expression analysis of amplified NKX2-1 in lung adenocarcinoma identifies LMO3 as a functional transcriptional target.

    Science.gov (United States)

    Watanabe, Hideo; Francis, Joshua M; Woo, Michele S; Etemad, Banafsheh; Lin, Wenchu; Fries, Daniel F; Peng, Shouyong; Snyder, Eric L; Tata, Purushothama Rao; Izzo, Francesca; Schinzel, Anna C; Cho, Jeonghee; Hammerman, Peter S; Verhaak, Roel G; Hahn, William C; Rajagopal, Jayaraj; Jacks, Tyler; Meyerson, Matthew

    2013-01-15

    The NKX2-1 transcription factor, a regulator of normal lung development, is the most significantly amplified gene in human lung adenocarcinoma. To study the transcriptional impact of NKX2-1 amplification, we generated an expression signature associated with NKX2-1 amplification in human lung adenocarcinoma and analyzed DNA-binding sites of NKX2-1 by genome-wide chromatin immunoprecipitation. Integration of these expression and cistromic analyses identified LMO3, itself encoding a transcription regulator, as a candidate direct transcriptional target of NKX2-1. Further cistromic and overexpression analyses indicated that NKX2-1 can cooperate with the forkhead box transcription factor FOXA1 to regulate LMO3 gene expression. RNAi analysis of NKX2-1-amplified cells compared with nonamplified cells demonstrated that LMO3 mediates cell survival downstream from NKX2-1. Our findings provide new insight into the transcriptional regulatory network of NKX2-1 and suggest that LMO3 is a transcriptional signal transducer in NKX2-1-amplified lung adenocarcinomas. PMID:23322301

  5. Identifying Canadian freshwater fishes through DNA barcodes.

    Directory of Open Access Journals (Sweden)

    Nicolas Hubert

    species can be efficiently identified through the use of DNA barcoding, especially the species complex of small-sized species, and that the present COI library can be used for subsequent applications in ecology and systematics.

  6. Identifying hidden sexual bridging communities in Chicago.

    Science.gov (United States)

    Youm, Yoosik; Mackesy-Amiti, Mary Ellen; Williams, Chyvette T; Ouellet, Lawrence J

    2009-07-01

    Bridge populations can play a central role in the spread of human immunodeficiency virus (HIV) by providing transmission links between higher and lower prevalence populations. While social network methods are well suited to the study of bridge populations, analyses tend to focus on dyads (i.e., risk between drug and/or sex partners) and ignore bridges between distinct subpopulations. This study takes initial steps toward moving the analysis of sexual network linkages beyond individual and risk group levels to a community level in which Chicago's 77 community areas are examined as subpopulations for the purpose of identifying potential bridging communities. Of particular interest are "hidden" bridging communities; that is, areas with above-average levels of sexual ties with other areas but whose below-average AIDS prevalence may hide their potential importance for HIV prevention. Data for this analysis came from the first wave of recruiting at the Chicago Sexual Acquisition and Transmission of HIV Cooperative Agreement Program site. Between August 2005 through October 2006, respondent-driven sampling was used to recruit users of heroin, cocaine, or methamphetamine, men who have sex with men regardless of drug use, the sex partners of these two groups, and sex partners of the sex partners. In this cross-sectional study of the sexual transmission of HIV, participants completed a network-focused computer-assisted self-administered interview, which included questions about the geographic locations of sexual contacts with up to six recent partners. Bridging scores for each area were determined using a matrix representing Chicago's 77 community areas and were assessed using two measures: non-redundant ties and flow betweenness. Bridging measures and acquired immunodeficiency syndrome (AIDS) case prevalence rates were plotted for each community area on charts representing four conditions: below-average bridging and AIDS prevalence, below-average bridging and above

  7. Identifying and Tracing Persistent Identifiers of Research Resources : Automation, Metrics and Analytics

    Science.gov (United States)

    Maull, K. E.; Hart, D.; Mayernik, M. S.

    2015-12-01

    Formal and informal citations and acknowledgements for research infrastructures, such as data collections, software packages, and facilities, are an increasingly important function of attribution in scholarly literature. While such citations provide the appropriate links, even if informally, to their origins, they are often done so inconsistently, making such citations hard to analyze. While significant progress has been made in the past few years in the development of recommendations, policies, and procedures for creating and promoting citable identifiers, progress has been mixed in tracking how data sets and other digital infrastructures have actually been identified and cited in the literature. Understanding the full extent and value of research infrastructures through the lens of scholarly literature requires significant resources, and thus, we argue must rely on automated approaches that mine and track persistent identifiers to scientific resources. Such automated approaches, however, face a number of unique challenges, from the inconsistent and informal referencing practices of authors, to unavailable, embargoed or hard-to-obtain full-text resources for text analytics, to inconsistent and capricious impact metrics. This presentation will discuss work to develop and evaluate tools for automating the tracing of research resource identification and referencing in the research literature via persistent citable identifiers. Despite the impediments, automated processes are of considerable importance in enabling these traceability efforts to scale, as the numbers of identifiers being created for unique scientific resources continues to grow rapidly. Such efforts, if successful, should improve the ability to answer meaningful questions about research resources as they continue to grow as a target of advanced analyses in research metrics.

  8. Genome-wide profiling of p63 DNA-binding sites identifies an element that regulates gene expression during limb development in the 7q21 SHFM1 locus.

    Directory of Open Access Journals (Sweden)

    Evelyn N Kouwenhoven

    2010-08-01

    Full Text Available Heterozygous mutations in p63 are associated with split hand/foot malformations (SHFM, orofacial clefting, and ectodermal abnormalities. Elucidation of the p63 gene network that includes target genes and regulatory elements may reveal new genes for other malformation disorders. We performed genome-wide DNA-binding profiling by chromatin immunoprecipitation (ChIP, followed by deep sequencing (ChIP-seq in primary human keratinocytes, and identified potential target genes and regulatory elements controlled by p63. We show that p63 binds to an enhancer element in the SHFM1 locus on chromosome 7q and that this element controls expression of DLX6 and possibly DLX5, both of which are important for limb development. A unique micro-deletion including this enhancer element, but not the DLX5/DLX6 genes, was identified in a patient with SHFM. Our study strongly indicates disruption of a non-coding cis-regulatory element located more than 250 kb from the DLX5/DLX6 genes as a novel disease mechanism in SHFM1. These data provide a proof-of-concept that the catalogue of p63 binding sites identified in this study may be of relevance to the studies of SHFM and other congenital malformations that resemble the p63-associated phenotypes.

  9. CFHT and VLT Identify Extremely Remote Galaxy

    Science.gov (United States)

    2003-05-01

    , the chances for detecting those distant objects are optimal. The astronomers talk about "maximizing the contrast" of objects showing emission lines at this wavelength. The CFHT Search Programme ESO PR Photo 13b/03 ESO PR Photo 13b/03 [Preview - JPEG: 494 x 400 pix - 83k [Normal - JPEG: 987 x 800 pix - 920k] Caption : PR Photo 13b/03 displays the image of a particular object (at the center), as seen at various wavelengths (colours) on CCD-frames obtained through different optical filters with the CFH12K camera at the CFHT. The object is only visible in the NB920 frame in which emission at the near-infrared wavelength 920 nm is registered (upper left). It is not seen in any of the others ( B lue [450 nm], V isual [550 nm], R ed [650 nm], I [800 nm]), nor in a combination of these (the "sum" of BVRI , the so-called "detection" image, here labeled as "Det"; it is used to detect closer objects from their optical colours for spectroscopic follow-up observations). The indicated object was later shown to be an extremely distant galaxy and has been designated z6VDF J022803-041618 . Each of the six photos covers 20 x 20 arcsec 2 ; North is up, East is right. Based on the above considerations, an international team of astronomers [2] installed a narrow-band optical filter centered at the near-infrared wavelength 920 nm on the CFH12K instrument at the Canada-France-Hawaii telescope on Mauna Kea (Hawaii, USA) to search for extremely distant galaxies. The CFH12K is a wide-field camera used at the prime focus of the CFHT, providing a field-of-view of approx. 30 x 40 arcmin 2 , somewhat larger than the full moon [5]. By comparing images of the same sky field taken through different filters, the astronomers were able to identify objects which appear comparatively "bright" in the NB920 image and "faint" (or are even not visible) in the corresponding images obtained through the other filters. A striking example is shown in PR Photo 13b/03 - the object at the center is well visible in

  10. Comparative in silico analysis identifies bona fide MyoD binding sites within the Myocyte Stress 1 gene promoter

    Directory of Open Access Journals (Sweden)

    Imbalzano Anthony N

    2008-05-01

    Full Text Available Abstract Background Myocyte stress 1 (MS1 is a striated muscle actin binding protein required for the muscle specific activity of the evolutionary ancient myocardin related transcription factor (MRTF/serum response factor (SRF transcriptional pathway. To date, little is known about the molecular mechanisms that govern skeletal muscle specific expression of MS1. Such mechanisms are likely to play a major role in modulating SRF activity and therefore muscle determination, differentiation and regeneration. In this study we employed a comparative in silico analysis coupled with an experimental promoter characterisation to delineate these mechanisms. Results Analysis of MS1 expression in differentiating C2C12 muscle cells demonstrated a temporal differentiation dependent up-regulation in ms1 mRNA. An in silico comparative sequence analysis identified two conserved putative myogenic regulatory domains within the proximal 1.5 kbp of 5' upstream sequence. Co-transfecting C2C12 myoblasts with ms1 promoter/luciferase reporters and myogenic regulatory factor (MRF over-expression plasmids revealed specific sensitivity of the ms1 promoter to MyoD. Subsequent mutagenesis and EMSA analysis demonstrated specific targeting of MyoD at two distinct E-Boxes (E1 and E2 within identified evolutionary conserved regions (ECRs, α and β. Chromatin immunoprecipitation (ChIP analysis indicates that co-ordinated binding of MyoD at E-Boxes located within ECRs α and β correlates with the temporal induction in ms1 mRNA. Conclusion These findings suggest that the tissue specific and differentiation dependent up-regulation in ms1 mRNA is mediated by temporal binding of MyoD at distinct evolutionary conserved E-Boxes within the ms1 5' upstream sequence. We believe, through its activation of ms1, this is the first study to demonstrate a direct link between MyoD activity and SRF transcriptional signalling, with clear implications for the understanding of muscle determination

  11. Systematic Mutational Analysis of Histidine Kinase Genes in the Nosocomial Pathogen Stenotrophomonas maltophilia Identifies BfmAK System Control of Biofilm Development.

    Science.gov (United States)

    Zheng, Liu; Wang, Fang-Fang; Ren, Bao-Zhen; Liu, Wei; Liu, Zhong; Qian, Wei

    2016-04-01

    The Gram-negative bacterium Stenotrophomonas maltophilialives in diverse ecological niches. As a result of its formidable capabilities of forming biofilm and its resistance to multiple antibiotic agents, the bacterium is also a nosocomial pathogen of serious threat to the health of patients whose immune systems are suppressed or compromised. Besides the histidine kinase RpfC, the two-component signal transduction system (TCS), which is the canonical regulatory machinery used by most bacterial pathogens, has never been experimentally investigated inS. maltophilia Here, we annotated 62 putative histidine kinase genes in the S. maltophilia genome and successfully obtained 51 mutants by systematical insertional inactivation. Phenotypic characterization identified a series of mutants with deficiencies in bacterial growth, swimming motility, and biofilm development. A TCS, named here BfmA-BfmK (Smlt4209-Smlt4208), was genetically confirmed to regulate biofilm formation inS. maltophilia Together with interacting partner prediction and chromatin immunoprecipitation screens, six candidate promoter regions bound by BfmA in vivo were identified. We demonstrated that, among them, BfmA acts as a transcription factor that binds directly to the promoter regions of bfmA-bfmK and Smlt0800(acoT), a gene encoding an acyl coenzyme A thioesterase that is associated with biofilm development, and positively controls their transcription. Genome-scale mutational analyses of histidine kinase genes and functional dissection of BfmK-BfmA regulation in biofilm provide genetic information to support more in-depth studies on cellular signaling inS. maltophilia, in the context of developing novel approaches to fight this important bacterial pathogen. PMID:26873318

  12. Cancer associated epigenetic transitions identified by genome-wide histone methylation binding profiles in human colorectal cancer samples and paired normal mucosa

    International Nuclear Information System (INIS)

    Despite their well-established functional roles, histone modifications have received less attention than DNA methylation in the cancer field. In order to evaluate their importance in colorectal cancer (CRC), we generated the first genome-wide histone modification profiles in paired normal colon mucosa and tumor samples. Chromatin immunoprecipitation and microarray hybridization (ChIP-chip) was used to identify promoters enriched for histone H3 trimethylated on lysine 4 (H3K4me3) and lysine 27 (H3K27me3) in paired normal colon mucosa and tumor samples from two CRC patients and for the CRC cell line HT29. By comparing histone modification patterns in normal mucosa and tumors, we found that alterations predicted to have major functional consequences were quite rare. Furthermore, when normal or tumor tissue samples were compared to HT29, high similarities were observed for H3K4me3. However, the differences found for H3K27me3, which is important in determining cellular identity, indicates that cell lines do not represent optimal tissue models. Finally, using public expression data, we uncovered previously unknown changes in CRC expression patterns. Genes positive for H3K4me3 in normal and/or tumor samples, which are typically already active in normal mucosa, became hyperactivated in tumors, while genes with H3K27me3 in normal and/or tumor samples and which are expressed at low levels in normal mucosa, became hypersilenced in tumors. Genome wide histone modification profiles can be used to find epigenetic aberrations in genes associated with cancer. This strategy gives further insights into the epigenetic contribution to the oncogenic process and may identify new biomarkers

  13. Nbs1 ChIP-Seq Identifies Off-Target DNA Double-Strand Breaks Induced by AID in Activated Splenic B Cells.

    Directory of Open Access Journals (Sweden)

    Lyne Khair

    2015-08-01

    Full Text Available Activation-induced cytidine deaminase (AID is required for initiation of Ig class switch recombination (CSR and somatic hypermutation (SHM of antibody genes during immune responses. AID has also been shown to induce chromosomal translocations, mutations, and DNA double-strand breaks (DSBs involving non-Ig genes in activated B cells. To determine what makes a DNA site a target for AID-induced DSBs, we identify off-target DSBs induced by AID by performing chromatin immunoprecipitation (ChIP for Nbs1, a protein that binds DSBs, followed by deep sequencing (ChIP-Seq. We detect and characterize hundreds of off-target AID-dependent DSBs. Two types of tandem repeats are highly enriched within the Nbs1-binding sites: long CA repeats, which can form Z-DNA, and tandem pentamers containing the AID target hotspot WGCW. These tandem repeats are not nearly as enriched at AID-independent DSBs, which we also identified. Msh2, a component of the mismatch repair pathway and important for genome stability, increases off-target DSBs, similar to its effect on Ig switch region DSBs, which are required intermediates during CSR. Most of the off-target DSBs are two-ended, consistent with generation during G1 phase, similar to DSBs in Ig switch regions. However, a minority are one-ended, presumably due to conversion of single-strand breaks to DSBs during replication. One-ended DSBs are repaired by processes involving homologous recombination, including break-induced replication repair, which can lead to genome instability. Off-target DSBs, especially those present during S phase, can lead to chromosomal translocations, deletions and gene amplifications, resulting in the high frequency of B cell lymphomas derived from cells that express or have expressed AID.

  14. Chromatin Immunoprecipitation to Investigate Origin Association of Replication Factors in Mammalian Cells

    OpenAIRE

    Leman, Adam R.; Noguchi, Eishi

    2014-01-01

    A variety of DNA-binding proteins regulate DNA transactions including DNA replication and DNA damage response. To initiate DNA replication in S phase of the cell cycle, numerous replication proteins must be recruited to the replication origin in order to unwind and synthesize DNA. Some replication factors stay at the origin, while replisome components move with the replication fork. When the replisome encounters DNA damage or other issues during DNA replication, the replication fork stalls an...

  15. Insights into the polerovirus-plant interactome revealed by co-immunoprecipitation and mass spectrometry

    Science.gov (United States)

    The identification of host proteins that interact with virus proteins is a major challenge for the field of virology. Phloem-limited viruses pose extraordinary challenges for in vivo protein interaction experiments because these viruses are localized in very few and highly specialized host cells. ...

  16. Whole genome sequencing identifies a deletion in protein phosphatase 2A that affects its stability and localization in Chlamydomonas reinhardtii.

    Directory of Open Access Journals (Sweden)

    Huawen Lin

    Full Text Available Whole genome sequencing is a powerful tool in the discovery of single nucleotide polymorphisms (SNPs and small insertions/deletions (indels among mutant strains, which simplifies forward genetics approaches. However, identification of the causative mutation among a large number of non-causative SNPs in a mutant strain remains a big challenge. In the unicellular biflagellate green alga Chlamydomonas reinhardtii, we generated a SNP/indel library that contains over 2 million polymorphisms from four wild-type strains, one highly polymorphic strain that is frequently used in meiotic mapping, ten mutant strains that have flagellar assembly or motility defects, and one mutant strain, imp3, which has a mating defect. A comparison of polymorphisms in the imp3 strain and the other 15 strains allowed us to identify a deletion of the last three amino acids, Y313F314L315, in a protein phosphatase 2A catalytic subunit (PP2A3 in the imp3 strain. Introduction of a wild-type HA-tagged PP2A3 rescues the mutant phenotype, but mutant HA-PP2A3 at Y313 or L315 fail to rescue. Our immunoprecipitation results indicate that the Y313, L315, or YFLΔ mutations do not affect the binding of PP2A3 to the scaffold subunit, PP2A-2r. In contrast, the Y313, L315, or YFLΔ mutations affect both the stability and the localization of PP2A3. The PP2A3 protein is less abundant in these mutants and fails to accumulate in the basal body area as observed in transformants with either wild-type HA-PP2A3 or a HA-PP2A3 with a V310T change. The accumulation of HA-PP2A3 in the basal body region disappears in mated dikaryons, which suggests that the localization of PP2A3 may be essential to the mating process. Overall, our results demonstrate that the terminal YFL tail of PP2A3 is important in the regulation on Chlamydomonas mating.

  17. 3 Drugs Identified to Potentially Fight Zika Virus

    Science.gov (United States)

    ... html 3 Drugs Identified to Potentially Fight Zika Virus But only one is already approved in the ... fetuses protection against the damaging effects of Zika virus, a new multicenter study reports. Researchers identified these ...

  18. Can a structured questionnaire identify patients with reduced renal function?

    DEFF Research Database (Denmark)

    Azzouz, Manal; Rømsing, Janne; Thomsen, Henrik

    2014-01-01

    To evaluate a structured questionnaire in identifying outpatients with renal dysfunction before MRI or CT in various age groups.......To evaluate a structured questionnaire in identifying outpatients with renal dysfunction before MRI or CT in various age groups....

  19. Identifying Critical Cross-Cultural School Psychology Competencies.

    Science.gov (United States)

    Rogers, Margaret R.; Lopez, Emilia C.

    2002-01-01

    Study sought to identify critical cross-cultural competencies for school psychologists. To identify the competencies, an extensive literature search about cross-cultural school psychology competencies was conducted, as well as a questionnaire to ask expert panelists. The 102 competencies identified cover 14 major domains of professional activities…

  20. 75 FR 14539 - Furnishing Identifying Number of Tax Return Preparer

    Science.gov (United States)

    2010-03-26

    ... Internal Revenue Service 26 CFR Part 1 RIN 1545-BI28 Furnishing Identifying Number of Tax Return Preparer... guidance to tax return preparers on furnishing an identifying number on tax returns and claims for refund of tax that they prepare. These proposed regulations provide guidance on the identifying number of...

  1. ChIP-on-chip analysis identifies IL-22 as direct target gene of ectopically expressed FOXP3 transcription factor in human T cells

    Directory of Open Access Journals (Sweden)

    Jeron Andreas

    2012-12-01

    Full Text Available Abstract Background The transcription factor (TF forkhead box P3 (FOXP3 is constitutively expressed at high levels in naturally occurring CD4+CD25+ regulatory T cells (nTregs. It is not only the most accepted marker for that cell population but is also considered lineage determinative. Chromatin immunoprecipitation (ChIP of TFs in combination with genomic tiling microarray analysis (ChIP-on-chip has been shown to be an appropriate tool for identifying FOXP3 transcription factor binding sites (TFBSs on a genome-wide scale. In combination with microarray expression analysis, the ChIP-on-chip technique allows identification of direct FOXP3 target genes. Results ChIP-on-chip analysis of the human FOXP3 expressed in resting and PMA/ionomycin–stimulated Jurkat T cells revealed several thousand putative FOXP3 binding sites and demonstrated the importance of intronic regions for FOXP3 binding. The analysis of expression data showed that the stimulation-dependent down-regulation of IL-22 was correlated with direct FOXP3 binding in the IL-22 promoter region. This association was confirmed by real-time PCR analysis of ChIP-DNA. The corresponding ChIP-region also contained a matching FOXP3 consensus sequence. Conclusions Knowledge of the general distribution patterns of FOXP3 TFBSs in the human genome under resting and activated conditions will contribute to a better understanding of this TF and its influence on direct target genes, as well as its importance for the phenotype and function of Tregs. Moreover, FOXP3-dependent repression of Th17-related IL-22 may be relevant to an understanding of the phenomenon of Treg/Th17 cell plasticity.

  2. [3H]Azidodantrolene photoaffinity labeling, synthetic domain peptides and monoclonal antibody reactivity identify the dantrolene binding sequence on RyR1

    Energy Technology Data Exchange (ETDEWEB)

    Paul-Pletzer, Kalanethee; Yamamoto, Takeshi; Bhat, Manju B.; Ma, Jianjie; Ikemoto, Noriaki; Jimenez, Leslie S.; Morimoto, Hiromi; Williams, Philip G.; Parness, Jerome

    2002-06-14

    Dantrolene is a drug that suppresses intracellular Ca2+ release from sarcoplasmic reticulum in normal skeletal muscle and is used as a therapeutic agent in individuals susceptible to malignant hyperthermia. Though its precise mechanism of action has not been elucidated, we have identified the N-terminal region (amino acids 1-1400) of the skeletal muscle isoform of the ryanodine receptor (RyR1), the primary Ca2+ release channel in sarcoplasmic reticulum, as a molecular target for dantrolene using the photoaffinity analog [3H]azidodantrolene(1). Here, we demonstrate that heterologously expressed RyR1 retains its capacity to be specifically labeled with [3H]azidodantrolene,indicating that muscle specific factors are not required for this ligand-receptor interaction. Synthetic domain peptides of RyR1, previously shown to affect RyR1 function in vitro and in vivo, were exploited as potential drug binding site mimics and used in photoaffinity labeling experiments. Only DP1 and DP1-2, peptide s containing the amino acid sequence corresponding to RyR1 residues 590-609, were specifically labeled by [3H]azidodantrolene. A monoclonal anti-RyR1 antibody which recognizes RyR1 and its 1400 amino acid N-terminal fragment, recognizes DP1 and DP1-2 in both Western blots and immunoprecipitation assays, and specifically inhibits [3H]azidodantrolene photolabeling of RyR1 and its N-terminal fragment in sarcoplasmic reticulum. Our results indicate that synthetic domain peptides can mimic a native, ligand binding conformation in vitro, and that the dantrolene binding site and the epitope for the monoclonal antibody on RyR1 are equivalent and composed of amino-acids 590-609.

  3. HIV-1 RNAs are Not Part of the Argonaute 2 Associated RNA Interference Pathway in Macrophages.

    Directory of Open Access Journals (Sweden)

    Valentina Vongrad

    Full Text Available MiRNAs and other small noncoding RNAs (sncRNAs are key players in post-transcriptional gene regulation. HIV-1 derived small noncoding RNAs (sncRNAs have been described in HIV-1 infected cells, but their biological functions still remain to be elucidated. Here, we approached the question whether viral sncRNAs may play a role in the RNA interference (RNAi pathway or whether viral mRNAs are targeted by cellular miRNAs in human monocyte derived macrophages (MDM.The incorporation of viral sncRNAs and/or their target RNAs into RNA-induced silencing complex was investigated using photoactivatable ribonucleoside-induced cross-linking and immunoprecipitation (PAR-CLIP as well as high-throughput sequencing of RNA isolated by cross-linking immunoprecipitation (HITS-CLIP, which capture Argonaute2-bound miRNAs and their target RNAs. HIV-1 infected monocyte-derived macrophages (MDM were chosen as target cells, as they have previously been shown to express HIV-1 sncRNAs. In addition, we applied small RNA deep sequencing to study differential cellular miRNA expression in HIV-1 infected versus non-infected MDMs.PAR-CLIP and HITS-CLIP data demonstrated the absence of HIV-1 RNAs in Ago2-RISC, although the presence of a multitude of HIV-1 sncRNAs in HIV-1 infected MDMs was confirmed by small RNA sequencing. Small RNA sequencing revealed that 1.4% of all sncRNAs were of HIV-1 origin. However, neither HIV-1 derived sncRNAs nor putative HIV-1 target sequences incorporated into Ago2-RISC were identified suggesting that HIV-1 sncRNAs are not involved in the canonical RNAi pathway nor is HIV-1 targeted by this pathway in HIV-1 infected macrophages.

  4. Accuracy of ultrasound to identify chronic liver disease

    Institute of Scientific and Technical Information of China (English)

    Richard; Allan; Kerry; Thoirs; Maureen; Phillips

    2010-01-01

    AIM:To identify and assess studies reporting the diagnostic performance of ultrasound imaging for identifying chronic liver disease(CLD)in a high risk population. METHODS:A search was performed to identify studies investigating the diagnostic accuracy of ultrasound imaging for CLD.Two authors independently used the quality assessment of diagnostic accuracy studies(QUADAS)checklist to assess the methodological quality of the selected studies.Inter-observer reliability of the QUADAS tool was assessed by measu...

  5. Can "Federal Sanctuaries" be identified in Triphylia and Arkadia?

    DEFF Research Database (Denmark)

    Nielsen, Thomas Heine

    2013-01-01

    This paper discusses whether federal sanctuaries - such as are known from the Achaian and Aitolian Federations - can be identified in Triphylia and Arkadia in the Peloponnese. It is concluded that on present evidence it is not possible to identify such sanctuaries in these areas......This paper discusses whether federal sanctuaries - such as are known from the Achaian and Aitolian Federations - can be identified in Triphylia and Arkadia in the Peloponnese. It is concluded that on present evidence it is not possible to identify such sanctuaries in these areas...

  6. Identifying single points of failure in your organisation.

    Science.gov (United States)

    Bryant, Robby J

    2013-01-01

    Single points of failure may spell disaster for businesses that have not adequately identified and mitigated these critical risks. A single point of failure audit will identify the single points of failure in all functional areas that may negatively impact organisational processes and process flows. This paper provides a holistic approach to constructing a successful single point of failure audit and identifies the systems that are frequently the sources of single points of failure. It also examines the internal and external risks that may spawn single points of failure and provides various mitigation strategies for the systems identified. PMID:24113634

  7. Identifiability of causal effect for a simple causal model

    Institute of Scientific and Technical Information of China (English)

    郑忠国; 张艳艳; 童行伟

    2002-01-01

    Counterfactual model is put forward to discuss the causal inference in the directed acyclic graph and its corresponding identifiability is thus studied with the ancillary information based on conditional independence. It is shown that the assumption of ignorability can be expanded to the assumption of replaceability,under which the causal efiects are identifiable.

  8. On the Identifiability Conditions in Some Nonlinear Time Series Models

    OpenAIRE

    Noh, Jungsik; Lee, Sangyeol

    2013-01-01

    In this study, we consider the identifiability problem for nonlinear time series models. Special attention is paid to smooth transition GARCH, nonlinear Poisson autoregressive, and multiple regime smooth transition autoregressive models. Some sufficient conditions are obtained to establish the identifiability of these models.

  9. 44 CFR 5.27 - Deletion of identifying details.

    Science.gov (United States)

    2010-10-01

    ... 44 Emergency Management and Assistance 1 2010-10-01 2010-10-01 false Deletion of identifying details. 5.27 Section 5.27 Emergency Management and Assistance FEDERAL EMERGENCY MANAGEMENT AGENCY..., FEMA may delete identifying details when making available or publishing an opinion, statement of...

  10. 28 CFR 22.22 - Revelation of identifiable data.

    Science.gov (United States)

    2010-07-01

    ... 28 Judicial Administration 1 2010-07-01 2010-07-01 false Revelation of identifiable data. 22.22 Section 22.22 Judicial Administration DEPARTMENT OF JUSTICE CONFIDENTIALITY OF IDENTIFIABLE RESEARCH AND... subject, be expected to totally conceal subject identity....

  11. Identifying costs for capitation in psychiatric case management.

    Science.gov (United States)

    Baker, J J; Chiverton, P; Hines, V

    1998-01-01

    This article presents an example of how one hospital identified costs for capitation in psychiatric case management. An 18-month postacute case management pilot project collected data on a nurse-specific and patient-specific basis. Costs were identified using activity-based costing methodology. PMID:9502055

  12. Identifying Interbank Loans, Rates, and Claims Networks from Transactional Data

    NARCIS (Netherlands)

    Leon Rincon, C.E.; Cely, Jorge; Cadena, Carlos

    2015-01-01

    We identify interbank (i.e. non-collateralized) loans from the Colombian large-value payment system by implementing Furfine’s method. After identifying interbank loans from transactional data we obtain the interbank rates and claims without relying on financial institutions’ reported data. Contrasti

  13. Sampling in the frequency domain to identify a metamodel

    Energy Technology Data Exchange (ETDEWEB)

    Mara, T. A.; Laurent, P.

    2001-07-01

    The paper deals with regression analysis. We propose a special sampling the consists in oscillating each factor in its uncertainly range to identify the regression polynomial. We illustrate the method identifying the fifth order metamodel of eleven factors model. (Author) 2 refs.

  14. 36 CFR 1223.16 - How are vital records identified?

    Science.gov (United States)

    2010-07-01

    ... 36 Parks, Forests, and Public Property 3 2010-07-01 2010-07-01 false How are vital records identified? 1223.16 Section 1223.16 Parks, Forests, and Public Property NATIONAL ARCHIVES AND RECORDS... identify vital records in the context of the emergency management function. Vital records are those...

  15. Gasoline identifier based on SH0 plate acoustic waves.

    Science.gov (United States)

    Kuznetsova, Iren E; Zaitsev, Boris D; Seleznev, Eugenii P; Verona, Enrico

    2016-08-01

    The present paper is devoted to the development of gasoline identifier based on zero order shear-horizontal (SH0) acoustic wave propagating in piezoelectric plate. It has been found that the permittivity of gasoline is increased when its octane number rises. The development of such identifier is experimentally demonstrated to be possible. PMID:27125559

  16. National variety trials identify clones with high potential

    Science.gov (United States)

    Quality potato varieties are the backbone of a strong potato industry. Variety trials have been used to identify promising new varieties for well over a century. Trials are repeated and information collected over many years in order to confidently identify lines that may be well suited for productio...

  17. Integrating subpathway analysis to identify candidate agents for hepatocellular carcinoma.

    Science.gov (United States)

    Wang, Jiye; Li, Mi; Wang, Yun; Liu, Xiaoping

    2016-01-01

    Hepatocellular carcinoma (HCC) is the second most common cause of cancer-associated death worldwide, characterized by a high invasiveness and resistance to normal anticancer treatments. The need to develop new therapeutic agents for HCC is urgent. Here, we developed a bioinformatics method to identify potential novel drugs for HCC by integrating HCC-related and drug-affected subpathways. By using the RNA-seq data from the TCGA (The Cancer Genome Atlas) database, we first identified 1,763 differentially expressed genes between HCC and normal samples. Next, we identified 104 significant HCC-related subpathways. We also identified the subpathways associated with small molecular drugs in the CMap database. Finally, by integrating HCC-related and drug-affected subpathways, we identified 40 novel small molecular drugs capable of targeting these HCC-involved subpathways. In addition to previously reported agents (ie, calmidazolium), our method also identified potentially novel agents for targeting HCC. We experimentally verified that one of these novel agents, prenylamine, induced HCC cell apoptosis using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide, an acridine orange/ethidium bromide stain, and electron microscopy. In addition, we found that prenylamine not only affected several classic apoptosis-related proteins, including Bax, Bcl-2, and cytochrome c, but also increased caspase-3 activity. These candidate small molecular drugs identified by us may provide insights into novel therapeutic approaches for HCC. PMID:27022281

  18. 40 CFR 174.529 - Bacillus thuringiensis modified Cry1Ab protein as identified under OECD Unique Identifier SYN...

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Bacillus thuringiensis modified Cry1Ab protein as identified under OECD Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement of a tolerance. 174.529 Section 174.529 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS PROCEDURES...

  19. Identifying workflow disruptions in the cardiovascular operating room.

    Science.gov (United States)

    Cohen, T N; Cabrera, J S; Sisk, O D; Welsh, K L; Abernathy, J H; Reeves, S T; Wiegmann, D A; Shappell, S A; Boquet, A J

    2016-08-01

    The objectives of this study were to identify the frequency and nature of flow disruptions in the operating room with respect to three cardiac surgical team members: anaesthetists; circulating nurses; and perfusionists. Data collected from 15 cases and coded using a human factors taxonomy identified 878 disruptions. Significant differences were identified in frequency relative to discipline type. Circulating nurses experienced more coordination disruptions (χ(2) (2, N = 110) = 7.136, p role. PMID:27396248

  20. A System for Distributed Minting and Management of Persistent Identifiers

    Directory of Open Access Journals (Sweden)

    Łukasz Bolikowski

    2015-02-01

    Full Text Available Minting persistent identifiers and managing their metadata is typically governed by a single organization. Such a single point of failure poses a risk to longevity and long-term preservation of identifiers. In this paper we address the risk by proposing a radically different approach, in which minting and management of persistent identifiers is distributed, and the integrity of the distributed system is guaranteed by public-key cryptography. We describe the general architecture of the system, analyse its robustness and discuss potential deployment scenarios.

  1. On identifying transfer functions and state equations for linear systems.

    Science.gov (United States)

    Shieh, L. S.; Chen, C. F.; Huang, C. J.

    1972-01-01

    Two methods are established for identifying constant-coefficient, C to the 2n power type of noise-free linear systems if the time response data of the input-output or of all states are known. 2n response data are required to identify an nth-order transfer function or state equation for an unknown linear system. The order of the unknown system can be identified by checking a sequence of determinants. The Z transform and its inversion are mainly used.

  2. Research to Identify Effective Antifungal Agents, 1993 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Schreck, Carl

    1993-10-01

    This study is a continuation of ``Research to Identify Effective Antifungal Agents'' sponsored by Bonneville Power Administration (Schreck et al. 1990, 1991, and 1992). The objectives of the present study were to select and evaluate candidate fungicides.

  3. Research to Identify Effective Antifungal Agents, 1991 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Schreck, Carl

    1991-09-01

    This study is a continuation of ``Research to Identify Effective Antifungal Agents'' sponsored by Bonneville Power Administration (Schreck et al. 1990). The objectives of the present study was to evaluate up to 10 candidate fungicides.

  4. Comparing complete and partial classification for identifying customers at risk

    NARCIS (Netherlands)

    Bloemer, J.M.M.; Brijs, T.; Vanhoof, K.; Swinnen, S.P.

    2003-01-01

    This paper evaluates complete versus partial classification for the problem of identifying customers at risk. We define customers at risk as customers reporting overall satisfaction, but these customers also possess characteristics that are strongly associated with dissatisfied customers. This defin

  5. Identifying and Educating Gifted/Talented Nonhandicapped and Handicapped Preschoolers.

    Science.gov (United States)

    Karnes, Merle B.; Bertschi, Jane D.

    1978-01-01

    The Retrieval and Acceleration of Promising Young Handicapped and Talented program, part of the Joint Early Education Program for the Handicapped, identifies and educates preschool children who are both handicapped and gifted or talented. (PHR)

  6. Can Zebrafish be used to Identify Developmentally Neurotoxic Chemicals

    Science.gov (United States)

    Can Zebrafish be Used to Identify Developmentally Neurotoxic Chemicals? The U.S. Environmental Protection Agency is evaluating methods to screen and prioritize large numbers of chemicals for developmental neurotoxicity. We are exploring behavioral methods using zebrafish by desig...

  7. Time delay and partial coherence analyses to identify cortical connectivities

    CERN Document Server

    Govindan, R B; Deuschl, G; Kopper, F; Raethjen, J

    2005-01-01

    Recently it has been demonstrated by Albo that partial coherence analysis is sensitive to signal to noise ratio (SNR) and that it will always identify the signal with the highest SNR among the three signals as the main (driving) influence. We propose to use time delay analysis in parallel to partial coherence analysis to identify the connectivities between the multivariate time series. Both are applied to a theoretical model (used by Albo) to analyse the connections introduced in the model. Time delay analysis identifies the connections correctly. We also apply these analyses to the electroencephalogram (EEG) and electromyogram (EMG) of essential tremor patients and EEG of normal subjects while bimanually tapping their index fingers. Biologically plausible cortico-muscular and cortico-cortical connections are identified by these methods.

  8. Expression profiling identifies genes involved in emphysema severity

    Directory of Open Access Journals (Sweden)

    Bowman Rayleen V

    2009-09-01

    Full Text Available Abstract Chronic obstructive pulmonary disease (COPD is a major public health problem. The aim of this study was to identify genes involved in emphysema severity in COPD patients. Gene expression profiling was performed on total RNA extracted from non-tumor lung tissue from 30 smokers with emphysema. Class comparison analysis based on gas transfer measurement was performed to identify differentially expressed genes. Genes were then selected for technical validation by quantitative reverse transcriptase-PCR (qRT-PCR if also represented on microarray platforms used in previously published emphysema studies. Genes technically validated advanced to tests of biological replication by qRT-PCR using an independent test set of 62 lung samples. Class comparison identified 98 differentially expressed genes (p p Gene expression profiling of lung from emphysema patients identified seven candidate genes associated with emphysema severity including COL6A3, SERPINF1, ZNHIT6, NEDD4, CDKN2A, NRN1 and GSTM3.

  9. Novel lipid constituents identified in seeds of Nigella sativa (Linn)

    Energy Technology Data Exchange (ETDEWEB)

    Mehta, B.K.; Verma, Manjul; Gupta, Meenal [Vikram University (India). School of Studies in Chemistry and Biochemistry]. E-mail: bkmehta11@yahoo.com

    2008-07-01

    Novel lipids were isolated from the unsaponifiable matter extracted from seeds of Nigella sativa Linn by using n-hexane. The new dienoate and two monoesters were the new lipids identified by spectral (IR, {sup 1}H- and {sup 13}C-NMR spectra, mass spectrum, elemental analysis) and chemical analysis. The dienoate (1) was identified as methylnonadeca-15,17-dienoate and two monoesters were identified as pentyl hexadec-12-enoate (2) and pentyl pentadec-11-enoate (3). Linoleic acid, oleic acid, {beta}-sitosterol and stigmasterol were identified as part of the lipid structures. All compounds exhibited moderate activity against Staphylococcus aureus and poor activity against shigella spp, and Klebsiella pneumoniae. (author)

  10. Identifying refuge resources of concern and management priorities : A handbook

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This handbook provides a strategy for anyone who must identify priorities (refuge resources of concern) that will guide future refuge wildlife and habitat...

  11. Using the National Provider Identifier for Health Care...

    Data.gov (United States)

    U.S. Department of Health & Human Services — The establishment in recent years of a National Provider Identifier (NPI) offers a new method for counting and categorizing physicians and other health care...

  12. An improved anti-leech mechanism based on session identifier

    Science.gov (United States)

    Zhang, Jianbiao; Zhu, Tong; Zhang, Han; Lin, Li

    2012-01-01

    With the rapid development of information technology and extensive requirement of network resource sharing, plenty of resource hotlinking phenomenons appear on the internet. The hotlinking problem not only harms the interests of legal websites but also leads to a great affection to fair internet environment. The anti-leech technique based on session identifier is highly secure, but the transmission of session identifier in plaintext form causes some security flaws. In this paper, a proxy hotlinking technique based on session identifier is introduced firstly to illustrate these security flaws; next, this paper proposes an improved anti-leech mechanism based on session identifier, the mechanism takes the random factor as the core and detects hotlinking request using a map table that contains random factor, user's information and time stamp; at last the paper analyzes the security of mechanism in theory. The result reveals that the improved mechanism has the merits of simple realization, high security and great flexibility.

  13. Identifying victims of violence using register-based data

    DEFF Research Database (Denmark)

    Kruse, Marie; Sørensen, Jan; Brønnum-Hansen, Henrik;

    2010-01-01

    AIMS: The aim of this study was twofold. Firstly we identified victims of violence in national registers and discussed strengths and weaknesses of this approach. Secondly we assessed the magnitude of violence and the characteristics of the victims using register-based data. METHODS: We used three...... nationwide registers to identify victims of violence: The National Patient Register, the Victim Statistics, and the Causes of Death Register. We merged these data and assessed the degree of overlap between data sources. We identified a reference population by selecting all individuals in Denmark over 15....... RESULTS: In 2006, 22,000 individuals were registered as having been exposed to violence. About 70% of these victims were men. Most victims were identified from emergency room contacts and police records, and few from the Causes of Death Register. There was some overlap between the two large data sources...

  14. Communication difficulties in children identified with psychiatric problems

    OpenAIRE

    Helland, Wenche Andersen

    2010-01-01

    Several studies have pointed to an overlap between different developmental psychopathological conditions and language impairments, and difficulties with communication have been identified in children of various diagnostic backgrounds. This thesis is based on three empirical studies, and the purposes are to investigate communication difficulties as reported by parents, in children identified with psychiatric problems as well as to evaluate a Norwegian adaptation of the Children’...

  15. A Note on the Identifiability of Generalized Linear Mixed Models

    DEFF Research Database (Denmark)

    Labouriau, Rodrigo

    2014-01-01

    I present here a simple proof that, under general regularity conditions, the standard parametrization of generalized linear mixed model is identifiable. The proof is based on the assumptions of generalized linear mixed models on the first and second order moments and some general mild regularity...... conditions, and, therefore, is extensible to quasi-likelihood based generalized linear models. In particular, binomial and Poisson mixed models with dispersion parameter are identifiable when equipped with the standard parametrization...

  16. Identifying appropriate tasks for the preregistration year: modified Delphi technique

    OpenAIRE

    Stewart, J.; O'Halloran, Cath; Harrigan, P; Spencer, J; Barton, J. R.; Singleton, S. J.

    1999-01-01

    Objectives: To identify the tasks that should constitute the work of preregistration house officers to provide the basis for the development of a self evaluation instrument. Design: Literature review and modified Delphi technique. Setting: Northern Deanery within the Northern and Yorkshire office NHS executive. Subjects: 67 educational supervisors of preregistration house officers. Main outcome measures: Percentage of agreement by educational supervisors to tasks identified fr...

  17. Eight Unrecorded Higher Fungi Identified at the Korea National Arboretum

    OpenAIRE

    Han, Sang-Kuk; Oh, Seung-Hwan; Kim, Hyun-Joong

    2010-01-01

    A total of 560 higher fungal specimens were collected in the Gwangneung Forest from May to November of 2007. All of the collected specimens were identified; categorized into 8 classes, 19 orders, 69 families, 165 genera, and 296 species; and deposited in the herbarium of the Korea National Arboretum. Of the identified specimens, 8 were confirmed as being new to Korea and are as follows: Cudoniella acicularis (Korean name: Jeombakisotugubeoseos), Discina ancilis (Korean name: Jomwonbanbeoseos)...

  18. An Advanced Threshold Secret Sharing Scheme for Identifying Cheaters

    Institute of Scientific and Technical Information of China (English)

    XIE Shu-cui; ZHANG Jian-zhong

    2003-01-01

    In this paper an advanced threshold secret sharing scheme for identifying cheaters is proposed by using authentication codes. The performance of the scheme is discussed. The results show that in the scheme the valid shareholders can not only identify the impersonation of an adversary, but also detect cheating of some valid shareholders. In particular one honest shareholder is able to detect cheating of other participants forming a collection, and the information rate of the scheme is higher than that of others.

  19. Identifying the role that animals play in their social networks.

    OpenAIRE

    Lusseau, David; Newman, M.E.J.

    2004-01-01

    Techniques recently developed for the analysis of human social networks are applied to the social network of bottlenose dolphins living in Doubtful Sound, New Zealand. We identify communities and subcommunities within the dolphin population and present evidence that sex- and age-related homophily play a role in the formation of clusters of preferred companionship. We also identify brokers who act as links between sub-communities and who appear to be crucial to the social cohesion of the popul...

  20. SOFTWARE PURCHASING PROFESSIONAL : Identifying Competences and Capabilities in Software Purchasing

    OpenAIRE

    Tidenberg, Pia

    2012-01-01

    This study explores the existing purchasing and supply management competence theories and seeks to understand if these theories are applicable in evaluating the competence requirements in the specific business category, software purchasing. The aim of this study was to identify the meaning and content of individual competence and capability in the field of purchasing and supply chain management, and to take this information on the case organization level to identify the most important com...

  1. Identifying and recruiting sponsors for Uganda Olympic Committee

    OpenAIRE

    Nuwagaba, Godfrey; Delpy, Lisa

    2012-01-01

    Sponsorship is one of the biggest challenge facing Olympic sports in Uganda. Many sports disciplines have not been able to identify, recruit, and sustain sponsors.. This has hampered team preparations, training, provision of kits, and consequently poor performance of individuals and teams at all levels. To avert this situation, Uganda Olympic Committee (UOC) needs to identify and recruit capable sponsors in order to allow long term planning and execution of strategic plans. This research stud...

  2. Newly identified YSO candidates towards the LDN 1188

    CERN Document Server

    Marton, Gábor; Kiss, Csaba; Smidla, József

    2013-01-01

    We present an analysis of Young Stellar Object (YSO) candidates towards the LDN 1188 molecular cloud. The YSO candidates were selected from the WISE all-sky catalogue, based on a statistical method. We found 601 candidates in the region, and classified them as Class I, Flat and Class II YSOs. Groups were identified and described with the Minimal Spanning Tree (MST) method. Previously identified molecular cores show evidence of ongoing star formation at different stages throughout the cloud complex.

  3. Identifying patients at risk of emergency admission for colorectal cancer

    OpenAIRE

    Wallace, D.; Walker, K.; Kuryba, A; Finan, P; Scott, N.; Van Der Meulen, J.

    2014-01-01

    Background: Patients whose colorectal cancer is treated after an emergency admission tend to have late-stage cancer and a poor prognosis. We identified risk factors for an emergency admission by linking data from the National Bowel Cancer Audit (NBCA) and the English Hospital Episode Statistics (HES), an administrative database of all admissions to English National Health Service hospitals, which includes data on mode of admission. Methods: We identified all adults included in the NBCA with a...

  4. Identifying Cancer Driver Genes Using Replication-Incompetent Retroviral Vectors

    Directory of Open Access Journals (Sweden)

    Victor M. Bii

    2016-10-01

    Full Text Available Identifying novel genes that drive tumor metastasis and drug resistance has significant potential to improve patient outcomes. High-throughput sequencing approaches have identified cancer genes, but distinguishing driver genes from passengers remains challenging. Insertional mutagenesis screens using replication-incompetent retroviral vectors have emerged as a powerful tool to identify cancer genes. Unlike replicating retroviruses and transposons, replication-incompetent retroviral vectors lack additional mutagenesis events that can complicate the identification of driver mutations from passenger mutations. They can also be used for almost any human cancer due to the broad tropism of the vectors. Replication-incompetent retroviral vectors have the ability to dysregulate nearby cancer genes via several mechanisms including enhancer-mediated activation of gene promoters. The integrated provirus acts as a unique molecular tag for nearby candidate driver genes which can be rapidly identified using well established methods that utilize next generation sequencing and bioinformatics programs. Recently, retroviral vector screens have been used to efficiently identify candidate driver genes in prostate, breast, liver and pancreatic cancers. Validated driver genes can be potential therapeutic targets and biomarkers. In this review, we describe the emergence of retroviral insertional mutagenesis screens using replication-incompetent retroviral vectors as a novel tool to identify cancer driver genes in different cancer types.

  5. Identifying and retargeting transcriptional hot spots in the human genome.

    Science.gov (United States)

    Cheng, Joseph K; Lewis, Amanda M; Kim, Do Soon; Dyess, Timothy; Alper, Hal S

    2016-08-01

    Mammalian cell line development requires streamlined methodologies that will reduce both the cost and time to identify candidate cell lines. Improvements in site-specific genomic editing techniques can result in flexible, predictable, and robust cell line engineering. However, an outstanding question in the field is the specific site of integration. Here, we seek to identify productive loci within the human genome that will result in stable, high expression of heterologous DNA. Using an unbiased, random integration approach and a green fluorescent reporter construct, we identify ten single-integrant, recombinant human cell lines that exhibit stable, high-level expression. From these cell lines, eight unique corresponding integration loci were identified. These loci are concentrated in non-protein coding regions or intronic regions of protein coding genes. Expression mapping of the surrounding genes reveals minimal disruption of endogenous gene expression. Finally, we demonstrate that targeted de novo integration at one of the identified loci, the 12(th) exon-intron region of the GRIK1 gene on chromosome 21, results in superior expression and stability compared to the standard, illegitimate integration approach at levels approaching 4-fold. The information identified here along with recent advances in site-specific genomic editing techniques can lead to expedited cell line development.

  6. Fungi identify the geographic origin of dust samples.

    Directory of Open Access Journals (Sweden)

    Neal S Grantham

    Full Text Available There is a long history of archaeologists and forensic scientists using pollen found in a dust sample to identify its geographic origin or history. Such palynological approaches have important limitations as they require time-consuming identification of pollen grains, a priori knowledge of plant species distributions, and a sufficient diversity of pollen types to permit spatial or temporal identification. We demonstrate an alternative approach based on DNA sequencing analyses of the fungal diversity found in dust samples. Using nearly 1,000 dust samples collected from across the continental U.S., our analyses identify up to 40,000 fungal taxa from these samples, many of which exhibit a high degree of geographic endemism. We develop a statistical learning algorithm via discriminant analysis that exploits this geographic endemicity in the fungal diversity to correctly identify samples to within a few hundred kilometers of their geographic origin with high probability. In addition, our statistical approach provides a measure of certainty for each prediction, in contrast with current palynology methods that are almost always based on expert opinion and devoid of statistical inference. Fungal taxa found in dust samples can therefore be used to identify the origin of that dust and, more importantly, we can quantify our degree of certainty that a sample originated in a particular place. This work opens up a new approach to forensic biology that could be used by scientists to identify the origin of dust or soil samples found on objects, clothing, or archaeological artifacts.

  7. SitesIdentify: a protein functional site prediction tool

    Directory of Open Access Journals (Sweden)

    Doig Andrew J

    2009-11-01

    Full Text Available Abstract Background The rate of protein structures being deposited in the Protein Data Bank surpasses the capacity to experimentally characterise them and therefore computational methods to analyse these structures have become increasingly important. Identifying the region of the protein most likely to be involved in function is useful in order to gain information about its potential role. There are many available approaches to predict functional site, but many are not made available via a publicly-accessible application. Results Here we present a functional site prediction tool (SitesIdentify, based on combining sequence conservation information with geometry-based cleft identification, that is freely available via a web-server. We have shown that SitesIdentify compares favourably to other functional site prediction tools in a comparison of seven methods on a non-redundant set of 237 enzymes with annotated active sites. Conclusion SitesIdentify is able to produce comparable accuracy in predicting functional sites to its closest available counterpart, but in addition achieves improved accuracy for proteins with few characterised homologues. SitesIdentify is available via a webserver at http://www.manchester.ac.uk/bioinformatics/sitesidentify/

  8. Effectively identifying user profiles in network and host metrics

    Science.gov (United States)

    Murphy, John P.; Berk, Vincent H.; Gregorio-de Souza, Ian

    2010-04-01

    This work presents a collection of methods that is used to effectively identify users of computers systems based on their particular usage of the software and the network. Not only are we able to identify individual computer users by their behavioral patterns, we are also able to detect significant deviations in their typical computer usage over time, or compared to a group of their peers. For instance, most people have a small, and relatively unique selection of regularly visited websites, certain email services, daily work hours, and typical preferred applications for mandated tasks. We argue that these habitual patterns are sufficiently specific to identify fully anonymized network users. We demonstrate that with only a modest data collection capability, profiles of individual computer users can be constructed so as to uniquely identify a profiled user from among their peers. As time progresses and habits or circumstances change, the methods presented update each profile so that changes in user behavior can be reliably detected over both abrupt and gradual time frames, without losing the ability to identify the profiled user. The primary benefit of our methodology allows one to efficiently detect deviant behaviors, such as subverted user accounts, or organizational policy violations. Thanks to the relative robustness, these techniques can be used in scenarios with very diverse data collection capabilities, and data privacy requirements. In addition to behavioral change detection, the generated profiles can also be compared against pre-defined examples of known adversarial patterns.

  9. On the Identifiability of the Post-Nonlinear Causal Model

    CERN Document Server

    Zhang, Kun

    2012-01-01

    By taking into account the nonlinear effect of the cause, the inner noise effect, and the measurement distortion effect in the observed variables, the post-nonlinear (PNL) causal model has demonstrated its excellent performance in distinguishing the cause from effect. However, its identifiability has not been properly addressed, and how to apply it in the case of more than two variables is also a problem. In this paper, we conduct a systematic investigation on its identifiability in the two-variable case. We show that this model is identifiable in most cases; by enumerating all possible situations in which the model is not identifiable, we provide sufficient conditions for its identifiability. Simulations are given to support the theoretical results. Moreover, in the case of more than two variables, we show that the whole causal structure can be found by applying the PNL causal model to each structure in the Markov equivalent class and testing if the disturbance is independent of the direct causes for each va...

  10. Nursing diagnoses identified in children with acute respiration infection

    Directory of Open Access Journals (Sweden)

    Flávia Paula Magalhães Monteiro

    2006-08-01

    Full Text Available A cross-sectional study developed with 78 children with until five years old, bearers of acute respiration infection interned in pediatric hospital of the periphery of a great city, with the purpose to identify the nursing diagnoses presented by these children. The number of nursing diagnoses, defining characteristics, related factors and risk factors identified and other numerical variables were analyzed based in theirs central tendency and dispersion measures. It was identified a total of 26 nursing diagnoses, 43 related factors, 14 risk factors e 67 defining characteristics. In average, It was found 5,32 nursing diagnoses; 4,10 related factors; 2,03 risk factors and 7,33 defining characteristics. The nursing diagnoses with the biggest proportion were: Ineffective Breathing Pattern, Risk for delayed growth, Ineffective protection and Altered oral mucous membrane. We concluded that children with acute respiration infection present a complex diagnostic frame including human responses of multiples domains.

  11. Benchmarking in Identifying Priority Directions of Development of Telecommunication Operators

    Directory of Open Access Journals (Sweden)

    Zaharchenko Lolita A.

    2013-12-01

    Full Text Available The article analyses evolution of development and possibilities of application of benchmarking in the telecommunication sphere. It studies essence of benchmarking on the basis of generalisation of approaches of different scientists to definition of this notion. In order to improve activity of telecommunication operators, the article identifies the benchmarking technology and main factors, that determine success of the operator in the modern market economy, and the mechanism of benchmarking and component stages of carrying out benchmarking by a telecommunication operator. It analyses the telecommunication market and identifies dynamics of its development and tendencies of change of the composition of telecommunication operators and providers. Having generalised the existing experience of benchmarking application, the article identifies main types of benchmarking of telecommunication operators by the following features: by the level of conduct of (branch, inter-branch and international benchmarking; by relation to participation in the conduct (competitive and joint; and with respect to the enterprise environment (internal and external.

  12. Stochastic search variable selection for identifying multiple quantitative trait loci.

    Science.gov (United States)

    Yi, Nengjun; George, Varghese; Allison, David B

    2003-07-01

    In this article, we utilize stochastic search variable selection methodology to develop a Bayesian method for identifying multiple quantitative trait loci (QTL) for complex traits in experimental designs. The proposed procedure entails embedding multiple regression in a hierarchical normal mixture model, where latent indicators for all markers are used to identify the multiple markers. The markers with significant effects can be identified as those with higher posterior probability included in the model. A simple and easy-to-use Gibbs sampler is employed to generate samples from the joint posterior distribution of all unknowns including the latent indicators, genetic effects for all markers, and other model parameters. The proposed method was evaluated using simulated data and illustrated using a real data set. The results demonstrate that the proposed method works well under typical situations of most QTL studies in terms of number of markers and marker density. PMID:12871920

  13. Rapid identifying high-influence nodes in complex networks

    Institute of Scientific and Technical Information of China (English)

    宋波; 蒋国平; 宋玉蓉; 夏玲玲

    2015-01-01

    A tiny fraction of infl uential individuals play a critical role in the dynamics on complex systems. Identifying the infl uential nodes in complex networks has theoretical and practical significance. Considering the uncertainties of network scale and topology, and the timeliness of dynamic behaviors in real networks, we propose a rapid identifying method (RIM) to find the fraction of high-infl uential nodes. Instead of ranking all nodes, our method only aims at ranking a small number of nodes in network. We set the high-infl uential nodes as initial spreaders, and evaluate the performance of RIM by the susceptible–infected–recovered (SIR) model. The simulations show that in different networks, RIM performs well on rapid identifying high-infl uential nodes, which is verified by typical ranking methods, such as degree, closeness, betweenness, and eigenvector centrality methods.

  14. Family and academic performance: identifying high school student profiles

    Directory of Open Access Journals (Sweden)

    Alicia Aleli Chaparro Caso López

    2016-01-01

    Full Text Available The objective of this study was to identify profiles of high school students, based on variables related to academic performance, socioeconomic status, cultural capital and family organization. A total of 21,724 high school students, from the five municipalities of the state of Baja California, took part. A K-means cluster analysis was performed to identify the profiles. The analyses identified two clearly-defined clusters: Cluster 1 grouped together students with high academic performance and who achieved higher scores for socioeconomic status, cultural capital and family involvement, whereas Cluster 2 brought together students with low academic achievement, and who also obtained lower scores for socioeconomic status and cultural capital, and had less family involvement. It is concluded that the family variables analyzed form student profiles that can be related to academic achievement.

  15. A Study of Scientometric Methods to Identify Emerging Technologies

    Energy Technology Data Exchange (ETDEWEB)

    Abercrombie, Robert K [ORNL; Udoeyop, Akaninyene W [ORNL

    2011-01-01

    This work examines a scientometric model that tracks the emergence of an identified technology from initial discovery (via original scientific and conference literature), through critical discoveries (via original scientific, conference literature and patents), transitioning through Technology Readiness Levels (TRLs) and ultimately on to commercial application. During the period of innovation and technology transfer, the impact of scholarly works, patents and on-line web news sources are identified. As trends develop, currency of citations, collaboration indicators, and on-line news patterns are identified. The combinations of four distinct and separate searchable on-line networked sources (i.e., scholarly publications and citation, worldwide patents, news archives, and on-line mapping networks) are assembled to become one collective network (a dataset for analysis of relations). This established network becomes the basis from which to quickly analyze the temporal flow of activity (searchable events) for the example subject domain we investigated.

  16. Identifying Differentially Abundant Metabolic Pathways in Metagenomic Datasets

    Science.gov (United States)

    Liu, Bo; Pop, Mihai

    Enabled by rapid advances in sequencing technology, metagenomic studies aim to characterize entire communities of microbes bypassing the need for culturing individual bacterial members. One major goal of such studies is to identify specific functional adaptations of microbial communities to their habitats. Here we describe a powerful analytical method (MetaPath) that can identify differentially abundant pathways in metagenomic data-sets, relying on a combination of metagenomic sequence data and prior metabolic pathway knowledge. We show that MetaPath outperforms other common approaches when evaluated on simulated datasets. We also demonstrate the power of our methods in analyzing two, publicly available, metagenomic datasets: a comparison of the gut microbiome of obese and lean twins; and a comparison of the gut microbiome of infant and adult subjects. We demonstrate that the subpathways identified by our method provide valuable insights into the biological activities of the microbiome.

  17. Drosophila Cancer Models Identify Functional Differences between Ret Fusions.

    Science.gov (United States)

    Levinson, Sarah; Cagan, Ross L

    2016-09-13

    We generated and compared Drosophila models of RET fusions CCDC6-RET and NCOA4-RET. Both RET fusions directed cells to migrate, delaminate, and undergo EMT, and both resulted in lethality when broadly expressed. In all phenotypes examined, NCOA4-RET was more severe than CCDC6-RET, mirroring their effects on patients. A functional screen against the Drosophila kinome and a library of cancer drugs found that CCDC6-RET and NCOA4-RET acted through different signaling networks and displayed distinct drug sensitivities. Combining data from the kinome and drug screens identified the WEE1 inhibitor AZD1775 plus the multi-kinase inhibitor sorafenib as a synergistic drug combination that is specific for NCOA4-RET. Our work emphasizes the importance of identifying and tailoring a patient's treatment to their specific RET fusion isoform and identifies a multi-targeted therapy that may prove effective against tumors containing the NCOA4-RET fusion. PMID:27626672

  18. Identifying influential spreaders in complex networks based on gravity formula

    CERN Document Server

    Ma, Ling-Ling; Zhang, Hai-Feng

    2015-01-01

    How to identify the influential spreaders in social networks is crucial for accelerating/hindering information diffusion, increasing product exposure, controlling diseases and rumors, and so on. In this paper, by viewing the k-shell value of each node as its mass and the shortest path distance between any two nodes as their distance, then inspired by the idea of the gravity formula, we propose a gravity centrality index to identify the influential spreaders in complex networks. The comparison between the gravity centrality index with some well-known centralities, such as degree centrality, betweenness centrality, closeness centrality, and k-shell centrality, and so forth, indicates that our method can effectively identify the influential spreaders in real networks as well as artificial networks. We also use the classical Susceptible-Infected-Recovered (SIR) epidemic model to verify the good performance of our method.

  19. Identifying the interactions in a colored dynamical network

    Institute of Scientific and Technical Information of China (English)

    吴召艳; 弓晓利

    2015-01-01

    The interactions of a colored dynamical network play a great role in its dynamical behaviour and are denoted by outer and inner coupling matrices. In this paper, the outer and inner coupling matrices are assumed to be unknown and need to be identified. A corresponding network estimator is designed for identifying the unknown interactions by adopting proper adaptive laws. Based on the Lyapunov function method and Barbalat’s lemma, the obtained result is analytically proved. A colored network coupled with chaotic Lorenz, Chen, and L ¨u systems is considered as a numerical example to illustrate the effectiveness of the proposed method.

  20. A novel stroke locus identified in a northern Sweden pedigree

    DEFF Research Database (Denmark)

    Janunger, T.; Nilsson-Ardnor, S.; Wiklund, P.-G.;

    2009-01-01

    OBJECTIVES: The population of northern Sweden is characterized by reduced genetic diversity and a high incidence of stroke. We sought to reduce genetic variation further, using genealogic analysis in a set of nuclear families affected by stroke, and we subsequently performed a genome-wide scan to...... of 4.81 on chromosome 9q31-q33 was detected. Haplotype analysis identified a common 2.2-megabase interval in the chromosomal region in 4 of the nuclear families, where an overrepresentation of intracerebral hemorrhage was observed. CONCLUSIONS: We have identified a novel susceptibility locus for...... stroke. Haplotype analysis suggests that a shared genetic factor is of particular importance for intracerebral hemorrhage....

  1. Recent developments in methods for identifying reaction coordinates.

    Science.gov (United States)

    Li, Wenjin; Ma, Ao

    2014-01-01

    In the study of rare events in complex systems with many degrees of freedom, a key element is to identify the reaction coordinates of a given process. Over recent years, a number of methods and protocols have been developed to extract the reaction coordinates based on limited information from molecular dynamics simulations. In this review, we provide a brief survey over a number of major methods developed in the past decade, some of which are discussed in greater detail, to provide an overview of the problems that are partially solved and challenges that still remain. A particular emphasis has been placed on methods for identifying reaction coordinates that are related to the committor.

  2. Recent Developments in Methods for Identifying Reaction Coordinates

    CERN Document Server

    Li, Wenjin

    2015-01-01

    In the study of rare events in complex systems with many degrees of freedom, a key element is to identify the reaction coordinates of a given process. Over recent years, a number of methods and protocols have been developed to extract the reaction coordinates based on limited information from molecular dynamics simulations. In this review, we provide a brief survey over a number of major methods developed in the past decade, some of which are discussed in greater detail, to provide an overview of the problems that are partially solved and challenges that still remain. A particular emphasis has been placed on methods for identifying reaction coordinates that are related to the committor.

  3. Identifying information technology competencies needed in Singapore nursing education.

    Science.gov (United States)

    Yee, Chia Choon

    2002-01-01

    The purpose of the study was to identify Singapore's healthcare industry's minimum information technology (IT) performance standard expectations for nurses' competencies. A needs assessment was conducted with a panel representing nursing education, nursing management and nursing practice. The findings in this study would provide suggestions to improve the current diploma and advanced diploma nursing programs curricula to meet the present workforce demands. The experts agreed that information technology is necessary and there were two main categories of IT skills identified, basic IT skills and work-related IT skills.

  4. Identifying risks in the realm of enterprise risk management.

    Science.gov (United States)

    Carroll, Roberta

    2016-01-01

    An enterprise risk management (ERM) discipline is comprehensive and organization-wide. The effectiveness of ERM is governed in part by the strength and breadth of its practices and processes. An essential element in decision making is a thorough process by which organizational risks and value opportunities can be identified. This article will offer identification techniques that go beyond those used in traditional risk management programs and demonstrate how these techniques can be used to identify risks and opportunity in the ERM environment. PMID:26789745

  5. Identifying Lead Markets in the European Automotive Industry

    DEFF Research Database (Denmark)

    Cleff, Thomas; Grimpe, Christoph; Rammer, Christian

    2015-01-01

    This paper presents an indicator-based methodology to identify lead markets in the European automotive industry. The lead market approach tries to explain why certain countries are better positioned than others for developing and launching new products. While much research stresses the role...... from the automotive industry should exploit this diversity of market characteristics within Europe when developing and launching new products...... design. We use an indicator-based approach which has been successfully employed for individual products as well as for various industries in order to identify lead markets in the European automotive industry. Employing five lead market factors, our results show that the EU is by far no homogeneous market...

  6. Applications for unique identifiers in the geological sciences

    Science.gov (United States)

    Klump, J.; Lehnert, K. A.

    2012-12-01

    Even though geology has always been a generalist discipline in many parts, approaches towards questions about Earth's past have become increasingly interdisciplinary. At the same time, a wealth of samples has been collected, the resulting data have been stored in in disciplinary databases, the interpretations published in scientific literature. In the past these resources have existed alongside each other, semantically linked only by the knowledge of the researcher and his peers. One of the main drivers towards the inception of the world wide web was the ability to link scientific sources over the internet. The Uniform Resource Locator (URL) used to locate resources on the web soon turned out to be ephemeral in nature. A more reliable way of addressing objects was needed, a way of persistent identification to make digital objects, or digital representations of objects, part of the record of science. With their high degree of centralisation the scientific publishing houses were quick to implement and adopt a system for unique and persistent identification, the Digital Object Identifier (DOI) ®. At the same time other identifier systems exist alongside DOI, e.g. URN, ARK, handle ®, and others. There many uses for persistent identification in science, other than the identification of journal articles. DOI are already used for the identification of data, thus making data citable. There are several initiatives to assign identifiers to authors and institutions to allow unique identification. A recent development is the application of persistent identifiers for geological samples. As most data in the geosciences are derived from samples, it is crucial to be able to uniquely identify the samples from which a set of data were derived. Incomplete documentation of samples in publications, use of ambiguous sample names are major obstacles for synthesis studies and re-use of data. Access to samples for re-analysis and re-appraisal is limited due to the lack of a central

  7. Identifying Effective Classroom Practices Using Student Achievement Data

    Science.gov (United States)

    Kane, Thomas J.; Taylor, Eric S.; Tyler, John H.; Wooten, Amy L.

    2011-01-01

    Research continues to find large differences in student achievement gains across teachers' classrooms. The variability in teacher effectiveness raises the stakes on identifying effective teachers and teaching practices. This paper combines data from classroom observations of teaching practices and measures of teachers' ability to improve student…

  8. Assessing the identifiability in isotope exchange depth profiling measurements

    DEFF Research Database (Denmark)

    Ciucci, Francesco; Panagakos, Grigorios; Chen, Chi;

    2014-01-01

    of identifiability in Isotope Exchange Depth Profiling (IEDP), an important characterization tool in the ionics field, by exploring the measurability of k and D as a function of two dimensionless quantities, the Biot number, and the annealing time divided by the diffusional time scale. In addition, we show a novel...

  9. Identifying and Mitigating Sources of School Revenue Erosion

    Science.gov (United States)

    Prombo, Michael; Dalianis, Ares G.; Metcalf, Scott R.

    2009-01-01

    Preserving existing revenues is an essential component of the work of school business officials. The broad ranges of activities that can affect school district revenues make identifying potential threats difficult. By understanding the issues that affect school district revenue, school business officials are better able to diminish its erosion--a…

  10. Identifying Psychopathy Subtypes on the Basis of Personality Structure

    Science.gov (United States)

    Hicks, Brian M.; Markon, Kristian E.; Patrick, Christopher J.; Krueger, Robert F.; Newman, Joseph P.

    2004-01-01

    The authors used model-based cluster analysis to identify subtypes of criminal psychopaths on the basis of differences in personality structure. Participants included 96 male prisoners diagnosed as psychopathic, using the Psychopathy Checklist Revised (PCL-R; R. D. Hare, 1991). Personality was assessed using the brief form of the Multidimensional…

  11. Identifying populations at risk from environmental contamination from point sources

    OpenAIRE

    Williams, F; Ogston, S

    2002-01-01

    Objectives: To compare methods for defining the population at risk from a point source of air pollution. A major challenge for environmental epidemiology lies in correctly identifying populations at risk from exposure to environmental pollutants. The complexity of today's environment makes it essential that the methods chosen are accurate and sensitive.

  12. Identifying workers at risk of sickness absence by questionnaire

    NARCIS (Netherlands)

    Roelen, Corne A. M.; van der Pol, Tjepke R.; Koopmans, Petra C.; Groothoff, Johan W.

    2006-01-01

    Background Sickness absence is an important economic problem, because of high costs and lost productivity. Determining factors associated with increased risk of sickness absence may lead to the development of preventive measures. Aims To determine whether self-report questionnaires can identify thos

  13. Fetal alcohol-spectrum disorders: identifying at-risk mothers.

    Science.gov (United States)

    Montag, Annika C

    2016-01-01

    Fetal alcohol-spectrum disorders (FASDs) are a collection of physical and neurobehavioral disabilities caused by prenatal exposure to alcohol. To prevent or mitigate the costly effects of FASD, we must identify mothers at risk for having a child with FASD, so that we may reach them with interventions. Identifying mothers at risk is beneficial at all time points, whether prior to pregnancy, during pregnancy, or following the birth of the child. In this review, three approaches to identifying mothers at risk are explored: using characteristics of the mother and her pregnancy, using laboratory biomarkers, and using self-report assessment of alcohol-consumption risk. At present, all approaches have serious limitations. Research is needed to improve the sensitivity and specificity of biomarkers and screening instruments, and to link them to outcomes as opposed to exposure. Universal self-report screening of all women of childbearing potential should ideally be incorporated into routine obstetric and gynecologic care, followed by brief interventions, including education and personalized feedback for all who consume alcohol, and referral to treatment as indicated. Effective biomarkers or combinations of biomarkers may be used during pregnancy and at birth to determine maternal and fetal alcohol exposure. The combination of self-report and biomarker screening may help identify a greater proportion of women at risk for having a child with FASD, allowing them to access information and treatment, and empowering them to make decisions that benefit their children.

  14. Identifying Quality in Preschool Education: Progress and Challenge

    Science.gov (United States)

    Hughes, Jan N.

    2010-01-01

    In this article, the author comments on Dominguez, Vitiello, Maier, and Greenfield's (2010) article on identifying quality in preschool education. Dominguez et al. have conducted a methodologically sophisticated study describing the growth of learning behavior among Head Start children. By doing so, they contribute to a growing body of evidence…

  15. New technique for identifying varieties resistance to rice blast

    Institute of Scientific and Technical Information of China (English)

    ZHUPeiliang

    1994-01-01

    After 8 yrs lab experiments and field tests, an advanced technique for identifying varieties resistance to rice blast was developed by a research group in Plant Protection Institute, Zhejiang Academy of AgricuLltural Sciences. With this technique, the inoculum was prepared on a maizc-rice-straw-agar media which was suitable for sporulation of most rice blast pathogen isolates.

  16. Identifying Individual Excellence: The Dependable Strengths Articulation Process.

    Science.gov (United States)

    Boivin-Brown, Allen; Haldane, Jean; Forster, Jerald

    This paper was written to describe the essential tasks of a process known as Dependable Strengths Articulation (DSA) and how career development practitioners can acquire the skills to use the process. DSA, when combined with practices known as Job Magnet, helps participants identify their individual excellence and then use this knowledge to…

  17. Nuclear techniques to identify allergenic metals in orthodontic brackets

    International Nuclear Information System (INIS)

    The present study determines the elementary alloy composition of ten commercial brands of brackets, especially related to Ni, Cr, and Co metals, confirmed allergenic elements. The nuclear techniques applied in the analyses were X-ray fluorescence (XRF) - Centre National de la Recherche Scientifique, France (National Center of Scientific Research), and X-ray energy spectrometry (XRES), and Instrumental Neutron Activation Analysis (INAA) - CDTN/CNEN, Brazil. The XRES and XRF techniques identified Cr in the 10 samples analyzed and Ni in eight samples. The INAA technique identified the presence of Cr (14% to 19%) and Co (42% to 2400 ppm) in all samples. The semi-quantitative analysis performed by XRF also identified Co in two samples. The techniques were effective in the identification of metals in orthodontic brackets. The elements identified in this study can be considered one of the main reason for the allergic processes among the patients studied. This finding suggests that the patients should be tested for allergy and allergenic sensibility to metals prior to the prescription of orthodontic device. (author)

  18. Examination of Leadership Practices of Principals Identified as Servant Leaders

    Science.gov (United States)

    Taylor, Tim; Martin, Barbara N.; Hutchinson, Sandy; Jinks, Michael

    2007-01-01

    The purpose of this study was to examine the leadership practices of principals identified as servant leaders. The conceptual framework used to access the leadership behaviours was the leadership practices advocated by Kouzes and Posner. Statistical analysis included a multivariate test to determine if the demographic variables were significantly…

  19. Research to Identify Effective Antifungal Agents, 1992 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Schreck, Carl

    1993-03-01

    This study is a continuation of ``Research to Identify Effective Antifungal Agents'' sponsored by Bonneville Power Administration (Schreck et al. 1990 and Schreck et al. 1991). The objectives of the present study were to select and evaluate up to 10 candidate fungicides.

  20. Identifying Hearing Loss in Young Children: Technology Replaces the Bell

    Science.gov (United States)

    Eiserman, William; Shisler, Lenore

    2010-01-01

    Hearing loss can too easily be misdiagnosed or overlooked by providers serving young children. Parents and professionals may observe a language delay--an "invisible" condition--while failing to identify the underlying cause. Otoacoustic emissions (OAE) hearing screening technology, used extensively with newborns, is becoming an essential tool,…

  1. Identifying targets for quality improvement in hospital antibiotic prescribing

    NARCIS (Netherlands)

    Spreuwel, P.C. van; Blok, H.; Langelaar, M.F.; Kullberg, B.J.; Mouton, J.W.; Natsch, S.S.

    2015-01-01

    OBJECTIVES: To audit antibiotic use in a university hospital and to identify targets for quality improvement in a setting with low antibiotic use and resistance rates. METHODOLOGY: A point-prevalence survey (PPS), using a patient-based audit tool for antibiotic use, was executed in the Radboud Unive

  2. 7 CFR 70.55 - Check grading officially identified product.

    Science.gov (United States)

    2010-01-01

    ... AND STANDARDS UNDER THE AGRICULTURAL MARKETING ACT OF 1946 AND THE EGG PRODUCTS INSPECTION ACT (CONTINUED) VOLUNTARY GRADING OF POULTRY PRODUCTS AND RABBIT PRODUCTS Grading of Poultry Products and Rabbit... identified poultry or rabbit products may be subject to final check grading prior to their shipment....

  3. Researchers Develop Method to Identify Sparticles in Big Bang Conditions

    CERN Multimedia

    2008-01-01

    Three Northeastern University researchers have proposed a new approach for the highly anticipated discovery of supersymmetric particles, often called sparticles. The methodology, which was published in the December 21 issue of the Physical Review Letters, is based on identifying the hierarchical mass patterns of sparticles, which are assumed to exist in a new class of particle physics theories beyond the Standard Model.

  4. Development of microsatellite markers for identifying Brazilian coffee arabica varieties

    NARCIS (Netherlands)

    Vieira, E.S.N.; Pinho, Von E.V.R.; Carvalho, M.G.G.; Esselink, G.; Vosman, B.

    2010-01-01

    Microsatellite markers, also known as SSRs (Simple Sequence Repeats), have proved to be excellent tools for identifying variety and determining genetic relationships. A set of 127 SSR markers was used to analyze genetic similarity in twenty five Coffea arabica varieties. These were composed of ninet

  5. Identifying Food Safety Concerns when Communication Barriers Exist

    Science.gov (United States)

    Neal, Jack A.; Dawson, Mary; Madera, Juan M.

    2011-01-01

    Abstract: Students must be prepared to lead a diverse workforce. The objective of this study was to establish a teaching method that helps students identify barriers to food safety while working in a simulated environment with communication barriers. This study employed a perspective taking exercise based upon the principles of social learning…

  6. Text mining electronic health records to identify hospital adverse events

    DEFF Research Database (Denmark)

    Gerdes, Lars Ulrik; Hardahl, Christian

    2013-01-01

    Manual reviews of health records to identify possible adverse events are time consuming. We are developing a method based on natural language processing to quickly search electronic health records for common triggers and adverse events. Our results agree fairly well with those obtained using manual...... reviews, and we therefore believe that it is possible to develop automatic tools for monitoring aspects of patient safety....

  7. The Development of Procedures for Identifying Competitive Behavior in Children

    Science.gov (United States)

    Mithaug, Dennis E.

    1973-01-01

    Identifies events in the competitive process that could be employed to discriminate between competition and individual, nonsocial behaviors. If a subject is working for the competitive contingency and checks his progress against another's, his behavior may be classified as competitive rather than individual, nonsocial behavior. (DP)

  8. Identifying core domains to assess flare in rheumatoid arthritis

    DEFF Research Database (Denmark)

    Bartlett, Susan J; Hewlett, Sarah; Bingham, Clifton O;

    2012-01-01

    For rheumatoid arthritis (RA), there is no consensus on how to define and assess flare. Variability in flare definitions impairs understanding of findings across studies and limits ability to pool results. The OMERACT RA Flare Group sought to identify domains to define RA flares from patient...

  9. Identifying the "Truly Disadvantaged": A Comprehensive Biosocial Approach

    Science.gov (United States)

    Barnes, J. C.; Beaver, Kevin M.; Connolly, Eric J.; Schwartz, Joseph A.

    2016-01-01

    There has been significant interest in examining the developmental factors that predispose individuals to chronic criminal offending. This body of research has identified some social-environmental risk factors as potentially important. At the same time, the research producing these results has generally failed to employ genetically sensitive…

  10. Implications of Identifying Additional Cerebral Metastases during Gamma Knife Radiosurgery

    Directory of Open Access Journals (Sweden)

    Toral R. Patel

    2012-01-01

    Full Text Available Introduction. Gamma Knife radiosurgery (GK-SRS is commonly used to treat cerebral metastases. Although additional intracranial metastases are often found on the day of GK-SRS, the significance of finding them is unknown. Methods. A retrospective review of 133 patients undergoing GK-SRS for cerebral metastases was performed. The change in number of metastases detected between initial referral magnetic resonance imaging (MRI and subsequent treatment MRI was quantified. Multivariate and Kaplan-Meier analyses were employed to examine the significance of identifying additional lesions. Results. Additional lesions were identified in 41% of patients. An increasing number of metastases on referral MRI (=0.001 and the presence of progressive systemic disease (=0.003 were predictive of identifying additional metastases. Median survival was 6.9 months for patients with additional metastases, compared to 12.1 months for patients without additional metastases (hazard ratio 1.56, =0.021. Conclusions. Identifying additional metastases on the day of GK-SRS may add important prognostic information.

  11. Systems constellations : A better way to identify branding opportunities?

    NARCIS (Netherlands)

    Jurg, W.; Bloemer, J.; Doorewaard, H.; Peelen, E.

    2008-01-01

    Building strong brands has become one of the main marketing priorities for brand-supportive companies. The leading positivist paradigm in marketing may not be, however, the most-effective perspective in identifying branding opportunities. This paper offers an alternative phenomenological point of vi

  12. Neurobehavioral Mutants Identified in an ENU Mutagenesis Project

    Energy Technology Data Exchange (ETDEWEB)

    Cook, Melloni N. [University of Memphis; Dunning, Jonathan P [University of Memphis; Wiley, Ronald G [Vanderbilt University and Veterans Administration, Nashville, TN; Chesler, Elissa J [ORNL; Johnson, Dabney K [ORNL; Goldowitz, Daniel [University of Tennessee Health Science Center, Memphis

    2007-01-01

    We report on a behavioral screening test battery that successfully identified several neurobehavioral mutants among a large-scale ENU-mutagenized mouse population. Large numbers of ENU mutagenized mice were screened for abnormalities in central nervous system function based on abnormal performance in a series of behavior tasks. We developed and employed a high-throughput screen of behavioral tasks to detect behavioral outliers. Twelve mutant pedigrees, representing a broad range of behavioral phenotypes, have been identified. Specifically, we have identified two open field mutants (one displaying hyper-locomotion, the other hypo-locomotion), four tail suspension mutants (all displaying increased immobility), one nociception mutant (displaying abnormal responsiveness to thermal pain), two prepulse inhibition mutants (displaying poor inhibition of the startle response), one anxiety-related mutant (displaying decreased anxiety in the light/dark test), and one learning and memory mutant (displaying reduced response to the conditioned stimulus) These findings highlight the utility of a set of behavioral tasks used in a high throughput screen to identify neurobehavioral mutants. Further analysis (i.e., behavioral and genetic mapping studies) of mutants is in progress with the ultimate goal of identification of novel genes and mouse models relevant to human disorders as well as the identification of novel therapeutic targets.

  13. Challenges of Identifying Communities with Shared Semantics in Enterprise Modeling

    NARCIS (Netherlands)

    Hoppenbrouwers, Stijn; Linden, D. van der

    2012-01-01

    In this paper we discuss the use and challenges of identifying communities with shared semantics in Enterprise Modeling. People tend to understand modeling meta-concepts (i.e., a modeling language’s constructs or types) in a certain way and can be grouped by this understanding. Having an insight int

  14. Identifying slip systems around indentations in FCC metals

    International Nuclear Information System (INIS)

    Atomic force and orientation imaging microscopy can be used to identify slip planes responsible for slip step formation around indentations in FCC polycrystalline engineering alloys. The character of the slip steps provides insight into the material's slip mode and the step patterns can be used to study dislocation reactions

  15. Identifying slip systems around indentations in FCC metals

    Energy Technology Data Exchange (ETDEWEB)

    Nibur, K.A.; Bahr, D.F

    2003-12-15

    Atomic force and orientation imaging microscopy can be used to identify slip planes responsible for slip step formation around indentations in FCC polycrystalline engineering alloys. The character of the slip steps provides insight into the material's slip mode and the step patterns can be used to study dislocation reactions.

  16. Beyond basic citation—What to identify, when, and why

    Science.gov (United States)

    Parsons, M. A.

    2015-12-01

    Persistent identifiers (and locators) have emerged as a critical component in designing and implementing information systems and networks. This is especially evident in the use of the Digital Object Identifier in association with formal bibliographic citation of literature and increasingly of data sets. Indeed, the principles and methods of data citation have been a hot topic in the informatics community over the last decade or so. To date the focus has typically been on closely linking data sets to associated literature and generally emulating bibliographic-style citation. To design a sustainable, trusted data infrastructure, however, requires us to unambiguously reference many things in many ways, be they data, software, instruments, methods, or people. Design of this infrastructure also requires us to consider the entire data lifecycle and when important elements come into play and need to be identified. This paper will advocate an "ecological" model of data sharing that takes a more holistic perspective than many traditional data publication approaches. It will explore a variety of use cases around what elements of an information ecosystem need to be unambiguously identified and located, at what point in the data production process, and to what explicit purpose.

  17. IDENTIFYING FEATURES OF PERSONALITY WHICH ENSURES PROFFESIONAL SUCCES OF ATTORNEYS

    OpenAIRE

    Craiovan, Petru Mihai; Bordeianu, Stefania

    2011-01-01

    The paper " Identifying features of personality which ensures professional succes of attorneys" tries to capture the personality dimensions that support the success of professional attorneys. In this approach we have used the following methods of psihodiagnostic: EPI, Questionnaire "mentality towards working" and Questionnaire "satisfaction towards working". The objectives of this study are : identification of psychoprofesionals features that promote the professional success of young lawyers ...

  18. From Unresolved Anger to Sadness: Identifying Physiological Correlates

    Science.gov (United States)

    Rochman, Daniel; Diamond, Gary M.

    2008-01-01

    This study was designed to identify physiological correlates of unresolved anger and sadness, and the shift between these emotions, in a context similar to that of emotion-focused, experiential psychotherapy. Twenty-seven university students reporting unresolved anger toward an attachment figure were induced to experience and express unresolved…

  19. Fetal alcohol-spectrum disorders: identifying at-risk mothers

    Science.gov (United States)

    Montag, Annika C

    2016-01-01

    Fetal alcohol-spectrum disorders (FASDs) are a collection of physical and neurobehavioral disabilities caused by prenatal exposure to alcohol. To prevent or mitigate the costly effects of FASD, we must identify mothers at risk for having a child with FASD, so that we may reach them with interventions. Identifying mothers at risk is beneficial at all time points, whether prior to pregnancy, during pregnancy, or following the birth of the child. In this review, three approaches to identifying mothers at risk are explored: using characteristics of the mother and her pregnancy, using laboratory biomarkers, and using self-report assessment of alcohol-consumption risk. At present, all approaches have serious limitations. Research is needed to improve the sensitivity and specificity of biomarkers and screening instruments, and to link them to outcomes as opposed to exposure. Universal self-report screening of all women of childbearing potential should ideally be incorporated into routine obstetric and gynecologic care, followed by brief interventions, including education and personalized feedback for all who consume alcohol, and referral to treatment as indicated. Effective biomarkers or combinations of biomarkers may be used during pregnancy and at birth to determine maternal and fetal alcohol exposure. The combination of self-report and biomarker screening may help identify a greater proportion of women at risk for having a child with FASD, allowing them to access information and treatment, and empowering them to make decisions that benefit their children. PMID:27499649

  20. Identifying Children at High Risk for a Child Maltreatment Report

    Science.gov (United States)

    Dubowitz, Howard; Kim, Jeongeun; Black, Maureen M.; Weisbart, Cindy; Semiatin, Joshua; Magder, Laurence S.

    2011-01-01

    Objective: To help professionals identify factors that place families at risk for future child maltreatment, to facilitate necessary services and to potentially help prevent abuse and neglect. Method: The data are from a prospective, longitudinal study of 332 low-income families recruited from urban pediatric primary care clinics, followed for…

  1. On the Identifiability of Transmission Dynamic Models for Infectious Diseases.

    Science.gov (United States)

    Lintusaari, Jarno; Gutmann, Michael U; Kaski, Samuel; Corander, Jukka

    2016-03-01

    Understanding the transmission dynamics of infectious diseases is important for both biological research and public health applications. It has been widely demonstrated that statistical modeling provides a firm basis for inferring relevant epidemiological quantities from incidence and molecular data. However, the complexity of transmission dynamic models presents two challenges: (1) the likelihood function of the models is generally not computable, and computationally intensive simulation-based inference methods need to be employed, and (2) the model may not be fully identifiable from the available data. While the first difficulty can be tackled by computational and algorithmic advances, the second obstacle is more fundamental. Identifiability issues may lead to inferences that are driven more by prior assumptions than by the data themselves. We consider a popular and relatively simple yet analytically intractable model for the spread of tuberculosis based on classical IS6110 fingerprinting data. We report on the identifiability of the model, also presenting some methodological advances regarding the inference. Using likelihood approximations, we show that the reproductive value cannot be identified from the data available and that the posterior distributions obtained in previous work have likely been substantially dominated by the assumed prior distribution. Further, we show that the inferences are influenced by the assumed infectious population size, which generally has been kept fixed in previous work. We demonstrate that the infectious population size can be inferred if the remaining epidemiological parameters are already known with sufficient precision.

  2. Invisible Kids: Preventing School Violence by Identifying Kids in Trouble.

    Science.gov (United States)

    Bender, William N.; Shubert, Terresa H.; McLaughlin, Phillip J.

    2001-01-01

    Discussion of school violence compares possible causes of the school shootings in Colorado and Georgia with a prior analysis of possible causes of school shootings. Characteristics of these violent perpetrators are discussed as a possible guide to help identify these seemingly "invisible kids." Identification options include warning…

  3. Identifying and prioritising services in European terrestrial and freshwater ecosystems

    NARCIS (Netherlands)

    Harrison, P.A.; Vandewalle, M.; Sykes, M.T.; Berry, P.M.; Bugter, R.J.F.; Bello, de F.; Feld, C.K.; Grandin, U.; Harrington, R.; Haslett, J.R.; Jongman, R.H.G.; Luck, G.W.; Martins da Silva, P.; Moora, M.; Settele, J.; Sousa, J.P.; Zobel, M.

    2010-01-01

    Ecosystems are multifunctional and provide humanity with a broad array of vital services. Effective management of services requires an improved evidence base, identifying the role of ecosystems in delivering multiple services, which can assist policy-makers in maintaining them. Here, information fro

  4. Opportunistic Beacon Networks: Information Dissemination via Wireless Network Identifiers

    NARCIS (Netherlands)

    Türkes, Okan; Scholten, Hans; Havinga, Paul J.M.

    2016-01-01

    This paper presents OBN, a universal opportunistic ad hoc networking model particularly intended for smart mobile devices. It enables fast and lightweight data dissemination in wireless community networks through the utilization of universally-available wireless network identifiers. As a ubiquitous

  5. Identifying multiple submissions in Internet research: preserving data integrity.

    Science.gov (United States)

    Bowen, Anne M; Daniel, Candice M; Williams, Mark L; Baird, Grayson L

    2008-11-01

    Internet-based sexuality research with hidden populations has become increasingly popular. Respondent anonymity may encourage participation and lower social desirability, but associated disinhibition may promote multiple submissions, especially when incentives are offered. The goal of this study was to identify the usefulness of different variables for detecting multiple submissions from repeat responders and to explore incentive effects. The data included 1,900 submissions from a three-session Internet intervention with a pretest and three post-test questionnaires. Participants were men who have sex with men and incentives were offered to rural participants for completing each questionnaire. The final number of submissions included 1,273 "unique", 132 first submissions by "repeat responders" and 495 additional submissions by the "repeat responders" (N = 1,900). Four categories of repeat responders were identified: "infrequent" (2-5 submissions), "persistent" (6-10 submissions), "very persistent" (11-30 submissions), and "hackers" (more than 30 submissions). Internet Provider (IP) addresses, user names, and passwords were the most useful for identifying "infrequent" repeat responders. "Hackers" often varied their IP address and identifying information to prevent easy identification, but investigating the data for small variations in IP, using reverse telephone look up, and patterns across usernames and passwords were helpful. Incentives appeared to play a role in stimulating multiple submissions, especially from the more sophisticated "hackers". Finally, the web is ever evolving and it will be necessary to have good programmers and staff who evolve as fast as "hackers". PMID:18240015

  6. BIOELECTRICAL IMPEDANCE VECTOR ANALYSIS IDENTIFIES SARCOPENIA IN NURSING HOME RESIDENTS

    Science.gov (United States)

    Loss of muscle mass and water shifts between body compartments are contributing factors to frailty in the elderly. The body composition changes are especially pronounced in institutionalized elderly. We investigated the ability of single-frequency bioelectrical impedance analysis (BIA) to identify b...

  7. 77 FR 8753 - Furnishing Identifying Number of Tax Return Preparer

    Science.gov (United States)

    2012-02-15

    ... published in the Federal Register on June 3, 2011 (76 FR 32286)). For purposes of these requirements, a tax... the Internal Revenue Service published in the Federal Register on September 30, 2010 (75 FR 60309... Internal Revenue Service 26 CFR Part 1 RIN 1545-BK37 Furnishing Identifying Number of Tax Return...

  8. Identifying and Researching Market Opportunities for New High Technology Products.

    Science.gov (United States)

    Dunstan, Peter

    Using a product called the synchro-pulse welder as a case study example, this paper discusses the activities of CSIRO (Commonwealth Scientific and Industrial Research Organisation) in identifying and marketing new high-technology products. A general discussion of CSIRO's market research plans includes two goals to be attained within the next 5…

  9. Identifying intrinsic and reflexive contributions to low-back stabilization

    NARCIS (Netherlands)

    Van Drunen, P.; Maaswinkel, E.; Van der Helm, F.C.T.; Van Dieën, J.H.; Happee, R.

    2013-01-01

    Motor control deficits have been suggested as potential cause and/or effect of a-specific chronic low-back pain and its recurrent behavior. Therefore, the goal of this study is to identify motor control in low-back stabilization by simultaneously quantifying the intrinsic and reflexive contributions

  10. Identifying Codes in the Complementary Prism of Cycles

    OpenAIRE

    Cappelle, Marcia R.; Coelho, Erika M. M.; Coelho, Hebert; Penso, Lucia D.; Rautenbach, Dieter

    2015-01-01

    We show that an identifying code of minimum order in the complementary prism of a cycle of order $n$ has order $7n/9+\\Theta(1)$. Furthermore, we observe that the clique-width of the complementary prism of a graph of clique-width $k$ is at most $4k$, and discuss some algorithmic consequences.

  11. Identifying Emotions through Language Means in Early Childhood

    Directory of Open Access Journals (Sweden)

    Malanov S.V.

    2015-08-01

    Full Text Available The paper focuses on the development of higher mental functions responsible for emotional regulation and describes a study revealing the stages in which young children acquire certain language means that help them to identify emotional states and understand emotional relationships. The sample of the study consisted of 94 children aged from 1.8 to 7.5 years. The outcomes suggest that at the age of 1.8 the children begin to acquire skills necessary for recognizing emotions basing on what the adults tell them. The revealed general tendency in the development of object reference of words is as follows: at first the children are able to identify emotional states and relationships according to the context of intersubjective interactions; later, basing on facial expressions; and finally, basing on pictograms of facial expressions. At the age of 2.4 years the children begin to employ language tools for identifying and naming emotions in others by themselves. Basing on their experience of analyzing emotions in others, the children then gradually develop the skills for identifying and partly recognizing their own emotions. Such skills may actually be found in some children at the age of 3.5 years, but usually it is not until the age of 7.5 that they can be observed in most preschoolers

  12. Blood Pressure Loci Identified with a Gene-Centric Array

    NARCIS (Netherlands)

    Johnson, Toby; Gaunt, Tom R.; Newhouse, Stephen J.; Padmanabhan, Sandosh; Tomaszewski, Maciej; Kumari, Meena; Morris, Richard W.; Tzoulaki, Ioanna; O'Brien, Eoin T.; Poulter, Neil R.; Sever, Peter; Shields, Denis C.; Thom, Simon; Wannamethee, Sasiwarang G.; Whincup, Peter H.; Brown, Morris J.; Connell, John M.; Dobson, Richard J.; Howard, Philip J.; Mein, Charles A.; Onipinla, Abiodun; Shaw-Hawkins, Sue; Zhang, Yun; Smith, George Davey; Day, Ian N. M.; Lawlor, Debbie A.; Goodall, Alison H.; Fowkes, F. Gerald; Abecasis, Goncalo R.; Elliott, Paul; Gateva, Vesela; Braund, Peter S.; Burton, Paul R.; Nelson, Christopher P.; Tobin, Martin D.; van der Harst, Pim; Glorioso, Nicola; Neuvrith, Hani; Salvi, Erika; Staessen, Jan A.; Stucchi, Andrea; Devos, Nabila; Jeunemaitre, Xavier; Plouin, Pierre-Francois; Tichet, Jean; Juhanson, Peeter; Org, Elin; Putku, Margus; Sober, Siim; Veldre, Gudrun; Viigimaa, Margus; Levinsson, Anna; Rosengren, Annika; Thelle, Dag S.; Hastie, Claire E.; Hedner, Thomas; Lee, Wai K.; Melander, Olle; Wahlstrand, Bjoern; Hardy, Rebecca; Wong, Andrew; Cooper, Jackie A.; Palmen, Jutta; Chen, Li; Stewart, Alexandre F. R.; Wells, George A.; Westra, Harm-Jan; Wolfs, Marcel G. M.; Clarke, Robert; Franzosi, Maria Grazia; Goel, Anuj; Hamsten, Anders; Lathrop, Mark; Peden, John F.; Seedorf, Udo; Watkins, Hugh; Ouwehand, Willem H.; Sambrook, Jennifer; Stephens, Jonathan; Casas, Juan-Pablo; Drenos, Fotios; Holmes, Michael V.; Kivimaki, Mika; Shah, Sonia; Shah, Tina; Talmud, Philippa J.; Whittaker, John; Wallace, Chris; Delles, Christian; Laan, Mans; Kuh, Diana; Humphries, Steve E.; Nyberg, Fredrik; Cusi, Daniele; Roberts, Robert; Newton-Cheh, Christopher; Franke, Lude; Stanton, Alice V.; Dominiczak, Anna F.; Farrall, Martin; Hingorani, Aroon D.; Samani, Nilesh J.; Caulfield, Mark J.; Munroe, Patricia B.

    2011-01-01

    Raised blood pressure (BP) is a major risk factor for cardiovascular disease. Previous studies have identified 47 distinct genetic variants robustly associated with BP, but collectively these explain only a few percent of the heritability for BP phenotypes. To find additional BP loci, we used a besp

  13. Modelling intelligence-led policing to identify its potential

    NARCIS (Netherlands)

    Hengst-Bruggeling, M. den; Graaf, H.A.L.M. de; Scheepstal, P.G.M. van

    2014-01-01

    lntelligence-led policing is a concept of policing that has been applied throughout the world. Despite some encouraging reports, the effect of intelligence-led policing is largely unknown. This paper presents a method with which it is possible to identify intelligence-led policing's potential to inc

  14. Identifying the methodological characteristics of European green city rankings

    NARCIS (Netherlands)

    Meijering, J.V.; Kern, K.; Tobi, H.

    2014-01-01

    City rankings that aim to measure the environmental sustainability of European cities may contribute to the evaluation and development of environmental policy of European cities. The objective of this study is to identify and evaluate the methodological characteristics of these city rankings. First,

  15. Identifying structures of continuously-varying weighted networks

    Science.gov (United States)

    Mei, Guofeng; Wu, Xiaoqun; Chen, Guanrong; Lu, Jun-An

    2016-05-01

    Identifying network structures from dynamical observations is a fundamental problem currently pervading scientific research on complex systems, as understanding and modeling the structure of a complex network will lead to greater knowledge of its evolutionary mechanisms and to a better understanding of its functional behaviors. Usually, one needs to identify a network’s structure through a limited number of observations. Particularly, couplings of many real-world networks are sparse and continuously varying with time. In this study, a new framework is developed via optimization for identifying structures of continuously-varying weighted networks formed by sparsely-connected dynamical systems. Furthermore, a regularization technique is employed to increase the numerical stability of the parameter estimation algorithm. Three numerical examples are provided to illustrate the feasibility and effectiveness of the proposed identification method. In comparison with other existing techniques, the main advantages of our method include its ability to identify structures of continuously-varying weighted networks in addition to static ones, as well as its requirement of a relatively small number of observations. The proposed method has a potential applicability to a variety of evolving complex dynamical networks.

  16. Easy Long-Term Identifiers and the "Data Paper"

    Science.gov (United States)

    Kunze, John

    2011-05-01

    A new publishing paradigm is needed to cope with the deluge of data artifacts produced by data-intensive science, many of which are vital to data re-use and verification of published scientific conclusions. Due to the limitations of traditional publishing, most of these artifacts are not usually disseminated, cited, or preserved. At the California Digital Library (CDL), one promising approach to the problem is to wrap these artifacts in the metaphor of a "data paper", assigning and managing data citations with our EZID (easy-eye-dee) identifier service. A data paper is a somewhat unfamiliar bundle of scholarly output with a familiar facade: minimally, a set of links to archived artifacts and a cover sheet containing familiar elements such as title, authors, date, abstract, and persistent identifier _ just enough to create basic citations, build "overlay journals", and enable discovery of data by internet search engines. Over time, we expect to add elements that permit deeper domain-specific discovery and re-use, such as variable names, methods, etc. At the same time, for data and identifiers that we manage, we will leverage as much domain-agnosticism data and identifier as possible.

  17. Developing Communities of Innovation by Identifying Innovation Champions

    Science.gov (United States)

    Coakes, Elayne; Smith, Peter

    2007-01-01

    Purpose: The purpose of this paper is to propose that a form of communities of practice (CoP), a community of innovation (CoInv), is the best support for sustainable innovation. It aims to outline a method for identifying champions of innovation in organisation. Design/methodology/approach: The paper draws on extant research to argue that…

  18. Identifying Indicators Related to Constructs for Engineering Design Outcome

    Science.gov (United States)

    Wilhelmsen, Cheryl A.; Dixon, Raymond A.

    2016-01-01

    This study ranked constructs articulated by Childress and Rhodes (2008) and identified the key indicators for each construct as a starting point to explore what should be included on an instrument to measure the engineering design process and outcomes of students in high schools that use the PLTW and EbDTM curricula in Idaho. A case-study design…

  19. Identifying the Key Weaknesses in Network Security at Colleges.

    Science.gov (United States)

    Olsen, Florence

    2000-01-01

    A new study identifies and ranks the 10 security gaps responsible for most outsider attacks on college computer networks. The list is intended to help campus system administrators establish priorities as they work to increase security. One network security expert urges that institutions utilize multiple security layers. (DB)

  20. Identifying Heterogeneities in Subsurface Environment using the Level Set Method

    Energy Technology Data Exchange (ETDEWEB)

    Lei, Hongzhuan [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Lu, Zhiming [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Vesselinov, Velimir Valentinov [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2016-08-25

    These are slides from a presentation on identifying heterogeneities in subsurface environment using the level set method. The slides start with the motivation, then explain Level Set Method (LSM), the algorithms, some examples are given, and finally future work is explained.

  1. The Patent Literature As A Shortcut To Identify Knowledge Suppliers

    DEFF Research Database (Denmark)

    Søberg, Peder Veng

    patents which decreases the time span between a patent is filed and its value can be evaluated when searching the patent literature. A potential benefit thereof could be that the patent literature could become relevant in order to identify potential knowledge suppliers....

  2. Identifying Different Registers of Digital Literacy in Virtual Learning Environments

    Science.gov (United States)

    Knutsson, Ola; Blasjo, Mona.; Hallsten, Stina; Karlstrom, Petter

    2012-01-01

    In this paper social semiotics, and systemic functional linguistics in particular, are used in order to identify registers of digital literacy in the use of virtual learning environments. The framework of social semiotics provides means to systemize and discuss digital literacy as a linguistic and semiotic issue. The following research question…

  3. Identifying 21st Century STEM Competencies Using Workplace Data

    Science.gov (United States)

    Jang, Hyewon

    2016-01-01

    Gaps between science, technology, engineering, and mathematics (STEM) education and required workplace skills have been identified in industry, academia, and government. Educators acknowledge the need to reform STEM education to better prepare students for their future careers. We pursue this growing interest in the skills needed for STEM…

  4. Identifying Predictors of Negative Psychological Reactions to Stalking Victimization

    Science.gov (United States)

    Johnson, Matthew C.; Kercher, Glen A.

    2009-01-01

    Victims of stalking often experience a number of negative psychological problems including such things as fear, symptoms of depression, and anger. However, research on factors that lead to these outcomes is limited. The goal of this study was to first identify distinct subgroups of stalking victims based on measures of psychological problems…

  5. Identifying Genes Responsible for Tamoxifen Resistance in Breast Cancer

    NARCIS (Netherlands)

    D. Meijer (Daniëlle)

    2008-01-01

    textabstractBreast cancer is one of the leading causes of death of women in western countries. It affects one out of eight females in the USA (1) and one out of nine females in The Netherlands (www.kankerregistratie.nl) during their lifetime. Many risk factors for breast cancer have been identified

  6. Identifying cognitive predictors of reactive and proactive aggression

    NARCIS (Netherlands)

    Brugman, S.; Lobbestael, J.; Arntz, A.R.; Cima, M.; Schumann, T.; Dambacher, F.

    2015-01-01

    The aim of this study was to identify implicit cognitive predictors of aggressive behavior. Specifically, the predictive value of an attentional bias for aggressive stimuli and automatic association of the self and aggression was examined for reactive and proactive aggressive behavior in a non-clini

  7. Identifying cognitive predictors of reactive and proactive aggression

    NARCIS (Netherlands)

    S. Brugman; J. Lobbestael; A. Arntz; M. Cima; T. Schuhmann; F. Dambacher; A.T. Sack

    2014-01-01

    The aim of this study was to identify implicit cognitive predictors of aggressive behavior. Specifically, the predictive value of an attentional bias for aggressive stimuli and automatic association of the self and aggression was examined for reactive and proactive aggressive behavior in a non-clini

  8. Identifying high dose activities in industrial site radiography

    International Nuclear Information System (INIS)

    Although the radiation doses received by industrial radiographers in the UK have progressively fallen over the last few years, with most now receiving less than 1 mSv/y, a few still receive, relative to the rest, much higher doses. As a percentage of all radiographers the number stays surprisingly constant from year to year. This paper describes a survey to identify the work causing these doses and suggest possible solutions. The UK Central Index of Dose Information was interrogated to identify the industrial radiography companies having staff (not necessarily the same person) with doses of greater than 5mSv/y in the last three years for which information was available. This was 15 in total. The people on the staff receiving these doses were identified and a questionnaire sent to the companies concerned requesting information about their work. A general questionnaire about the operation of the company was also included. With the agreement of the company these questionnaires were followed up by a visit to the company to interviews a number of the management and the radiographers if available. Both groups were generally very open about their problems and every discussion had a positive outcome. Several areas of work/reasons for the doses have been identified. These are: pipeline radiography, ultra sound radiographers working on nuclear reactors, complex plant work often with several teams in the area, inability to retreat from the wind out equipment due to height or access problems, site pressure to not follow the best practices and a lack of appreciation when a dose was being received or, alternatively, carelessness. Some o these problem areas are very difficult to resolve. However ways in which the Health and Safety can help influence the doses have been identified together with practical suggestions radiographers could adopt. These will be reported. (author)

  9. Antibody Arrays Identify Potential Diagnostic Markers of Hepatocellular Carcinoma

    Directory of Open Access Journals (Sweden)

    Brian J. Peter

    2008-01-01

    Full Text Available Hepatocellular carcinoma (HCC is the third leading cause of cancer deaths worldwide. Effective treatment of HCC patients is hampered by the lack of sensitive and specific diagnostic markers of HCC. Alpha-fetoprotein (AFP, the currently used HCC marker, misses 30%–50% of HCC patients, who therefore remain undiagnosed and untreated. In order to identify novel diagnostic markers that can be used individually or in combination with AFP, we used an antibody array platform to detect the levels of candidate proteins in the plasma of HCC patients (n = 48 and patients with chronic hepatitis B or C viral infections (n = 19 (both of which are the major risk factors of HCC. We identified 7 proteins that significantly differentiate HCC patients from hepatitis patients (p < 0.05 (AFP, CTNNB, CSF1, SELL, IGFBP6, IL6R, and VCAM1.Importantly, we also identified 8 proteins that significantly differentiate HCC patients with ‘normal’ levels of AFP (<20 ng/ml from hepatitis patients (p < 0.05 (IL1RN, IFNG, CDKN1A, RETN, CXCL14, CTNNB, FGF2, and SELL. These markers are potentially important complementary markers to AFP. Using an independent immunoassay method in an independent group of 23 HCC patients and 22 hepatitis patients, we validated that plasma levels of CTNNB were significantly higher in the HCC group (p = 0.020. In conclusion, we used an antibody array platform to identify potential circulating diagnostic markers of HCC, some of which may be valuable when used in combination with AFP. The clinical utility of these newly identified HCC diagnostic markers needs to be systematically evaluated.

  10. Postural control deficits identify lingering post-concussion neurological deficits

    Institute of Scientific and Technical Information of China (English)

    Thomas A. Buckley; Jessie R. Oldham; Jaclyn B. Caccese

    2016-01-01

    Concussion, or mild traumatic brain injury, incidence rates have reached epidemic levels and impaired postural control is a cardinal symptom. The purpose of this review is to provide an overview of the linear and non-linear assessments of post-concussion postural control. The current acute evaluation for concussion utilizes the subjective balance error scoring system (BESS) to assess postural control. While the sensitivity of the overall test battery is high, the sensitivity of the BESS is unacceptably low and, with repeat administration, is unable to accurately identify recovery. Sophisticated measures of postural control, utilizing traditional linear assessments, have identified impairments in postural control well beyond BESS recovery. Both assessments of quiet stance and gait have identified lingering impairments for at least 1 month post-concussion. Recently, the application of non-linear metrics to concussion recovery have begun to receive limited attention with the most commonly utilized metric being approximate entropy (ApEn). ApEn, most commonly in the medial-lateral plane, has successfully identified impaired postural control in the acute post-concussion timeframe even when linear assessments of instrumented measures are equivalent to healthy pre-injury values;unfortunately these studies have not gone beyond the acute phase of recovery. One study has identified lingering deficits in postural control, utilizing Shannon and Renyi entropy metrics, which persist at least through clinical recovery and return to participation. Finally, limited evidence from two studies suggest that individuals with a previous history of a single concussion, even months or years prior, may display altered ApEn metrics. Overall, non-linear metrics provide a fertile area for future study to further the understanding of postural control impairments acutely post-concussion and address the current challenge of sensitive identification of recovery.

  11. Identifying acute coronary syndrome patients approaching end-of-life.

    Directory of Open Access Journals (Sweden)

    Stephen Fenning

    Full Text Available BACKGROUND: Acute coronary syndrome (ACS is common in patients approaching the end-of-life (EoL, but these patients rarely receive palliative care. We compared the utility of a palliative care prognostic tool (Gold Standards Framework (GSF and the Global Registry of Acute Coronary Events (GRACE score, to help identify patients approaching EoL. METHODS AND FINDINGS: 172 unselected consecutive patients with confirmed ACS admitted over an eight-week period were assessed using prognostic tools and followed up for 12 months. GSF criteria identified 40 (23% patients suitable for EoL care while GRACE identified 32 (19% patients with ≥ 10% risk of death within 6 months. Patients meeting GSF criteria were older (p = 0.006, had more comorbidities (1.6 ± 0.7 vs. 1.2 ± 0.9, p = 0.007, more frequent hospitalisations before (p = 0.001 and after (0.0001 their index admission, and were more likely to die during follow-up (GSF+ 20% vs GSF- 7%, p = 0.03. GRACE score was predictive of 12-month mortality (C-statistic 0.75 and this was improved by the addition of previous hospital admissions and previous history of stroke (C-statistic 0.88. CONCLUSIONS: This study has highlighted a potentially large number of ACS patients eligible for EoL care. GSF or GRACE could be used in the hospital setting to help identify these patients. GSF identifies ACS patients with more comorbidity and at increased risk of hospital readmission.

  12. Antifungal chemical compounds identified using a C. elegans pathogenicity assay.

    Directory of Open Access Journals (Sweden)

    Julia Breger

    2007-02-01

    Full Text Available There is an urgent need for the development of new antifungal agents. A facile in vivo model that evaluates libraries of chemical compounds could solve some of the main obstacles in current antifungal discovery. We show that Candida albicans, as well as other Candida species, are ingested by Caenorhabditis elegans and establish a persistent lethal infection in the C. elegans intestinal track. Importantly, key components of Candida pathogenesis in mammals, such as filament formation, are also involved in nematode killing. We devised a Candida-mediated C. elegans assay that allows high-throughput in vivo screening of chemical libraries for antifungal activities, while synchronously screening against toxic compounds. The assay is performed in liquid media using standard 96-well plate technology and allows the study of C. albicans in non-planktonic form. A screen of 1,266 compounds with known pharmaceutical activities identified 15 (approximately 1.2% that prolonged survival of C. albicans-infected nematodes and inhibited in vivo filamentation of C. albicans. Two compounds identified in the screen, caffeic acid phenethyl ester, a major active component of honeybee propolis, and the fluoroquinolone agent enoxacin exhibited antifungal activity in a murine model of candidiasis. The whole-animal C. elegans assay may help to study the molecular basis of C. albicans pathogenesis and identify antifungal compounds that most likely would not be identified by in vitro screens that target fungal growth. Compounds identified in the screen that affect the virulence of Candida in vivo can potentially be used as "probe compounds" and may have antifungal activity against other fungi.

  13. Identifying and relating biological concepts in the Catalogue of Life

    Directory of Open Access Journals (Sweden)

    Jones Andrew C

    2011-10-01

    Full Text Available Abstract Background In this paper we describe our experience of adding globally unique identifiers to the Species 2000 and ITIS Catalogue of Life, an on-line index of organisms which is intended, ultimately, to cover all the world's known species. The scientific species names held in the Catalogue are names that already play an extensive role as terms in the organisation of information about living organisms in bioinformatics and other domains, but the effectiveness of their use is hindered by variation in individuals' opinions and understanding of these terms; indeed, in some cases more than one name will have been used to refer to the same organism. This means that it is desirable to be able to give unique labels to each of these differing concepts within the catalogue and to be able to determine which concepts are being used in other systems, in order that they can be associated with the concepts in the catalogue. Not only is this needed, but it is also necessary to know the relationships between alternative concepts that scientists might have employed, as these determine what can be inferred when data associated with related concepts is being processed. A further complication is that the catalogue itself is evolving as scientific opinion changes due to an increasing understanding of life. Results We describe how we are using Life Science Identifiers (LSIDs as globally unique identifiers in the Catalogue of Life, explaining how the mapping to species concepts is performed, how concepts are associated with specific editions of the catalogue, and how the Taxon Concept Schema has been adopted in order to express information about concepts and their relationships. We explore the implications of using globally unique identifiers in order to refer to abstract concepts such as species, which incorporate at least a measure of subjectivity in their definition, in contrast with the more traditional use of such identifiers to refer to more tangible

  14. To identify morbidity and mortality predictors in acute organophosphate poisoning

    Directory of Open Access Journals (Sweden)

    Arti Muley

    2014-01-01

    Full Text Available Background: Organophosphorus poisoning remains an important cause of morbidity and mortality, but no definite parameters have been identified as predictors of outcome. Prediction of morbidity at presentation might help in decision making in places of limited resources like rural settings in developing countries. Materials and Methods: A total of 76 cases were included in this retrospective cohort study. Logged relative risk of requirement of mechanical ventilation and hospital stay >7 days was measured in patients with serum acetylcholinesterase (s. acetylcholinesterase 1000, presenting in 12 and in patients with SpO 2 7 days. Conclusion: S. acetylcholinesterase, SpO 2 at room air, GCS, and duration of exposure at presentation can be used to identify the requirement of special care in acute organophosphorus poisoning. This can aid in decision making regarding admission to intensive care unit and referral in the places with limited resources.

  15. Proteogenomic Analysis Identifies a Novel Human SHANK3 Isoform

    Directory of Open Access Journals (Sweden)

    Fahad Benthani

    2015-05-01

    Full Text Available Mutations of the SHANK3 gene have been associated with autism spectrum disorder. Individuals harboring different SHANK3 mutations display considerable heterogeneity in their cognitive impairment, likely due to the high SHANK3 transcriptional diversity. In this study, we report a novel interaction between the Mutated in colorectal cancer (MCC protein and a newly identified SHANK3 protein isoform in human colon cancer cells and mouse brain tissue. Hence, our proteogenomic analysis identifies a new human long isoform of the key synaptic protein SHANK3 that was not predicted by the human reference genome. Taken together, our findings describe a potential new role for MCC in neurons, a new human SHANK3 long isoform and, importantly, highlight the use of proteomic data towards the re-annotation of GC-rich genomic regions.

  16. Identifying Influential Spreaders of Epidemics on Community Networks

    CERN Document Server

    Luo, Shi-Long; Kang, Li

    2016-01-01

    An efficient strategy for the identification of influential spreaders that could be used to control epidemics within populations would be of considerable importance. Generally, populations are characterized by its community structures and by the heterogeneous distributions of weak ties among nodes bridging over communities. A strategy for community networks capable of identifying influential spreaders that accelerate the spread of disease is here proposed. In this strategy, influential spreaders serve as target nodes. This is based on the idea that, in k-shell decomposition, weak ties and strong ties are processed separately. The strategy was used on empirical networks constructed from online social networks, and results indicated that this strategy is more accurate than other strategies. Its effectiveness stems from the patterns of connectivity among neighbors, and it successfully identified the important nodes. In addition, the performance of the strategy remained robust even when there were errors in the s...

  17. Identifying Semantic Relations for DiseaseTreatment in Medline

    Directory of Open Access Journals (Sweden)

    P. Menaka

    2012-03-01

    Full Text Available The Machine Learning (ML is almost used in any domain of research and now it has become a reliable tool in the medical domain.ML is a tool by which medical field is integrated with the computer based systems to provide more efficient medical care. The main objective of this work is to show what Natural Language Processing (NLP and Machine Learning (ML techniques used for representation of information and what classification algorithms are suitable for identifying and classifying relevant medical information in short texts. It acknowledges the fact that tools capable of identifying reliable information in the medical domain stand as building blocks for a healthcare system that is up-to-date with the latest discoveries. In this research, it focuses on diseases and treatment information, and the relation that exists between these two entities.

  18. A Framework for Identifying and Understanding Enterprise Systems Benefits

    DEFF Research Database (Denmark)

    Schubert, Petra; Williams, Susan P.

    2011-01-01

    and business change, which addresses the identified limitations of previous research and provides a more detailed analysis of benefits and their contextual variation. Design/methodology/approach – Drawing on data gathered from 31 real-world organizations (case studies) of differing size, maturity, and industry...... sector, the study adopts an iterative content analysis to empirically derive a comprehensive benefits framework. Findings – The content analysis provides a detailed classification of expectations and benefits, which is described in a four-level framework. The four levels (areas) are further subdivided......Purpose – Identifying the benefits arising from implementations of enterprise systems and realizing business value remains a significant challenge for both research and industry. This paper aims to consolidate previous work. It presents a framework for investigating enterprise systems benefits...

  19. Identifying Sentiment in Web Multi-topic Documents

    Directory of Open Access Journals (Sweden)

    Na Fan

    2012-02-01

    Full Text Available Most of web documents coverage multiple topic. Identifying sentiment of multi-topic documents is a challenge task. In this paper, we proposed a new method to solve this problem. The method firstly reveals the latent topical facets in documents by Parametric Mixture Model. By focusing on modeling the generation process of a document with multiple topics, we can extract specific properties of documents with multiple topics. PMM models documents with multiple topics by mixing model parameters of each single topic. In order to analyze sentiment of each topic, conditional random fields techniques is used to identify sentiment. Empirical experiments on test datasets show that this approach is effective for extracting subtopics and revealing sentiments of each topic. Moreover, this method is quite general and can be applied to any kinds of text collections.

  20. Identifying critical factors for implementing good agricultural practice

    Directory of Open Access Journals (Sweden)

    Nelson Gutiérrez Guzmán

    2010-05-01

    Full Text Available This paper deals with identifying the critical factors (CFs involved in implementing a good agricultural practice (GAP programme for coffee and fruit farmers in the Huila department of Colombia. An exploratory factor analysis using principal component analy- sis (PCA factorisation was used. Data matrixes were constructed from the results of applying two defined-structure assessment tools to the populations being studied: Starbucks’ coffee and farmer equity (CAFE practices for small-scale coffee growers and coffee-producers and the EUREPGAP V2.1 Oct.2004 / checklist for fruit and vegetables, as applied to fruit-producers. This inves- tigation led to identifying 6 CFs which must be considered when implementing a GAP programme: infrastructure, established production activities, preparing and maintaining records, environmental awareness, workers’ welfare and safety and quality con- trol.

  1. Identifying and Ranking the Determinants of Tourism Performance

    DEFF Research Database (Denmark)

    Assaf, A.George; Josiassen, Alexander

    2012-01-01

    After a prolonged period of growth, driven, in part, by an increasing number of affluent consumers, the international tourism industry is now suffering the effects of a weaker world economy. These tougher market conditions have, in turn, led to increasing competition. As a result, countries......, their tourism industries, and tourism businesses seek to improve the performance of the tourism industry and its constituents by vigorously promoting themselves to international tourists, cutting costs, and identifying synergies in their tourism endeavors. In seeking to improve the tourism industry...... and their relative importance. The present study addresses this important gap. We identify and rank the determinants of tourism performance. We also provide performance measures of international tourism destinations. The results are derived using the Data Envelopment Analysis (DEA) and bootstrap truncated regression...

  2. Comparison of Algorithms for an Electronic Nose in Identifying Liquors

    Institute of Scientific and Technical Information of China (English)

    Zhi-biao Shi; Tao Yu; Qun Zhao; Yang Li; Yu-bin Lan

    2008-01-01

    When the electronic nose is used to identify different varieties of distilled liquors, the pattern recognition algorithm is chosen on the basis of the experience, which lacks the guiding principle. In this research, the different brands of distilled spirits were identified using the pattern recognition algorithms (principal component analysis and the artificial neural network). The recognition rates of different algorithms were compared. The recognition rate of the Back Propagation Neural Network (BPNN) is the highest. Owing to the slow convergence speed of the BPNN, it tends easily to get into a local minimum. A chaotic BPNN was tried in order to overcome the disadvantage of the BPNN. The convergence speed of the chaotic BPNN is 75.5 times faster than that of the BPNN.

  3. Identifiability and identification of a Synthesis Load Model

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    A Synthesis Load Model (SLM) including both the power load and the distribution network has been proposed in the references. The identifiability of SLM is analyzed at first, it is concluded that the model parameters are identifiable if one of the resistance, reactance and the ratio of them is known. The conclusion is validated through a simulation example. A strategy for parameter identification of SLM is proposed with the combination of the component based approach and the measurement based approach. During parameter identification, only the key parameters playing very important roles in the dynamics of the load and the system are estimated, while the other parameters playing limited role are set as the default values. The proposed strategy is verified by the field measurements.

  4. Identifying the ejected population from disintegrating multiple systems

    CERN Document Server

    Yip, A K P; Kurtev, R; Gromadzki, M; Marocco, F

    2016-01-01

    Kinematic studies of the Hipparcos catalogue have revealed associations that are best explained as disintegrating multiple systems, presumably resulting from a dynamical encounter between single/multiple systems in the field (Li et al. 2009). In this work we explore the possibility that known ultra-cool dwarfs may be components of disintegrating multiple systems, and consider the implications for the properties of these objects. We will present here the methods/techniques that can be used to search for and identify disintegrating benchmark systems in three database/catalogues: Dwarf Archive, the Hipparcos Main Catalogue, and the Gliese-Jahrei{\\ss} Catalogue. Placing distance constraints on objects with parallax or colour-magnitude information from spectrophotometry allowed us to identify common distance associations. Proper motion measurements allowed us to separate common proper motion multiples from our sample of disintegrating candidates. Moreover, proper motion and positional information allowed us to sel...

  5. [Dialysis and quality of life: identifying and managing critical aspects].

    Science.gov (United States)

    Del Corso, C; Caravello, G; Betti, M G; Ferretti, S; Lunardi, W; Tavolaro, A; Capitanini, A; Petrone, I; Rossi, A; Cerri, A; Galati, V; Marini, M; Sardi, T; Valenti, I

    2008-01-01

    Living with a chronic disease is for the patient a ''disease experience'' that also affects the psychosocial sphere and has a negative impact on perceived quality of life. To estimate the effect of dialysis on the perceived quality of life and to identify by means of a specific questionnaire the aspects that are compromised most. From our results it emerged that the examined patients had a sufficiently good total perception of quality of life, even though about 30% of the patients reported critical aspects related to daily life and, in some age groups, also related to dialysis method. This study confirms the importance of developing educational and supportive predialysis programs in order to identify and reduce the critical aspects. PMID:18350501

  6. Identifying 21st century STEM competencies using workplace data

    CERN Document Server

    Jang, Hyewon

    2015-01-01

    Gaps between Science, Technology, Engineering, and Mathematics (STEM) education and required workplace skills have been identified in industry, academia, and government. Educators acknowledge the need to reform STEM education to better prepare students for their future careers. We pursue this growing interest in the skills needed for STEM disciplines and ask whether frameworks for 21st century skills and engineering education cover all of important STEM competencies. In this study, we identify important STEM competencies and evaluate the relevance of current frameworks applied in education using the standardized job-specific database operated and maintained by the United States Department of Labor. Our analysis of the importance of 109 skills, types of knowledge and work activities, revealed 18 skills, seven categories of knowledge, and 27 work activities important for STEM workers. We investigate the perspectives of STEM and non-STEM job incumbents, comparing the importance of each skill, knowledge, and work...

  7. Adaptive algorithms for identifying large flows in IP traffic

    CERN Document Server

    Chabchoub, Yousra; Guillemin, Fabrice; Robert, Philippe

    2009-01-01

    We develop in this paper an adaptive algorithm based on Bloom filters in order to identify large flows. While most algorithms proposed so far in the technical literature rely on a periodic erasure of the Bloom filter, we propose in this paper to progressively decrement the various counters of the filter according to some overload criteria. When tested against real traffic traces, the proposed algorithm performs well in the sense that a high percentage of large flows in traffic are detected by the algorithm. In order to improve the accuracy of the algorithm, we introduce a shadow Bloom filter, which is less frequently decremented so that elephants have more chance of being identified. Since elephant detection issue is very close to flood attack detection, we adapt the proposed algorithm in order to detect SYN and volume flood attack in Internet traffic. The attack detection algorithm is tested against traffic traces from France Telecom collect and transit networks. Some performance issues are finally discussed...

  8. Pharmacy students' ability to identify plagiarism after an educational intervention.

    Science.gov (United States)

    Degeeter, Michelle; Harris, Kira; Kehr, Heather; Ford, Carolyn; Lane, Daniel C; Nuzum, Donald S; Compton, Cynthia; Gibson, Whitney

    2014-03-12

    Objective. To determine if an educational intervention in a doctor of pharmacy (PharmD) degree program increases pharmacy students' ability to identify plagiarism. Methods. First-year (P1), second-year (P2), and third-year (P3) pharmacy students attended an education session during which types of plagiarism and methods for avoiding plagiarism were reviewed. Students completed a preintervention assessment immediately prior to the session and a postintervention assessment the following semester to measure their ability. Results. Two hundred fifty-two students completed both preintervention and postintervention assessments. There was a 4% increase from preintervention to postintervention in assessment scores for the overall student sample (pplagiarism can significantly improve students' ability to identify plagiarism.

  9. Staff resistance to restraint reduction: identifying & overcoming barriers.

    Science.gov (United States)

    Curran, Staci Silver

    2007-05-01

    Professional organizations, regulating agencies, and hospital administrators have taken a strong stance on restraint reduction policies. When implementing a restraint reduction initiative, it is important to identify the barriers to restraint reduction, such as concern for personal safety, lack of knowledge about and practice using alternate de-escalation skills, and fear of disrupting the therapeutic milieu by using a variety of de-escalation methods. Education aimed to reduce the use of restraints needs to do more than simply provide information. It is important to acknowledge the emotional response of the nursing staff and the culture of the current practice. A variety of educational strategies, including role-playing, and case studies will help identify attitudes, beliefs, and behaviors that are congruent with reducing the use of restraints. If the ultimate goal of restraint reduction is philosophical change, it will eventually lead to a new culture of practice. PMID:17526330

  10. Identifying Diabetic Parameters in Cochlear Mechanics and Models

    Directory of Open Access Journals (Sweden)

    Mrs. Nirmala N. Kamble,

    2014-01-01

    Full Text Available Hearing impairment is one of the most prevalent chronic disability identified with the elderly people over the age of 65.The peripheral portion of the cochlea and auditory nerve are known to deteriorate with age. The prevalence of hearing loss in diabetes has been shown in many studies to be moderately high, progressive and bilateral. The predominant mechanism of hearing loss in diabetes appears to be related to microangiopathy of inner ear. Mathematical modelling of cochlear dynamics had been attempted over the years with various parameters. This paper, attempts to study the correlation between diabetes and hearing loss and try to identify key parameters in cochlear model which leads to hearing loss.

  11. On Codes with w-identifiable Parent Property

    Institute of Scientific and Technical Information of China (English)

    MA Jun; XIONG Yu

    2008-01-01

    A code is said to be a w-identifiable parent property code (or w-IPP code for short) if whenever d is a descendant of w (or fewer) codewords, and one can always identify at least one of the parents of d. Let C be an (N, w + 1, q)-code and C* an (w + 1)-color graph for C. If a graph G is a subgraph of C* and consists of w + 1 edges with different colors, then G is called a (w + 1)-pattern of C*. In this paper, we proved that C is a w-IPP code if and only if there exists at most one vertex with color degree more than 1 in any (w + 1)-pattern of C*.

  12. Quantitative High-Throughput Luciferase Screening in Identifying CAR Modulators.

    Science.gov (United States)

    Lynch, Caitlin; Zhao, Jinghua; Wang, Hongbing; Xia, Menghang

    2016-01-01

    The constitutive androstane receptor (CAR, NR1I3) is responsible for the transcription of multiple drug metabolizing enzymes and transporters. There are two possible methods of activation for CAR, direct ligand binding and a ligand-independent method, which makes this a unique nuclear receptor. Both of these mechanisms require translocation of CAR from the cytoplasm into the nucleus. Interestingly, CAR is constitutively active in immortalized cell lines due to the basal nuclear location of this receptor. This creates an important challenge in most in vitro assay models because immortalized cells cannot be used without inhibiting the high basal activity. In this book chapter, we go into detail of how to perform quantitative high-throughput screens to identify hCAR1 modulators through the employment of a double stable cell line. Using this line, we are able to identify activators, as well as deactivators, of the challenging nuclear receptor, CAR. PMID:27518621

  13. Identifying sources and estimating glandular output of salivary TIMP-1

    DEFF Research Database (Denmark)

    Holten-Andersen, Lars; Jensen, Siri Beier; Jensen, Allan Bardow;

    2008-01-01

    -1 measurements in a non-invasive manner. Material and methods. Samples of unstimulated and stimulated whole saliva and saliva collected from individual glands were analysed for TIMP-1 content. A TIMP-1 ELISA was validated for use in saliva testing and the most optimal sampling and handling......Objective. Tissue inhibitor of metalloproteinases 1 (TIMP-1) has been identified as a potential biomarker in diseases such as cancer, cardiovascular diseases and diabetes. Since TIMP-1 resides in most tissues and bodily fluids, we evaluated the potential of using saliva to obtain reproducible TIMP...... procedures for reproducible measurements identified. Western blotting and MALDI-TOF mass spectrometry were used for confirmatory analyses. Results. The TIMP-1 ELISA was found suitable for saliva measurements. All saliva secretions contained TIMP-1, but in different concentrations ranging from 2.81 ng...

  14. Identifying False Alarms in the Kepler Planet Candidate Catalog

    CERN Document Server

    Mullally, F; Thompson, Susan E; Christiansen, Jessie; Burke, Christopher; Clarke, Bruce D; Haas, Michael R

    2016-01-01

    We present a new automated method to identify instrumental features masquerading as small, long period planets in the \\kepler\\ planet candidate catalog. These systematics, mistakenly identified as planet transits, can have a strong impact on occurrence rate calculations because they cluster in a region of parameter space where Kepler's sensitivity to planets is poor. We compare individual transit-like events to a variety of models of real transits and systematic events, and use a Bayesian Information Criterion to evaluate the likelihood that each event is real. We describe our technique and test its performance on simulated data. Results from this technique are incorporated in the \\kepler\\ Q1-17 DR24 planet candidate catalog of \\citet{Coughlin15}.

  15. Identifying incident oral and pharyngeal cancer cases using Medicare claims

    Directory of Open Access Journals (Sweden)

    Mahnken Jonathan D

    2013-01-01

    Full Text Available Abstract Background Baseline and trend data for oral and pharyngeal cancer incidence is limited. A new algorithm was derived using the Surveillance, Epidemiology, and End Results (SEER-Medicare linked database to create an algorithm to identify incident cases of oral and pharyngeal cancer using Medicare claims. Methods Using a split-sample approach, Medicare claims’ procedure and diagnosis codes were used to generate a new algorithm to identify oral and pharyngeal cancer cases and validate its operating characteristics. Results The algorithm had high sensitivity (95% and specificity (97%, which varied little by age group, sex, and race and ethnicity. Conclusion Examples of the utility of this algorithm and its operating characteristics include using it to derive baseline and trend estimates of oral and pharyngeal cancer incidence. Such measures could be used to provide incidence estimates where they are lacking or to serve as comparator estimates for tumor registries.

  16. Identifying microRNA/mRNA dysregulations in ovarian cancer

    Directory of Open Access Journals (Sweden)

    Miles Gregory D

    2012-03-01

    Full Text Available Abstract Background MicroRNAs are a class of noncoding RNA molecules that co-regulate the expression of multiple genes via mRNA transcript degradation or translation inhibition. Since they often target entire pathways, they may be better drug targets than genes or proteins. MicroRNAs are known to be dysregulated in many tumours and associated with aggressive or poor prognosis phenotypes. Since they regulate mRNA in a tissue specific manner, their functional mRNA targets are poorly understood. In previous work, we developed a method to identify direct mRNA targets of microRNA using patient matched microRNA/mRNA expression data using an anti-correlation signature. This method, applied to clear cell Renal Cell Carcinoma (ccRCC, revealed many new regulatory pathways compromised in ccRCC. In the present paper, we apply this method to identify dysregulated microRNA/mRNA mechanisms in ovarian cancer using data from The Cancer Genome Atlas (TCGA. Methods TCGA Microarray data was normalized and samples whose class labels (tumour or normal were ambiguous with respect to consensus ensemble K-Means clustering were removed. Significantly anti-correlated and correlated genes/microRNA differentially expressed between tumour and normal samples were identified. TargetScan was used to identify gene targets of microRNA. Results We identified novel microRNA/mRNA mechanisms in ovarian cancer. For example, the expression level of RAD51AP1 was found to be strongly anti-correlated with the expression of hsa-miR-140-3p, which was significantly down-regulated in the tumour samples. The anti-correlation signature was present separately in the tumour and normal samples, suggesting a direct causal dysregulation of RAD51AP1 by hsa-miR-140-3p in the ovary. Other pairs of potentially biological relevance include: hsa-miR-145/E2F3, hsa-miR-139-5p/TOP2A, and hsa-miR-133a/GCLC. We also identified sets of positively correlated microRNA/mRNA pairs that are most likely result from

  17. Identifiability, stratification and minimum variance estimation of causal effects.

    Science.gov (United States)

    Tong, Xingwei; Zheng, Zhongguo; Geng, Zhi

    2005-10-15

    The weakest sufficient condition for the identifiability of causal effects is the weakly ignorable treatment assignment, which implies that potential responses are independent of treatment assignment in each fine subpopulation stratified by a covariate. In this paper, we expand the independence that holds in fine subpopulations to the case that the independence may also hold in several coarse subpopulations, each of which consists of several fine subpopulations and may have overlaps with other coarse subpopulations. We first show that the identifiability of causal effects occurs if and only if the coarse subpopulations partition the whole population. We then propose a principle, called minimum variance principle, which says that the estimator possessing the minimum variance is preferred, in dealing with the stratification and the estimation of the causal effects. The simulation results with the detail programming and a practical example demonstrate that it is a feasible and reasonable way to achieve our goals. PMID:16149123

  18. Covert Flow Graph Approach to Identifying Covert Channels

    Directory of Open Access Journals (Sweden)

    XiangMei Song

    2011-12-01

    Full Text Available In this paper, the approach for identifying covert channels using a graph structure called Covert Flow Graph is introduced. Firstly, the construction of Covert Flow Graph which can offer information flows of the system for covert channel detection is proposed, and the search and judge algorithm used to identify covert channels in Covert Flow Graph is given. Secondly, an example file system analysis using Covert Flow Graph approach is provided, and the analysis result is compared with that of Shared Resource Matrix and Covert Flow Tree method. Finally, the comparison between Covert Flow Graph approach and other two methods is discussed. Different from previous methods, Covert Flow Graph approach provides a deep insight for system’s information flows, and gives an effective algorithm for covert channel identification.

  19. Short period eclipsing binary candidates identified using SuperWASP

    CERN Document Server

    Norton, A J; Evans, T; West, R G; Wheatley, P J; Anderson, D R; Barros, S C C; Butters, O W; Cameron, A Collier; Christian, D J; Enoch, B; Faedi, F; Haswell, C A; Hellier, C; Holmes, S; Horne, K D; Lister, T A; Maxted, P F L; Parley, N; Pollacco, D; Simpson, E K; Skillen, I; Smalley, B; Southworth, J; Street, R A

    2011-01-01

    We present light curves and periods of 53 candidates for short period eclipsing binary stars identified by SuperWASP. These include 48 newly identified objects with periods <2x10^4 seconds (~0.23d), as well as the shortest period binary known with main sequence components (GSC2314-0530 = 1SWASP J022050.85+332047.6) and four other previously known W UMa stars (although the previously reported periods for two of these four are shown to be incorrect). The period distribution of main sequence contact binaries shows a sharp cut-off at a lower limit of around 0.22d, but until now, very few systems were known close to this limit. These new candidates will therefore be important for understanding the evolution of low mass stars and to allow investigation of the cause of the period cut-off.

  20. Challenges of Identifying Clinically Actionable Genetic Variants for Precision Medicine

    Directory of Open Access Journals (Sweden)

    Tonia C. Carter

    2016-01-01

    Full Text Available Advances in genomic medicine have the potential to change the way we treat human disease, but translating these advances into reality for improving healthcare outcomes depends essentially on our ability to discover disease- and/or drug-associated clinically actionable genetic mutations. Integration and manipulation of diverse genomic data and comprehensive electronic health records (EHRs on a big data infrastructure can provide an efficient and effective way to identify clinically actionable genetic variants for personalized treatments and reduce healthcare costs. We review bioinformatics processing of next-generation sequencing (NGS data, bioinformatics infrastructures for implementing precision medicine, and bioinformatics approaches for identifying clinically actionable genetic variants using high-throughput NGS data and EHRs.

  1. Hidden chromosomal abnormalities in pleuropulmonary blastomas identified by multiplex FISH

    Directory of Open Access Journals (Sweden)

    Coze Carole

    2006-01-01

    Full Text Available Abstract Background Pleuropulmonary blastoma (PPB is a rare childhood dysontogenetic intrathoracic neoplasm associated with an unfavourable clinical behaviour. Cases presentation We report pathological and cytogenetic findings in two cases of PPB at initial diagnosis and recurrence. Both tumors were classified as type III pneumoblastoma and histological findings were similar at diagnosis and relapse. In both cases, conventional cytogenetic techniques revealed complex numerical and structural chromosomal abnormalities. Molecular cytogenetic analysis (interphase/metaphase FISH and multicolor FISH identified accurately chromosomal aberrations. In one case, TP53 gene deletion was detected on metaphase FISH. To date, only few cytogenetic data have been published about PPB. Conclusion The PPB genetic profile remains to be established and compared to others embryonal neoplasia. Our cytogenetic data are discussed reviewing cytogenetics PPBs published cases, illustrating the contribution of multicolor FISH in order to identify pathogenetically important recurrent aberrations in PPB.

  2. Identifying decision strategies in a consumer choice situation

    Directory of Open Access Journals (Sweden)

    Nils Reisen

    2008-12-01

    Full Text Available In two studies on mobile phone purchase decisions, we investigated consumers' decision strategies with a newly developed process tracing tool called extit{InterActive Process Tracing} (IAPT. This tool is a combination of several process tracing techniques (Active Information Search, Mouselab, and retrospective verbal protocol. After repeatedly choosing one of four mobile phones, participants formalized their strategy so that it could be used to make choices for them. The choices made by the identified strategies correctly predicted the observed choices in 73\\% (Experiment 1 and 67\\% (Experiment 2 of the cases. Moreover, in Experiment 2 we directly compared Mouselab and eye tracking with respect to their impact on information search and strategy description. We found only minor differences between these two methods. We conclude that IAPT is a useful research tool to identify choice strategies, and that using eye tracking technology did not increase its validity beyond that gained with Mouselab.

  3. Detecting, locating and identifying failed fuel in Canadian power reactors

    International Nuclear Information System (INIS)

    This document summarizes how defected fuel elements are detected, located and identified in Canadian CANDU power reactors. Fuel defects are detected by monitoring the primary coolant for gaseous fission products and radioiodines, while location in core is usually performed on-power by delayed neutron monitoring of coolant samples from individual fuel channels or off-power by gamma-ray monitoring of the channel feeder pipes. The systems and techniques used to detect and locate defected fuel in both Ontario Hydro and CANDU 6 power stations are described, along with examples provided by station experience. The ability to detect and locate defected fuel in power stations was greatly enhanced by a fundamental R and D program, which provided an understanding and models of fission-product release and transport, and the post-defect deterioration of failed fuel. Techniques and equipment used to identify and store defected fuel after it has been discharged from the reactor are briefly reviewed

  4. Identifying Parents Who Are Amenable to Pro-Vaccination Conversations

    Directory of Open Access Journals (Sweden)

    Emily K. Brunson MPH, PhD

    2015-11-01

    Full Text Available While health care providers are often cited as parents’ most trusted source for information and advice about vaccination, parents differ in their level of receptiveness to pro-vaccination conversations. The purpose of this research was to identify points in individual parents’ decision-making processes when parents are particularly open to receiving information and advice from their children’s health care providers. Interview data were collected from 20 mothers and 5 couples. Analysis of these data suggested 3 primary circumstances when parents were particularly open to receiving information and advice: during parents’ initial decision-making, as parents continued to assess vaccination options, and during particular circumstances that prompted parents to reconsider previously made vaccination choices. These results provide a mechanism for providers to identify parents who may be particularly receptive to pro-vaccination conversations. By prioritizing conversations with parents at one of these points, health care providers’ efforts at promoting vaccination may be more effective.

  5. Vulnerable Earthworm Species Identified from Nilgiri Biosphere Reserve

    Directory of Open Access Journals (Sweden)

    E.V. Ramasamy

    2011-01-01

    Full Text Available Diversity of earthworms at Nilgiri Biosphere Reserve is less known even though it is one among the biodiversity hot spots. Unless an authentic record of available earthworm species is made, the consequences of human alternation or climate change on the earthworm species diversity cannot be assessed. In this regard, the present study is relevant. Earthworms were collected from twenty three sites of NBR. The findings of this study showed that out of the total earthworm species identified from selected areas of NBR, 83.4% are native species and 16.6% are exotic. This indicates the predominance of native species in the study area possibly due to low level of disturbance in the area. Among the species identified from Mukurthi, Priodichaeta pellucida (Bourne which is listed as vulnerable and has not been encountered since its discovery about 100 years ago.

  6. Hidden chromosomal abnormalities in pleuropulmonary blastomas identified by multiplex FISH

    International Nuclear Information System (INIS)

    Pleuropulmonary blastoma (PPB) is a rare childhood dysontogenetic intrathoracic neoplasm associated with an unfavourable clinical behaviour. We report pathological and cytogenetic findings in two cases of PPB at initial diagnosis and recurrence. Both tumors were classified as type III pneumoblastoma and histological findings were similar at diagnosis and relapse. In both cases, conventional cytogenetic techniques revealed complex numerical and structural chromosomal abnormalities. Molecular cytogenetic analysis (interphase/metaphase FISH and multicolor FISH) identified accurately chromosomal aberrations. In one case, TP53 gene deletion was detected on metaphase FISH. To date, only few cytogenetic data have been published about PPB. The PPB genetic profile remains to be established and compared to others embryonal neoplasia. Our cytogenetic data are discussed reviewing cytogenetics PPBs published cases, illustrating the contribution of multicolor FISH in order to identify pathogenetically important recurrent aberrations in PPB

  7. How do we identify and foster talent in medical schools?

    DEFF Research Database (Denmark)

    Christensen, Mette Krogh; Cristiancho, Sayra; Jensen, Rune Dall

    2016-01-01

    Background: Talent is highly regarded in high performance sports as a key feature for athletes to succeed. In medicine, talent is not a commonly held conversation, even though, medical students are usually identified as high achieving, internally motivated individuals. We suggest that bringing...... talent into the conversation of medical education research, will help us enrich how medical schools design selection processes. In this workshop we will bring awareness into the notion of talent from sports science research and invite discussion around how to embrace talent identification and development....... Finally, the workshop aim to extent participants’ repertoire of strategies in identifying and fostering talent at their institutions. Structure of Workshop: The latest research on talent identification and development will be presented and discussed. Participants will engage in an exercise including...

  8. Identify influential spreaders in complex networks, the role of neighborhood

    CERN Document Server

    Liu, Ying; Zhou, Tao; Do, Younghae

    2015-01-01

    Identifying the most influential spreaders is an important issue in controlling the spreading processes in complex networks. Centrality measures are used to rank node influence in a spreading dynamics. Here we propose a node influence measure based on the centrality of a node and its neighbors' centrality, which we call the neighborhood centrality. By simulating the spreading processes in six real-world networks, we find that the neighborhood centrality greatly outperforms the basic centrality of a node such as the degree and coreness in ranking node influence and identifying the most influential spreaders. Interestingly, we discover a saturation effect in considering the neighborhood of a node, which is not the case of the larger the better. Specifically speaking, considering the 2-step neighborhood of nodes is a good choice that balances the cost and performance. If further step of neighborhood is taken into consideration, there is no obvious improvement and even decrease in the ranking performance. The sat...

  9. The Invisible Hunger: Is Famine Identifiable from the Archaeological Record?

    Directory of Open Access Journals (Sweden)

    Johanna Morgan

    2013-06-01

    Full Text Available Famine, as defined by an acute (short-term or chronic (long-term or cyclical period of starvation, is identifiable in the historical period from written records and potentially with archaeological corroboration, but in prehistory other approaches must be employed. Several of these are discussed including studies of diet and nutrition, paleodemography, environmental catalysts, and funerary ritual. Despite a multifactorial analysis integrating palynology, dendrochronology, stable isotope analyses, osteoarchaeology, and social archaeology, difficulties in contemporizing paleodemographic events them with osteological assemblages are substantial enough that the detection of a famine is not possible solely from the archaeological record. More significant is the conclusion that all apparent indicators for acute or chronic starvation are also representative of epidemic disease. Because of this uncertainty, it is not possible to identify famine in prehistory.

  10. Candidate olfaction genes identified within the Helicoverpa armigera Antennal Transcriptome.

    Directory of Open Access Journals (Sweden)

    Yang Liu

    Full Text Available Antennal olfaction is extremely important for insect survival, mediating key behaviors such as host preference, mate choice, and oviposition site selection. Multiple antennal proteins are involved in olfactory signal transduction pathways. Of these, odorant receptors (ORs and ionotropic receptors (IRs confer specificity on olfactory sensory neuron responses. In this study, we identified the olfactory gene repertoire of the economically important agricultural pest moth, Helicoverpa armigera, by assembling the adult male and female antennal transcriptomes. Within the male and female antennal transcriptomes we identified a total of 47 OR candidate genes containing 6 pheromone receptor candidates. Additionally, 12 IR genes as well as 26 odorant-binding proteins and 12 chemosensory proteins were annotated. Our results allow a systematic functional analysis across much of conventional ORs repertoire and newly reported IRs mediating the key olfaction-mediated behaviors of H. armigera.

  11. Emotion at work: identifying the emotional climate of night nursing.

    Science.gov (United States)

    Brown, Reva Berman; Brooks, Ian

    2002-01-01

    This paper introduces the concept of the emotional climate of the workplace and explores how it both shapes and is shaped by the emotions experienced, expressed and redefined by nurses. It extracts emotional aspects of an organizational climate framework developed by Litwin and Stringer and examines these with respect to nurse's experiences. The primary research was carried out at a general hospital NHS Trust in the East Midlands of the UK using a grounded theory methodology. The research methods included semi-structured interviews and observation. The themes identified include many of those found by Litwin and Stringer, others which represent variations upon these, and a new set, which, when combined, identify the emotional climate of the organization. The findings have confirmed that the "experiment" of using a 33-year-old positivistic framework to investigate aspects of qualitative research has enabled a robust contribution to the conceptual area of emotional climate. PMID:12463648

  12. Identifying False Alarms in the Kepler Planet Candidate Catalog

    Science.gov (United States)

    Mullally, F.; Coughlin, Jeffery L.; Thompson, Susan E.; Christiansen, Jessie; Burke, Christopher; Clarke, Bruce D.; Haas, Michael R.

    2016-07-01

    We present a new automated method to identify instrumental features masquerading as small, long-period planets in the Kepler planet candidate catalog. These systematics, mistakenly identified as planet transits, can have a strong impact on occurrence rate calculations because they cluster in a region of parameter space where Kepler’s sensitivity to planets is poor. We compare individual transit-like events to a variety of models of real transits and systematic events and use a Bayesian information criterion to evaluate the likelihood that each event is real. We describe our technique and test its performance on simulated data. Results from this technique are incorporated in the Kepler Q1–Q17 DR24 planet candidate catalog of Coughlin et al.

  13. Community and law: identifying the locus of law in community

    OpenAIRE

    Yaylali, Mustafa

    2012-01-01

    "Community and law approach" provides an illuminating insight into alternative legal orderings within a social unit. The comprehensiveness of legal systems within a community or a social unit, provides a suitable basis for a structural framework of alternative legal systems or Legal Pluralism, which is missing in the discourse on Legal Pluralism. "Identifying the locus of law within a community", provides us with an indication on how autopoetic a legal system can be within a social unit, taki...

  14. Methods To Identify Aptamers against Cell Surface Biomarkers

    OpenAIRE

    Frédéric Ducongé; Daniel Miotto Dupont; Agnes Cibiel

    2011-01-01

    Aptamers are nucleic acid-based ligands identified through a process of molecular evolution named SELEX (Systematic Evolution of Ligands by Exponential enrichment). During the last 10-15 years, numerous aptamers have been developed specifically against targets present on or associated with the surface of human cells or infectious pathogens such as viruses, bacteria, fungi or parasites. Several of the aptamers have been described as potent probes, rivalling antibodies, for use in flow cytometr...

  15. Data Mining and Pattern Recognition Models for Identifying Inherited Diseases

    DEFF Research Database (Denmark)

    Iddamalgoda, Lahiru; Das, Partha S; Aponso, Achala;

    2016-01-01

    Data mining and pattern recognition methods reveal interesting findings in genetic studies, especially on how the genetic makeup is associated with inherited diseases. Although researchers have proposed various data mining models for biomedical approaches, there remains a challenge in accurately...... prioritizing the single nucleotide polymorphisms (SNP) associated with the disease. In this commentary, we review the state-of-art data mining and pattern recognition models for identifying inherited diseases and deliberate the need of binary classification- and scoring-based prioritization methods...

  16. Identifying program critical success factors in construction industry

    OpenAIRE

    Sarmad Kiani; Vahidreza Yousefi; Siamak Haji Yakhchali; Aghil Mellatdust

    2014-01-01

    In project management literature, the concept of program is a group of related projects managed in a coordinated way to obtain benefits not available from managing them individually. This paper attempts to identify program critical success factors focusing on Iran’s construction industry so that the level of relative importance of various factors could be determined for key stakeholders. Furthermore, since a program includes a set of projects, another objective of this study is to find out wh...

  17. Classifying and identifying servers for biomedical information retrieval.

    OpenAIRE

    Patrick, T. B.; Springer, G K

    1994-01-01

    Useful retrieval of biomedical information from network information sources requires methods for organized access to those information sources. This access must be organized in terms of the information content of information sources and in terms of the discovery of the network location of those information sources. We have developed an approach to providing organized access to information sources based on a scheme of hierarchical classifiers and identifiers of the servers providing access to ...

  18. Identifying Bank Frauds Using CRISP-DM and Decision Trees

    OpenAIRE

    Bruno Carneiro da Rocha; Rafael Timóteo de Sousa Júnior

    2010-01-01

    This article aims to evaluate the use of techniques of decision trees, in conjunction with the managementmodel CRISP-DM, to help in the prevention of bank fraud. This article offers a study on decision trees, animportant concept in the field of artificial intelligence. The study is focused on discussing how these treesare able to assist in the decision making process of identifying frauds by the analysis of informationregarding bank transactions. This information is captured with the use of t...

  19. Identifying the needs of brain tumor patients and their caregivers.

    Science.gov (United States)

    Parvataneni, Rupa; Polley, Mei-Yin; Freeman, Teresa; Lamborn, Kathleen; Prados, Michael; Butowski, Nicholas; Liu, Raymond; Clarke, Jennifer; Page, Margaretta; Rabbitt, Jane; Fedoroff, Anne; Clow, Emelia; Hsieh, Emily; Kivett, Valerie; Deboer, Rebecca; Chang, Susan

    2011-09-01

    The purpose of this study is to identify the needs of brain tumor patients and their caregivers to provide improved health services to these populations. Two different questionnaires were designed for patients and caregivers. Both questionnaires contained questions pertaining to three realms: disease symptoms/treatment, health care provider, daily living/finances. The caregivers' questionnaires contained an additional domain on emotional needs. Each question was evaluated for the degree of importance and satisfaction. Exploratory analyses determined whether baseline characteristics affect responder importance or satisfaction. Also, areas of high agreement/disagreement in satisfaction between the participating patient-caregiver pairs were identified. Questions for which >50% of the patients and caregivers thought were "very important" but >30% were dissatisfied include: understanding the cause of brain tumors, dealing with patients' lower energy, identifying healthful foods and activities for patients, telephone access to health care providers, information on medical insurance coverage, and support from their employer. In the emotional realm, caregivers identified 9 out of 10 items as important but need further improvement. Areas of high disagreement in satisfaction between participating patient-caregiver pairs include: getting help with household chores (P value = 0.006) and finding time for personal needs (P value < 0.001). This study provides insights into areas to improve services for brain tumor patients and their caregivers. The caregivers' highest amount of burden is placed on their emotional needs, emphasizing the importance of providing appropriate medical and psychosocial support for caregivers to cope with emotional difficulties they face during the patients' treatment process.

  20. Identifying Fine Aggregates Prone to Polishing in PCC Pavements

    OpenAIRE

    Fowler, David W; Rached, Marc M.

    2012-01-01

    Surface polishing in portland cement concrete (PCC) pavements leads to higher incidences of skid-related accidents on highways. This type of failure is often associated with the usage of softer fine aggregate such as limestone sands. To identify polish resistance aggregates, state agencies like TxDOT have adopted tests such as the acid insoluble residue test (AIR). Since calcium carbonate is soluble in acid, no carbonate sand passes the AIR test which has a minimum limit of 60% in Texas. This...

  1. Identifying seasonal variations in store‐level visitor grocery demand

    OpenAIRE

    Newing, A.; Clarke, GP; Clarke, MC

    2013-01-01

    Purpose: The purpose of this paper is to understand the contribution of visitor demand to the seasonal sales variations experienced at grocery retailers in Cornwall, South West England. Design/methodology/approach: Working collaboratively with a major UK retailer provides access to store trading information and customer data from a popular loyalty card scheme. The authors use spatial analysis to identify revenue originating from outside the store catchment, and explore the spatial and tempora...

  2. A framework for identifying carbon hotspots and forest management drivers.

    Science.gov (United States)

    Timilsina, Nilesh; Escobedo, Francisco J; Cropper, Wendell P; Abd-Elrahman, Amr; Brandeis, Thomas J; Delphin, Sonia; Lambert, Samuel

    2013-01-15

    Spatial analyses of ecosystem system services that are directly relevant to both forest management decision making and conservation in the subtropics are rare. Also, frameworks that identify and map carbon stocks and corresponding forest management drivers using available regional, national, and international-level forest inventory datasets could provide insights into key forest structural characteristics and management practices that are optimal for carbon storage. To address this need we used publicly available USDA Forest Service Forest Inventory and Analysis data and spatial analyses to develop a framework for mapping "carbon hotspots" (i.e. areas of significantly high tree and understory aboveground carbon stocks) across a range of forest types using the state of Florida, USA as an example. We also analyzed influential forest management variables (e.g. forest types, fire, hurricanes, tenure, management activities) using generalized linear mixed modeling to identify drivers associated with these hotspots. Most of the hotspots were located in the northern third of the state some in peri-urban areas, and there were no identifiable hotspots in South Florida. Forest silvicultural treatments (e.g. site preparation, thinning, logging, etc) were not significant predictors of hotspots. Forest types, site quality, and stand age were however significant predictors. Higher site quality and stand age increased the probability of forests being classified as a hotspot. Disturbance type and time since disturbance were not significant predictors in our analyses. This framework can use globally available forest inventory datasets to analyze and map ecosystems service provision areas and bioenergy supplies and identify forest management practices that optimize these services in forests. PMID:23171606

  3. Identifying Basketball Performance Indicators in Regular Season and Playoff Games

    OpenAIRE

    García, Javier; Ibáñez, Sergio J.; De Santos, Raúl Martinez; Leite, Nuno; Sampaio, Jaime

    2013-01-01

    The aim of the present study was to identify basketball game performance indicators which best discriminate winners and losers in regular season and playoffs. The sample used was composed by 323 games of ACB Spanish Basketball League from the regular season (n=306) and from the playoffs (n=17). A previous cluster analysis allowed splitting the sample in balanced (equal or below 12 points), unbalanced (between 13 and 28 points) and very unbalanced games (above 28 points). A discriminant analys...

  4. Using a polyphasic approach to identify wild Brazilian fungal strains

    OpenAIRE

    Lima, M. Sanitá; Santos, C.; Lima, Nelson; Maria de Lourdes T. M. Polizeli

    2012-01-01

    [Aim] The species must be delineated based on a polyphasic approach, including morphology, physiology, profile of secondary metabolites and molecular biology [1]. According to Santos et al. [2;3] it is clearer that spectral analyses add value to the polyphasic approach. This work aimed to perform a polyphasic approach based on morphological, biochemical and spectral analysis by MALDI-TOF ICMS for identify Aspergilli isolates from different environments of Brazil.

  5. Asthma trajectories in early childhood: identifying modifiable factors.

    Directory of Open Access Journals (Sweden)

    Lidia Panico

    Full Text Available BACKGROUND: There are conflicting views as to whether childhood wheezing represents several discreet entities or a single but variable disease. Classification has centered on phenotypes often derived using subjective criteria, small samples, and/or with little data for young children. This is particularly problematic as asthmatic features appear to be entrenched by age 6/7. In this paper we aim to: identify longitudinal trajectories of wheeze and other atopic symptoms in early childhood; characterize the resulting trajectories by the socio-economic background of children; and identify potentially modifiable processes in infancy correlated with these trajectories. DATA AND METHODS: The Millennium Cohort Study is a large, representative birth cohort of British children born in 2000-2002. Our analytical sample includes 11,632 children with data on key variables (wheeze in the last year; ever hay-fever and/or eczema reported by the main carers at age 3, 5 and 7 using a validated tool, the International Study of Asthma and Allergies in Childhood module. We employ longitudinal Latent Class Analysis, a clustering methodology which identifies classes underlying the observed population heterogeneity. RESULTS: Our model distinguished four latent trajectories: a trajectory with both low levels of wheeze and other atopic symptoms (54% of the sample; a trajectory with low levels of wheeze but high prevalence of other atopic symptoms (29%; a trajectory with high prevalence of both wheeze and other atopic symptoms (9%; and a trajectory with high levels of wheeze but low levels of other atopic symptoms (8%. These groups differed in terms of socio-economic markers and potential intervenable factors, including household damp and breastfeeding initiation. CONCLUSION: Using data-driven techniques, we derived four trajectories of asthmatic symptoms in early childhood in a large, population based sample. These groups differ in terms of their socio-economic profiles

  6. Identifying Nanotechnological Linkages in the Finnish Economy - An Explorative Study

    OpenAIRE

    Nikulainen, Tuomo

    2007-01-01

    Nanotechnology, as an emerging science-based technology, is seen to have great potential both in scientific as well as economic terms. In this paper the focus is on identifying the technological linkages between the Finnish nanotechnology community and the industrial incumbents. These technological link-ages are first observed at a broader level in comparison with the technological strengths of the Finnish industries, and then in greater detail at the level of companies. In addition, the abso...

  7. A saltwater flotation technique to identify unincubated eggs

    Science.gov (United States)

    Devney, C.A.; Kondrad, S.L.; Stebbins, K.R.; Brittingham, K.D.; Hoffman, D.J.; Heinz, G.H.

    2009-01-01

    Field studies on nesting birds sometimes involve questions related to nest initiation dates, length of the incubation period, or changes in parental incubation behavior during various stages of incubation. Some of this information can be best assessed when a nest is discovered before the eggs have undergone any incubation, and this has traditionally been assessed by floating eggs in freshwater. However, because the freshwater method is not particularly accurate in identifying unincubated eggs, we developed a more reliable saltwater flotation method. The saltwater method involves diluting a saturated saltwater solution with freshwater until a salt concentration is reached where unincubated eggs sink to the bottom and incubated eggs float to the surface. For Laughing Gulls (Leucophaeus atricilla), floating eggs in freshwater failed to identify 39.0% (N = 251) of eggs that were subsequently found by candling to have undergone incubation prior to collection. By contrast, in a separate collection of gull eggs, no eggs that passed the saltwater test (N = 225) were found by a later candling to have been incubated prior to collection. For Double-crested Cormorants (Phalacrocorax auritus), floating eggs in freshwater failed to identify 15.6% (N = 250) of eggs that had undergone incubation prior to collection, whereas in a separate collection, none of the eggs that passed the saltwater test (N = 85) were found by a later candling to have been incubated prior to collection. Immersion of eggs in saltwater did not affect embryo survival. Although use of the saltwater method is likely limited to colonial species and requires calibrating a saltwater solution, it is a faster and more accurate method of identifying unincubated eggs than the traditional method of floating eggs in freshwater.

  8. SPIDERz: SuPport vector classification for IDEntifying Redshifts

    Science.gov (United States)

    Jones, Evan; Singal, J.

    2016-08-01

    SPIDERz (SuPport vector classification for IDEntifying Redshifts) applies powerful support vector machine (SVM) optimization and statistical learning techniques to custom data sets to obtain accurate photometric redshift (photo-z) estimations. It is written for the IDL environment and can be applied to traditional data sets consisting of photometric band magnitudes, or alternatively to data sets with additional galaxy parameters (such as shape information) to investigate potential correlations between the extra galaxy parameters and redshift.

  9. Magnetism based System for Detecting and Identifying buried Networks

    OpenAIRE

    Sultan Buzid; Danielle Nuzillard; Fabien Belloir; Larbi Beheim; Jean-Louis Nicolas

    2009-01-01

    An innovative magnetic based system for detectingand identifying networks of buried pipes is presented. Currentlywhen a pipe is buried, a warning colored plastic is placed aboveit and its color indicates the nature of its fluid. Its locationis reported on maps. This system developed here consists ofa magnetic sensor block associated to a detector based on anelectromagnetic induction balance. The detector emits a sine waveof frequency f0 and picks up the harmonics generated by thepossible pres...

  10. Taming Trojan Horses: Identifying and Mitigating Corporate Social Responsibility Risks

    OpenAIRE

    Heugens, Pursey; Dentchev, Nikolay

    2007-01-01

    textabstractOrganizations are exposed to increasing pressures from their constituents to integrate corporate social responsibility (CSR) principles into their ongoing business practices. But accepting new and potentially open-ended commitments is not a harmless exercise, and companies may well expose themselves to serious risks when embracing such principles. To identify these risks, we conducted two naturalistic studies: one exploratory, the other corroborative. The results show that CSR ado...

  11. Identifying Diabetic Parameters in Cochlear Mechanics and Models

    OpenAIRE

    Mrs. Nirmala N. Kamble,; Dr V R Mankar

    2014-01-01

    Hearing impairment is one of the most prevalent chronic disability identified with the elderly people over the age of 65.The peripheral portion of the cochlea and auditory nerve are known to deteriorate with age. The prevalence of hearing loss in diabetes has been shown in many studies to be moderately high, progressive and bilateral. The predominant mechanism of hearing loss in diabetes appears to be related to microangiopathy of inner ear. Mathematical modelling ...

  12. Ontology integration to identify protein complex in protein interaction networks

    OpenAIRE

    Yang Zhihao; Lin Hongfei; Xu Bo

    2011-01-01

    Abstract Background Protein complexes can be identified from the protein interaction networks derived from experimental data sets. However, these analyses are challenging because of the presence of unreliable interactions and the complex connectivity of the network. The integration of protein-protein interactions with the data from other sources can be leveraged for improving the effectiveness of protein complexes detection algorithms. Methods We have developed novel semantic similarity metho...

  13. Computational approaches to identify functional genetic variants in cancer genomes

    Science.gov (United States)

    Gonzalez-Perez, Abel; Mustonen, Ville; Reva, Boris; Ritchie, Graham R.S.; Creixell, Pau; Karchin, Rachel; Vazquez, Miguel; Fink, J. Lynn; Kassahn, Karin S.; Pearson, John V.; Bader, Gary; Boutros, Paul C.; Muthuswamy, Lakshmi; Ouellette, B.F. Francis; Reimand, Jüri; Linding, Rune; Shibata, Tatsuhiro; Valencia, Alfonso; Butler, Adam; Dronov, Serge; Flicek, Paul; Shannon, Nick B.; Carter, Hannah; Ding, Li; Sander, Chris; Stuart, Josh M.; Stein, Lincoln D.; Lopez-Bigas, Nuria

    2014-01-01

    The International Cancer Genome Consortium (ICGC) aims to catalog genomic abnormalities in tumors from 50 different cancer types. Genome sequencing reveals hundreds to thousands of somatic mutations in each tumor, but only a minority drive tumor progression. We present the result of discussions within the ICGC on how to address the challenge of identifying mutations that contribute to oncogenesis, tumor maintenance or response to therapy, and recommend computational techniques to annotate somatic variants and predict their impact on cancer phenotype. PMID:23900255

  14. Fetal alcohol-spectrum disorders: identifying at-risk mothers

    Directory of Open Access Journals (Sweden)

    Montag AC

    2016-07-01

    Full Text Available Annika C Montag Department of Pediatrics, Division of Dysmorphology and Teratology, University of California San Diego, San Diego, CA, USA Abstract: Fetal alcohol-spectrum disorders (FASDs are a collection of physical and neuro­behavioral disabilities caused by prenatal exposure to alcohol. To prevent or mitigate the costly effects of FASD, we must identify mothers at risk for having a child with FASD, so that we may reach them with interventions. Identifying mothers at risk is beneficial at all time points, whether prior to pregnancy, during pregnancy, or following the birth of the child. In this review, three approaches to identifying mothers at risk are explored: using characteristics of the mother and her pregnancy, using laboratory biomarkers, and using self-report assessment of alcohol-consumption risk. At present, all approaches have serious limitations. Research is needed to improve the sensitivity and specificity of biomarkers and screening instruments, and to link them to outcomes as opposed to exposure. Universal self-report screening of all women of childbearing potential should ideally be incorporated into routine obstetric and gynecologic care, followed by brief interventions, including education and personalized feedback for all who consume alcohol, and referral to treatment as indicated. Effective biomarkers or combinations of biomarkers may be used during pregnancy and at birth to determine maternal and fetal alcohol exposure. The combination of self-report and biomarker screening may help identify a greater proportion of women at risk for having a child with FASD, allowing them to access information and treatment, and empowering them to make decisions that benefit their children. Keywords: fetal alcohol-spectrum disorder (FASD, alcohol, pregnancy, screening, biomarkers, SBIRT

  15. Identifying industry clusters in Colombia based on graph theory

    OpenAIRE

    Juan C. Duque; Rey, S.J.; Gómez, D. A.

    2009-01-01

    This paper presents a new way to identify and understand the industry clusters in the Colombian economy. The analysis relies on a recent methodology proposed by Duque and Rey (2008) where intricate input-output linkages between industries are simplified using network analysis. In addition to other techniques for cluster identification available in the literature, this novel methodology allows us not only to classify each industry in a given cluster, but also to understand how industries are r...

  16. Mass spectrometry identifies multiple organophosphorylated sites on tubulin

    OpenAIRE

    Grigoryan, Hasmik; Schopfer, Lawrence M.; Peeples, Eric S.; Duysen, Ellen G.; Grigoryan, Marine; Thompson, Charles M.; Lockridge, Oksana

    2009-01-01

    Acute toxicity of organophosphorus poisons (OP) is explained by inhibition of acetylcholinesterase in nerve synapses. Low dose effects are hypothesized to result from modification of other proteins, whose identity is not yet established. The goal of the present work was to obtain information that would make it possible to identify tubulin as a target of OP exposure. Tubulin was selected for study because live mice injected with a nontoxic dose of a biotinylated organophosphorus agent appeared...

  17. High-Throughput Screening of Small Molecules Identifies Hepcidin Antagonists

    OpenAIRE

    Fung, Eileen; Sugianto, Priscilla; Hsu, Jason; Damoiseaux, Robert; Ganz, Tomas; Nemeth, Elizabeta

    2013-01-01

    Anemia of inflammation (AI) is common in patients with infection, autoimmune diseases, cancer, and chronic kidney disease. Unless the underlying condition can be reversed, treatment options are limited to erythropoiesis-stimulating agents with or without intravenous iron therapy, modalities that are not always effective and can cause serious adverse effects. Hepcidin, the iron regulatory hormone, has been identified as a pathogenic factor in the development of AI. To explore new therapeutic o...

  18. A Bayesian Approach to Identifying New Risk Factors for Dementia

    OpenAIRE

    Wen, Yen-Hsia; Wu, Shihn-Sheng; Lin, Chun-Hung Richard; Tsai, Jui-Hsiu; Yang, Pinchen; Chang, Yang-Pei; Tseng, Kuan-Hua

    2016-01-01

    Abstract Dementia is one of the most disabling and burdensome health conditions worldwide. In this study, we identified new potential risk factors for dementia from nationwide longitudinal population-based data by using Bayesian statistics. We first tested the consistency of the results obtained using Bayesian statistics with those obtained using classical frequentist probability for 4 recognized risk factors for dementia, namely severe head injury, depression, diabetes mellitus, and vascular...

  19. DNA Barcode for Identifying Folium Artemisiae Argyi from Counterfeits.

    Science.gov (United States)

    Mei, Quanxi; Chen, Xiaolu; Xiang, Li; Liu, Yue; Su, Yanyan; Gao, Yuqiao; Dai, Weibo; Dong, Pengpeng; Chen, Shilin

    2016-01-01

    Folium Artemisiae Argyi is an important herb in traditional Chinese medicine. It is commonly used in moxibustion, medicine, etc. However, identifying Artemisia argyi is difficult because this herb exhibits similar morphological characteristics to closely related species and counterfeits. To verify the applicability of DNA barcoding, ITS2 and psbA-trnH were used to identify A. argyi from 15 closely related species and counterfeits. Results indicated that total DNA was easily extracted from all the samples and that both ITS2 and psbA-trnH fragments can be easily amplified. ITS2 was a more ideal barcode than psbA-trnH and ITS2+psbA-trnH to identify A. argyi from closely related species and counterfeits on the basis of sequence character, genetic distance, and tree methods. The sequence length was 225 bp for the 56 ITS2 sequences of A. argyi, and no variable site was detected. For the ITS2 sequences, A. capillaris, A. anomala, A. annua, A. igniaria, A. maximowicziana, A. princeps, Dendranthema vestitum, and D. indicum had single nucleotide polymorphisms (SNPs). The intraspecific Kimura 2-Parameter distance was zero, which is lower than the minimum interspecific distance (0.005). A. argyi, the closely related species, and counterfeits, except for Artemisia maximowicziana and Artemisia sieversiana, were separated into pairs of divergent clusters by using the neighbor joining, maximum parsimony, and maximum likelihood tree methods. Thus, the ITS2 sequence was an ideal barcode to identify A. argyi from closely related species and counterfeits to ensure the safe use of this plant. PMID:27582332

  20. Identifying nurses' rewards: a qualitative categorization study in Belgium

    OpenAIRE

    Du Bois Cindy; Caers Ralf; Pepermans Roland; De Cooman Rein; De Gieter Sara; Jegers Marc

    2006-01-01

    Abstract Background Rewards are important in attracting, motivating and retaining the most qualified employees, and nurses are no exception to this rule. This makes the establishment of an efficient reward system for nurses a true challenge for every hospital manager. A reward does not necessarily have a financial connotation: non-financial rewards may matter too, or may even be more important. Therefore, the present study examines nurses' reward perceptions, in order to identify potential re...

  1. Identifying and ranking factors affecting entrepreneurship success in palm industry

    OpenAIRE

    N. Mina; S. Habobollah; Ebrahim, H.

    2013-01-01

    Influencing physical environment and valued-entrepreneurship effects on community; it reduces unemployment by creating value; it also leads the society to employment and production rather than consumption. This study aimed to identify and rank factors affecting entrepreneurship success in palm industry in Saravan. After reviewing literatures as well as doing interviews, a questionnaire with 66 items was developed by the researcher. Using snowball sampling method, 106 executives and experts re...

  2. Multidisciplinary approach to identify aquifer-peatland connectivity

    Science.gov (United States)

    Larocque, Marie; Pellerin, Stéphanie; Cloutier, Vincent; Ferlatte, Miryane; Munger, Julie; Quillet, Anne; Paniconi, Claudio

    2015-04-01

    In southern Quebec (Canada), wetlands sustain increasing pressures from agriculture, urban development, and peat exploitation. To protect both groundwater and ecosystems, it is important to be able to identify how, where, and to what extent shallow aquifers and wetlands are connected. This study focuses on peatlands which are especially abundant in Quebec. The objective of this research was to better understand aquifer-peatland connectivity and to identify easily measured indicators of this connectivity. Geomorphology, hydrogeochemistry, and vegetation were selected as key indicators of connectivity. Twelve peatland transects were instrumented and monitored in the Abitibi (slope peatlands associated with eskers) and Centre-du-Quebec (depression peatlands) regions of Quebec (Canada). Geomorphology, geology, water levels, water chemistry, and vegetation species were identified/measured on all transects. Flow conditions were simulated numerically on two typical transects. Results show that a majority of peatland transects receives groundwater from a shallow aquifer. In slope peatlands, groundwater flows through the organic deposits towards the peatland center. In depression peatlands, groundwater flows only 100-200 m within the peatland before being redirected through surface routes towards the outlet. Flow modeling and sensitivity analysis have identified that the thickness and hydraulic conductivity of permeable deposits close to the peatland and beneath the organic deposits influence flow directions within the peatland. Geochemical data have confirmed the usefulness of total dissolved solids (TDS) exceeding 14 mg/L as an indicator of the presence of groundwater within the peatland. Vegetation surveys have allowed the identification of species and groups of species that occur mostly when groundwater is present, for instance Carex limosa and Sphagnum russowii. Geomorphological conditions (slope or depression peatland), TDS, and vegetation can be measured

  3. De-Identifying Facial Images Using Projections on Hyperspheres

    OpenAIRE

    Chriskos, P.; Zoidi, O.; Tefas, A; Pitas, Ioannis

    2015-01-01

    A major issue that arises from mass visual media distribution in modern video sharing, social media and cloud services, is the issue of privacy. Malicious users can use these services to track the actions of certain individuals and/or groupsthus violating their privacy. As a result the need to hinder automatic facial image identification in images and videos arises. In this paper we propose a method for de-identifying facial images. Contrary to most de-identification methods, thismethod manip...

  4. An in vivo platform for identifying inhibitors of protein aggregation

    OpenAIRE

    Saunders, JC; Young, LM; Mahood, RA; Jackson, MP; Revill, CH; Foster, RJ; Smith, DA; Ashcroft, AE; Brockwell, DJ; Radford, SE

    2016-01-01

    Protein aggregation underlies an array of human diseases, yet only one small molecule therapeutic has been successfully developed to date. Here, we introduce an in vivo system, based on a β-lactamase tripartite fusion construct, capable of identifying aggregation-prone sequences in the periplasm of Escherichia coli and inhibitors that prevent their aberrant self-assembly. We demonstrate the power of the system using a range of proteins, from small unstructured peptides (islet amyloid polypept...

  5. Identifying Distraction: Kinematic Detection of Off-Road Eye Glances

    OpenAIRE

    Rainey, Cameron; McLaughlin, Shane B.

    2015-01-01

    Visual attention is a key component of the driving task. Identifying times when the driver is not looking toward the forward views has been shown to be a successful indicator of distracted driving (Olson, Hanowski, Hickman, & Bocanegra, 2009). Previous technologies have successfully captured eye-glance location, but have come at great expense in terms of both cost and intrusiveness. This project explored the possibility of using a low cost and unobtrusive Inertial Measurement Unit (IMU). Thro...

  6. Parameter Trajectory Analysis to Identify Treatment Effects of Pharmacological Interventions

    OpenAIRE

    Tiemann, Christian A.; Vanlier, Joep; Oosterveer, Maaike H.; Albert K Groen; Hilbers, Peter A. J.; Natal A W van Riel

    2013-01-01

    The field of medical systems biology aims to advance understanding of molecular mechanisms that drive disease progression and to translate this knowledge into therapies to effectively treat diseases. A challenging task is the investigation of long-term effects of a (pharmacological) treatment, to establish its applicability and to identify potential side effects. We present a new modeling approach, called Analysis of Dynamic Adaptations in Parameter Trajectories (ADAPT), to analyze the long-t...

  7. Bioinformatics approaches for identifying new therapeutic bioactive peptides in food

    OpenAIRE

    Nora Khaldi

    2012-01-01

    ABSTRACT:The traditional methods for mining foods for bioactive peptides are tedious and long. Similar to the drug industry, the length of time to identify and deliver a commercial health ingredient that reduces disease symptoms can take anything between 5 to 10 years. Reducing this time and effort is crucial in order to create new commercially viable products with clear and important health benefits. In the past few years, bioinformatics, the science that brings together fast computational b...

  8. Human strongyloidiasis: identifying knowledge gaps, with emphasis on environmental control

    OpenAIRE

    Taylor, Michael

    2014-01-01

    Michael J Taylor, Tara A Garrard, Francis J O'Donahoo, Kirstin E Ross Health and Environment, School of the Environment, Flinders University, Adelaide, SA, Australia Abstract: Strongyloides is a human parasitic nematode that is poorly understood outside a clinical context. This article identifies gaps within the literature, with particular emphasis on gaps that are hindering environmental control of Strongyloides. The prevalence and distribution of Strongyloides is unclear. An estima...

  9. Human strongyloidiasis: identifying knowledge gaps, with emphasis on environmental control

    OpenAIRE

    Taylor MJ; Garrard TA; O'Donahoo FJ; Ross KE

    2014-01-01

    Michael J Taylor, Tara A Garrard, Francis J O'Donahoo, Kirstin E Ross Health and Environment, School of the Environment, Flinders University, Adelaide, SA, Australia Abstract: Strongyloides is a human parasitic nematode that is poorly understood outside a clinical context. This article identifies gaps within the literature, with particular emphasis on gaps that are hindering environmental control of Strongyloides. The prevalence and distribution of Strongyloides is unclear. An estimate o...

  10. Parameter trajectory analysis to identify treatment effects of pharmacological interventions.

    Directory of Open Access Journals (Sweden)

    Christian A Tiemann

    Full Text Available The field of medical systems biology aims to advance understanding of molecular mechanisms that drive disease progression and to translate this knowledge into therapies to effectively treat diseases. A challenging task is the investigation of long-term effects of a (pharmacological treatment, to establish its applicability and to identify potential side effects. We present a new modeling approach, called Analysis of Dynamic Adaptations in Parameter Trajectories (ADAPT, to analyze the long-term effects of a pharmacological intervention. A concept of time-dependent evolution of model parameters is introduced to study the dynamics of molecular adaptations. The progression of these adaptations is predicted by identifying necessary dynamic changes in the model parameters to describe the transition between experimental data obtained during different stages of the treatment. The trajectories provide insight in the affected underlying biological systems and identify the molecular events that should be studied in more detail to unravel the mechanistic basis of treatment outcome. Modulating effects caused by interactions with the proteome and transcriptome levels, which are often less well understood, can be captured by the time-dependent descriptions of the parameters. ADAPT was employed to identify metabolic adaptations induced upon pharmacological activation of the liver X receptor (LXR, a potential drug target to treat or prevent atherosclerosis. The trajectories were investigated to study the cascade of adaptations. This provided a counter-intuitive insight concerning the function of scavenger receptor class B1 (SR-B1, a receptor that facilitates the hepatic uptake of cholesterol. Although activation of LXR promotes cholesterol efflux and -excretion, our computational analysis showed that the hepatic capacity to clear cholesterol was reduced upon prolonged treatment. This prediction was confirmed experimentally by immunoblotting measurements of SR-B1

  11. Identifying the big question in international business research

    OpenAIRE

    Mike W. Peng

    2004-01-01

    Buckley (2002) argues that the international business (IB) research agenda may be running out of steam, because no big research question has currently been identified. Buckley also asks whether the field needs a big question, and if so challenges IB scholars to discover it. Buckley and Ghauri (2004) elaborate on the third question of globalization discussed in Buckley (2002) as a possible candidate for the big question. In response, this article is written to take up Buckley's challenge and a...

  12. A comparison of computational methods for identifying virulence factors.

    Directory of Open Access Journals (Sweden)

    Lu-Lu Zheng

    Full Text Available Bacterial pathogens continue to threaten public health worldwide today. Identification of bacterial virulence factors can help to find novel drug/vaccine targets against pathogenicity. It can also help to reveal the mechanisms of the related diseases at the molecular level. With the explosive growth in protein sequences generated in the postgenomic age, it is highly desired to develop computational methods for rapidly and effectively identifying virulence factors according to their sequence information alone. In this study, based on the protein-protein interaction networks from the STRING database, a novel network-based method was proposed for identifying the virulence factors in the proteomes of UPEC 536, UPEC CFT073, P. aeruginosa PAO1, L. pneumophila Philadelphia 1, C. jejuni NCTC 11168 and M. tuberculosis H37Rv. Evaluated on the same benchmark datasets derived from the aforementioned species, the identification accuracies achieved by the network-based method were around 0.9, significantly higher than those by the sequence-based methods such as BLAST, feature selection and VirulentPred. Further analysis showed that the functional associations such as the gene neighborhood and co-occurrence were the primary associations between these virulence factors in the STRING database. The high success rates indicate that the network-based method is quite promising. The novel approach holds high potential for identifying virulence factors in many other various organisms as well because it can be easily extended to identify the virulence factors in many other bacterial species, as long as the relevant significant statistical data are available for them.

  13. A unique, consistent identifier for alternatively spliced transcript variants.

    Directory of Open Access Journals (Sweden)

    Alberto Riva

    Full Text Available BACKGROUND: As research into alternative splicing reveals the fundamental importance of this phenomenon in the genome expression of higher organisms, there is an increasing need for a standardized, consistent and unique identifier for alternatively spliced isoforms. Such an identifier would be useful to eliminate ambiguities in references to gene isoforms, and would allow for the reliable comparison of isoforms from different sources (e.g., known genes vs. computational predictions. Commonly used identifiers for gene transcripts prove to be unsuitable for this purpose. METHODOLOGY: We propose an algorithm to compute an isoform signature based on the arrangement of exons and introns in a primary transcript. The isoform signature uniquely identifies a transcript structure, and can therefore be used as a key in databases of alternatively spliced isoforms, or to compare alternative splicing predictions produced by different methods. In this paper we present the algorithm to generate isoform signatures, we provide some examples of its application, and we describe a web-based resource to generate isoform signatures and use them in database searches. CONCLUSIONS: Isoform signatures are simple, so that they can be easily generated and included in publications and databases, but flexible enough to unambiguously represent all possible isoform structures, including information about coding sequence position and variable transcription start and end sites. We believe that the adoption of isoform signatures can help establish a consistent, unambiguous nomenclature for alternative splicing isoforms. The system described in this paper is freely available at http://genome.ufl.edu/genesig/, and supplementary materials can be found at http://genome.ufl.edu/genesig-files/.

  14. Engaging basic scientists in translational research: identifying opportunities, overcoming obstacles

    Directory of Open Access Journals (Sweden)

    Hobin Jennifer A

    2012-04-01

    Full Text Available Abstract This report is based on the Federation of American Societies for Experimental Biology’s symposium, “Engaging basic Scientists in Translational Research: Identifying Opportunities, Overcoming Obstacles,” held in Chevy Chase, MD, March 24–25, 2011. Meeting participants examined the benefits of engaging basic scientists in translational research, the challenges to their participation in translational research, and the roles that research institutions, funding organizations, professional societies, and scientific publishers can play to address these challenges.

  15. Identifying critical factors for implementing good agricultural practice

    OpenAIRE

    Nelson Gutiérrez Guzmán; Juan Antonio Serra Belenguer; Gonzalo Clemente Marín

    2010-01-01

    This paper deals with identifying the critical factors (CFs) involved in implementing a good agricultural practice (GAP) programme for coffee and fruit farmers in the Huila department of Colombia. An exploratory factor analysis using principal component analy- sis (PCA) factorisation was used. Data matrixes were constructed from the results of applying two defined-structure assessment tools to the populations being studied: Starbucks’ coffee and farmer equity (CAFE) practices for small-scal...

  16. Rice transcriptome analysis to identify possible herbicide quinclorac detoxification genes

    OpenAIRE

    Xu, Wenying; Di, Chao; Zhou, Shaoxia; Liu, Jia; LI Li; Liu, Fengxia; Yang, Xinling; Ling, Yun; Su, Zhen

    2015-01-01

    Quinclorac is a highly selective auxin-type herbicide and is widely used in the effective control of barnyard grass in paddy rice fields, improving the world's rice yield. The herbicide mode of action of quinclorac has been proposed, and hormone interactions affecting quinclorac signaling has been identified. Because of widespread use, quinclorac may be transported outside rice fields with the drainage waters, leading to soil and water pollution and other environmental health problems. In thi...

  17. Identifying Competitive Positioning Strategies of Universities: Evidence from Turkey

    Directory of Open Access Journals (Sweden)

    Burçak Cagla Garipagaoglu

    2015-06-01

    Full Text Available This research aims to identify the factors affecting the students’ and parents’ choice of university in Turkey and strives to understand how they classify or position the universities in their minds. Since the focus of this research is to explore the main factors leading to the students’ and parents’ choice of university and to identify the dimensions for segmentation within the universities in Turkey, this research is qualitative in nature. Data was collected with a series of in-depth interviews with prospective university students and two focus group discussions with parents. Based on the findings, three dimensions, which were used to segment universities by the Turkish higher education market, were identified: 1 the diploma value of the program in a university, in terms of graduate employment, 2 the student social-life that the students expect to experience throughout their undergraduate years, and 3 the constraints limiting the students’ choice of university. Using these dimensions as a basis for segmentation, a simplified conceptual framework of competitive positioning strategies for universities was generated and four university types were identified: goal-oriented, exclusive, commodity and honeymoon. Turkish universities were then advised to consider their competitive positioning styles in the marketplace that is already perceived by the market and to develop appropriate marketing strategies, accordingly. By doing so, this research both aims to assist university leaders in developing their offerings with a unique and strong brand promise with the help of marketing orientation and make a significant contribution to a little researched, but increasingly topical, issue in the literature.

  18. Identifying indicators of soil suppressiveness to fungal diseases

    OpenAIRE

    Siegel, Katarzyna; Aime, Sébastien; Chapelle, Emilie; Edel Hermann, Veronique; Raaijmakers, Jos M; Lemanceau, Philippe; Steinberg, Christian

    2013-01-01

    Soils suppressive to soil-borne diseases are defined by a low disease incidence in spite of the presence of a virulent pathogen and a susceptible plant. In many cases, the inhibition of the disease development relies on the activity of the resident soil microbiome. To identify taxonomic microbial indicators linked to the suppressiveness phenotype of soils, culture independent-based methods have been employed to analyse and compare microbial dynamics in two different soils suppressive to eithe...

  19. Identifying Differences in Cultural Behavior in Online Groups

    Energy Technology Data Exchange (ETDEWEB)

    Gregory, Michelle L.; Engel, David W.; Bell, Eric B.; Mcgrath, Liam R.

    2012-07-23

    We have developed methods to identify online communities, or groups, using a combination of structural information variables and content information variables from weblog posts and their comments to build a characteristic footprint for groups. We have worked with both explicitly connected groups and 'abstract' groups, in which the connection between individuals is in interest (as determined by content based features) and behavior (metadata based features) as opposed to explicit links. We find that these variables do a good job at identifying groups, placing members within a group, and helping determine the appropriate granularity for group boundaries. The group footprint can then be used to identify differences between the online groups. In the work described here we are interested in determining how an individual's online behavior is influenced by their membership in more than one group. For example, individuals belong to a certain culture; they may belong as well to a demographic group, and other 'chosen' groups such as churches or clubs. There is a plethora of evidence surrounding the culturally sensitive adoption, use, and behavior on the Internet. In this work we begin to investigate how culturally defined internet behaviors may influence behaviors of subgroups. We do this through a series of experiments in which we analyze the interaction between culturally defined behaviors and the behaviors of the subgroups. Our goal is to (a) identify if our features can capture cultural distinctions in internet use, and (b) determine what kinds of interaction there are between levels and types of groups.

  20. Classes of secondary metabolites identified in three legume species

    OpenAIRE

    Delci de Deus Nepomuceno; João Carlos de Carvalho Almeida; Mário Geraldo de Carvalho; Renata Duarte Fernandes; Francisco Eduardo Aragão Catunda Júnior

    2013-01-01

    The objective of this study was to identify secondary metabolite classes of tropical kudzu, perennial soybean and archer legumes through identification by phytochemical screening and confirmation by infrared (IR), ¹H and carbon-13 NMR spectroscopy of fractions obtained by organic solvents partition of crude extracts. These analyses allowed for proposing the presence of the following metabolite classes: reducing sugars, saccharides, saponins, cardiac glucosides, terpenes, coumarins, tannins, a...