WorldWideScience

Sample records for hrp regulon predicts

  1. RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach

    Energy Technology Data Exchange (ETDEWEB)

    Novichkov, Pavel S.; Rodionov, Dmitry A.; Stavrovskaya, Elena D.; Novichkova, Elena S.; Kazakov, Alexey E.; Gelfand, Mikhail S.; Arkin, Adam P.; Mironov, Andrey A.; Dubchak, Inna

    2010-05-26

    RegPredict web server is designed to provide comparative genomics tools for reconstruction and analysis of microbial regulons using comparative genomics approach. The server allows the user to rapidly generate reference sets of regulons and regulatory motif profiles in a group of prokaryotic genomes. The new concept of a cluster of co-regulated orthologous operons allows the user to distribute the analysis of large regulons and to perform the comparative analysis of multiple clusters independently. Two major workflows currently implemented in RegPredict are: (i) regulon reconstruction for a known regulatory motif and (ii) ab initio inference of a novel regulon using several scenarios for the generation of starting gene sets. RegPredict provides a comprehensive collection of manually curated positional weight matrices of regulatory motifs. It is based on genomic sequences, ortholog and operon predictions from the MicrobesOnline. An interactive web interface of RegPredict integrates and presents diverse genomic and functional information about the candidate regulon members from several web resources. RegPredict is freely accessible at http://regpredict.lbl.gov.

  2. PePPER : a webserver for prediction of prokaryote promoter elements and regulons

    NARCIS (Netherlands)

    de Jong, Anne; Pietersma, Hilco; Cordes, Martijn; Kuipers, Oscar P.; Kok, Jan

    2012-01-01

    Background: Accurate prediction of DNA motifs that are targets of RNA polymerases, sigma factors and transcription factors (TFs) in prokaryotes is a difficult mission mainly due to as yet undiscovered features in DNA sequences or structures in promoter regions. Improved prediction and comparison

  3. Review of HRP Positions

    Energy Technology Data Exchange (ETDEWEB)

    Center for Reliability Studies

    2007-01-01

    The Department of Energy (DOE) Human Reliability Program (HRP), published as 10 CFR Part 712, is currently being reviewed and revised to address concerns identified during its implementation. Although these ''page changes'' primarily incorporate clarification of terms and language, the following discussion relates to broadening the definition of positions that require HRP certification that is found in {section}712.10.

  4. The sigma(54) regulon (sigmulon) of Pseudomonas putida

    DEFF Research Database (Denmark)

    Cases, I.; Ussery, David; de Lorenzo, V.

    2003-01-01

    , the sigma(54) regulon has been studied both in Escherichia coli, Salmonella typhimurium and several species of the Rhizobiaceae. Here we present the analysis of the sigma(54) regulon (sigmulon) in the complete genome of Pseudomonas putida KT2440. We have developed an improved method for the prediction...

  5. Computational prediction of the Crc regulon identifies genus-wide and species-specific targets of catabolite repression control in Pseudomonas bacteria

    Directory of Open Access Journals (Sweden)

    O'Gara Fergal

    2010-11-01

    Full Text Available Abstract Background Catabolite repression control (CRC is an important global control system in Pseudomonas that fine tunes metabolism in order optimise growth and metabolism in a range of different environments. The mechanism of CRC in Pseudomonas spp. centres on the binding of a protein, Crc, to an A-rich motif on the 5' end of an mRNA resulting in translational down-regulation of target genes. Despite the identification of several Crc targets in Pseudomonas spp. the Crc regulon has remained largely unexplored. Results In order to predict direct targets of Crc, we used a bioinformatics approach based on detection of A-rich motifs near the initiation of translation of all protein-encoding genes in twelve fully sequenced Pseudomonas genomes. As expected, our data predict that genes related to the utilisation of less preferred nutrients, such as some carbohydrates, nitrogen sources and aromatic carbon compounds are targets of Crc. A general trend in this analysis is that the regulation of transporters is conserved across species whereas regulation of specific enzymatic steps or transcriptional activators are often conserved only within a species. Interestingly, some nucleoid associated proteins (NAPs such as HU and IHF are predicted to be regulated by Crc. This finding indicates a possible role of Crc in indirect control over a subset of genes that depend on the DNA bending properties of NAPs for expression or repression. Finally, some virulence traits such as alginate and rhamnolipid production also appear to be regulated by Crc, which links nutritional status cues with the regulation of virulence traits. Conclusions Catabolite repression control regulates a broad spectrum of genes in Pseudomonas. Some targets are genus-wide and are typically related to central metabolism, whereas other targets are species-specific, or even unique to particular strains. Further study of these novel targets will enhance our understanding of how Pseudomonas

  6. Computational prediction of the Crc regulon identifies genus-wide and species-specific targets of catabolite repression control in Pseudomonas bacteria.

    Science.gov (United States)

    Browne, Patrick; Barret, Matthieu; O'Gara, Fergal; Morrissey, John P

    2010-11-25

    Catabolite repression control (CRC) is an important global control system in Pseudomonas that fine tunes metabolism in order optimise growth and metabolism in a range of different environments. The mechanism of CRC in Pseudomonas spp. centres on the binding of a protein, Crc, to an A-rich motif on the 5' end of an mRNA resulting in translational down-regulation of target genes. Despite the identification of several Crc targets in Pseudomonas spp. the Crc regulon has remained largely unexplored. In order to predict direct targets of Crc, we used a bioinformatics approach based on detection of A-rich motifs near the initiation of translation of all protein-encoding genes in twelve fully sequenced Pseudomonas genomes. As expected, our data predict that genes related to the utilisation of less preferred nutrients, such as some carbohydrates, nitrogen sources and aromatic carbon compounds are targets of Crc. A general trend in this analysis is that the regulation of transporters is conserved across species whereas regulation of specific enzymatic steps or transcriptional activators are often conserved only within a species. Interestingly, some nucleoid associated proteins (NAPs) such as HU and IHF are predicted to be regulated by Crc. This finding indicates a possible role of Crc in indirect control over a subset of genes that depend on the DNA bending properties of NAPs for expression or repression. Finally, some virulence traits such as alginate and rhamnolipid production also appear to be regulated by Crc, which links nutritional status cues with the regulation of virulence traits. Catabolite repression control regulates a broad spectrum of genes in Pseudomonas. Some targets are genus-wide and are typically related to central metabolism, whereas other targets are species-specific, or even unique to particular strains. Further study of these novel targets will enhance our understanding of how Pseudomonas bacteria integrate nutritional status cues with the regulation

  7. Computational prediction of the Crc regulon identifies genus-wide and species-specific targets of catabolite repression control in Pseudomonas bacteria

    LENUS (Irish Health Repository)

    Browne, Patrick

    2010-11-25

    Abstract Background Catabolite repression control (CRC) is an important global control system in Pseudomonas that fine tunes metabolism in order optimise growth and metabolism in a range of different environments. The mechanism of CRC in Pseudomonas spp. centres on the binding of a protein, Crc, to an A-rich motif on the 5\\' end of an mRNA resulting in translational down-regulation of target genes. Despite the identification of several Crc targets in Pseudomonas spp. the Crc regulon has remained largely unexplored. Results In order to predict direct targets of Crc, we used a bioinformatics approach based on detection of A-rich motifs near the initiation of translation of all protein-encoding genes in twelve fully sequenced Pseudomonas genomes. As expected, our data predict that genes related to the utilisation of less preferred nutrients, such as some carbohydrates, nitrogen sources and aromatic carbon compounds are targets of Crc. A general trend in this analysis is that the regulation of transporters is conserved across species whereas regulation of specific enzymatic steps or transcriptional activators are often conserved only within a species. Interestingly, some nucleoid associated proteins (NAPs) such as HU and IHF are predicted to be regulated by Crc. This finding indicates a possible role of Crc in indirect control over a subset of genes that depend on the DNA bending properties of NAPs for expression or repression. Finally, some virulence traits such as alginate and rhamnolipid production also appear to be regulated by Crc, which links nutritional status cues with the regulation of virulence traits. Conclusions Catabolite repression control regulates a broad spectrum of genes in Pseudomonas. Some targets are genus-wide and are typically related to central metabolism, whereas other targets are species-specific, or even unique to particular strains. Further study of these novel targets will enhance our understanding of how Pseudomonas bacteria integrate

  8. Prediction of DtxR regulon: Identification of binding sites and operons controlled by Diphtheria toxin repressor in Corynebacterium diphtheriae

    Directory of Open Access Journals (Sweden)

    Hasnain Seyed

    2004-09-01

    Full Text Available Abstract Background The diphtheria toxin repressor, DtxR, of Corynebacterium diphtheriae has been shown to be an iron-activated transcription regulator that controls not only the expression of diphtheria toxin but also of iron uptake genes. This study aims to identify putative binding sites and operons controlled by DtxR to understand the role of DtxR in patho-physiology of Corynebacterium diphtheriae. Result Positional Shannon relative entropy method was used to build the DtxR-binding site recognition profile and the later was used to identify putative regulatory sites of DtxR within C. diphtheriae genome. In addition, DtxR-regulated operons were also identified taking into account the predicted DtxR regulatory sites and genome annotation. Few of the predicted motifs were experimentally validated by electrophoretic mobility shift assay. The analysis identifies motifs upstream to the novel iron-regulated genes that code for Formamidopyrimidine-DNA glycosylase (FpG, an enzyme involved in DNA-repair and starvation inducible DNA-binding protein (Dps which is involved in iron storage and oxidative stress defense. In addition, we have found the DtxR motifs upstream to the genes that code for sortase which catalyzes anchoring of host-interacting proteins to the cell wall of pathogenic bacteria and the proteins of secretory system which could be involved in translocation of various iron-regulated virulence factors including diphtheria toxin. Conclusions We have used an in silico approach to identify the putative binding sites and genes controlled by DtxR in Corynebacterium diphtheriae. Our analysis shows that DtxR could provide a molecular link between Fe+2-induced Fenton's reaction and protection of DNA from oxidative damage. DtxR-regulated Dps prevents lethal combination of Fe+2 and H2O2 and also protects DNA by nonspecific DNA-binding. In addition DtxR could play an important role in host interaction and virulence by regulating the levels of sortase

  9. Reconstruction of the core and extended regulons of global transcription factors.

    Directory of Open Access Journals (Sweden)

    Yann S Dufour

    2010-07-01

    Full Text Available The processes underlying the evolution of regulatory networks are unclear. To address this question, we used a comparative genomics approach that takes advantage of the large number of sequenced bacterial genomes to predict conserved and variable members of transcriptional regulatory networks across phylogenetically related organisms. Specifically, we developed a computational method to predict the conserved regulons of transcription factors across alpha-proteobacteria. We focused on the CRP/FNR super-family of transcription factors because it contains several well-characterized members, such as FNR, FixK, and DNR. While FNR, FixK, and DNR are each proposed to regulate different aspects of anaerobic metabolism, they are predicted to recognize very similar DNA target sequences, and they occur in various combinations among individual alpha-proteobacterial species. In this study, the composition of the respective FNR, FixK, or DNR conserved regulons across 87 alpha-proteobacterial species was predicted by comparing the phylogenetic profiles of the regulators with the profiles of putative target genes. The utility of our predictions was evaluated by experimentally characterizing the FnrL regulon (a FNR-type regulator in the alpha-proteobacterium Rhodobacter sphaeroides. Our results show that this approach correctly predicted many regulon members, provided new insights into the biological functions of the respective regulons for these regulators, and suggested models for the evolution of the corresponding transcriptional networks. Our findings also predict that, at least for the FNR-type regulators, there is a core set of target genes conserved across many species. In addition, the members of the so-called extended regulons for the FNR-type regulators vary even among closely related species, possibly reflecting species-specific adaptation to environmental and other factors. The comparative genomics approach we developed is readily applicable to other

  10. Genome-wide identification of HrpL-regulated genes in the necrotrophic phytopathogen Dickeya dadantii 3937.

    Directory of Open Access Journals (Sweden)

    Shihui Yang

    Full Text Available BACKGROUND: Dickeya dadantii is a necrotrophic pathogen causing disease in many plants. Previous studies have demonstrated that the type III secretion system (T3SS of D. dadantii is required for full virulence. HrpL is an alternative sigma factor that binds to the hrp box promoter sequence of T3SS genes to up-regulate their expression. METHODOLOGY/PRINCIPAL FINDINGS: To explore the inventory of HrpL-regulated genes of D. dadantii 3937 (3937, transcriptome profiles of wild-type 3937 and a hrpL mutant grown in a T3SS-inducing medium were examined. Using a cut-off value of 1.5, significant differential expression was observed in sixty-three genes, which are involved in various cellular functions such as type III secretion, chemotaxis, metabolism, regulation, and stress response. A hidden Markov model (HMM was used to predict candidate hrp box binding sites in the intergenic regions of 3937, including the promoter regions of HrpL-regulated genes identified in the microarray assay. In contrast to biotrophic phytopathgens such as Pseudomonas syringae, among the HrpL up-regulated genes in 3937 only those within the T3SS were found to contain a hrp box sequence. Moreover, direct binding of purified HrpL protein to the hrp box was demonstrated for hrp box-containing DNA fragments of hrpA and hrpN using the electrophoretic mobility shift assay (EMSA. In this study, a putative T3SS effector DspA/E was also identified as a HrpL-upregulated gene, and shown to be translocated into plant cells in a T3SS-dependent manner. CONCLUSION/SIGNIFICANCES: We provide the genome-wide study of HrpL-regulated genes in a necrotrophic phytopathogen (D. dadantii 3937 through a combination of transcriptomics and bioinformatics, which led to identification of several effectors. Our study indicates the extent of differences for T3SS effector protein inventory requirements between necrotrophic and biotrophic pathogens, and may allow the development of different strategies for

  11. Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation.

    Science.gov (United States)

    Krin, Evelyne; Pierlé, Sebastian Aguilar; Sismeiro, Odile; Jagla, Bernd; Dillies, Marie-Agnès; Varet, Hugo; Irazoki, Oihane; Campoy, Susana; Rouy, Zoé; Cruveiller, Stéphane; Médigue, Claudine; Coppée, Jean-Yves; Mazel, Didier

    2018-05-21

    The SOS response is an almost ubiquitous response of cells to genotoxic stresses. The full complement of genes in the SOS regulon for Vibrio species has only been addressed through bioinformatic analyses predicting LexA binding box consensus and in vitro validation. Here, we perform whole transcriptome sequencing from Vibrio cholerae treated with mitomycin C as an SOS inducer to characterize the SOS regulon and other pathways affected by this treatment. Comprehensive transcriptional profiling allowed us to define the full landscape of promoters and transcripts active in V. cholerae. We performed extensive transcription start site (TSS) mapping as well as detection/quantification of the coding and non-coding RNA (ncRNA) repertoire in strain N16961. To improve TSS detection, we developed a new technique to treat RNA extracted from cells grown in various conditions. This allowed for identification of 3078 TSSs with an average 5'UTR of 116 nucleotides, and peak distribution between 16 and 64 nucleotides; as well as 629 ncRNAs. Mitomycin C treatment induced transcription of 737 genes and 28 ncRNAs at least 2 fold, while it repressed 231 genes and 17 ncRNAs. Data analysis revealed that in addition to the core genes known to integrate the SOS regulon, several metabolic pathways were induced. This study allowed for expansion of the Vibrio SOS regulon, as twelve genes (ubiEJB, tatABC, smpA, cep, VC0091, VC1190, VC1369-1370) were found to be co-induced with their adjacent canonical SOS regulon gene(s), through transcriptional read-through. Characterization of UV and mitomycin C susceptibility for mutants of these newly identified SOS regulon genes and other highly induced genes and ncRNAs confirmed their role in DNA damage rescue and protection. We show that genotoxic stress induces a pervasive transcriptional response, affecting almost 20% of the V. cholerae genes. We also demonstrate that the SOS regulon is larger than previously known, and its syntenic organization is

  12. Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria.

    Science.gov (United States)

    Sun, Eric I; Leyn, Semen A; Kazanov, Marat D; Saier, Milton H; Novichkov, Pavel S; Rodionov, Dmitry A

    2013-09-02

    In silico comparative genomics approaches have been efficiently used for functional prediction and reconstruction of metabolic and regulatory networks. Riboswitches are metabolite-sensing structures often found in bacterial mRNA leaders controlling gene expression on transcriptional or translational levels.An increasing number of riboswitches and other cis-regulatory RNAs have been recently classified into numerous RNA families in the Rfam database. High conservation of these RNA motifs provides a unique advantage for their genomic identification and comparative analysis. A comparative genomics approach implemented in the RegPredict tool was used for reconstruction and functional annotation of regulons controlled by RNAs from 43 Rfam families in diverse taxonomic groups of Bacteria. The inferred regulons include ~5200 cis-regulatory RNAs and more than 12000 target genes in 255 microbial genomes. All predicted RNA-regulated genes were classified into specific and overall functional categories. Analysis of taxonomic distribution of these categories allowed us to establish major functional preferences for each analyzed cis-regulatory RNA motif family. Overall, most RNA motif regulons showed predictable functional content in accordance with their experimentally established effector ligands. Our results suggest that some RNA motifs (including thiamin pyrophosphate and cobalamin riboswitches that control the cofactor metabolism) are widespread and likely originated from the last common ancestor of all bacteria. However, many more analyzed RNA motifs are restricted to a narrow taxonomic group of bacteria and likely represent more recent evolutionary innovations. The reconstructed regulatory networks for major known RNA motifs substantially expand the existing knowledge of transcriptional regulation in bacteria. The inferred regulons can be used for genetic experiments, functional annotations of genes, metabolic reconstruction and evolutionary analysis. The obtained genome

  13. Immunocytochemical localization of HrpA and HrpZ supports a role for the Hrp pilus in the transfer of effector proteins from Pseudomonas syringae pv. tomato across the host plant cell wall.

    Science.gov (United States)

    Brown, I R; Mansfield, J W; Taira, S; Roine, E; Romantschuk, M

    2001-03-01

    The Hrp pilus, composed of HrpA subunits, is an essential component of the type III secretion system in Pseudomonas syringae. We used electron microscopy (EM) and immunocytochemistry to examine production of the pilus in vitro from P. syringae pv. tomato strain DC3000 grown under hrp-inducing conditions on EM grids. Pili, when labeled with antibodies to HrpA, developed rapidly in a nonpolar manner shortly after the detection of the hrpA transcript and extended up to 5 microm into surrounding media. Structures at the base of the pilus were clearly differentiated from the basal bodies of flagella. The HrpZ protein, also secreted via the type III system, was found by immunogold labeling to be associated with the pilus in vitro. Accumulation and secretion of HrpA and HrpZ were also examined quantitatively after the inoculation of wild-type DC3000 and hrpA and hrpZ mutants into leaves of Arabidopsis thaliana. The functional pilus crossed the plant cell wall to generate tracks of immunogold labeling for HrpA and HrpZ. Mutants that produced HrpA but did not assemble pili were nonpathogenic, did not secrete HrpA protein, and were compromised for the accumulation of HrpZ. A model is proposed in which the rapidly elongating Hrp pilus acts as a moving conveyor, facilitating transfer of effector proteins from bacteria to the plant cytoplasm across the formidable barrier of the plant cell wall.

  14. The cys regulon of Xanthomonas citri

    Energy Technology Data Exchange (ETDEWEB)

    Moutran, A.; Balan, A. [Laboratorio Nacional de Biociencias - LNBIO, Campinas, SP (Brazil)

    2012-07-01

    Full text: In Escherichia coli, genes involved in metabolic pathway of sulfate and sulfonate compounds are clustered in a cys regulon, which includes three ABC transport system (operons: sbpcysWUA; ssuABC and tauABC), thirteen genes involved in the sulfur reduction (ssuDE; tauD and cysDNCHIJGK) and two regulatory proteins that belong to LysR transcription family: CysB and Cbl. Notably, a search and comparative analysis of these genes in the genomes of the citrus pathogen Xanthomonas citri and other phylogenetically related Xanthomonas species revealed the presence of genes involved with alkanesulfonate, sulfate ester and taurine, only in X. citri, suggesting that proteins from this regulon might be associated with pathogenicity in citrus. Using the molecular modeling associated with a system biology view, we modeled all the protein structures of the X. citri cys regulon as well as characterized the important residues forming the putative active sites. Comparison with orthologs from different microorganisms was made in order to get a phylogenetic relationships. We showed that proteins that are responsible for the affinity and specificity of the alkanesulfonate, sulfate and taurine transport systems conserved the residues involved in the sulfate coordination but are organized in different branches in evolution. Inside these phylogenetic branches, proteins involved in the sulfate transporter are highly conserved when compared to the others. Moreover, we identified that the taurine-binding protein (TauA) of the X. citri belongs to a different evolutionary branch from that one that described for E. coli. These differences were also noticed for components of the tau operon, including a putative new regulator. The function and mechanism of action of each protein is discussed in order to bring light for the sulfur assimilation processes and their importance for X. citri physiology. (author)

  15. The cys regulon of Xanthomonas citri

    International Nuclear Information System (INIS)

    Moutran, A.; Balan, A.

    2012-01-01

    Full text: In Escherichia coli, genes involved in metabolic pathway of sulfate and sulfonate compounds are clustered in a cys regulon, which includes three ABC transport system (operons: sbpcysWUA; ssuABC and tauABC), thirteen genes involved in the sulfur reduction (ssuDE; tauD and cysDNCHIJGK) and two regulatory proteins that belong to LysR transcription family: CysB and Cbl. Notably, a search and comparative analysis of these genes in the genomes of the citrus pathogen Xanthomonas citri and other phylogenetically related Xanthomonas species revealed the presence of genes involved with alkanesulfonate, sulfate ester and taurine, only in X. citri, suggesting that proteins from this regulon might be associated with pathogenicity in citrus. Using the molecular modeling associated with a system biology view, we modeled all the protein structures of the X. citri cys regulon as well as characterized the important residues forming the putative active sites. Comparison with orthologs from different microorganisms was made in order to get a phylogenetic relationships. We showed that proteins that are responsible for the affinity and specificity of the alkanesulfonate, sulfate and taurine transport systems conserved the residues involved in the sulfate coordination but are organized in different branches in evolution. Inside these phylogenetic branches, proteins involved in the sulfate transporter are highly conserved when compared to the others. Moreover, we identified that the taurine-binding protein (TauA) of the X. citri belongs to a different evolutionary branch from that one that described for E. coli. These differences were also noticed for components of the tau operon, including a putative new regulator. The function and mechanism of action of each protein is discussed in order to bring light for the sulfur assimilation processes and their importance for X. citri physiology. (author)

  16. DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli.

    Science.gov (United States)

    Lemmens, Karen; De Bie, Tijl; Dhollander, Thomas; De Keersmaecker, Sigrid C; Thijs, Inge M; Schoofs, Geert; De Weerdt, Ami; De Moor, Bart; Vanderleyden, Jos; Collado-Vides, Julio; Engelen, Kristof; Marchal, Kathleen

    2009-01-01

    We present DISTILLER, a data integration framework for the inference of transcriptional module networks. Experimental validation of predicted targets for the well-studied fumarate nitrate reductase regulator showed the effectiveness of our approach in Escherichia coli. In addition, the condition dependency and modularity of the inferred transcriptional network was studied. Surprisingly, the level of regulatory complexity seemed lower than that which would be expected from RegulonDB, indicating that complex regulatory programs tend to decrease the degree of modularity.

  17. Computational analysis of LexA regulons in Cyanobacteria

    Directory of Open Access Journals (Sweden)

    Su Zhengchang

    2010-09-01

    Full Text Available Abstract Background The transcription factor LexA plays an important role in the SOS response in Escherichia coli and many other bacterial species studied. Although the lexA gene is encoded in almost every bacterial group with a wide range of evolutionary distances, its precise functions in each group/species are largely unknown. More recently, it has been shown that lexA genes in two cyanobacterial genomes Nostoc sp. PCC 7120 and Synechocystis sp. PCC 6803 might have distinct functions other than the regulation of the SOS response. To gain a general understanding of the functions of LexA and its evolution in cyanobacteria, we conducted the current study. Results Our analysis indicates that six of 33 sequenced cyanobacterial genomes do not harbor a lexA gene although they all encode the key SOS response genes, suggesting that LexA is not an indispensable transcription factor in these cyanobacteria, and that their SOS responses might be regulated by different mechanisms. Our phylogenetic analysis suggests that lexA was lost during the course of evolution in these six cyanobacterial genomes. For the 26 cyanobacterial genomes that encode a lexA gene, we have predicted their LexA-binding sites and regulons using an efficient binding site/regulon prediction algorithm that we developed previously. Our results show that LexA in most of these 26 genomes might still function as the transcriptional regulator of the SOS response genes as seen in E. coli and other organisms. Interestingly, putative LexA-binding sites were also found in some genomes for some key genes involved in a variety of other biological processes including photosynthesis, drug resistance, etc., suggesting that there is crosstalk between the SOS response and these biological processes. In particular, LexA in both Synechocystis sp. PCC6803 and Gloeobacter violaceus PCC7421 has largely diverged from those in other cyanobacteria in the sequence level. It is likely that LexA is no longer a

  18. Involvement of hrpX and hrpG in the Virulence of Acidovorax citrulli Strain Aac5, Causal Agent of Bacterial Fruit Blotch in Cucurbits

    Directory of Open Access Journals (Sweden)

    Xiaoxiao Zhang

    2018-03-01

    Full Text Available Acidovorax citrulli causes bacterial fruit blotch, a disease that poses a global threat to watermelon and melon production. Despite its economic importance, relatively little is known about the molecular mechanisms of pathogenicity and virulence of A. citrulli. Like other plant-pathogenic bacteria, A. citrulli relies on a type III secretion system (T3SS for pathogenicity. On the basis of sequence and operon arrangement analyses, A. citrulli was found to have a class II hrp gene cluster similar to those of Xanthomonas and Ralstonia spp. In the class II hrp cluster, hrpG and hrpX play key roles in the regulation of T3SS effectors. However, little is known about the regulation of the T3SS in A. citrulli. This study aimed to investigate the roles of hrpG and hrpX in A. citrulli pathogenicity. We found that hrpG or hrpX deletion mutants of the A. citrulli group II strain Aac5 had reduced pathogenicity on watermelon seedlings, failed to induce a hypersensitive response in tobacco, and elicited higher levels of reactive oxygen species in Nicotiana benthamiana than the wild-type strain. Additionally, we demonstrated that HrpG activates HrpX in A. citrulli. Moreover, transcription and translation of the type 3-secreted effector (T3E gene Aac5_2166 were suppressed in hrpG and hrpX mutants. Notably, hrpG and hrpX appeared to modulate biofilm formation. These results suggest that hrpG and hrpX are essential for pathogenicity, regulation of T3Es, and biofilm formation in A. citrulli.

  19. 10 CFR 712.11 - General requirements for HRP certification.

    Science.gov (United States)

    2010-01-01

    ..., “Drug-Free Federal Workplace Testing Implementation Program,” for DOE employees; (9) An initial alcohol... the HRP and complete initial instruction on the importance of security, safety, reliability, and... the Manager, the NNSA Administrator, his or her designee, or the appropriate Lead Program Secretarial...

  20. HRP's Healthcare Spin-Offs Through Computational Modeling and Simulation Practice Methodologies

    Science.gov (United States)

    Mulugeta, Lealem; Walton, Marlei; Nelson, Emily; Peng, Grace; Morrison, Tina; Erdemir, Ahmet; Myers, Jerry

    2014-01-01

    Spaceflight missions expose astronauts to novel operational and environmental conditions that pose health risks that are currently not well understood, and perhaps unanticipated. Furthermore, given the limited number of humans that have flown in long duration missions and beyond low Earth-orbit, the amount of research and clinical data necessary to predict and mitigate these health and performance risks are limited. Consequently, NASA's Human Research Program (HRP) conducts research and develops advanced methods and tools to predict, assess, and mitigate potential hazards to the health of astronauts. In this light, NASA has explored the possibility of leveraging computational modeling since the 1970s as a means to elucidate the physiologic risks of spaceflight and develop countermeasures. Since that time, substantial progress has been realized in this arena through a number of HRP funded activates such as the Digital Astronaut Project (DAP) and the Integrated Medical Model (IMM). Much of this success can be attributed to HRP's endeavor to establish rigorous verification, validation, and credibility (VV&C) processes that ensure computational models and simulations (M&S) are sufficiently credible to address issues within their intended scope. This presentation summarizes HRP's activities in credibility of modeling and simulation, in particular through its outreach to the community of modeling and simulation practitioners. METHODS: The HRP requires all M&S that can have moderate to high impact on crew health or mission success must be vetted in accordance to NASA Standard for Models and Simulations, NASA-STD-7009 (7009) [5]. As this standard mostly focuses on engineering systems, the IMM and DAP have invested substantial efforts to adapt the processes established in this standard for their application to biological M&S, which is more prevalent in human health and performance (HHP) and space biomedical research and operations [6,7]. These methods have also generated

  1. Genome-wide analysis of the RpoN regulon in Geobacter sulfurreducens

    Directory of Open Access Journals (Sweden)

    Núñez Cinthia

    2009-07-01

    Full Text Available Abstract Background The role of the RNA polymerase sigma factor RpoN in regulation of gene expression in Geobacter sulfurreducens was investigated to better understand transcriptional regulatory networks as part of an effort to develop regulatory modules for genome-scale in silico models, which can predict the physiological responses of Geobacter species during groundwater bioremediation or electricity production. Results An rpoN deletion mutant could not be obtained under all conditions tested. In order to investigate the regulon of the G. sulfurreducens RpoN, an RpoN over-expression strain was made in which an extra copy of the rpoN gene was under the control of a taclac promoter. Combining both the microarray transcriptome analysis and the computational prediction revealed that the G. sulfurreducens RpoN controls genes involved in a wide range of cellular functions. Most importantly, RpoN controls the expression of the dcuB gene encoding the fumarate/succinate exchanger, which is essential for cell growth with fumarate as the terminal electron acceptor in G. sulfurreducens. RpoN also controls genes, which encode enzymes for both pathways of ammonia assimilation that is predicted to be essential under all growth conditions in G. sulfurreducens. Other genes that were identified as part of the RpoN regulon using either the computational prediction or the microarray transcriptome analysis included genes involved in flagella biosynthesis, pili biosynthesis and genes involved in central metabolism enzymes and cytochromes involved in extracellular electron transfer to Fe(III, which are known to be important for growth in subsurface environment or electricity production in microbial fuel cells. The consensus sequence for the predicted RpoN-regulated promoter elements is TTGGCACGGTTTTTGCT. Conclusion The G. sulfurreducens RpoN is an essential sigma factor and a global regulator involved in a complex transcriptional network controlling a variety of

  2. The Flagellar Regulon of Legionella—A Review

    Science.gov (United States)

    Appelt, Sandra; Heuner, Klaus

    2017-01-01

    The Legionella genus comprises more than 60 species. In particular, Legionella pneumophila is known to cause severe illnesses in humans. Legionellaceae are ubiquitous inhabitants of aquatic environments. Some Legionellaceae are motile and their motility is important to move around in habitats. Motility can be considered as a potential virulence factor as already shown for various human pathogens. The genes of the flagellar system, regulator and structural genes, are structured in hierarchical levels described as the flagellar regulon. Their expression is modulated by various environmental factors. For L. pneumophila it was shown that the expression of genes of the flagellar regulon is modulated by the actual growth phase and temperature. Especially, flagellated Legionella are known to express genes during the transmissive phase of growth that are involved in the expression of virulence traits. It has been demonstrated that the alternative sigma-28 factor is part of the link between virulence expression and motility. In the following review, the structure of the flagellar regulon of L. pneumophila is discussed and compared to other flagellar systems of different Legionella species. Recently, it has been described that Legionella micdadei and Legionella fallonii contain a second putative partial flagellar system. Hence, the report will focus on flagellated and non-flagellated Legionella strains, phylogenetic relationships, the role and function of the alternative sigma factor (FliA) and its anti-sigma-28 factor (FlgM). PMID:29104863

  3. Alternative Sigma Factor HrpL of Pectobacterium carotovorum 35 is Important for the Development of Soft-rot Symptoms

    Directory of Open Access Journals (Sweden)

    Hyo-Song Nam

    2011-08-01

    Full Text Available A bacterial artificial chromosome library of Pectobacterium carotovorum 35 was constructed to characterize the genome and to sequence its hrp region. The hrp cluster of P. carotovorum 35 consisted of 26 open reading frames in five operons. A promoter-based green fluorescent protein technology was used to identify the genes regulated by the alternative sigma factor, HrpL, in P. carotovorum 35. The majority of the selected clones contained the hrpJ operon promoter sequence, which harbors a hrp box, but no putative hrp boxes were detected within the promoter sequences of two other hrpL-regulated genes encoding for pectate lyase and large repetitive protein. Although the promoters of five other hrp operons also contained hrp boxes, their expression was not HrpL-dependent in the promoter-based selection in E. coli. However, transcriptional analysis showed that expression from all operons harboring hrp boxes, except for the hrpN operon, was reduced significantly in the hrpL mutant. The severity of soft-rot symptoms when the hrpL mutant was applied to the surface of tobacco leaves, mimicking natural infection, was greatly attenuated. These results indicate that the hrpL gene of P. carotovorum 35 may be involved in the development of soft-rot symptoms.

  4. Identification of self-consistent modulons from bacterial microarray expression data with the help of structured regulon gene sets

    KAUST Repository

    Permina, Elizaveta A.; Medvedeva, Yulia; Baeck, Pia M.; Hegde, Shubhada R.; Mande, Shekhar C.; Makeev, Vsevolod J.

    2013-01-01

    interactions helps to evaluate parameters for regulatory subnetwork inference. We suggest a procedure for modulon construction where a seed regulon is iteratively updated with genes having expression patterns similar to those for regulon member genes. A set

  5. Characterization of the SOS meta-regulon in the human gut microbiome.

    Science.gov (United States)

    Cornish, Joseph P; Sanchez-Alberola, Neus; O'Neill, Patrick K; O'Keefe, Ronald; Gheba, Jameel; Erill, Ivan

    2014-05-01

    Data from metagenomics projects remain largely untapped for the analysis of transcriptional regulatory networks. Here, we provide proof-of-concept that metagenomic data can be effectively leveraged to analyze regulatory networks by characterizing the SOS meta-regulon in the human gut microbiome. We combine well-established in silico and in vitro techniques to mine the human gut microbiome data and determine the relative composition of the SOS network in a natural setting. Our analysis highlights the importance of translesion synthesis as a primary function of the SOS response. We predict the association of this network with three novel protein clusters involved in cell wall biogenesis, chromosome partitioning and restriction modification, and we confirm binding of the SOS response transcriptional repressor to sites in the promoter of a cell wall biogenesis enzyme, a phage integrase and a death-on-curing protein. We discuss the implications of these findings and the potential for this approach for metagenome analysis.

  6. Global gene expression under nitrogen starvation in Xylella fastidiosa: contribution of the σ54 regulon

    Directory of Open Access Journals (Sweden)

    da Silva Neto José F

    2010-08-01

    Full Text Available Abstract Background Xylella fastidiosa, a Gram-negative fastidious bacterium, grows in the xylem of several plants causing diseases such as citrus variegated chlorosis. As the xylem sap contains low concentrations of amino acids and other compounds, X. fastidiosa needs to cope with nitrogen limitation in its natural habitat. Results In this work, we performed a whole-genome microarray analysis of the X. fastidiosa nitrogen starvation response. A time course experiment (2, 8 and 12 hours of cultures grown in defined medium under nitrogen starvation revealed many differentially expressed genes, such as those related to transport, nitrogen assimilation, amino acid biosynthesis, transcriptional regulation, and many genes encoding hypothetical proteins. In addition, a decrease in the expression levels of many genes involved in carbon metabolism and energy generation pathways was also observed. Comparison of gene expression profiles between the wild type strain and the rpoN null mutant allowed the identification of genes directly or indirectly induced by nitrogen starvation in a σ54-dependent manner. A more complete picture of the σ54 regulon was achieved by combining the transcriptome data with an in silico search for potential σ54-dependent promoters, using a position weight matrix approach. One of these σ54-predicted binding sites, located upstream of the glnA gene (encoding glutamine synthetase, was validated by primer extension assays, confirming that this gene has a σ54-dependent promoter. Conclusions Together, these results show that nitrogen starvation causes intense changes in the X. fastidiosa transcriptome and some of these differentially expressed genes belong to the σ54 regulon.

  7. Characterization of the YdeO regulon in Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Yuki Yamanaka

    Full Text Available Enterobacteria are able to survive under stressful conditions within animals, such as acidic conditions in the stomach, bile salts during transfer to the intestine and anaerobic conditions within the intestine. The glutamate-dependent (GAD system plays a major role in acid resistance in Escherichia coli, and expression of the GAD system is controlled by the regulatory cascade consisting of EvgAS > YdeO > GadE. To understand the YdeO regulon in vivo, we used ChIP-chip to interrogate the E. coli genome for candidate YdeO binding sites. All of the seven operons identified by ChIP-chip as being potentially regulated by YdeO were confirmed as being under the direct control of YdeO using RT-qPCR, EMSA, DNaseI-footprinting and reporter assays. Within this YdeO regulon, we identified four stress-response transcription factors, DctR, NhaR, GadE, and GadW and enzymes for anaerobic respiration. Both GadE and GadW are involved in regulation of the GAD system and NhaR is an activator for the sodium/proton antiporter gene. In conjunction with co-transcribed Slp, DctR is involved in protection against metabolic endoproducts under acidic conditions. Taken all together, we suggest that YdeO is a key regulator of E. coli survival in both acidic and anaerobic conditions.

  8. Analysis of the Pho regulon in Streptomyces tsukubaensis.

    Science.gov (United States)

    Ordóñez-Robles, María; Santos-Beneit, Fernando; Rodríguez-García, Antonio; Martín, Juan F

    2017-12-01

    Phosphate regulation of antibiotic biosynthesis in Streptomyces has been studied due to the importance of this genus as a source of secondary metabolites with biological activity. Streptomyces tsukubaensis is the main producer of tacrolimus (or FK506), an immunosuppressant macrolide that generates important benefits for the pharmaceutical market. However, the production of tacrolimus is under a negative control by phosphate and, therefore, is important to know the molecular mechanism of this regulation. Despite its important role, there are no reports about the Pho regulon in S. tsukubaensis. In this work we combined transcriptional studies on the response to phosphate starvation with the search for PHO boxes in the whole genome sequence of S. tsukubaensis. As a result, we identified a set of genes responding to phosphate starvation and containing PHO boxes that include common Pho regulon members but also new species-specific candidates. In addition, we demonstrate for the first time the functional activity of PhoP from S. tsukubaensis through complementation studies in a Streptomyces coelicolor ΔphoP strain. For this purpose, we developed an anhydrotetracycline inducible system that can be applied to the controlled expression of target genes. Copyright © 2017 Elsevier GmbH. All rights reserved.

  9. NASA HRP Immunology Discipline - Use of Terrestrial Analogs

    Science.gov (United States)

    Crucian, Brian

    2014-01-01

    Due to the cost and operational constraints, as well as technical implementation limitations, it is desirous to perform relevant space physiology investigations first in terrestrial 'space analogs'. This is particularly true for initial investigations, which may then provide appropriate focus for subsequent flight investigations, or for mechanistic investigations that simply cannot be performed during spaceflight. Appropriate analog choice is extremely important. There are a wide variety of terrestrial space analogs, each relevant to a particular physiological discipline (or disciplines) and each with a particular fidelity (or lack thereof) to spaceflight, and each with unique operational constraints. The HRP Immunology Discipline is tasked with managing the HRP Risk concerning clinical risk for Astronaut crews related to spaceflight-associated immune dysregulation. Such dysregulation has been documented to occur during spaceflight, and found to persist for the duration of a 6-month ISS mission. Studies continue to characterize the onorbit phenomenon, but it generally consists of diminished immunocyte function, dysregulated cytokine profiles, and persistent herpesvirus reactivation. Causes are thought to synergistically include microgravity, psychological or physiological stress, radiation, and/or circadian misalignment. An appropriate terrestrial analog for immune dysregulation would replicate as many of these influences as possible. Such analogs may include clinostat or bioreactor cell culture (microgravity), hindlimb suspension (stress, fluid shifts, hypokinesis), or human deployment to remote or extreme environments (isolation, stress, circadian). Also, the laboratory setting may be used as an analog, or to augment analogs, such as sleep deprivation/misalignment or human centrifugation to replicate gravitational stress. As an appropriate example of a NASA Disciplines use of Terrestrial space analogs, this talk will discuss spaceflight associated immune

  10. Phenol Removal from Industrial Wastewater by HRP Enzyme

    Directory of Open Access Journals (Sweden)

    Iran Alemzadeh

    2009-01-01

    Full Text Available In this research, horseradish peroxidase for phenol removal was utilized. First, the process was studied at the laboratory scale using a synthetic phenol solution (1-10 mM. Results showed that horseradish peroxidase (HRP could effectively remove phenolic compounds from wastewater and that the catalytic capability of the enzyme was maintained for a wide range of pH, temperature, and aromatic concentration levels. The performance conditions were optimized for at lease 95% and 100% removal of phenolic compounds for both actual and synthetic wastewaters under high and low phenol concentrations (1 and 10 mM. The phenolic wastewater used was an olive mill effluent with a phenol concentration of 1221 mg/L (13 mM and a pH value of 3.5. At the end of the reaction, the phenolic compounds changed to insoluble polymers and precipitated. Each enzyme/wastewater system was optimized for the following chemical dosages: hydrogen peroxide, enzyme, polyethylene glycol (PEG, and buffer. Furthermore, the reaction time to achieve at least 95% phenol removal was determined. According to the results, COD and BOD reduced to 58% and 78%, respectively. Experimental results showed an increase in H2O2 concentration beyond the optimum dose resulting from enzyme inactivation, thus reducing the phenol removal efficiency. On the other hand, increasing the enzyme, PEG, and/or reaction time beyond the optimum values resulted in only a marginal increase in removal efficiency.

  11. Cross-species comparison of the Burkholderia pseudomallei, Burkholderia thailandensis, and Burkholderia mallei quorum-sensing regulons.

    Science.gov (United States)

    Majerczyk, Charlotte D; Brittnacher, Mitchell J; Jacobs, Michael A; Armour, Christopher D; Radey, Matthew C; Bunt, Richard; Hayden, Hillary S; Bydalek, Ryland; Greenberg, E Peter

    2014-11-01

    Burkholderia pseudomallei, Burkholderia thailandensis, and Burkholderia mallei (the Bptm group) are close relatives with very different lifestyles: B. pseudomallei is an opportunistic pathogen, B. thailandensis is a nonpathogenic saprophyte, and B. mallei is a host-restricted pathogen. The acyl-homoserine lactone quorum-sensing (QS) systems of these three species show a high level of conservation. We used transcriptome sequencing (RNA-seq) to define the quorum-sensing regulon in each species, and we performed a cross-species analysis of the QS-controlled orthologs. Our analysis revealed a core set of QS-regulated genes in all three species, as well as QS-controlled factors shared by only two species or unique to a given species. This global survey of the QS regulons of B. pseudomallei, B. thailandensis, and B. mallei serves as a platform for predicting which QS-controlled processes might be important in different bacterial niches and contribute to the pathogenesis of B. pseudomallei and B. mallei. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  12. Cross-Species Comparison of the Burkholderia pseudomallei, Burkholderia thailandensis, and Burkholderia mallei Quorum-Sensing Regulons

    Science.gov (United States)

    Majerczyk, Charlotte D.; Brittnacher, Mitchell J.; Jacobs, Michael A.; Armour, Christopher D.; Radey, Matthew C.; Bunt, Richard; Hayden, Hillary S.; Bydalek, Ryland

    2014-01-01

    Burkholderia pseudomallei, Burkholderia thailandensis, and Burkholderia mallei (the Bptm group) are close relatives with very different lifestyles: B. pseudomallei is an opportunistic pathogen, B. thailandensis is a nonpathogenic saprophyte, and B. mallei is a host-restricted pathogen. The acyl-homoserine lactone quorum-sensing (QS) systems of these three species show a high level of conservation. We used transcriptome sequencing (RNA-seq) to define the quorum-sensing regulon in each species, and we performed a cross-species analysis of the QS-controlled orthologs. Our analysis revealed a core set of QS-regulated genes in all three species, as well as QS-controlled factors shared by only two species or unique to a given species. This global survey of the QS regulons of B. pseudomallei, B. thailandensis, and B. mallei serves as a platform for predicting which QS-controlled processes might be important in different bacterial niches and contribute to the pathogenesis of B. pseudomallei and B. mallei. PMID:25182491

  13. Nanobody Based Immunoassay for Human Soluble Epoxide Hydrolase Detection Using Polymeric Horseradish Peroxidase (PolyHRP) for Signal Enhancement: The Rediscovery of PolyHRP?

    Science.gov (United States)

    Li, Dongyang; Cui, Yongliang; Morisseau, Christophe; Gee, Shirley J; Bever, Candace S; Liu, Xiangjiang; Wu, Jian; Hammock, Bruce D; Ying, Yibin

    2017-06-06

    Soluble epoxide hydrolase (sEH) is a potential pharmacological target for treating hypertension, vascular inflammation, cancer, pain, and multiple cardiovascular related diseases. A variable domain of the heavy chain antibody (termed single domain antibody (sdAb), nanobody, or VHH) possesses the advantages of small size, high stability, ease of genetic manipulation, and ability for continuous manufacture, making such nanobody a superior choice as an immunoreagent. In this work, we developed an ultrasensitive nanobody based immunoassay for human sEH detection using polymeric horseradish peroxidase (PolyHRP) for signal enhancement. Llama nanobodies against human sEH were used as the detection antibody in sandwich enzyme linked immunosorbent assays (ELISA) with polyclonal anti-sEH as the capture antibody. A conventional sandwich ELISA using a horseradish peroxidase (HRP) labeled anti-hemeagglutinin (HA) tag as the tracer showed a marginal sensitivity (0.0015 optical density (OD)·mL/ng) and limit of detection (LOD) of 3.02 ng/mL. However, the introduction of the PolyHRP as the tracer demonstrated a 141-fold increase in the sensitivity (0.21 OD·mL/ng) and 57-fold decrease in LOD (0.05 ng/mL). Systematic comparison of three different tracers in four ELISA formats demonstrated the overwhelming advantage of PolyHRP as a label for nanobody based immunoassay. This enhanced sEH immunoassay was further evaluated in terms of selectivity against other epoxide hydrolases and detection of the target protein in human tissue homogenate samples. Comparison with an enzyme activity based assay and a Western blot for sEH detection reveals good correlation with the immunoassay. This work demonstrates increased competiveness of nanobodies for practical sEH protein detection utilizing PolyHRP. It is worthwhile to rediscover the promising potential of PolyHRP in nanobody and other affinity based methods after its low-profile existence for decades.

  14. Accuracy of PfHRP2 versus Pf-pLDH antigen detection by malaria rapid diagnostic tests in hospitalized children in a seasonal hyperendemic malaria transmission area in Burkina Faso.

    Science.gov (United States)

    Maltha, Jessica; Guiraud, Issa; Lompo, Palpouguini; Kaboré, Bérenger; Gillet, Philippe; Van Geet, Chris; Tinto, Halidou; Jacobs, Jan

    2014-01-13

    In most sub-Saharan African countries malaria rapid diagnostic tests (RDTs) are now used for the diagnosis of malaria. Most RDTs used detect Plasmodium falciparum histidine-rich protein-2 (PfHRP2), though P. falciparum-specific parasite lactate dehydrogenase (Pf-pLDH)-detecting RDTs may have advantages over PfHRP2-detecting RDTs. Only few data are available on the use of RDTs in severe illness and the present study compared Pf-pLDH to PfHRP2-detection. Hospitalized children aged one month to 14 years presenting with fever or severe illness were included over one year. Venous blood samples were drawn for malaria diagnosis (microscopy and RDT), culture and complete blood count. Leftovers were stored at -80 °C and used for additional RDT analysis and PCR. An RDT targeting both PfHRP2 and Pf-pLDH was performed on all samples for direct comparison of diagnostic accuracy with microscopy as reference method. PCR was performed to explore false-positive RDT results. In 376 of 694 (54.2%) included children, malaria was microscopically confirmed. Sensitivity, specificity, positive predictive value (PPV) and negative predictive value were 100.0, 70.9, 69.4 and 100.0%, respectively for PfHRP2-detection and 98.7, 94.0, 91.6 and 99.1%, respectively for Pf-pLDH-detection. Specificity and PPV were significantly lower for PfHRP2-detection (p <0.001). For both detection antigens, specificity was lowest for children one to five years and in the rainy season. PPV for both antigens was highest in the rainy season, because of higher malaria prevalence. False positive PfHRP2 results were associated with prior anti-malarial treatment and positive PCR results (98/114 (86.0%) samples tested). Among children presenting with severe febrile illness in a seasonal hyperendemic malaria transmission area, the present study observed similar sensitivity but lower specificity and PPV of PfHRP2 compared to Pf-pLDH-detection. Further studies should assess the diagnostic accuracy and safety of an

  15. The components of the unique Zur regulon of Cupriavidus metallidurans mediate cytoplasmic zinc handling.

    Science.gov (United States)

    Bütof, Lucy; Schmidt-Vogler, Christopher; Herzberg, Martin; Große, Cornelia; Nies, Dietrich H

    2017-08-14

    Zinc is an essential trace element and at the same time it is toxic at high concentrations. In the beta-proteobacterium Cupriavidus metallidurans the highly efficient removal of surplus zinc from the periplasm is responsible for its outstanding metal resistance. Rather than having a typical Zur-dependent, high-affinity ATP-binding cassette transporter of the ABC protein superfamily for zinc uptake at low concentrations, C. metallidurans instead has the secondary zinc importer ZupT of the ZRT/IRT (ZIP) family. It is important to understand, therefore, how this zinc-resistant bacterium copes when it is exposed to low zinc concentrations. Members of the Zur regulon in C. metallidurans were identified by comparing the transcriptomes of a Δ zur mutant and its parent strain. The consensus sequence of the Zur-binding box was derived for the zupTp promoter-regulatory region using a truncation assay. The motif was used to predict possible Zur-boxes upstream of Zur regulon members. Binding of Zur to these boxes was confirmed. Two Zur-boxes upstream of the cobW 1 gene, encoding a putative zinc chaperone, proved to be required for complete repression of cobW 1 and its downstream genes in cells cultivated in mineral salts medium. A Zur box upstream of each of zur-cobW 2 , cobW 3 and zupT permitted low-expression level of these genes plus their up-regulation under zinc starvation conditions. This demonstrates a compartmentalization of zinc homeostasis in C. metallidurans with the periplasm being responsible for removal of surplus zinc and cytoplasmic components for management of zinc as an essential co-factor, with both compartments connected by ZupT. Importance Elucidating zinc homeostasis is necessary to understand both host-pathogen interactions and performance of free-living bacteria in their natural environment. Escherichia coli acquires zinc under low zinc concentrations by the Zur-controlled ZnuABC importer of the ABC superfamily, and this was also the paradigm for other

  16. Bradyrhizobium elkanii nod regulon: insights through genomic analysis

    Directory of Open Access Journals (Sweden)

    Luciane M. P. Passaglia

    2017-07-01

    Full Text Available Abstract A successful symbiotic relationship between soybean [Glycine max (L. Merr.] and Bradyrhizobium species requires expression of the bacterial structural nod genes that encode for the synthesis of lipochitooligosaccharide nodulation signal molecules, known as Nod factors (NFs. Bradyrhizobium diazoefficiens USDA 110 possesses a wide nodulation gene repertoire that allows NF assembly and modification, with transcription of the nodYABCSUIJnolMNOnodZ operon depending upon specific activators, i.e., products of regulatory nod genes that are responsive to signaling molecules such as flavonoid compounds exuded by host plant roots. Central to this regulatory circuit of nod gene expression are NodD proteins, members of the LysR-type regulator family. In this study, publicly available Bradyrhizobium elkanii sequenced genomes were compared with the closely related B. diazoefficiens USDA 110 reference genome to determine the similarities between those genomes, especially with regards to the nod operon and nod regulon. Bioinformatics analyses revealed a correlation between functional mechanisms and key elements that play an essential role in the regulation of nod gene expression. These analyses also revealed new genomic features that had not been clearly explored before, some of which were unique for some B. elkanii genomes.

  17. The Rcs regulon in Proteus mirabilis: implications for motility, biofilm formation, and virulence.

    Science.gov (United States)

    Howery, Kristen E; Clemmer, Katy M; Rather, Philip N

    2016-11-01

    The overall role of the Rcs phosphorelay in Proteus mirabilis is largely unknown. Previous work had demonstrated that the Rcs phosphorelay represses the flhDC operon and activates the minCDE cell division inhibition system. To identify additional cellular functions regulated by the Rcs phosphorelay, an analysis of RNA-seq data was undertaken. In this report, the results of the RNA-sequencing are discussed with an emphasis on the predicted roles of the Rcs phosphorelay in swarmer cell differentiation, motility, biofilm formation, and virulence. RcsB is shown to activate genes important for differentiation and fimbriae formation, while repressing the expression of genes important for motility and virulence. Additionally, to follow up on the RNA-Seq data, we demonstrate that an rcsB mutant is deficient in its ability to form biofilm and exhibits enhanced virulence in a Galleria mellonella waxworm model. Overall, these results indicate the Rcs regulon in P. mirabilis extends beyond flagellar genes to include those involved in biofilm formation and virulence. Furthermore, the information presented in this study may provide clues to additional roles of the Rcs phosphorelay in other members of the Enterobacteriaceae.

  18. Thermometric sensing of peroxide in organic media. Application to monitor the stability of RBP-retinol-HRP complex.

    Science.gov (United States)

    Ramanathan, K; Jönsson, B R; Danielsson, B

    2000-08-01

    The stability of horseradish peroxidase (HRP) in aqueous and organic solvents is applied to develop a simple thermometric procedure to detect the binding of retinoic acid-HRP conjugate to retinol binding protein (RBP). Butanone peroxide (BP) in organic phase and hydrogen peroxide in aqueous phase is detected thermometrically on a HRP column, immobilized by cross-linking with glutaraldehyde on controlled pore glass (CPG). Acetone, acetonitrile, methanol, and 2-butanol are used for detection of BP, in the flow injection analysis (FIA) mode. A linear range between 1 and 50 mM BP is obtained in all the organic solvents with a precision of 5-7% (CV%). The magnitude and nature of the thermometric response is significantly different in each organic solvent. The stability of HRP in the organic phase is used to study the stability of a retinoic acid-HRP conjugate bound to immobilized RBP. The response of HRP (to 20 mM BP) in the retinoic acid-HRP conjugate is used as an indicator of the stability of the RBP-retinoic acid-HRP complex, after challenges with various organic/aqueous solvents. Both immobilized HRP and RBP are stable at least for 6 months. The effect of o-phenylene diamine on the thermometric response of HRP is also investigated. A scheme for the design of a thermometric retinol (vitamin A) biosensor is proposed.

  19. Plasmodium falciparum HRP2 ELISA for analysis of dried blood spot samples in rural Zambia.

    Science.gov (United States)

    Gibson, Lauren E; Markwalter, Christine F; Kimmel, Danielle W; Mudenda, Lwiindi; Mbambara, Saidon; Thuma, Philip E; Wright, David W

    2017-08-23

    Dried blood spots are commonly used for sample collection in clinical and non-clinical settings. This method is simple, and biomolecules in the samples remain stable for months at room temperature. In the field, blood samples for the study and diagnosis of malaria are often collected on dried blood spot cards, so development of a biomarker extraction and analysis method is needed. A simple extraction procedure for the malarial biomarker Plasmodium falciparum histidine-rich protein 2 (HRP2) from dried blood spots was optimized to achieve maximum extraction efficiency. This method was used to assess the stability of HRP2 in dried blood spots. Furthermore, 328 patient samples made available from rural Zambia were analysed for HRP2 using the developed method. These samples were collected at the initial administration of artemisinin-based combination therapy and at several points following treatment. An average extraction efficiency of 70% HRP2 with a low picomolar detection limit was achieved. In specific storage conditions HRP2 was found to be stable in dried blood spots for at least 6 months. Analysis of patient samples showed the method to have a sensitivity of 94% and a specificity of 89% when compared with microscopy, and trends in HRP2 clearance after treatment were observed. The dried blood spot ELISA for HRP2 was found to be sensitive, specific and accurate. The method was effectively used to assess biomarker clearance characteristics in patient samples, which prove it to be ideal for gaining further insight into the disease and epidemiological applications.

  20. RpfF-dependent regulon of Xylella fastidiosa.

    Science.gov (United States)

    Wang, Nian; Li, Jian-Liang; Lindow, Steven E

    2012-11-01

    ABSTRACT Xylella fastidiosa regulates traits important to both virulence of grape as well as colonization of sharpshooter vectors via its production of a fatty acid signal molecule known as DSF whose production is dependent on rpfF. Although X. fastidiosa rpfF mutants exhibit increased virulence to plants, they are unable to be spread from plant to plant by insect vectors. To gain more insight into the traits that contribute to these processes, a whole-genome Agilent DNA microarray for this species was developed and used to determine the RpfF-dependent regulon by transcriptional profiling. In total, 446 protein coding genes whose expression was significantly different between the wild type and an rpfF mutant (false discovery rate genes were downregulated in the rpfF mutant compared with the wild-type strain whereas 281 genes were over-expressed. RpfF function was required for regulation of 11 regulatory and σ factors, including rpfE, yybA, PD1177, glnB, rpfG, PD0954, PD0199, PD2050, colR, rpoH, and rpoD. In general, RpfF is required for regulation of genes involved in attachment and biofilm formation, enhancing expression of hemagglutinin genes hxfA and hxfB, and suppressing most type IV pili and gum genes. A large number of other RpfF-dependent genes that might contribute to virulence or insect colonization were also identified such as those encoding hemolysin and colicin V, as well as genes with unknown functions.

  1. Analysis of Erwinia chrysanthemi EC16 pelE::uidA, pelL::uidA, and hrpN::uidA mutants reveals strain-specific atypical regulation of the Hrp type III secretion system.

    Science.gov (United States)

    Ham, Jong Hyun; Cui, Yaya; Alfano, James R; Rodríguez-Palenzuela, Pablo; Rojas, Clemencia M; Chatterjee, Arun K; Collmer, Alan

    2004-02-01

    The plant pathogen Erwinia chrysanthemi produces a variety of factors that have been implicated in its ability to cause soft-rot diseases in various hosts. These include HrpN, a harpin secreted by the Hrp type III secretion system; PelE, one of several major pectate lyase isozymes secreted by the type II system; and PelL, one of several secondary Pels secreted by the type II system. We investigated these factors in E. chrysanthemi EC16 with respect to the effects of medium composition and growth phase on gene expression (as determined with uidA fusions and Northern analyses) and effects on virulence. pelE was induced by polygalacturonic acid, but pelL was not, and hrpN was expressed unexpectedly in nutrient-rich King's medium B and in minimal salts medium at neutral pH. In contrast, the effect of medium composition on hrp expression in E. chrysanthemi CUCPB1237 and 3937 was like that of many other phytopathogenic bacteria in being repressed in complex media and induced in acidic pH minimal medium. Northern blot analysis of hrpN and hrpL expression by the wild-type and hrpL::omegaCmr and hrpS::omegaCmr mutants revealed that hrpN expression was dependent on the HrpL alternative sigma factor, whose expression, in turn, was dependent on the HrpS putative sigma54 enhancer binding protein. The expression of pelE and hrpN increased strongly in late logarithmic growth phase. To test the possible role of quorum sensing in this expression pattern, the expI/expR locus was cloned in Escherichia coli on the basis of its ability to direct production of acyl-homoserine lactone and then used to construct expI mutations in pelE::uidA, pelL::uidA, and hrpN::uidA Erwinia chrysanthemi strains. Mutation of expI had no apparent effect on the growth-phase-dependent expression of hrpN and pelE, or on the virulence of E. chrysanthemi in witloof chicory leaves. Overexpression of hrpN in E. chrysanthemi resulted in approximately 50% reduction of lesion size on chicory leaves without an

  2. Subchronic mild noise stress increases HRP permeability in rat small intestine in vitro.

    Science.gov (United States)

    Bijlsma, P B; van Raaij, M T; Dobbe, C J; Timmerman, A; Kiliaan, A J; Taminiau, J A; Groot, J A

    2001-05-01

    Recently we reported an increased trans- and paracellular protein permeability in rat small intestine after acute cold restraint stress. In the present study, we applied randomized 95- or 105-dB white noise pulses during 45 min/h, 12 h/day, duration 8 days, as a milder, but more chronic stressor to male rats. At 8 days before the noise experiments, 50% of the animals were cannulated in the vena cava for blood sampling during the experimental period. The other 50% of the animals were sacrificed at Day 9, segments of ileum were mounted in Ussing chambers and perfused at 37 degrees C. Horseradish peroxidase (HRP) was added mucosally, serosal appearance was detected enzymatically and tissues were fixed for electron microscopy. In the animals exposed to 95-dB noise, plasma corticosterone levels were enhanced twofold compared to controls, and ileal HRP flux was enhanced twofold. Electron micrographs of tissue from stressed or control animals showed no detectable paracellular staining of HRP. Quantification of HRP-containing endosomes in enterocytes revealed a twofold increase in endosome number in the animals exposed to 95-db noise indicating that the increased HRP permeability was primarily due to increased endocytosis. In contrast to the animals exposed to 95-dB noise, rats exposed to 105-dB noise showed no increase in corticosterone levels and ileal HRP fluxes were not significantly different from controls. We conclude that mild subchronic noise stress may cause a decrease in intestinal barrier function by increased transcytosis of luminal antigens.

  3. The BvgAS Regulon of Bordetella pertussis

    Directory of Open Access Journals (Sweden)

    Kyung Moon

    2017-10-01

    Full Text Available Nearly all virulence factors in Bordetella pertussis are activated by a master two-component system, BvgAS, composed of the sensor kinase BvgS and the response regulator BvgA. When BvgS is active, BvgA is phosphorylated (BvgA~P, and virulence-activated genes (vags are expressed [Bvg(+ mode]. When BvgS is inactive and BvgA is not phosphorylated, virulence-repressed genes (vrgs are induced [Bvg(− mode]. Here, we have used transcriptome sequencing (RNA-seq and reverse transcription-quantitative PCR (RT-qPCR to define the BvgAS-dependent regulon of B. pertussis Tohama I. Our analyses reveal more than 550 BvgA-regulated genes, of which 353 are newly identified. BvgA-activated genes include those encoding two-component systems (such as kdpED, multiple other transcriptional regulators, and the extracytoplasmic function (ECF sigma factor brpL, which is needed for type 3 secretion system (T3SS expression, further establishing the importance of BvgA~P as an apex regulator of transcriptional networks promoting virulence. Using in vitro transcription, we demonstrate that the promoter for brpL is directly activated by BvgA~P. BvgA-FeBABE cleavage reactions identify BvgA~P binding sites centered at positions −41.5 and −63.5 in bprL. Most importantly, we show for the first time that genes for multiple and varied metabolic pathways are significantly upregulated in the B. pertussis Bvg(− mode. These include genes for fatty acid and lipid metabolism, sugar and amino acid transporters, pyruvate dehydrogenase, phenylacetic acid degradation, and the glycolate/glyoxylate utilization pathway. Our results suggest that metabolic changes in the Bvg(− mode may be participating in bacterial survival, transmission, and/or persistence and identify over 200 new vrgs that can be tested for function.

  4. The Effect of Combined Treatment with the (ProRenin Receptor Blocker HRP and Quinapril in Type 1 Diabetic Rats

    Directory of Open Access Journals (Sweden)

    Gábor Kökény

    2017-04-01

    Full Text Available Background/Aims: Diabetic nephropathy remains a major clinical problem. The effects of prorenin might be adverse, but the literature data are controversial. We compared the renal effects of the (prorenin receptor ((PRR blockade and angiotensin converting enzyme (ACE inhibition on the progression of diabetic nephropathy in rats. Methods: Diabetes (DM was induced by ip. streptozotocin administration in adult male Sprague-Dawley rats, followed by eight weeks of treatment with the (PRR blocker „handle region” decoy peptide (HRP, 0,1 mg/kg/day or with the ACE inhibitor Quinapril (Q, 50 mg/kg/day and grouped as follows: 1. Control (n=10; 2. DM (n=8; 3. DM+HRP (n=6; 4. DM+Q (n=10; 5. DM+Q+HRP (n=10. Renal functional parameters, histology and gene expressions were evaluated. Results: HRP reduced glomerulosclerosis and podocyte desmin expression, but did not affect proteinuria and tubular ERK(1/2 phosphorylation. Both Q and Q+HRP treatment reduced proteinuria, glomerular and tubular damage, tubular TGF-ß1 expression and ERK(1/2 phosphorylation to the same extent. Conclusion: The effects of HRP were partially beneficial on diabetic kidney lesions as HRP reduced damage but did not improve tubular damage and failed to reduce ERK(1/2 phosphorylation in rats. The combination of HRP with Quinapril had no additive effects over Quinapril monotherapy on the progression of diabetic nephropathy.

  5. Definition of the sigma(W) Regulon of Bacillus subtilis in the Absence of Stress

    NARCIS (Netherlands)

    Zweers, Jessica C.; Nicolas, Pierre; Wiegert, Thomas; van Dijl, Jan Maarten; Denham, Emma L.

    2012-01-01

    Bacteria employ extracytoplasmic function (ECF) sigma factors for their responses to environmental stresses. Despite intensive research, the molecular dissection of ECF sigma factor regulons has remained a major challenge due to overlaps in the ECF sigma factor-regulated genes and the stimuli that

  6. The response of Bacillus licheniformis to heat and ethanol stress and the role of the SigB regulon.

    Science.gov (United States)

    Voigt, Birgit; Schroeter, Rebecca; Jürgen, Britta; Albrecht, Dirk; Evers, Stefan; Bongaerts, Johannes; Maurer, Karl-Heinz; Schweder, Thomas; Hecker, Michael

    2013-07-01

    The heat and ethanol stress response of Bacillus licheniformis DSM13 was analyzed at the transcriptional and/or translational level. During heat shock, regulons known to be heat-induced in Bacillus subtilis 168 are upregulated in B. licheniformis, such as the HrcA, SigB, CtsR, and CssRS regulon. Upregulation of the SigY regulon and of genes controlled by other extracytoplasmic function (ECF) sigma factors indicates a cell-wall stress triggered by the heat shock. Furthermore, tryptophan synthesis enzymes were upregulated in heat stressed cells as well as regulons involved in usage of alternative carbon and nitrogen sources. Ethanol stress led to an induction of the SigB, HrcA, and CtsR regulons. As indicated by the upregulation of a SigM-dependent protein, ethanol also triggered a cell wall stress. To characterize the SigB regulon of B. licheniformis, we analyzed the heat stress response of a sigB mutant. It is shown that the B. licheniformis SigB regulon comprises additional genes, some of which do not exist in B. subtilis, such as BLi03885, encoding a hypothetical protein, the Na/solute symporter gene BLi02212, the arginase homolog-encoding gene BLi00198 and mcrA, encoding a protein with endonuclease activity. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. SD Bioline malaria antigen Pf (HRP-2/pLHD) for assessing efficacy ...

    African Journals Online (AJOL)

    Pan African Medical Journal. Journal Home · ABOUT ... Higher proportions of false positive cases were observed on the HRP-2 band irrespective of patient parasite densities during the follow up but these were barely seen on the pLDH band.

  8. HRP facility for fabrication of ITER vertical target divertor full scale plasma facing units

    International Nuclear Information System (INIS)

    Visca, Eliseo; Roccella, S.; Candura, D.; Palermo, M.; Rossi, P.; Pizzuto, A.; Sanguinetti, G.P.; Mancini, A.; Verdini, L.; Cacciotti, E.; Cerri, V.; Mugnaini, G.; Reale, A.; Giacomi, G.

    2015-01-01

    Highlights: • R&D activities for the manufacturing of ITER divertor high heat flux plasma-facing components (HHFC). • ENEA and Ansaldo have jointly manufactured several actively cooled monoblock mock-ups and prototypical components. • ENEA and ANSALDO NUCLEARE jointly participate to the European program for the qualification of the manufacturing technology for the ITER divertor IVT. • Successful manufacturing by HRP (Hot Radial Pressing) of first full-scale full-W armored IVT qualification prototype. - Abstract: ENEA and Ansaldo Nucleare S.p.A. (ANN) have being deeply involved in the European development activities for the manufacturing of the ITER Divertor Inner Vertical Target (IVT) plasma-facing components. During normal operation the heat flux deposited on the bottom segment of divertor is 5–10 MW/m 2 but the capability to remove up to 20 MW/m 2 during transient events of 10 s must also be demonstrated. In order to fulfill ITER requirements, ENEA has set up and widely tested a manufacturing process, named Hot Radial Pressing (HRP). The last challenge is now to fabricate full-scale prototypes of the IVT, aimed to be qualified for the next step, i.e. the series production. On the basis of the experience of manufacturing hundreds of small mock-ups, ENEA designed and installed a new suitable HRP facility. The objective of getting a final shaped plasma facing unit (PFU) that satisfies these requirements is an ambitious target because tolerances set by ITER/F4E are very tight. The setting-up of the equipment started with the fabrication of full scale and representative ‘dummies’ in which stainless steel instead of CFC or W was used for monoblocks. The results confirmed that dimensions were compliant with the required tolerances. The paper reports a brief description of the innovative HRP equipment and the dimensional check results after HRP of the first full-scale full-W PFU.

  9. HRP facility for fabrication of ITER vertical target divertor full scale plasma facing units

    Energy Technology Data Exchange (ETDEWEB)

    Visca, Eliseo, E-mail: eliseo.visca@enea.it [Unità Tecnica Fusione, ENEA C. R. Frascati, via E. Fermi 45, IT-00044 Frascati (Roma) (Italy); Roccella, S. [Unità Tecnica Fusione, ENEA C. R. Frascati, via E. Fermi 45, IT-00044 Frascati (Roma) (Italy); Candura, D.; Palermo, M. [Ansaldo Nucleare S.p.A., Corso Perrone 25, IT-16152 Genova (Italy); Rossi, P.; Pizzuto, A. [Unità Tecnica Fusione, ENEA C. R. Frascati, via E. Fermi 45, IT-00044 Frascati (Roma) (Italy); Sanguinetti, G.P. [Ansaldo Nucleare S.p.A., Corso Perrone 25, IT-16152 Genova (Italy); Mancini, A.; Verdini, L.; Cacciotti, E.; Cerri, V.; Mugnaini, G.; Reale, A.; Giacomi, G. [Unità Tecnica Fusione, ENEA C. R. Frascati, via E. Fermi 45, IT-00044 Frascati (Roma) (Italy)

    2015-10-15

    Highlights: • R&D activities for the manufacturing of ITER divertor high heat flux plasma-facing components (HHFC). • ENEA and Ansaldo have jointly manufactured several actively cooled monoblock mock-ups and prototypical components. • ENEA and ANSALDO NUCLEARE jointly participate to the European program for the qualification of the manufacturing technology for the ITER divertor IVT. • Successful manufacturing by HRP (Hot Radial Pressing) of first full-scale full-W armored IVT qualification prototype. - Abstract: ENEA and Ansaldo Nucleare S.p.A. (ANN) have being deeply involved in the European development activities for the manufacturing of the ITER Divertor Inner Vertical Target (IVT) plasma-facing components. During normal operation the heat flux deposited on the bottom segment of divertor is 5–10 MW/m{sup 2} but the capability to remove up to 20 MW/m{sup 2} during transient events of 10 s must also be demonstrated. In order to fulfill ITER requirements, ENEA has set up and widely tested a manufacturing process, named Hot Radial Pressing (HRP). The last challenge is now to fabricate full-scale prototypes of the IVT, aimed to be qualified for the next step, i.e. the series production. On the basis of the experience of manufacturing hundreds of small mock-ups, ENEA designed and installed a new suitable HRP facility. The objective of getting a final shaped plasma facing unit (PFU) that satisfies these requirements is an ambitious target because tolerances set by ITER/F4E are very tight. The setting-up of the equipment started with the fabrication of full scale and representative ‘dummies’ in which stainless steel instead of CFC or W was used for monoblocks. The results confirmed that dimensions were compliant with the required tolerances. The paper reports a brief description of the innovative HRP equipment and the dimensional check results after HRP of the first full-scale full-W PFU.

  10. The GlnR Regulon in Streptococcus mutans Is Differentially Regulated by GlnR and PmrA.

    Directory of Open Access Journals (Sweden)

    Yi-Ywan M Chen

    Full Text Available GlnR-mediated repression of the GlnR regulon at acidic pH is required for optimal acid tolerance in Streptococcus mutans, the etiologic agent for dental caries. Unlike most streptococci, the GlnR regulon is also regulated by newly identified PmrA (SMUGS5_RS05810 at the transcriptional level in S. mutans GS5. Results from gel mobility shift assays confirmed that both GlnR and PmrA recognized the putative GlnR box in the promoter regions of the GlnR regulon genes. By using a chemostat culture system, we found that PmrA activated the expression of the GlnR regulon at pH 7, and that this activation was enhanced by excess glucose. Deletion of pmrA (strain ΔPmrA reduced the survival rate of S. mutans GS5 at pH 3 moderately, whereas the GlnR mutant (strain ΔGlnR exhibited an acid-sensitive phenotype in the acid killing experiments. Elevated biofilm formation in both ΔGlnR and ΔPmrA mutant strains is likely a result of indirect regulation of the GlnR regulon since GlnR and PmrA regulate the regulon differently. Taken together, it is suggested that activation of the GlnR regulon by PmrA at pH 7 ensures adequate biosynthesis of amino acid precursor, whereas repression by GlnR at acidic pH allows greater ATP generation for acid tolerance. The tight regulation of the GlnR regulon in response to pH provides an advantage for S. mutans to better survive in its primary niche, the oral cavity.

  11. Erwinia amylovora expresses fast and simultaneously hrp/dsp virulence genes during flower infection on apple trees.

    Directory of Open Access Journals (Sweden)

    Doris Pester

    Full Text Available BACKGROUND: Pathogen entry through host blossoms is the predominant infection pathway of the gram-negative bacterium Erwinia amylovora leading to manifestation of the disease fire blight. Like in other economically important plant pathogens, E. amylovora pathogenicity depends on a type III secretion system encoded by hrp genes. However, timing and transcriptional order of hrp gene expression during flower infections are unknown. METHODOLOGY/PRINCIPAL FINDINGS: Using quantitative real-time PCR analyses, we addressed the questions of how fast, strong and uniform key hrp virulence genes and the effector dspA/E are expressed when bacteria enter flowers provided with the full defense mechanism of the apple plant. In non-invasive bacterial inoculations of apple flowers still attached to the tree, E. amylovora activated expression of key type III secretion genes in a narrow time window, mounting in a single expression peak of all investigated hrp/dspA/E genes around 24-48 h post inoculation (hpi. This single expression peak coincided with a single depression in the plant PR-1 expression at 24 hpi indicating transient manipulation of the salicylic acid pathway as one target of E. amylovora type III effectors. Expression of hrp/dspA/E genes was highly correlated to expression of the regulator hrpL and relative transcript abundances followed the ratio: hrpA>hrpN>hrpL>dspA/E. Acidic conditions (pH 4 in flower infections led to reduced virulence/effector gene expression without the typical expression peak observed under natural conditions (pH 7. CONCLUSION/SIGNIFICANCE: The simultaneous expression of hrpL, hrpA, hrpN, and the effector dspA/E during early floral infection indicates that speed and immediate effector transmission is important for successful plant invasion. When this delicate balance is disturbed, e.g., by acidic pH during infection, virulence gene expression is reduced, thus partly explaining the efficacy of acidification in fire blight

  12. Identification of self-consistent modulons from bacterial microarray expression data with the help of structured regulon gene sets

    KAUST Repository

    Permina, Elizaveta A.

    2013-01-01

    Identification of bacterial modulons from series of gene expression measurements on microarrays is a principal problem, especially relevant for inadequately studied but practically important species. Usage of a priori information on regulatory interactions helps to evaluate parameters for regulatory subnetwork inference. We suggest a procedure for modulon construction where a seed regulon is iteratively updated with genes having expression patterns similar to those for regulon member genes. A set of genes essential for a regulon is used to control modulon updating. Essential genes for a regulon were selected as a subset of regulon genes highly related by different measures to each other. Using Escherichia coli as a model, we studied how modulon identification depends on the data, including the microarray experiments set, the adopted relevance measure and the regulon itself. We have found that results of modulon identification are highly dependent on all parameters studied and thus the resulting modulon varies substantially depending on the identification procedure. Yet, modulons that were identified correctly displayed higher stability during iterations, which allows developing a procedure for reliable modulon identification in the case of less studied species where the known regulatory interactions are sparse. Copyright © 2013 Taylor & Francis.

  13. Involvement and necessity of the Cpx regulon in the event of aberrant β-barrel outer membrane protein assembly

    Science.gov (United States)

    Gerken, Henri; Leiser, Owen P.; Bennion, Drew; Misra, Rajeev

    2010-01-01

    Summary The Cpx and σE regulons help maintain outer membrane integrity; the Cpx pathway monitors the biogenesis of cell surface structures, such as pili, while the σE pathway monitors the biogenesis of β-barrel outer membrane proteins (OMPs). In this study we revealed the importance of the Cpx regulon in the event of β-barrel OMP mis-assembly, by utilizing mutants expressing either a defective β-barrel OMP assembly machinery (Bam) or assembly defective β-barrel OMPs. Analysis of specific mRNAs showed that ΔcpxR bam double mutants failed to induce degP expression beyond the wild type level, despite activation of the σE pathway. The synthetic conditional lethal phenotype of ΔcpxR in mutant Bam or β-barrel OMP backgrounds was reversed by wild type DegP expressed from a heterologous plasmid promoter. Consistent with the involvement of the Cpx regulon in the event of aberrant β-barrel OMP assembly, the expression of cpxP, the archetypal member of the cpx regulon, was upregulated in defective Bam backgrounds or in cells expressing a single assembly-defective β-barrel OMP species. Together, these results showed that both the Cpx and σE regulons are required to reduce envelope stress caused by aberrant β-barrel OMP assembly, with the Cpx regulon principally contributing by controlling degP expression. PMID:20487295

  14. The nervus terminalis ganglion in Anguilla rostrata: an immunocytochemical and HRP histochemical analysis.

    Science.gov (United States)

    Grober, M S; Bass, A H; Burd, G; Marchaterre, M A; Segil, N; Scholz, K; Hodgson, T

    1987-12-08

    Immunocytochemistry and retrograde horseradish peroxidase (HRP) transport were used to study the ganglion of the nervus terminalis in the American eel, Anguilla rostrata. Luteinizing hormone releasing hormone (LHRH) like immunoreactivity was found in large, ganglion-like cells located ventromedially at the junction of the telencephalon and olfactory bulb and in fibers within the retina and olfactory epithelium. HRP transport from the retina demonstrated direct connections with both the ipsi- and contralateral populations of these ganglion-like cells. Given the well-documented role of both olfaction and vision during migratory and reproductive phases of the life cycle of eels, the robust nature of a nervus terminalis system in these fish may present a unique opportunity to study the behavioral correlates of structure-function organization in a discrete population of ganglion-like cells.

  15. A model for evolution and regulation of nicotine biosynthesis regulon in tobacco.

    Science.gov (United States)

    Kajikawa, Masataka; Sierro, Nicolas; Hashimoto, Takashi; Shoji, Tsubasa

    2017-06-03

    In tobacco, the defense alkaloid nicotine is produced in roots and accumulates mainly in leaves. Signaling mediated by jasmonates (JAs) induces the formation of nicotine via a series of structural genes that constitute a regulon and are coordinated by JA-responsive transcription factors of the ethylene response factor (ERF) family. Early steps in the pyrrolidine and pyridine biosynthesis pathways likely arose through duplication of the polyamine and nicotinamide adenine dinucleotide (NAD) biosynthetic pathways, respectively, followed by recruitment of duplicated primary metabolic genes into the nicotine biosynthesis regulon. Transcriptional regulation of nicotine biosynthesis by ERF and cooperatively-acting MYC2 transcription factors is implied by the frequency of cognate cis-regulatory elements for these factors in the promoter regions of the downstream structural genes. Indeed, a mutant tobacco with low nicotine content was found to have a large chromosomal deletion in a cluster of closely related ERF genes at the nicotine-controlling NICOTINE2 (NIC2) locus.

  16. The post-transcriptional regulator rsmA/csrA activates T3SS by stabilizing the 5' UTR of hrpG, the master regulator of hrp/hrc genes, in Xanthomonas.

    Directory of Open Access Journals (Sweden)

    Maxuel O Andrade

    2014-02-01

    Full Text Available The RsmA/CsrA family of the post-transcriptional regulators of bacteria is involved in the regulation of many cellular processes, including pathogenesis. In this study, we demonstrated that rsmA not only is required for the full virulence of the phytopathogenic bacterium Xanthomonas citri subsp. citri (XCC but also contributes to triggering the hypersensitive response (HR in non-host plants. Deletion of rsmA resulted in significantly reduced virulence in the host plant sweet orange and a delayed and weakened HR in the non-host plant Nicotiana benthamiana. Microarray, quantitative reverse-transcription PCR, western-blotting, and GUS assays indicated that RsmA regulates the expression of the type 3 secretion system (T3SS at both transcriptional and post-transcriptional levels. The regulation of T3SS by RsmA is a universal phenomenon in T3SS-containing bacteria, but the specific mechanism seems to depend on the interaction between a particular bacterium and its hosts. For Xanthomonads, the mechanism by which RsmA activates T3SS remains unknown. Here, we show that RsmA activates the expression of T3SS-encoding hrp/hrc genes by directly binding to the 5' untranslated region (UTR of hrpG, the master regulator of the hrp/hrc genes in XCC. RsmA stabilizes hrpG mRNA, leading to increased accumulation of HrpG proteins and subsequently, the activation of hrp/hrc genes. The activation of the hrp/hrc genes by RsmA via HrpG was further supported by the observation that ectopic overexpression of hrpG in an rsmA mutant restored its ability to cause disease in host plants and trigger HR in non-host plants. RsmA also stabilizes the transcripts of another T3SS-associated hrpD operon by directly binding to the 5' UTR region. Taken together, these data revealed that RsmA primarily activates T3SS by acting as a positive regulator of hrpG and that this regulation is critical to the pathogenicity of XCC.

  17. The hnRNP A1 homolog Hrp36 is essential for normal development ...

    Indian Academy of Sciences (India)

    2012-08-11

    Aug 11, 2012 ... Here we show that loss of both copies of hrp36 gene slows down development with .... larvae, pupae and adults were reared at 18°C or 24°C or. 30°C (±1°C) on ... of three days old 20 male and 20 female flies were set up: (a) wild type ... dissected out in Poels' salt solution (PSS; Lakhotia and. Tapadia ...

  18. The Streptococcus sanguinis Competence Regulon Is Not Required for Infective Endocarditis Virulence in a Rabbit Model

    OpenAIRE

    Callahan, Jill E.; Munro, Cindy L.; Kitten, Todd

    2011-01-01

    Streptococcus sanguinis is an important component of dental plaque and a leading cause of infective endocarditis. Genetic competence in S. sanguinis requires a quorum sensing system encoded by the early comCDE genes, as well as late genes controlled by the alternative sigma factor, ComX. Previous studies of Streptococcus pneumoniae and Streptococcus mutans have identified functions for the >100-gene com regulon in addition to DNA uptake, including virulence. We investigated this possibility i...

  19. Deep sequencing whole transcriptome exploration of the σE regulon in Neisseria meningitidis.

    Directory of Open Access Journals (Sweden)

    Robert Antonius Gerhardus Huis in 't Veld

    Full Text Available Bacteria live in an ever-changing environment and must alter protein expression promptly to adapt to these changes and survive. Specific response genes that are regulated by a subset of alternative σ(70-like transcription factors have evolved in order to respond to this changing environment. Recently, we have described the existence of a σ(E regulon including the anti-σ-factor MseR in the obligate human bacterial pathogen Neisseria meningitidis. To unravel the complete σ(E regulon in N. meningitidis, we sequenced total RNA transcriptional content of wild type meningococci and compared it with that of mseR mutant cells (ΔmseR in which σ(E is highly expressed. Eleven coding genes and one non-coding gene were found to be differentially expressed between H44/76 wildtype and H44/76ΔmseR cells. Five of the 6 genes of the σ(E operon, msrA/msrB, and the gene encoding a pepSY-associated TM helix family protein showed enhanced transcription, whilst aniA encoding a nitrite reductase and nspA encoding the vaccine candidate Neisserial surface protein A showed decreased transcription. Analysis of differential expression in IGRs showed enhanced transcription of a non-coding RNA molecule, identifying a σ(E dependent small non-coding RNA. Together this constitutes the first complete exploration of an alternative σ-factor regulon in N. meningitidis. The results direct to a relatively small regulon indicative for a strictly defined response consistent with a relatively stable niche, the human throat, where N. meningitidis resides.

  20. Transcriptome analysis of the Lactococcus lactis ArgR and AhrC regulons

    DEFF Research Database (Denmark)

    Larsen, Rasmus; van Hijum, Sacha A. F. T.; Martinussen, Jan

    2008-01-01

    In previous studies, we have shown that direct protein-protein. interaction between the two regulators ArgR and AhrC in Lactococcus lactis is required for arginine-dependent repression of the biosynthetic argC promoter and the activation of the catabolic arcA promoter. Here, we establish the global...... ArgR and AhrC regulons by transcriptome analyses and show that both regulators are dedicated to the control of arginine metabolism in L. lactis....

  1. Formal Development of the HRP Prover - Part 1: Syntax and Semantics

    International Nuclear Information System (INIS)

    Sivertsen, Terje

    1996-01-01

    This report describes the formal development of a new version of the HRP Prover. The new version of the tool will have functionality almost identical to the current version, but is developed in accordance to established principles for applying algebraic specification in formal software development. The development project provides results of relevance to the formal development of a wide range of language-oriented tools, including programming language compilers, as well as to the automatic generation of code from specifications. Since the overall scope of this report is the analysis of algebraic specifications, emphasis is given to topics related to what is usually understood as the ''front end'' of compilers. This includes lexical and syntax analysis of the specifications, static semantics through type checking, and dynamic semantics through evaluation. All the different phases are specified in algebraic specification and supported by the current version of the HRP Prover. In subsequent work, the completed parts of the new version will complement the tool support in the development. The work presented will be followed up by formal specification of theorem proving and transformation, as well as code generation into conventional programming languages. The new version of the HRP Prover is incrementally developed in coherence with the specifications produced in these activities. At the same time, the development of the tool demonstrates the efficient use of the methodology through real application on an increasingly important class of software. (author)

  2. Human myeloperoxidase (MPO) and horseradish peroxidase (HRP) catalyzed oxidation of phenol

    International Nuclear Information System (INIS)

    Ross, D.; Eastmond, D.A.; Ruzo, L.O.; Smith, M.T.

    1986-01-01

    MPO-catalyzed conversion of phenolic metabolites of benzene may be involved in benzene-induced myelotoxicity. The authors have studied the metabolism and protein binding of phenol - the major metabolite of benzene - during peroxidatic oxidation. The major metabolite observed during MPO- and HRP- catalyzed oxidation was characterized as 4,4 biphenol using HPLC and combined GC-MS. When glutathione (GSH) was added to the incubation mixtures, two additional compounds were observed during HPLC analysis which were characterized as GSH-conjugates of 4,4-diphenoquinone by fast atom bombardment MS and by NMR. ESR spectroscopy showed that both MPO-and HRP-catalyzed oxidation of phenol proceeded via the generation of free radical intermediates. Using 14 C-phenol, both MPO- and HRP-catalyzed oxidations resulted in the production of species which bound covalently to boiled liver microsomal protein. The increase in binding correlated well with removal of substrate. Thus, peroxidatic oxidation of phenolic metabolites of benzene in the bone marrow may be involved in benzene-induced myelotoxicity

  3. The Streptococcus sanguinis competence regulon is not required for infective endocarditis virulence in a rabbit model.

    Directory of Open Access Journals (Sweden)

    Jill E Callahan

    Full Text Available Streptococcus sanguinis is an important component of dental plaque and a leading cause of infective endocarditis. Genetic competence in S. sanguinis requires a quorum sensing system encoded by the early comCDE genes, as well as late genes controlled by the alternative sigma factor, ComX. Previous studies of Streptococcus pneumoniae and Streptococcus mutans have identified functions for the >100-gene com regulon in addition to DNA uptake, including virulence. We investigated this possibility in S. sanguinis. Strains deleted for the comCDE or comX master regulatory genes were created. Using a rabbit endocarditis model in conjunction with a variety of virulence assays, we determined that both mutants possessed infectivity equivalent to that of a virulent control strain, and that measures of disease were similar in rabbits infected with each strain. These results suggest that the com regulon is not required for S. sanguinis infective endocarditis virulence in this model. We propose that the different roles of the S. sanguinis, S. pneumoniae, and S. mutans com regulons in virulence can be understood in relation to the pathogenic mechanisms employed by each species.

  4. The Streptococcus sanguinis competence regulon is not required for infective endocarditis virulence in a rabbit model.

    Science.gov (United States)

    Callahan, Jill E; Munro, Cindy L; Kitten, Todd

    2011-01-01

    Streptococcus sanguinis is an important component of dental plaque and a leading cause of infective endocarditis. Genetic competence in S. sanguinis requires a quorum sensing system encoded by the early comCDE genes, as well as late genes controlled by the alternative sigma factor, ComX. Previous studies of Streptococcus pneumoniae and Streptococcus mutans have identified functions for the >100-gene com regulon in addition to DNA uptake, including virulence. We investigated this possibility in S. sanguinis. Strains deleted for the comCDE or comX master regulatory genes were created. Using a rabbit endocarditis model in conjunction with a variety of virulence assays, we determined that both mutants possessed infectivity equivalent to that of a virulent control strain, and that measures of disease were similar in rabbits infected with each strain. These results suggest that the com regulon is not required for S. sanguinis infective endocarditis virulence in this model. We propose that the different roles of the S. sanguinis, S. pneumoniae, and S. mutans com regulons in virulence can be understood in relation to the pathogenic mechanisms employed by each species.

  5. Immobilization of HRP in Mesoporous Silica and Its Application for the Construction of Polyaniline Modified Hydrogen Peroxide Biosensor

    Directory of Open Access Journals (Sweden)

    Chien-Chung Chen

    2009-06-01

    Full Text Available Polyaniline (PANI, an attractive conductive polymer, has been successfully applied in fabricating various types of enzyme-based biosensors. In this study, we have employed mesoporous silica SBA-15 to stably entrap horseradish peroxidase (HRP, and then deposited the loaded SBA-15 on the PANI modified platinum electrode to construct a GA/SBA-15(HRP/PANI/Pt biosensor. The mesoporous structures and morphologies of SBA-15 with or without HRP were characterized. Enzymatic protein assays were employed to evaluate HRP immobilization efficiency. Our results demonstrated that the constructed biosensor displayed a fine linear correlation between cathodic response and H2O2 concentration in the range of 0.02 to 18.5 mM, with enhanced sensitivity. In particular, the current approach provided the PANI modified biosensor with improved stability for multiple measurements.

  6. Study on Enhancement Principle and Stabilization for the Luminol-H2O2-HRP Chemiluminescence System.

    Directory of Open Access Journals (Sweden)

    Lihua Yang

    Full Text Available A luminol-H2O2-HRP chemiluminescence system with high relative luminescent intensity (RLU and long stabilization time was investigated. First, the comparative study on the enhancement effect of ten compounds as enhancers to the luminol-H2O2-HRP chemiluminescence system was carried out, and the results showed that 4-(imidazol-1-ylphenol (4-IMP, 4-iodophenol (4-IOP, 4-bromophenol (4-BOP and 4-hydroxy-4'-iodobiphenyl (HIOP had the best performance. Based on the experiment, the four enhancers were dissolved in acetone, acetonitrile, methanol, and dimethylformamide (DMF with various concentrations, the results indicated that 4-IMP, 4-IOP, 4-BOP and HIOP dissolved in DMF with the concentrations of 0.2%, 3.2%, 1.6% and 3.2% could get the highest RLU values. Subsequently, the influences of pH, ionic strength, HRP, 4-IMP, 4-IOP, 4-BOP, HIOP, H2O2 and luminol on the stabilization of the luminol-H2O2-HRP chemiluminescence system were studied, and we found that pH value, ionic strength, 4-IMP, 4-IOP, 4-BOP, HIOP, H2O2 and luminol have little influence on luminescent stabilization, while HRP has a great influence. In different ranges of HRP concentration, different enhancers should be selected. When the concentration is within the range of 0~6 ng/mL, 4-IMP should be selected. When the concentration of HRP ranges from 6 to 25 ng/mL, 4-IOP was the best choice. And when the concentration is within the range of 25~80 ng/mL, HIOP should be selected as the enhancer. Finally, the three well-performing chemiluminescent enhanced solutions (CESs have been further optimized according to the three enhancers (4-IMP, 4-IOP and HIOP in their utilized HRP concentration ranges.

  7. Identification of genes for small non-coding RNAs that belong to the regulon of the two-component regulatory system CiaRH in Streptococcus

    Directory of Open Access Journals (Sweden)

    Hakenbeck Regine

    2010-11-01

    Full Text Available Abstract Background Post-transcriptional regulation by small RNAs (sRNAs in bacteria is now recognized as a wide-spread regulatory mechanism modulating a variety of physiological responses including virulence. In Streptococcus pneumoniae, an important human pathogen, the first sRNAs to be described were found in the regulon of the CiaRH two-component regulatory system. Five of these sRNAs were detected and designated csRNAs for cia-dependent small RNAs. CiaRH pleiotropically affects β-lactam resistance, autolysis, virulence, and competence development by yet to be defined molecular mechanisms. Since CiaRH is highly conserved among streptococci, it is of interest to determine if csRNAs are also included in the CiaRH regulon in this group of organisms consisting of commensal as well as pathogenic species. Knowledge on the participation of csRNAs in CiaRH-dependent regulatory events will be the key to define the physiological role of this important control system. Results Genes for csRNAs were predicted in streptococcal genomes and data base entries other than S. pneumoniae by searching for CiaR-activated promoters located in intergenic regions that are followed by a transcriptional terminator. 61 different candidate genes were obtained specifying csRNAs ranging in size from 51 to 202 nt. Comparing these genes among each other revealed 40 different csRNA types. All streptococcal genomes harbored csRNA genes, their numbers varying between two and six. To validate these predictions, S. mitis, S. oralis, and S. sanguinis were subjected to csRNA-specific northern blot analysis. In addition, a csRNA gene from S. thermophilus plasmid pST0 introduced into S. pneumoniae was also tested. Each of the csRNAs was detected on these blots and showed the anticipated sizes. Thus, the method applied here is able to predict csRNAs with high precision. Conclusions The results of this study strongly suggest that genes for small non-coding RNAs, csRNAs, are part of

  8. Formation of target-specific binding sites in enzymes: solid-phase molecular imprinting of HRP

    Science.gov (United States)

    Czulak, J.; Guerreiro, A.; Metran, K.; Canfarotta, F.; Goddard, A.; Cowan, R. H.; Trochimczuk, A. W.; Piletsky, S.

    2016-05-01

    Here we introduce a new concept for synthesising molecularly imprinted nanoparticles by using proteins as macro-functional monomers. For a proof-of-concept, a model enzyme (HRP) was cross-linked using glutaraldehyde in the presence of glass beads (solid-phase) bearing immobilized templates such as vancomycin and ampicillin. The cross-linking process links together proteins and protein chains, which in the presence of templates leads to the formation of permanent target-specific recognition sites without adverse effects on the enzymatic activity. Unlike complex protein engineering approaches commonly employed to generate affinity proteins, the method proposed can be used to produce protein-based ligands in a short time period using native protein molecules. These affinity materials are potentially useful tools especially for assays since they combine the catalytic properties of enzymes (for signaling) and molecular recognition properties of antibodies. We demonstrate this concept in an ELISA-format assay where HRP imprinted with vancomycin and ampicillin replaced traditional enzyme-antibody conjugates for selective detection of templates at micromolar concentrations. This approach can potentially provide a fast alternative to raising antibodies for targets that do not require high assay sensitivities; it can also find uses as a biochemical research tool, as a possible replacement for immunoperoxidase-conjugates.Here we introduce a new concept for synthesising molecularly imprinted nanoparticles by using proteins as macro-functional monomers. For a proof-of-concept, a model enzyme (HRP) was cross-linked using glutaraldehyde in the presence of glass beads (solid-phase) bearing immobilized templates such as vancomycin and ampicillin. The cross-linking process links together proteins and protein chains, which in the presence of templates leads to the formation of permanent target-specific recognition sites without adverse effects on the enzymatic activity. Unlike

  9. The SOS and RpoS Regulons Contribute to Bacterial Cell Robustness to Genotoxic Stress by Synergistically Regulating DNA Polymerase Pol II.

    Science.gov (United States)

    Dapa, Tanja; Fleurier, Sébastien; Bredeche, Marie-Florence; Matic, Ivan

    2017-07-01

    Mitomycin C (MMC) is a genotoxic agent that induces DNA cross-links, DNA alkylation, and the production of reactive oxygen species (ROS). MMC induces the SOS response and RpoS regulons in Escherichia coli SOS-encoded functions are required for DNA repair, whereas the RpoS regulon is typically induced by metabolic stresses that slow growth. Thus, induction of the RpoS regulon by MMC may be coincidental, because DNA damage slows growth; alternatively, the RpoS regulon may be an adaptive response contributing to cell survival. In this study, we show that the RpoS regulon is primarily induced by MMC-induced ROS production. We also show that RpoS regulon induction is required for the survival of MMC-treated growing cells. The major contributor to RpoS-dependent resistance to MMC treatment is DNA polymerase Pol II, which is encoded by the polB gene belonging to the SOS regulon. The observation that polB gene expression is controlled by the two major stress response regulons that are required to maximize survival and fitness further emphasizes the key role of this DNA polymerase as an important factor in genome stability. Copyright © 2017 by the Genetics Society of America.

  10. Definition of the σ(W) regulon of Bacillus subtilis in the absence of stress.

    Science.gov (United States)

    Zweers, Jessica C; Nicolas, Pierre; Wiegert, Thomas; van Dijl, Jan Maarten; Denham, Emma L

    2012-01-01

    Bacteria employ extracytoplasmic function (ECF) sigma factors for their responses to environmental stresses. Despite intensive research, the molecular dissection of ECF sigma factor regulons has remained a major challenge due to overlaps in the ECF sigma factor-regulated genes and the stimuli that activate the different ECF sigma factors. Here we have employed tiling arrays to single out the ECF σ(W) regulon of the Gram-positive bacterium Bacillus subtilis from the overlapping ECF σ(X), σ(Y), and σ(M) regulons. For this purpose, we profiled the transcriptome of a B. subtilis sigW mutant under non-stress conditions to select candidate genes that are strictly σ(W)-regulated. Under these conditions, σ(W) exhibits a basal level of activity. Subsequently, we verified the σ(W)-dependency of candidate genes by comparing their transcript profiles to transcriptome data obtained with the parental B. subtilis strain 168 grown under 104 different conditions, including relevant stress conditions, such as salt shock. In addition, we investigated the transcriptomes of rasP or prsW mutant strains that lack the proteases involved in the degradation of the σ(W) anti-sigma factor RsiW and subsequent activation of the σ(W)-regulon. Taken together, our studies identify 89 genes as being strictly σ(W)-regulated, including several genes for non-coding RNAs. The effects of rasP or prsW mutations on the expression of σ(W)-dependent genes were relatively mild, which implies that σ(W)-dependent transcription under non-stress conditions is not strictly related to RasP and PrsW. Lastly, we show that the pleiotropic phenotype of rasP mutant cells, which have defects in competence development, protein secretion and membrane protein production, is not mirrored in the transcript profile of these cells. This implies that RasP is not only important for transcriptional regulation via σ(W), but that this membrane protease also exerts other important post-transcriptional regulatory

  11. Human Research Program (HRP) Exploration Medical Capability (ExMC) Standing Review Panel (SRP)

    Science.gov (United States)

    Cintron, Nitza; Dutson, Eric; Friedl, Karl; Hyman, William; Jemison, Mae; Klonoff, David

    2009-01-01

    The SRP believes strongly that regularly performed in-flight crew assessments are needed in order to identify a change in health status before a medical condition becomes clinically apparent. It is this early recognition in change that constitutes the foundation of the "occupational health model" expounded in the HRP Requirements Document as a key component of the HRP risk mitigation strategy that will enable its objective of "prevention and mitigation of human health and performance risks". A regular crew status examination of physiological and clinical performance is needed. This can be accomplished through instrumented monitoring of routine embedded tasks. The SRP recommends addition of a new gap to address this action under Category 3.0 Mitigate the Risk. This new gap is closely associated with Task 4.19 which addresses the lack of adequate biomedical monitoring capabilities for performing periodic clinical status evaluations and contingency medical monitoring. A corollary to these gaps is the critical emphasis on preventive medicine, not only during pre- and post-flight phases of a mission as is the current practice, but continued into the in-flight phases of exploration class missions.

  12. In silico discovery of the dormancy regulons in a number of Actinobacteria genomes

    Energy Technology Data Exchange (ETDEWEB)

    Gerasimova, Anna; Dubchak, Inna; Arkin, Adam; Gelfand, Mikhail

    2010-11-16

    Mycobacterium tuberculosis is a dangerous Actinobacteria infecting nearly one third of the human population. It becomes dormant and phenotypically drug resistant in response to stresses. An important feature of the M. tuberculosis pathogenesis is the prevalence of latent infection without disease, making understanding of the mechanisms used by the bacteria to exist in this state and to switch to metabolically active infectious form a vital problem to consider. M. tuberculosis dormancy is regulated by the three-component regulatory system of two kinases (DosT and DevS) and transcriprional regulator (DevR). DevR activates transcription of a set of genes, which allow the bacteria to survive long periods of anaerobiosis, and may be important for long-term survival within the host during latent infection. The DevR-regulon is studied experimentally in M. tuberculosis and few other phylogenetically close Mycobacteria spp. As many other two-component systems, the devRS operon is autoregulated. However, the mechanism of the dormancy is not completely clear even for these bacteria and there is no data describing the dormancy regulons in other species.

  13. Technological review of the HRP manufacturing process R and D activity

    International Nuclear Information System (INIS)

    Visca, Eliseo; Pizzuto, A.; Gavila, P.; Riccardi, B.; Roccella, S.; Candura, D.; Sanguinetti, G.P.

    2013-01-01

    Highlights: • R and D activities for the manufacturing of ITER divertor high heat flux plasma-facing components (HHFC). • ENEA and Ansaldo have jointly manufactured several actively cooled monoblock mock-ups and prototypical components. • Successful manufacturing by HRP (hot radial pressing) and PBC (pre-brazed casting) of both W and CFC armoured small and medium scale mockups. • ENEA-ANSALDO participate to the European programme for the qualification of the manufacturing technology for the ITER divertor IVT. • A qualification divertor inner vertical target prototype successfully tested at ITER relevant thermal heat fluxes. -- Abstract: ENEA and Ansaldo Nucleare S.p.A. have been deeply involved in the European International Thermonuclear Experimental Reactor (ITER) R and D activities for the manufacturing of high heat flux plasma-facing components (HHFC), and in particular for the inner vertical target (IVT) of the ITER divertor. This component has to be manufactured by using both armour and structural materials whose properties are defined by ITER. Their physical properties prevent the use of standard joining techniques. The reference armour materials are tungsten and carbon/carbon fibre composite (CFC). The cooling pipe is made of copper alloy (CuCrZr-IG). During the last years ENEA and Ansaldo have jointly manufactured several actively cooled monoblock mock-ups and prototypical components of different length, geometry and materials, by using innovative processes: HRP (hot radial pressing) and PBC (pre-brazed casting). The history of the technical issues solved during the R and D phase and the improvements implemented to the assembling tools and equipments are reviewed in the paper together with the testing results. The optimization of the processes started from the successful manufacturing of both W and CFC armoured small scale mockups thermal fatigue tested in the worst ITER operating condition (20 MW/m 2 ) through the achievement of record

  14. Technological review of the HRP manufacturing process R and D activity

    Energy Technology Data Exchange (ETDEWEB)

    Visca, Eliseo, E-mail: eliseo.visca@enea.it [Associazione EURATOM-ENEA sulla Fusione, C.R. Frascati, Via E. Fermi 45, IT-00044 Frascati (Italy); Pizzuto, A. [Associazione EURATOM-ENEA sulla Fusione, C.R. Frascati, Via E. Fermi 45, IT-00044 Frascati (Italy); Gavila, P.; Riccardi, B. [Fusion For Energy, C. Josep Pla 2, ES-08019 Barcelona (Spain); Roccella, S. [Associazione EURATOM-ENEA sulla Fusione, C.R. Frascati, Via E. Fermi 45, IT-00044 Frascati (Italy); Candura, D.; Sanguinetti, G.P. [Ansaldo Nucleare S.p.A., Corso Perrone 25, IT-16121 Genova (Italy)

    2013-10-15

    Highlights: • R and D activities for the manufacturing of ITER divertor high heat flux plasma-facing components (HHFC). • ENEA and Ansaldo have jointly manufactured several actively cooled monoblock mock-ups and prototypical components. • Successful manufacturing by HRP (hot radial pressing) and PBC (pre-brazed casting) of both W and CFC armoured small and medium scale mockups. • ENEA-ANSALDO participate to the European programme for the qualification of the manufacturing technology for the ITER divertor IVT. • A qualification divertor inner vertical target prototype successfully tested at ITER relevant thermal heat fluxes. -- Abstract: ENEA and Ansaldo Nucleare S.p.A. have been deeply involved in the European International Thermonuclear Experimental Reactor (ITER) R and D activities for the manufacturing of high heat flux plasma-facing components (HHFC), and in particular for the inner vertical target (IVT) of the ITER divertor. This component has to be manufactured by using both armour and structural materials whose properties are defined by ITER. Their physical properties prevent the use of standard joining techniques. The reference armour materials are tungsten and carbon/carbon fibre composite (CFC). The cooling pipe is made of copper alloy (CuCrZr-IG). During the last years ENEA and Ansaldo have jointly manufactured several actively cooled monoblock mock-ups and prototypical components of different length, geometry and materials, by using innovative processes: HRP (hot radial pressing) and PBC (pre-brazed casting). The history of the technical issues solved during the R and D phase and the improvements implemented to the assembling tools and equipments are reviewed in the paper together with the testing results. The optimization of the processes started from the successful manufacturing of both W and CFC armoured small scale mockups thermal fatigue tested in the worst ITER operating condition (20 MW/m{sup 2}) through the achievement of record

  15. Diagnosing severe falciparum malaria in parasitaemic African children: a prospective evaluation of plasma PfHRP2 measurement.

    Directory of Open Access Journals (Sweden)

    Ilse C E Hendriksen

    Full Text Available In African children, distinguishing severe falciparum malaria from other severe febrile illnesses with coincidental Plasmodium falciparum parasitaemia is a major challenge. P. falciparum histidine-rich protein 2 (PfHRP2 is released by mature sequestered parasites and can be used to estimate the total parasite burden. We investigated the prognostic significance of plasma PfHRP2 and used it to estimate the malaria-attributable fraction in African children diagnosed with severe malaria.Admission plasma PfHRP2 was measured prospectively in African children (from Mozambique, The Gambia, Kenya, Tanzania, Uganda, Rwanda, and the Democratic Republic of the Congo aged 1 month to 15 years with severe febrile illness and a positive P. falciparum lactate dehydrogenase (pLDH-based rapid test in a clinical trial comparing parenteral artesunate versus quinine (the AQUAMAT trial, ISRCTN 50258054. In 3,826 severely ill children, Plasmadium falciparum PfHRP2 was higher in patients with coma (p = 0.0209, acidosis (p<0.0001, and severe anaemia (p<0.0001. Admission geometric mean (95%CI plasma PfHRP2 was 1,611 (1,350-1,922 ng/mL in fatal cases (n = 381 versus 1,046 (991-1,104 ng/mL in survivors (n = 3,445, p<0.0001, without differences in parasitaemia as assessed by microscopy. There was a U-shaped association between log(10 plasma PfHRP2 and risk of death. Mortality increased 20% per log(10 increase in PfHRP2 above 174 ng/mL (adjusted odds ratio [AOR] 1.21, 95%CI 1.05-1.39, p = 0.009. A mechanistic model assuming a PfHRP2-independent risk of death in non-malaria illness closely fitted the observed data and showed malaria-attributable mortality less than 50% with plasma PfHRP2≤174 ng/mL. The odds ratio (OR for death in artesunate versus quinine-treated patients was 0.61 (95%CI 0.44-0.83, p = 0.0018 in the highest PfHRP2 tertile, whereas there was no difference in the lowest tertile (OR 1.05; 95%CI 0.69-1.61; p = 0.82. A limitation of the study is that some

  16. Immobilization of HRP Enzyme on Layered Double Hydroxides for Biosensor Application

    Directory of Open Access Journals (Sweden)

    Zouhair M. Baccar

    2011-01-01

    Full Text Available We present a new biosensor for hydrogen peroxide (H2O2 detection. The biosensor was based on the immobilization of horseradish peroxidase (HRP enzyme on layered double hydroxides- (LDH- modified gold surface. The hydrotalcite LDH (Mg2Al was prepared by coprecipitation in constant pH and in ambient temperature. The immobilization of the peroxidase on layered hybrid materials was realized via electrostatic adsorption autoassembly process. The detection of hydrogen peroxide was successfully observed in PBS buffer with cyclic voltammetry and the chronoamperometry techniques. A limit detection of 9 μM of H2O2 was obtained with a good reproducibility. We investigate the sensitivity of our developed biosensor for H2O2 detection in raw milk.

  17. Poly(ADP-ribose) Glycohydrolase and Poly(ADP-ribose)-interacting Protein Hrp38 Regulate Pattern Formation during Drosophila Eye Development

    Science.gov (United States)

    Ji, Yingbiao; Jarnik, Michael; Tulin, Alexei V.

    2013-01-01

    Drosophila Hrp38, a homolog of human hnRNP A1, has been shown to regulate splicing, but its function can be modified by poly(ADP-ribosyl)ation. Notwithstanding such findings, our understanding of the roles of poly(ADP-ribosyl)ated Hrp38 on development is limited. Here, we have demonstrated that Hrp38 is essential for fly eye development based on a rough-eye phenotype with disorganized ommatidia observed in adult escapers of the hrp38 mutant. We also observed that Poly(ADP-ribose) Glycohydrolase (Parg) loss-of-function, which caused increased Hrp38 poly(ADP-ribosyl)ation, also resulted in the rough-eye phenotype with disrupted ommatidial lattice and reduced number of photoreceptor cells. In addition, ectopic expression of DE-cadherin, which is required for retinal morphogenesis, fully rescued the rough-eye phenotype of the hrp38 mutant. Similarly, Parg mutant eye clones had decreased expression level of DE-cadherin with orientation defects, which is reminiscent of DE-cadherin mutant eye phenotype. Therefore, our results suggest that Hrp38 poly(ADP-ribosyl)ation controls eye pattern formation via regulation of DE-cadherin expression, a finding which has implications for understanding the pathogenic mechanisms of Hrp38-related Fragile X syndrome and PARP1-related retinal degeneration diseases. PMID:23711619

  18. H2O2 sensing using HRP modified catalyst-free ZnO nanorods synthesized by RF sputtering

    Science.gov (United States)

    Srivastava, Amit; Kumar, Naresh; Singh, Priti; Singh, Sunil Kumar

    2017-06-01

    Catalyst-free ( 00 l) oriented ZnO nanorods (NRs) -based biosensor for the H2O2 sensing has been reported. The (002) oriented ZnO NRs as confirmed by X-ray diffraction were successfully grown on indium tin oxide (ITO) coated glass substrate by radio frequency (RF) sputtering technique without using any catalyst. Horseradish peroxidase (HRP) enzyme was immobilized on ZnO NRs by physical adsorption technique to prepare the biosensor. In this HRP/ZnO NR/ITO bioelectrode, nafion solution was added to form a tight membrane on surface. The prepared bioelectrode has been used for biosensing measurements by electrochemical analyzer. The electrochemical studies reveal that the prepared HRP/ZnO NR/ITO biosensor is highly sensitive to the detection of H2O2 over a linear range of 0.250-10 μM. The ZnO NR-based biosensor showed lower value of detection limit (0.125 μM) and higher sensitivity (13.40 µA/µM cm2) towards H2O2. The observed value of higher sensitivity attributed to larger surface area of ZnO nanostructure for effective loading of HRP besides its high electron communication capability. In addition, the biosensor also shows lower value of enzyme's kinetic parameter (Michaelis-Menten constant, K m) of 0.262 μM which indicates enhanced enzyme affinity of HRP to H2O2. The reported biosensor may be useful for various applications in biosensing, clinical, food, and beverage industry.

  19. Effect of a glucose impulse on the CcpA regulon in Staphylococcus aureus

    Directory of Open Access Journals (Sweden)

    Engelmann Susanne

    2009-05-01

    Full Text Available Abstract Background The catabolite control protein A (CcpA is a member of the LacI/GalR family of transcriptional regulators controlling carbon-metabolism pathways in low-GC Gram-positive bacteria. It functions as a catabolite repressor or activator, allowing the bacteria to utilize the preferred carbon source over secondary carbon sources. This study is the first CcpA-dependent transcriptome and proteome analysis in Staphylococcus aureus, focussing on short-time effects of glucose under stable pH conditions. Results The addition of glucose to exponentially growing S. aureus increased the expression of genes and enzymes of the glycolytic pathway, while genes and proteins of the tricarboxylic acid (TCA cycle, required for the complete oxidation of glucose, were repressed via CcpA. Phosphotransacetylase and acetate kinase, converting acetyl-CoA to acetate with a concomitant substrate-level phosphorylation, were neither regulated by glucose nor by CcpA. CcpA directly repressed genes involved in utilization of amino acids as secondary carbon sources. Interestingly, the expression of a larger number of genes was found to be affected by ccpA inactivation in the absence of glucose than after glucose addition, suggesting that glucose-independent effects due to CcpA may have a particular impact in S. aureus. In the presence of glucose, CcpA was found to regulate the expression of genes involved in metabolism, but also that of genes coding for virulence determinants. Conclusion This study describes the CcpA regulon of exponentially growing S. aureus cells. As in other bacteria, CcpA of S. aureus seems to control a large regulon that comprises metabolic genes as well as virulence determinants that are affected in their expression by CcpA in a glucose-dependent as well as -independent manner.

  20. A comparison of the low temperature transcriptomes and CBF regulons of three plant species that differ in freezing tolerance: Solanum commersonii, Solanum tuberosum, and Arabidopsis thaliana

    OpenAIRE

    Carvallo, Marcela A.; Pino, María-Teresa; Jeknić, Zoran; Zou, Cheng; Doherty, Colleen J.; Shiu, Shin-Han; Chen, Tony H. H.; Thomashow, Michael F.

    2011-01-01

    Solanum commersonii and Solanum tuberosum are closely related plant species that differ in their abilities to cold acclimate; whereas S. commersonii increases in freezing tolerance in response to low temperature, S. tuberosum does not. In Arabidopsis thaliana, cold-regulated genes have been shown to contribute to freezing tolerance, including those that comprise the CBF regulon, genes that are controlled by the CBF transcription factors. The low temperature transcriptomes and CBF regulons of ...

  1. PecS and PecT coregulate the synthesis of HrpN and pectate lyases, two virulence determinants in Erwinia chrysanthemi 3937.

    Science.gov (United States)

    Nasser, William; Reverchon, Sylvie; Vedel, Regine; Boccara, Martine

    2005-11-01

    Erwinia chrysanthemi strain 3937 is a necrotrophic bacterial plant pathogen. Pectinolytic enzymes and, in particular, pectate lyases play a key role in soft rot symptoms; however, the efficient colonization of plants by E. chrysanthemi requires additional factors. These factors include HrpN (harpin), a heat-stable, glycine-rich hydrophilic protein, which is secreted by the type III secretion system. We investigated the expression of hrpN in E. chrysanthemi 3937 in various environmental conditions and different regulatory backgrounds. Using lacZ fusions, hrpN expression was markedly influenced by the carbon source, osmolarity, growth phase, and growth substrate. hrpN was repressed when pectinolysis started and negatively regulated by the repressors of pectate lyase synthesis, PecS and PecT. Primer extension data and in vitro DNA-protein interaction experiments support a model whereby PecS represses hrpN expression by binding to the hrpN regulatory region and inhibiting transcript elongation. The results suggest coordinated regulation of HrpN and pectate lyases by PecS and PecT. A putative model of the synthesis of these two virulence factors in E. chrysanthemi during pathogenesis is presented.

  2. Comparison of the performance of the borax buffer-based HRP-enhanced reagent and the 'Lumi-Phos 530' chemiluminescence systems in the detection of biotinylated DNA.

    Science.gov (United States)

    Cercek, B; Roby, K; Siaw, M

    1995-01-01

    A comparison of two chemiluminescence methods, the borax buffer-based HRP-enhanced reagent and Lumi-Phos 530, applied to the detection of a biotinylated 30-mer DNA slot blotted onto a nylon membrane, is presented. A streptavidin-HRP and streptavidin-ALP mediated detection system was used. The HRP-enhanced system is up to 15-fold greater with respect to the signal/background ratios than the Lumi-Phos 530 system at 0.5 microgram biotinylated DNA with at least a two-fold improvement in detection sensitivity for 0.5 ng biotinylated DNA.

  3. Lex marks the spot: the virulent side of SOS and a closer look at the LexA regulon.

    Science.gov (United States)

    Kelley, William L

    2006-12-01

    The SOS response that responds to DNA damage induces many genes that are under LexA repression. A detailed examination of LexA regulons using genome-wide techniques has recently been undertaken in both Escherichia coli and Bacillus subtilis. These extensive and elegant studies have now charted the extent of the LexA regulons, uncovered many new genes, and exposed a limited overlap in the LexA regulon between the two bacteria. As more bacterial genomes are analysed, more curiosities in LexA regulons arise. Several notable examples include the discovery of a LexA-like protein, HdiR, in Lactococcus lactis, organisms with two lexA genes, and small DNA damage-inducible cassettes under LexA control. In the cyanobacterium Synechocystis, genetic and microarray studies demonstrated that a LexA paralogue exerts control over an entirely different set of carbon-controlled genes and is crucial to cells facing carbon starvation. An examination of SOS induction evoked by common therapeutic drugs has shed new light on unsuspected consequences of drug exposure. Certain antibiotics, most notably fluoroquinolones such as ciprofloxacin, can induce an SOS response and can modulate the spread of virulence factors and drug resistance. SOS induction by beta-lactams in E. coli triggers a novel form of antibiotic defence that involves cell wall stress and signal transduction by the DpiAB two-component system. In this review, we provide an overview of these new directions in SOS and LexA research with emphasis on a few themes: identification of genes under LexA control, the identification of new endogenous triggers, and antibiotic-induced SOS response and its consequences.

  4. Optimization of Photosynthetic Productivity in Contrasting Environments by Regulons Controlling Plant Form and Function

    Directory of Open Access Journals (Sweden)

    Barbara Demmig-Adams

    2018-03-01

    Full Text Available We review the role of a family of transcription factors and their regulons in maintaining high photosynthetic performance across a range of challenging environments with a focus on extreme temperatures and water availability. Specifically, these transcription factors include CBFs (C-repeat binding factors and DREBs (dehydration-responsive element-binding, with CBF/DREB1 primarily orchestrating cold adaptation and other DREBs serving in heat, drought, and salinity adaptation. The central role of these modulators in plant performance under challenging environments is based on (i interweaving of these regulators with other key signaling networks (plant hormones and redox signals as well as (ii their function in integrating responses across the whole plant, from light-harvesting and sugar-production in the leaf to foliar sugar export and water import and on to the plant’s sugar-consuming sinks (growth, storage, and reproduction. The example of Arabidopsis thaliana ecotypes from geographic origins with contrasting climates is used to describe the links between natural genetic variation in CBF transcription factors and the differential acclimation of plant anatomical and functional features needed to support superior photosynthetic performance in contrasting environments. Emphasis is placed on considering different temperature environments (hot versus cold and light environments (limiting versus high light, on trade-offs between adaptations to contrasting environments, and on plant lines minimizing such trade-offs.

  5. Characterization and in vivo regulon determination of an ECF sigma factor and its cognate anti-sigma factor in Nostoc punctiforme.

    Science.gov (United States)

    Bell, Nicole; Lee, Jamie J; Summers, Michael L

    2017-04-01

    Based on primary sequence comparisons and genomic context, Npun_F4153 (SigG)/Npun_F4154 (SapG) of the cyanobacterium Nostoc punctiforme were hypothesized to encode an ECF sigma factor/anti-sigma factor pair. Transcription of sigG increased in heterocysts and akinetes, and after EDTA treatment. Interaction between SigG and the predicted cytoplasmic domain of SapG was observed in vitro. A SigG-GFP translational fusion protein localized to the periphery of vegetative cells in vivo, but lost this association following heat stress. A sigG mutant was unable to survive envelope damage caused by heat or EDTA, but was able to form functional heterocysts. Akinetes in the mutant strain appeared normal, but these cultures were less resistant to lysozyme and cold treatments than those of the wild-type strain. The SigG in vivo regulon was determined before and during akinete differentiation using DNA microarray analysis, and found to include multiple genes with putative association to the cell envelope. Mapped promoters common to both arrays enabled identification of a SigG promoter-binding motif that was supported in vivo by reporter studies, and in vitro by run-off transcription experiments. These findings support SigG/SapG as a sigma/anti-sigma pair involved in repair of envelope damage resulting from exogenous sources or cellular differentiation. © 2017 John Wiley & Sons Ltd.

  6. A mutant crp allele that differentially activates the operons of the fuc regulon in Escherichia coli.

    Science.gov (United States)

    Zhu, Y; Lin, E C

    1988-05-01

    L-Fucose is used by Escherichia coli through an inducible pathway mediated by a fucP-encoded permease, a fucI-encoded isomerase, a fucK-encoded kinase, and a fucA-encoded aldolase. The adolase catalyzes the formation of dihydroxyacetone phosphate and L-lactaldehyde. Anaerobically, lactaldehyde is converted by a fucO-encoded oxidoreductase to L-1,2-propanediol, which is excreted. The fuc genes belong to a regulon comprising four linked operons: fucO, fucA, fucPIK, and fucR. The positive regulator encoded by fucR responds to fuculose 1-phosphate as the effector. Mutants serially selected for aerobic growth on propanediol became constitutive in fucO and fucA [fucO(Con) fucA(Con)], but noninducible in fucPIK [fucPIK(Non)]. An external suppressor mutation that restored growth on fucose caused constitutive expression of fucPIK. Results from this study indicate that this suppressor mutation occurred in crp, which encodes the cyclic AMP-binding (or receptor) protein. When the suppressor allele (crp-201) was transduced into wild-type strains, the recipient became fucose negative and fucose sensitive (with glycerol as the carbon and energy source) because of impaired expression of fucA. The fucPIK operon became hyperinducible. The growth rate on maltose was significantly reduced, but growth on L-rhamnose, D-galactose, L-arabinose, glycerol, or glycerol 3-phosphate was close to normal. Lysogenization of fuc+ crp-201 cells by a lambda bacteriophage bearing crp+ restored normal growth ability on fucose. In contrast, lysogenization of [fucO(Con)fucA(Con)fucPIK(Non)crp-201] cells by the same phage retarded their growth on fucose.

  7. Identification and characterization of PhoP regulon members in Yersinia pestis biovar Microtus

    Directory of Open Access Journals (Sweden)

    Du Zongmin

    2008-03-01

    Full Text Available Abstract Background The transcription regulator PhoP has been shown to be important for Y. pestis survival in macrophages and under various in vitro stresses. However, the mechanism by which PhoP promotes bacterial intracellular survival is not fully understood. Our previous microarray analysis suggested that PhoP governed a wide set of cellular pathways in Y. pestis. A series of biochemical experiments were done herein to study members of the PhoP regulon of Y. pestis biovar Microtus. Results By using gel mobility shift assay and quantitative RT-PCR, a total of 30 putative transcription units were characterized as direct PhoP targets. The primer extension assay was further used to determine the transcription start sites of 18 PhoP-dependent promoters and to localize the -10 and -35 elements. The DNase I footprinting was used to identify the PhoP-binding sites within 17 PhoP-dependent promoters, enabling the identification of PhoP box and matrix that both represented the conserved signals for PhoP recognition in Y. pestis. Data presented here providing a good basis for modeling PhoP-promoter DNA interactions that is crucial to the PhoP-mediated transcriptional regulation. Conclusion The proven direct PhoP targets include nine genes encoding regulators and 21 genes or operons with functions of detoxification, protection against DNA damages, resistance to antimicrobial peptides, and adaptation to magnesium limitation. We can presume that PhoP is a global regulator that controls a complex regulatory cascade by a mechanism of not only directly controlling the expression of specific genes, but also indirectly regulating various cellular pathways by acting on a set of dedicated regulators. These results help us gain insights into the PhoP-dependent mechanisms by which Y. pestis survives the antibacterial strategies employed by host macrophages.

  8. Field evaluation of a PfHRP-2/pLDH rapid diagnostic test and light microscopy for diagnosis and screening of falciparum malaria during the peak seasonal transmission in an endemic area in Yemen.

    Science.gov (United States)

    Alareqi, Lina M Q; Mahdy, Mohammed A K; Lau, Yee-Ling; Fong, Mun-Yik; Abdul-Ghani, Rashad; Ali, Arwa A; Cheong, Fei-Wen; Tawfek, Rehab; Mahmud, Rohela

    2016-01-28

    Malaria is a public health threat in Yemen, with 149,451 cases being reported in 2013. Of these, Plasmodium falciparum represents 99%. Prompt diagnosis by light microscopy (LM) and rapid diagnostic tests (RTDs) is a key element in the national strategy of malaria control. The heterogeneous epidemiology of malaria in the country necessitates the field evaluation of the current diagnostic strategies, especially RDTs. Thus, the present study aimed to evaluate LM and an RDT, combining both P. falciparum histidine-rich protein-2 (PfHRP-2) and Plasmodium lactate dehydrogenase (pLDH), for falciparum malaria diagnosis and survey in a malaria-endemic area during the transmission season against nested polymerase chain reaction (PCR) as the reference method. A household-based, cross-sectional malaria survey was conducted in Mawza District, a malaria-endemic area in Taiz governorate. A total of 488 participants were screened using LM and PfHRP-2/pLDH RDT. Positive samples (160) and randomly selected negative samples (52) by both RDT and LM were further analysed using 18S rRNA-based nested PCR. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of the RDT were 96.0% (95% confidence interval (CI): 90.9-98.3), 56.0% (95% CI: 44.7-66.8), 76.3% (95% CI: 69.0-82.3), and 90.4% (95% CI: 78.8-96.8), respectively. On the other hand, LM showed sensitivity of 37.6% (95% CI: 29.6-46.3), specificity of 97.6% (95% CI: 91.7-99.7), PPV of 95.9% (95% CI: 86.3-98.9), and NPV of 51.3% (95% CI: 43.2-59.2). The sensitivity of LM dropped to 8.5% for detecting asymptomatic malaria. Malaria prevalence was 32.8% (32.1 and 37.5% for ≥10 and <10 years, respectively) with the RDT compared with 10.7% (10.8 and 9.4% for age groups of ≥10 and <10 years, respectively) with LM. Among asymptomatic malaria individuals, LM and RDT-based prevalence rates were 1.6 and 25.6%, respectively. However, rates of 88.2 and 94.1% of infection with P. falciparum were found

  9. Transcriptome analysis of the Dickeya dadantii PecS regulon during the early stages of interaction with Arabidopsis thaliana.

    Science.gov (United States)

    Pédron, Jacques; Chapelle, Emilie; Alunni, Benoît; Van Gijsegem, Frédérique

    2018-03-01

    PecS is one of the major global regulators controlling the virulence of Dickeya dadantii, a broad-host-range phytopathogenic bacterium causing soft rot on several plant families. To define the PecS regulon during plant colonization, we analysed the global transcriptome profiles in wild-type and pecS mutant strains during the early colonization of the leaf surfaces and in leaf tissue just before the onset of symptoms, and found that the PecS regulon consists of more than 600 genes. About one-half of these genes are down-regulated in the pecS mutant; therefore, PecS has both positive and negative regulatory roles that may be direct or indirect. Indeed, PecS also controls the regulation of a few dozen regulatory genes, demonstrating that this global regulator is at or near the top of a major regulatory cascade governing adaptation to growth in planta. Notably, PecS acts mainly at the very beginning of infection, not only to prevent virulence gene induction, but also playing an active role in the adaptation of the bacterium to the epiphytic habitat. Comparison of the patterns of gene expression inside leaf tissues and during early colonization of leaf surfaces in the wild-type bacterium revealed 637 genes modulated between these two environments. More than 40% of these modulated genes are part of the PecS regulon, emphasizing the prominent role of PecS during plant colonization. © 2017 BSPP AND JOHN WILEY & SONS LTD.

  10. Caminata del robot humanoide RH-2 en la plataforma de simulación OpenHRP

    OpenAIRE

    Torre Doblas, Carlos de

    2010-01-01

    En primer lugar, en este proyecto se trabajará con el simulador OpenHRP3, intentando comprender su funcionamiento interno (carga de archivos, lenguajes, funcionalidades, etc.). También se adaptará el modelo del robot humanoide Rh-2 al entorno del mismo, pudiendo así realizar simulaciones. La verdadera finalidad de este proyecto, y en lo que se ha hecho especial incapié, es simular el robot sosteniendo una caja, validando así las fuerzas que sienten las distintas partes del cuerpo en los momen...

  11. The Vibrio cholerae var regulon encodes a metallo-β-lactamase and an antibiotic efflux pump, which are regulated by VarR, a LysR-type transcription factor.

    Directory of Open Access Journals (Sweden)

    Hong-Ting Victor Lin

    Full Text Available The genome sequence of V. cholerae O1 Biovar Eltor strain N16961 has revealed a putative antibiotic resistance (var regulon that is predicted to encode a transcriptional activator (VarR, which is divergently transcribed relative to the putative resistance genes for both a metallo-β-lactamase (VarG and an antibiotic efflux-pump (VarABCDEF. We sought to test whether these genes could confer antibiotic resistance and are organised as a regulon under the control of VarR. VarG was overexpressed and purified and shown to have β-lactamase activity against penicillins, cephalosporins and carbapenems, having the highest activity against meropenem. The expression of VarABCDEF in the Escherichia coli (ΔacrAB strain KAM3 conferred resistance to a range of drugs, but most significant resistance was to the macrolide spiramycin. A gel-shift analysis was used to determine if VarR bound to the promoter regions of the resistance genes. Consistent with the regulation of these resistance genes, VarR binds to three distinct intergenic regions, varRG, varGA and varBC located upstream and adjacent to varG, varA and varC, respectively. VarR can act as a repressor at the varRG promoter region; whilst this repression was relieved upon addition of β-lactams, these did not dissociate the VarR/varRG-DNA complex, indicating that the de-repression of varR by β-lactams is indirect. Considering that the genomic arrangement of VarR-VarG is strikingly similar to that of AmpR-AmpC system, it is possible that V. cholerae has evolved a system for resistance to the newer β-lactams that would prove more beneficial to the bacterium in light of current selective pressures.

  12. Streptococcus mutans NADH oxidase lies at the intersection of overlapping regulons controlled by oxygen and NAD+ levels.

    Science.gov (United States)

    Baker, J L; Derr, A M; Karuppaiah, K; MacGilvray, M E; Kajfasz, J K; Faustoferri, R C; Rivera-Ramos, I; Bitoun, J P; Lemos, J A; Wen, Z T; Quivey, R G

    2014-06-01

    NADH oxidase (Nox, encoded by nox) is a flavin-containing enzyme used by the oral pathogen Streptococcus mutans to reduce diatomic oxygen to water while oxidizing NADH to NAD(+). The critical nature of Nox is 2-fold: it serves to regenerate NAD(+), a carbon cycle metabolite, and to reduce intracellular oxygen, preventing formation of destructive reactive oxygen species (ROS). As oxygen and NAD(+) have been shown to modulate the activity of the global transcription factors Spx and Rex, respectively, Nox is potentially poised at a critical junction of two stress regulons. In this study, microarray data showed that either addition of oxygen or loss of nox resulted in altered expression of genes involved in energy metabolism and transport and the upregulation of genes encoding ROS-metabolizing enzymes. Loss of nox also resulted in upregulation of several genes encoding transcription factors and signaling molecules, including the redox-sensing regulator gene rex. Characterization of the nox promoter revealed that nox was regulated by oxygen, through SpxA, and by Rex. These data suggest a regulatory loop in which the roles of nox in reduction of oxygen and regeneration of NAD(+) affect the activity levels of Spx and Rex, respectively, and their regulons, which control several genes, including nox, crucial to growth of S. mutans under conditions of oxidative stress. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  13. Analysis of the ArcA regulon in anaerobically grown Salmonella enterica sv. Typhimurium

    Directory of Open Access Journals (Sweden)

    Porwollik Steffen

    2011-03-01

    Full Text Available Abstract Background Salmonella enterica serovar Typhimurium (S. Typhimurium is a Gram-negative pathogen that must successfully adapt to the broad fluctuations in the concentration of dissolved dioxygen encountered in the host. In Escherichia coli, ArcA (Aerobic Respiratory Control helps the cells to sense and respond to the presence of dioxygen. The global role of ArcA in E. coli is well characterized; however, little is known about its role in anaerobically grown S. Typhimurium. Results We compared the transcriptional profiles of the virulent wild-type (WT strain (ATCC 14028s and its isogenic arcA mutant grown under anaerobic conditions. We found that ArcA directly or indirectly regulates 392 genes (8.5% of the genome; of these, 138 genes are poorly characterized. Regulation by ArcA in S. Typhimurium is similar, but distinct from that in E. coli. Thus, genes/operons involved in core metabolic pathways (e.g., succinyl-CoA, fatty acid degradation, cytochrome oxidase complexes, flagellar biosynthesis, motility, and chemotaxis were regulated similarly in the two organisms. However, genes/operons present in both organisms, but regulated differently by ArcA in S. Typhimurium included those coding for ethanolamine utilization, lactate transport and metabolism, and succinate dehydrogenases. Salmonella-specific genes/operons regulated by ArcA included those required for propanediol utilization, flagellar genes (mcpAC, cheV, Gifsy-1 prophage genes, and three SPI-3 genes (mgtBC, slsA, STM3784. In agreement with our microarray data, the arcA mutant was non-motile, lacked flagella, and was as virulent in mice as the WT. Additionally, we identified a set of 120 genes whose regulation was shared with the anaerobic redox regulator, Fnr. Conclusion(s We have identified the ArcA regulon in anaerobically grown S. Typhimurium. Our results demonstrated that in S. Typhimurium, ArcA serves as a transcriptional regulator coordinating cellular metabolism, flagella

  14. Common fur and mystacial vibrissae parallel sensory pathways: 14C 2-deoxyglucose and WGA-HRP studies in the rat

    International Nuclear Information System (INIS)

    Sharp, F.R.; Gonzalez, M.F.; Morgan, C.W.; Morton, M.T.; Sharp, J.W.

    1988-01-01

    Stimulation of mystacial vibrissae in rows A,B, and C increased (14C) 2-deoxyglucose (2DG) uptake in spinal trigeminal nucleus pars caudalis (Sp5c) mostly in ventral portions of laminae III-IV with less activation of II and V. Stimulation of common fur above the whiskers mainly activated lamina II, with less activation in deeper layers. The patterns of activation were compatible with an inverted head, onion skin Sp5c somatotopy. Wheatgerm Agglutinin-Horseradish Peroxidase (WGA-HRP) injections into common fur between mystacial vibrissae rows A-B and B-C led to anterograde transganglionic labeling only of Sp5c, mainly of lamina II with less label in layer V, and very sparse label in III and IV. WGA-HRP skin injections appear to primarily label small fibers, which along with larger fibers, were metabolically activated during common fur stimulation. Mystacial vibrissae stimulation increased 2DG uptake in ventral ipsilateral spinal trigeminal nuclei pars interpolaris (Sp5i) and oralis (Sp5o) and principal trigeminal sensory nucleus (Pr5). Common fur stimulation above the whiskers slightly increased 2DG uptake in ventral Sp5i, Sp5o, and possibly Pr5. The most dorsal aspect of the ventroposteromedial (VPM) nucleus of thalamus was activated contralateral to whisker stimulation. Stimulation of the common fur dorsal to the whiskers activated a region of dorsal VPM caudal to the VPM region activated during whisker stimulation. This is consistent with previous data showing that ventral whiskers and portions of the face are represented rostrally in VPM, and more dorsal whiskers and dorsal portions of the face are represented progressively more caudally in VPM. Mystacial vibrissae stimulation activated the contralateral primary sensory SI barrelfield cortex and a separate region in the second somatosensory SII cortex

  15. Anterograde axonal transport and intercellular transfer of WGA-HRP in trigeminal-innervated sensory receptors of rat incisive papilla.

    Science.gov (United States)

    Chan, K Y; Byers, M R

    1985-04-08

    The ultrastructure and identification of WGA-HRP-labeled sensory receptors in the rat incisive papilla (the most anterior part of hard palate) were studied using semiserial thin sections. Various sensory receptors were organized according to three locations: dome region (ventral), chemosensory corpuscle region (medial to orifice of incisive canal), and lateral labium (apposing the incisive canal). In the dome region, the sensory receptors were localized in three sensory zones that were associated with surface ridges (one medial and two lateral). In each of these zones, intraepithelial receptor axons and Merkel receptors occurred in the epithelium, while simple unencapsulated corpuscles, glomerular-Meissner corpuscles, and incisive (encapsulated) corpuscles occurred in the lamina propria. In the chemosensory corpuscle region, chemosensory corpuscles and intraepithelial receptor axons were located in the epithelium, and incisive corpuscles were present in the lamina propria. In the lateral labium, only intraepithelial receptor axons were prominent. In all these sensory receptors, the preterminal axons and axon terminals were labeled with the tracer protein. In addition, some nonneuronal cells closely associated with the axon terminals were selectively labeled, e.g., terminal Schwann cells, lamellar Schwann cells, Merkel cells, corpuscular basal cells and chemosensory cells. Other adjacent cells were not labeled, e.g., unspecialized epithelial cells, capsular cells, corpuscular sustentacular cells, and fibroblasts. In both labeled axons and cells, WGA-HRP was incorporated into vesicles, tubules, and vacuolar organelles. The specific intercellular transfer of tracer protein may indicate trophic interactions between axon terminals and support cells in sensory receptors. The specific organization of multiple sensory receptors in the rat incisive papilla may provide a useful alternative system for studying somatosensory physiology.

  16. Manufacturing and testing of W/Cu mono-block small scale mock-up for EAST by HIP and HRP technologies

    Energy Technology Data Exchange (ETDEWEB)

    Li, Qiang [Institute of Plasma Physics, Chinese Academy of Sciences (ASIPP), Hefei, Anhui (China); Qin, Sigui [Advanced Technology and Materials Co., Ltd, Beijing (China); Wang, Wanjing; Qi, Pan [Institute of Plasma Physics, Chinese Academy of Sciences (ASIPP), Hefei, Anhui (China); Roccella, Selanna; Visca, Eliseo [Associazione EURATOM-ENEA sulla Fusione, Frascati (Italy); Liu, Guohui [Advanced Technology and Materials Co., Ltd, Beijing (China); Luo, Guang-Nan, E-mail: liqiang577@ipp.ac.cn [Institute of Plasma Physics, Chinese Academy of Sciences (ASIPP), Hefei, Anhui (China)

    2013-10-15

    ITER-like W/Cu mono-block plasma-facing components (PFCs) will be used in vertical target regions of the experimental advanced superconducting tokamak (EAST) divertor. The first W/Cu mono-block small scale mock-up with five W mono-blocks has been manufactured successfully by technological combination of hot isostatic pressing (HIP) and hot radial pressing (HRP). The joining of a W mono-block and a pure copper interlayer was achieved by means of HIP technology and the bonding strength was over 150 MPa. The good bonding between the pure copper interlayer and a CuCrZr cooling tube was obtained by means of HRP technology. In order to understand deeply the process of HRP, the stress distribution of the mock-up during HRP process was simulated using ANSYS code. Ultrasonic Nondestructive Testing (NDT) of the W/Cu and Cu/CuCrZr interfaces was performed, showing that excellent bonding of the W/Cu and Cu/CuCrZr interfaces. The thermal cycle fatigue testing of the mock-up has been carried out by means of an e-beam device in Southwest Institute of Physics, Chengdu (SWIP) and the mock-up withstood 1000 cycles of heat loads up to 8.4 MW/m{sup 2} with the cooling water of 2 m/s, 20 °C, 0.2 MPa.

  17. Genetic variation of pfhrp2 in Plasmodium falciparum isolates from Yemen and the performance of HRP2-based malaria rapid diagnostic test.

    Science.gov (United States)

    Atroosh, Wahib M; Al-Mekhlafi, Hesham M; Al-Jasari, Adel; Sady, Hany; Al-Delaimy, Ahmed K; Nasr, Nabil A; Dawaki, Salwa; Abdulsalam, Awatif M; Ithoi, Init; Lau, Yee Ling; Fong, Mun Yik; Surin, Johari

    2015-07-22

    The genetic variation in the Plasmodium falciparum histidine-rich protein 2 (pfhrp2) gene that may compromise the use of pfhrp2-based rapid diagnostic tests (RDTs) for the diagnosis of malaria was assessed in P. falciparum isolates from Yemen. This study was conducted in Hodeidah and Al-Mahwit governorates, Yemen. A total of 622 individuals with fever were examined for malaria by CareStart malaria HRP2-RDT and Giemsa-stained thin and thick blood films. The Pfhrp2 gene was amplified and sequenced from 180 isolates, and subjected to amino acid repeat types analysis. A total of 188 (30.2%) participants were found positive for P. falciparum by the RDT. Overall, 12 different amino acid repeat types were identified in Yemeni isolates. Six repeat types were detected in all the isolates (100%) namely types 1, 2, 6, 7, 10 and 12 while types 9 and 11 were not detected in any of the isolates. Moreover, the sensitivity and specificity of the used PfHRP2-based RDTs were high (90.5% and 96.1%, respectively). The present study provides data on the genetic variation within the pfhrp2 gene, and its potential impact on the PfHRP2-based RDTs commonly used in Yemen. CareStart Malaria HRP2-based RDT showed high sensitivity and specificity in endemic areas of Yemen.

  18. Phosphoribosyl diphosphate synthetase-independent NAD de novo synthesis in Escherichia coli: a new phenotype of phosphate regulon mutants

    DEFF Research Database (Denmark)

    Hove-Jensen, Bjarne

    1996-01-01

    Phosphoribosyl diphosphate-lacking (Δprs) mutant strains of Escherichia coli require NAD, guanosine, uridine, histidine, and tryptophan for growth. NAD is required by phosphoribosyl diphosphate-lacking mutants because of lack of one of the substrates for the quinolinate phosphoribosyltransferase...... reaction, an enzyme of the NAD de novo pathway. Several NAD-independent mutants of a host from which prs had been deleted were isolated; all of them were shown to have lesions in the pstSCAB-phoU operon, in which mutations lead to derepression of the Pho regulon. In addition NAD-independent growth...... was dependent on a functional quinolinate phosphoribosyltransferase. The prs suppressor mutations led to the synthesis of a new phosphoryl compound that may act as a precursor for a new NAD biosynthetic pathway. This compound may be synthesized by the product of an unknown phosphate starvation-inducible gene...

  19. Comparative Genomics Identifies a Novel Conserved Protein, HpaT, in Proteobacterial Type III Secretion Systems that Do Not Possess the Putative Translocon Protein HrpF

    Directory of Open Access Journals (Sweden)

    Céline Pesce

    2017-06-01

    Full Text Available Xanthomonas translucens is the causal agent of bacterial leaf streak, the most common bacterial disease of wheat and barley. To cause disease, most xanthomonads depend on a highly conserved type III secretion system, which translocates type III effectors into host plant cells. Mutagenesis of the conserved type III secretion gene hrcT confirmed that the X. translucens type III secretion system is required to cause disease on the host plant barley and to trigger a non-host hypersensitive response (HR in pepper leaves. Type III effectors are delivered to the host cell by a surface appendage, the Hrp pilus, and a translocon protein complex that inserts into the plant cell plasma membrane. Homologs of the Xanthomonas HrpF protein, including PopF from Ralstonia solanacearum and NolX from rhizobia, are thought to act as a translocon protein. Comparative genomics revealed that X. translucens strains harbor a noncanonical hrp gene cluster, which rather shares features with type III secretion systems from Ralstonia solanacearum, Paraburkholderia andropogonis, Collimonas fungivorans, and Uliginosibacterium gangwonense than other Xanthomonas spp. Surprisingly, none of these bacteria, except R. solanacearum, encode a homolog of the HrpF translocon. Here, we aimed at identifying a candidate translocon from X. translucens. Notably, genomes from strains that lacked hrpF/popF/nolX instead encode another gene, called hpaT, adjacent to and co-regulated with the type III secretion system gene cluster. An insertional mutant in the X. translucens hpaT gene, which is the first gene of a two-gene operon, hpaT-hpaH, was non-pathogenic on barley and did not cause the HR or programmed cell death in non-host pepper similar to the hrcT mutant. The hpaT mutant phenotypes were partially complemented by either hpaT or the downstream gene, hpaH, which has been described as a facilitator of translocation in Xanthomonas oryzae. Interestingly, the hpaT mutant was also complemented

  20. Accuracy of PfHRP2 versus Pf-pLDH antigen detection by malaria rapid diagnostic tests in hospitalized children in a seasonal hyperendemic malaria transmission area in Burkina Faso

    OpenAIRE

    Maltha, Jessica; Guiraud, Issa; Lompo, Palpouguini; Kaboré, Bérenger; Gillet, Philippe; Van Geet, Chris; Tinto, Halidou; Jacobs, Jan

    2014-01-01

    Background In most sub-Saharan African countries malaria rapid diagnostic tests (RDTs) are now used for the diagnosis of malaria. Most RDTs used detect Plasmodium falciparum histidine-rich protein-2 (PfHRP2), though P. falciparum-specific parasite lactate dehydrogenase (Pf-pLDH)-detecting RDTs may have advantages over PfHRP2-detecting RDTs. Only few data are available on the use of RDTs in severe illness and the present study compared Pf-pLDH to PfHRP2-detection. Methods Hospitalized children...

  1. Genome-wide analysis of the Pho regulon in a pstCA mutant of Citrobacter rodentium.

    Directory of Open Access Journals (Sweden)

    Catherine Cheng

    Full Text Available The phosphate-specific transport operon, pstSCAB-phoU, of Gram-negative bacteria is an essential part of the Pho regulon. Its key roles are to encode a high-affinity inorganic phosphate transport system and to prevent activation of PhoB in phosphate-rich environments. In general, mutations in pstSCAB-phoU lead to the constitutive expression of the Pho regulon. Previously, we constructed a pstCA deletion mutant of Citrobacter rodentium and found it to be attenuated for virulence in mice, its natural host. This attenuation was dependent on PhoB or PhoB-regulated gene(s because a phoB mutation restored virulence for mice to the pstCA mutant. To investigate how downstream genes may contribute to the virulence of C. rodentium, we used microarray analysis to investigate global gene expression of C. rodentium strain ICC169 and its isogenic pstCA mutant when grown in phosphate-rich medium. Overall 323 genes of the pstCA mutant were differentially expressed by at least 1.5-fold compared to the wild-type C. rodentium. Of these 145 were up-regulated and 178 were down-regulated. Differentially expressed genes included some involved in phosphate homoeostasis, cellular metabolism and protein metabolism. A large number of genes involved in stress responses and of unknown function were also differentially expressed, as were some virulence-associated genes. Up-regulated virulence-associated genes in the pstCA mutant included that for DegP, a serine protease, which appeared to be directly regulated by PhoB. Down-regulated genes included those for the production of the urease, flagella, NleG8 (a type III-secreted protein and the tad focus (which encodes type IVb pili in Yersinia enterocolitica. Infection studies using C57/BL6 mice showed that DegP and NleG8 play a role in bacterial virulence. Overall, our study provides evidence that Pho is a global regulator of gene expression in C. rodentium and indicates the presence of at least two previously unrecognized

  2. A Novel Conductive Poly(3,4-ethylenedioxythiophene-BSA Film for the Construction of a Durable HRP Biosensor Modified with NanoAu Particles

    Directory of Open Access Journals (Sweden)

    Fangcheng Xu

    2016-03-01

    Full Text Available In this study, we have investigated the contribution of bovine serum albumin (BSA to the durability of the electrochemically synthesized poly(3,4-ethylenedioxythiophene (PEDOT film on a platinum (Pt electrode. The electrode was capable to effectively adsorb the nano Au particles (AuNPs to form a uniform layout, which was then able to immobilize the horseradish peroxidase (HRP to construct a functional HRP/AuNPs/PEDOT(BSA/Pt biosensor. Cyclic voltammetry was employed to evaluate the performance of the biosensor through the measurement of hydrogen peroxide. Our results revealed a satisfied linear correlation between the cathodic current and the concentration of H2O2. Furthermore, the addition of oxidized form of nicotinamide adenine dinucleotide, or NAD+, as the electron transfer mediator in the detection solution could dramatically enhance the sensitivity of detection by about 35.5%. The main advantages of the current biosensor are its durability, sensitivity, reliability, and biocompatibility.

  3. Horseradish Peroxidase (HRP Immobilized Poly(aniline-co-m-aminophenol Film Electrodes–fabrication and Evaluation as Hydrogen Peroxide Sensor

    Directory of Open Access Journals (Sweden)

    Seong-Ho Choi

    2007-05-01

    Full Text Available Enzyme modified electrodes were fabricated with poly(aniline-co-m-aminophenol. Electrochemical polymerization of aniline and m-aminophenol wasperformed to get the film of copolymer on the surface of gold electrode. Modifiedelectrodes were fabricated by two methods, physical entrapment and covalent cross-linking.In one of the method, gold nanoparticles were loaded into the copolymer film andhorseradish peroxidase (HRP was immobilized into the Au nanoparticle loaded copolymerfilm through physical entrapment. In the other method, the amino and -OH groups in thecopolymer are utilized to form covalent functionalization with HRP via glutaric dialdehydeas cross-linker/mediator. The conducting copolymer/enzyme modified electrodes preparedby physical entrapment/covalent functionalization of enzyme were tested forelectrocatalytic activities towards sensing of H2O2. Amperometric results indicate thatenzyme modified electrode via physical entrapment possesses better electrocatalyticperformance over covalent functionalized enzyme electrode.

  4. Use of HRP-2-based rapid diagnostic test for Plasmodium falciparum malaria: assessing accuracy and cost-effectiveness in the villages of Dielmo and Ndiop, Senegal

    Directory of Open Access Journals (Sweden)

    Trape Jean-François

    2010-06-01

    Full Text Available Abstract Background In 2006, the Senegalese National Malaria Control Programme (NMCP has recommended artemisinin-based combination therapy (ACT as the first-line treatment for uncomplicated malaria and, in 2007, mandated testing for all suspected cases of malaria with a Plasmodium falciparum HRP-2-based rapid diagnostic test for malaria (RDT(Paracheck®. Given the higher cost of ACT compared to earlier anti-malarials, the objectives of the present study were i to study the accuracy of Paracheck® compared to the thick blood smear (TBS in two areas with different levels of malaria endemicity and ii analyse the cost-effectiveness of the strategy of the parasitological confirmation of clinically suspected malaria cases management recommended by the NMCP. Methods A cross-sectional study was undertaken in the villages of Dielmo and Ndiop (Senegal nested in a cohort study of about 800 inhabitants. For all the individuals consulting between October 2008 and January 2009 with a clinical diagnosis of malaria, a questionnaire was filled and finger-prick blood samples were taken both for microscopic examination and RDT. The estimated costs and cost-effectiveness analysis were made considering five scenarios, the recommendations of the NMCP being the reference scenario. In addition, a sensitivity analysis was performed assuming that all the RDT-positive patients and 50% of RDT-negative patients were treated with ACT. Results A total of 189 consultations for clinically suspected malaria occurred during the study period. The sensitivity, specificity, positive and negative predictive values were respectively 100%, 98.3%, 80.0% and 100%. The estimated cost of the reference scenario was close to 700€ per 1000 episodes of illness, approximately twice as expensive as most of the other scenarios. Nevertheless, it appeared to us cost-effective while ensuring the diagnosis and the treatment of 100% of malaria attacks and an adequate management of 98.4% of episodes

  5. Use of HRP-2-based rapid diagnostic test for Plasmodium falciparum malaria: assessing accuracy and cost-effectiveness in the villages of Dielmo and Ndiop, Senegal.

    Science.gov (United States)

    Ly, Alioune Badara; Tall, Adama; Perry, Robert; Baril, Laurence; Badiane, Abdoulaye; Faye, Joseph; Rogier, Christophe; Touré, Aissatou; Sokhna, Cheikh; Trape, Jean-François; Michel, Rémy

    2010-06-04

    In 2006, the Senegalese National Malaria Control Programme (NMCP) has recommended artemisinin-based combination therapy (ACT) as the first-line treatment for uncomplicated malaria and, in 2007, mandated testing for all suspected cases of malaria with a Plasmodium falciparum HRP-2-based rapid diagnostic test for malaria (RDT(Paracheck). Given the higher cost of ACT compared to earlier anti-malarials, the objectives of the present study were i) to study the accuracy of Paracheck compared to the thick blood smear (TBS) in two areas with different levels of malaria endemicity and ii) analyse the cost-effectiveness of the strategy of the parasitological confirmation of clinically suspected malaria cases management recommended by the NMCP. A cross-sectional study was undertaken in the villages of Dielmo and Ndiop (Senegal) nested in a cohort study of about 800 inhabitants. For all the individuals consulting between October 2008 and January 2009 with a clinical diagnosis of malaria, a questionnaire was filled and finger-prick blood samples were taken both for microscopic examination and RDT. The estimated costs and cost-effectiveness analysis were made considering five scenarios, the recommendations of the NMCP being the reference scenario. In addition, a sensitivity analysis was performed assuming that all the RDT-positive patients and 50% of RDT-negative patients were treated with ACT. A total of 189 consultations for clinically suspected malaria occurred during the study period. The sensitivity, specificity, positive and negative predictive values were respectively 100%, 98.3%, 80.0% and 100%. The estimated cost of the reference scenario was close to 700 euros per 1000 episodes of illness, approximately twice as expensive as most of the other scenarios. Nevertheless, it appeared to us cost-effective while ensuring the diagnosis and the treatment of 100% of malaria attacks and an adequate management of 98.4% of episodes of illness. The present study also demonstrated

  6. The cytoskeleton is disrupted by the bacterial effector HrpZ, but not by the bacterial PAMP flg22, in tobacco BY-2 cells.

    Science.gov (United States)

    Guan, Xin; Buchholz, Günther; Nick, Peter

    2013-04-01

    Plant innate immunity is composed of two layers. Basal immunity is triggered by pathogen-associated molecular patterns (PAMPs) such as the flagellin-peptide flg22 and is termed PAMP-triggered immunity (PTI). In addition, effector-triggered immunity (ETI) linked with programmed cell death and cytoskeletal reorganization can be induced by pathogen-derived factors, such as the Harpin proteins originating from phytopathogenic bacteria. To get insight into the link between cytoskeleton and PTI or ETI, this study followed the responses of actin filaments and microtubules to flg22 and HrpZ in vivo by spinning-disc confocal microscopy in GFP-tagged marker lines of tobacco BY-2. At a concentration that clearly impairs mitosis, flg22 can induce only subtle cytoskeletal responses. In contrast, HrpZ causes a rapid and massive bundling of actin microfilaments (completed in ~20 min, i.e. almost simultaneously with extracellular alkalinization), which is followed by progressive disintegration of actin cables and cytoplasmic microtubules, a loss of cytoplasmic structure, and vacuolar disintegration. Cytoskeletal disruption is proposed as an early event that discriminates HrpZ-triggered ETI-like defence from flg22-triggered PTI.

  7. Influencia del Estado de Oxidación del Ión Cobalto en la Estabilidad de Electrodos Modificados con Monocapas SAM-TOA-ANTA-Con+-HRP-NHis.

    Directory of Open Access Journals (Sweden)

    Pedro R. Matheus*

    Full Text Available Influence of state oxidation of cobalt ion in the stability electrodes modified with monolayers SAM-TOA-ANTA-Con+-HRP-NHis. Quartz Crystal Microbalance (QCM was used to investigate the adsorption of the HRP-NHis enzyme (horseradish peroxidase, which was modified by the addition of a tail of six histidine on its extreme N-terminal. The QCM operating at flow of 0.025 mL min-1 on a crystal whose gold electrode was modified with monolayers of SAM-TOA-ANTA-Co2+ and SAM-TOA-ANTA -Co3+. The oxidize form was obtained from the electrochemical oxidation of a monolayer of SAM-TOA-ANTA-Co2+. The results suggest that the HRP-NHis is attached to both monolayers in a similar way; on the contrary, the desortion of the attached protein is dramatically different. Thus, whereas the ligand-Co2+ bonds are reversible, which allows that the anchored protein is easily replaced by imidazol molecules. The 3+ oxidation state of the metal does not allow the interchange of protein by the imidazol molecules.

  8. A survey of Type III restriction-modification systems reveals numerous, novel epigenetic regulators controlling phase-variable regulons; phasevarions

    Science.gov (United States)

    Atack, John M; Yang, Yuedong; Jennings, Michael P

    2018-01-01

    Abstract Many bacteria utilize simple DNA sequence repeats as a mechanism to randomly switch genes on and off. This process is called phase variation. Several phase-variable N6-adenine DNA-methyltransferases from Type III restriction-modification systems have been reported in bacterial pathogens. Random switching of DNA methyltransferases changes the global DNA methylation pattern, leading to changes in gene expression. These epigenetic regulatory systems are called phasevarions — phase-variable regulons. The extent of these phase-variable genes in the bacterial kingdom is unknown. Here, we interrogated a database of restriction-modification systems, REBASE, by searching for all simple DNA sequence repeats in mod genes that encode Type III N6-adenine DNA-methyltransferases. We report that 17.4% of Type III mod genes (662/3805) contain simple sequence repeats. Of these, only one-fifth have been previously identified. The newly discovered examples are widely distributed and include many examples in opportunistic pathogens as well as in environmental species. In many cases, multiple phasevarions exist in one genome, with examples of up to 4 independent phasevarions in some species. We found several new types of phase-variable mod genes, including the first example of a phase-variable methyltransferase in pathogenic Escherichia coli. Phasevarions are a common epigenetic regulation contingency strategy used by both pathogenic and non-pathogenic bacteria. PMID:29554328

  9. Listeria monocytogenes differential transcriptome analysis reveals temperature-dependent Agr regulation and suggests overlaps with other regulons.

    Science.gov (United States)

    Garmyn, Dominique; Augagneur, Yoann; Gal, Laurent; Vivant, Anne-Laure; Piveteau, Pascal

    2012-01-01

    Listeria monocytogenes is a ubiquitous, opportunistic pathogenic organism. Environmental adaptation requires constant regulation of gene expression. Among transcriptional regulators, AgrA is part of an auto-induction system. Temperature is an environmental cue critical for in vivo adaptation. In order to investigate how temperature may affect AgrA-dependent transcription, we compared the transcriptomes of the parental strain L. monocytogenes EGD-e and its ΔagrA mutant at the saprophytic temperature of 25°C and in vivo temperature of 37°C. Variations of transcriptome were higher at 37°C than at 25°C. Results suggested that AgrA may be involved in the regulation of nitrogen transport, amino acids, purine and pyrimidine biosynthetic pathways and phage-related functions. Deregulations resulted in a growth advantage at 37°C, but affected salt tolerance. Finally, our results suggest overlaps with PrfA, σB, σH and CodY regulons. These overlaps may suggest that through AgrA, Listeria monocytogenes integrates information on its biotic environment.

  10. Divergent regulation of CBF regulon on cold tolerance and plant phenotype in cassava overexpressing Arabidopsis CBF3 gene

    Directory of Open Access Journals (Sweden)

    Dong An

    2016-12-01

    Full Text Available Cassava is a tropical origin plant that is sensitive to chilling stress. In order to understand the CBF cold response pathway, a well-recognized regulatory mechanism in temperate plants, in cassava, overexpression of an Arabidopsis CBF3 gene is studied. This gene renders cassava increasingly tolerant to cold and drought stresses but is associated with retarded plant growth, leaf curling, reduced storage root yield, and reduced anthocyanin accumulation in a transcript abundance-dependent manner. Physiological analysis revealed that the transgenic cassava increased proline accumulation, reduced malondialdehyde production, and electrolyte leakage under cold stress. These transgenic lines also showed high relative water content when faced with drought. The expression of partial CBF-targeted genes in response to cold displayed temporal and spatial variations in the wild-type and transgenic plants: highly inducible in leaves and less altered in apical buds. In addition, anthocyanin accumulation was inhibited by downregulating the expression of genes involved in its biosynthesis and by interplaying between the CBF3 and the endogenous transcription factors. Thus, the heterologous CBF3 modulates the expression of stress-related genes and carries out a series of physiological adjustments under stressful conditions, showing a varied regulation pattern of CBF regulon from that of cassava CBFs.

  11. Computational prediction of cAMP receptor protein (CRP binding sites in cyanobacterial genomes

    Directory of Open Access Journals (Sweden)

    Su Zhengchang

    2009-01-01

    Full Text Available Abstract Background Cyclic AMP receptor protein (CRP, also known as catabolite gene activator protein (CAP, is an important transcriptional regulator widely distributed in many bacteria. The biological processes under the regulation of CRP are highly diverse among different groups of bacterial species. Elucidation of CRP regulons in cyanobacteria will further our understanding of the physiology and ecology of this important group of microorganisms. Previously, CRP has been experimentally studied in only two cyanobacterial strains: Synechocystis sp. PCC 6803 and Anabaena sp. PCC 7120; therefore, a systematic genome-scale study of the potential CRP target genes and binding sites in cyanobacterial genomes is urgently needed. Results We have predicted and analyzed the CRP binding sites and regulons in 12 sequenced cyanobacterial genomes using a highly effective cis-regulatory binding site scanning algorithm. Our results show that cyanobacterial CRP binding sites are very similar to those in E. coli; however, the regulons are very different from that of E. coli. Furthermore, CRP regulons in different cyanobacterial species/ecotypes are also highly diversified, ranging from photosynthesis, carbon fixation and nitrogen assimilation, to chemotaxis and signal transduction. In addition, our prediction indicates that crp genes in modern cyanobacteria are likely inherited from a common ancestral gene in their last common ancestor, and have adapted various cellular functions in different environments, while some cyanobacteria lost their crp genes as well as CRP binding sites during the course of evolution. Conclusion The CRP regulons in cyanobacteria are highly diversified, probably as a result of divergent evolution to adapt to various ecological niches. Cyanobacterial CRPs may function as lineage-specific regulators participating in various cellular processes, and are important in some lineages. However, they are dispensable in some other lineages. The

  12. ENCAPSULATION OF HORSERADISH PEROXIDASE-GLUCOSE OXIDASE (HRP-GOx IN SILICA AQUAGEL SYNTHESIZED FROM RICE HULL ASH FOR ENZYMATIC REACTION OF GLUCOSE

    Directory of Open Access Journals (Sweden)

    Nuryono Nuryono

    2010-06-01

    Full Text Available In recent years, the sol-gel technique has attracted increasing interest as a unique approach to immobilize biomolecules for bioanalytical applications as well as biochemical and biophysical studies. In this research, encapsulation of Horseradish peroxidase-Glucose oxidase (HRP-GOx enzymes in silica aquagel from rice hull ash by sol-gel process has been carried out. In addition, the effect of several parameters (weight ratio of HRP to GOx, pH, temperature, sodium ion concentration on enzyme activity was studied, as well. Rice hull ash, which was produced by ashing at 700 °C, was extracted it's silika by NaOH solution 1 M at 100 °C for two hours to produce sodium silikate (Na2SiO3 solution. The Na2SiO3 solution with pH of 13 was added with a strong cation exchanger resin, to produce sol solution with the pH of 4. Encapsulation was emphasized by mixing sol solution and phosphate buffer pH 7 containing HRP-GOx solution at volume ratio of buffer to sol solution 1:5. The mixture was transferred into 96-microwell plate and was aged for 24 hours. Enzymatic reaction was carried out by adding chromogenic solution of phenol and 4-aminoantipyrine (4-AAP and b-D-glucose solution (as substrate into the microwell. Enzymatic activity was examined by measuring absorbance of product solution at 490 nm with ELISA reader. Result of enzymatic activity for encapsulated enzymes (SGE was compared to that for free enzymes (EB. Results showed that at the investigated condition, HRP-GOx enzymes gave high activity at weight ratio of HRP to GOx 10:1 and pH 7 for both SGE and EB. Encapsulation caused the enzymes activity decrease to 53.0±0.2 %. However, SGE was observed to be more stable on pH and temperature changes than EB. Study on the effect of sodium concentration showed that the increase of sodium concentration from 0.10 to 0.37 M decreased the enzymatic activity to 56±0.2%. Reusability test showed that the synthesized SGE was reusable with activity decrease of 60

  13. Effect of BMI and body weight on pregnancy rates with LNG as emergency contraception: analysis of four WHO HRP studies.

    Science.gov (United States)

    Festin, Mario Philip R; Peregoudov, Alexandre; Seuc, Armando; Kiarie, James; Temmerman, Marleen

    2017-01-01

    To estimate the effect of increased body weight and body mass index (BMI) on pregnancy rates with levonorgestrel (LNG) 1.5mg used as emergency contraception (EC). The study reviewed data from 6873 women in four WHO-HRP randomized trials on EC conducted between 1993 and 2010. Participants took either 1.5mg of LNG as a single dose or in two doses 12h apart, up to 120h of unprotected intercourse. Contraceptive efficacy (pregnancy rates) at different weight and BMI categories was evaluated. Overall pregnancy rate was low at 1.2%. Pregnancy rates were also low in women weighing over 80kg (0.7%) and who were obese (BMI over 30kg/m 2 ) (2.0%). The pooled analyses for pregnancy demonstrated that BMI over 30kg/m 2 decreased efficacy significantly (odds ratio 8.27, 95% confidence interval = 2.70-25.37) when compared to women in lower BMI categories, mainly influenced by pregnancies in obese women from one study site. Sensitivity analyses excluding that site showed that obesity was no longer a risk factor; however, the other studies included too few obese women in the sample to exclude a substantial decrease in efficacy. Pregnancy rates with use of LNG 1.5mg for EC were low at less than 3% across different weight and BMI categories. Pooled analyses showed an increase in pregnancy rates among obese women (BMI more than 30kg/m 2 ) compared to women with normal BMI levels, influenced by pregnancies all coming from one study site. Access to LNG as EC should still be promoted to women who need them, and not be restricted in any weight or BMI category, with additional attention for counselling and advice for obese women. Copyright © 2016. Published by Elsevier Inc.

  14. Proposed megakaryocytic regulon of p53: the genes engaged to control cell cycle and apoptosis during megakaryocytic differentiation

    Science.gov (United States)

    Apostolidis, Pani A.; Lindsey, Stephan; Miller, William M.

    2012-01-01

    During endomitosis, megakaryocytes undergo several rounds of DNA synthesis without division leading to polyploidization. In primary megakaryocytes and in the megakaryocytic cell line CHRF, loss or knock-down of p53 enhances cell cycling and inhibits apoptosis, leading to increased polyploidization. To support the hypothesis that p53 suppresses megakaryocytic polyploidization, we show that stable expression of wild-type p53 in K562 cells (a p53-null cell line) attenuates the cells' ability to undergo polyploidization during megakaryocytic differentiation due to diminished DNA synthesis and greater apoptosis. This suggested that p53's effects during megakaryopoiesis are mediated through cell cycle- and apoptosis-related target genes, possibly by arresting DNA synthesis and promoting apoptosis. To identify candidate genes through which p53 mediates these effects, gene expression was compared between p53 knock-down (p53-KD) and control CHRF cells induced to undergo terminal megakaryocytic differentiation using microarray analysis. Among substantially downregulated p53 targets in p53-KD megakaryocytes were cell cycle regulators CDKN1A (p21) and PLK2, proapoptotic FAS, TNFRSF10B, CASP8, NOTCH1, TP53INP1, TP53I3, DRAM1, ZMAT3 and PHLDA3, DNA-damage-related RRM2B and SESN1, and actin component ACTA2, while antiapoptotic CKS1B, BCL2, GTSE1, and p53 family member TP63 were upregulated in p53-KD cells. Additionally, a number of cell cycle-related, proapoptotic, and cytoskeleton-related genes with known functions in megakaryocytes but not known to carry p53-responsive elements were differentially expressed between p53-KD and control CHRF cells. Our data support a model whereby p53 expression during megakaryopoiesis serves to control polyploidization and the transition from endomitosis to apoptosis by impeding cell cycling and promoting apoptosis. Furthermore, we identify a putative p53 regulon that is proposed to orchestrate these effects. PMID:22548738

  15. The new pLAI (lux regulon based auto-inducible expression system for recombinant protein production in Escherichia coli

    Directory of Open Access Journals (Sweden)

    Nocadello Salvatore

    2012-01-01

    Full Text Available Abstract Background After many years of intensive research, it is generally assumed that no universal expression system can exist for high-level production of a given recombinant protein. Among the different expression systems, the inducible systems are the most popular for their tight regulation. However, induction is in many cases less favorable due to the high cost and/or toxicity of inducers, incompatibilities with industrial scale-up or detrimental growth conditions. Expression systems using autoinduction (or self-induction prove to be extremely versatile allowing growth and induction of recombinant proteins without the need to monitor cell density or add inducer. Unfortunately, almost all the actual auto inducible expression systems need endogenous or induced metabolic changes during the growth to trigger induction, both frequently linked to detrimental condition to cell growth. In this context, we use a simple modular approach for a cell density-based genetic regulation in order to assemble an autoinducible recombinant protein expression system in E. coli. Result The newly designed pLAI expression system places the expression of recombinant proteins in Escherichia coli under control of the regulatory genes of the lux regulon of Vibrio fischeri's Quorum Sensing (QS system. The pLAI system allows a tight regulation of the recombinant gene allowing a negligible basal expression and expression only at high cell density. Sequence optimization of regulative genes of QS of V. fischeri for expression in E. coli upgraded the system to high level expression. Moreover, partition of regulative genes between the plasmid and the host genome and introduction of a molecular safety lock permitted tighter control of gene expression. Conclusion Coupling gene expression to cell density using cell-to-cell communication provides a promising approach for recombinant protein production. The system allows the control of expression of the target recombinant gene

  16. Comprehensive Definition of the SigH Regulon of Mycobacterium tuberculosis Reveals Transcriptional Control of Diverse Stress Responses.

    Directory of Open Access Journals (Sweden)

    Jared D Sharp

    Full Text Available Expression of SigH, one of 12 Mycobacterium tuberculosis alternative sigma factors, is induced by heat, oxidative and nitric oxide stresses. SigH activation has been shown to increase expression of several genes, including genes involved in maintaining redox equilibrium and in protein degradation. However, few of these are known to be directly regulated by SigH. The goal of this project is to comprehensively define the Mycobacterium tuberculosis genes and operons that are directly controlled by SigH in order to gain insight into the role of SigH in regulating M. tuberculosis physiology. We used ChIP-Seq to identify in vivo SigH binding sites throughout the M. tuberculosis genome, followed by quantification of SigH-dependent expression of genes linked to these sites and identification of SigH-regulated promoters. We identified 69 SigH binding sites, which are located both in intergenic regions and within annotated coding sequences in the annotated M. tuberculosis genome. 41 binding sites were linked to genes that showed greater expression following heat stress in a SigH-dependent manner. We identified several genes not previously known to be regulated by SigH, including genes involved in DNA repair, cysteine biosynthesis, translation, and genes of unknown function. Experimental and computational analysis of SigH-regulated promoter sequences within these binding sites identified strong consensus -35 and -10 promoter sequences, but with tolerance for non-consensus bases at specific positions. This comprehensive identification and validation of SigH-regulated genes demonstrates an extended SigH regulon that controls an unexpectedly broad range of stress response functions.

  17. Comprehensive Definition of the SigH Regulon of Mycobacterium tuberculosis Reveals Transcriptional Control of Diverse Stress Responses.

    Science.gov (United States)

    Sharp, Jared D; Singh, Atul K; Park, Sang Tae; Lyubetskaya, Anna; Peterson, Matthew W; Gomes, Antonio L C; Potluri, Lakshmi-Prasad; Raman, Sahadevan; Galagan, James E; Husson, Robert N

    2016-01-01

    Expression of SigH, one of 12 Mycobacterium tuberculosis alternative sigma factors, is induced by heat, oxidative and nitric oxide stresses. SigH activation has been shown to increase expression of several genes, including genes involved in maintaining redox equilibrium and in protein degradation. However, few of these are known to be directly regulated by SigH. The goal of this project is to comprehensively define the Mycobacterium tuberculosis genes and operons that are directly controlled by SigH in order to gain insight into the role of SigH in regulating M. tuberculosis physiology. We used ChIP-Seq to identify in vivo SigH binding sites throughout the M. tuberculosis genome, followed by quantification of SigH-dependent expression of genes linked to these sites and identification of SigH-regulated promoters. We identified 69 SigH binding sites, which are located both in intergenic regions and within annotated coding sequences in the annotated M. tuberculosis genome. 41 binding sites were linked to genes that showed greater expression following heat stress in a SigH-dependent manner. We identified several genes not previously known to be regulated by SigH, including genes involved in DNA repair, cysteine biosynthesis, translation, and genes of unknown function. Experimental and computational analysis of SigH-regulated promoter sequences within these binding sites identified strong consensus -35 and -10 promoter sequences, but with tolerance for non-consensus bases at specific positions. This comprehensive identification and validation of SigH-regulated genes demonstrates an extended SigH regulon that controls an unexpectedly broad range of stress response functions.

  18. Diverse Genetic Regulon of the Virulence-Associated Transcriptional Regulator MucR in Brucella abortus 2308

    Science.gov (United States)

    Caswell, Clayton C.; Elhassanny, Ahmed E. M.; Planchin, Emilie E.; Roux, Christelle M.; Weeks-Gorospe, Jenni N.; Ficht, Thomas A.; Dunman, Paul M.

    2013-01-01

    The Ros-type regulator MucR is one of the few transcriptional regulators that have been linked to virulence in Brucella. Here, we show that a Brucella abortus in-frame mucR deletion strain exhibits a pronounced growth defect during in vitro cultivation and, more importantly, that the mucR mutant is attenuated in cultured macrophages and in mice. The genetic basis for the attenuation of Brucella mucR mutants has not been defined previously, but in the present study the genes regulated by MucR in B. abortus have been elucidated using microarray analysis and real-time reverse transcription-PCR (RT-PCR). In B. abortus 2308, MucR regulates a wide variety of genes whose products may function in establishing and maintaining cell envelope integrity, polysaccharide biosynthesis, iron homeostasis, genome plasticity, and transcriptional regulation. Particularly notable among the MucR-regulated genes identified is arsR6 (nolR), which encodes a transcriptional regulator previously linked to virulence in Brucella melitensis 16 M. Importantly, electrophoretic mobility shift assays (EMSAs) determined that a recombinant MucR protein binds directly to the promoter regions of several genes repressed by MucR (including arsR6 [nolR]), and in Brucella, as in other alphaproteobacteria, MucR binds to its own promoter to repress expression of the gene that encodes it. Overall, these studies have uncovered the diverse genetic regulon of MucR in Brucella, and in doing so this work has begun to define the MucR-controlled genetic circuitry whose misregulation contributes to the virulence defect of Brucella mucR mutants. PMID:23319565

  19. Cysteine-mediated gene expression and characterization of the CmbR regulon in Streptococcus pneumoniae

    Directory of Open Access Journals (Sweden)

    Muhammad Afzal

    2016-12-01

    Full Text Available In this study, we investigated the transcriptomic response of Streptococcus pneumoniae D39 to cysteine. Transcriptome comparison of the D39 wild-type strain grown at a restricted concentration of cysteine (0.03 mM to one grown at a high concentration of cysteine (50 mM in chemically-define medium (CDM revealed elevated expression of various genes/operons, i.e. spd-0150, metQ, spd-0431, metEF, gshT, spd-0618, fhs, tcyB, metB-csd, metA, spd-1898, yvdE, and cysK, likely to be involved in the transport and utilization of cysteine and/or methionine. Microarray-based data were further confirmed by quantitative RT-PCR. Promoter lacZ-fusion studies and quantitative RT-PCR data showed that the transcriptional regulator CmbR acts as a transcriptional repressor of spd-0150, metEF, gshT, spd-0618, tcyB, metA, and yvdE, putatively involved in cysteine uptake and utilization. The operator site of CmbR in the promoter regions of CmbR-regulated genes is predicted and confirmed by mutating or deleting CmbR operator sites from the promoter regions of these genes.

  20. Global Analysis of the Burkholderia thailandensis Quorum Sensing-Controlled Regulon

    Science.gov (United States)

    Majerczyk, Charlotte; Brittnacher, Mitchell; Jacobs, Michael; Armour, Christopher D.; Radey, Mathew; Schneider, Emily; Phattarasokul, Somsak; Bunt, Richard

    2014-01-01

    Burkholderia thailandensis contains three acyl-homoserine lactone quorum sensing circuits and has two additional LuxR homologs. To identify B. thailandensis quorum sensing-controlled genes, we carried out transcriptome sequencing (RNA-seq) analyses of quorum sensing mutants and their parent. The analyses were grounded in the fact that we identified genes coding for factors shown previously to be regulated by quorum sensing among a larger set of quorum-controlled genes. We also found that genes coding for contact-dependent inhibition were induced by quorum sensing and confirmed that specific quorum sensing mutants had a contact-dependent inhibition defect. Additional quorum-controlled genes included those for the production of numerous secondary metabolites, an uncharacterized exopolysaccharide, and a predicted chitin-binding protein. This study provides insights into the roles of the three quorum sensing circuits in the saprophytic lifestyle of B. thailandensis, and it provides a foundation on which to build an understanding of the roles of quorum sensing in the biology of B. thailandensis and the closely related pathogenic Burkholderia pseudomallei and Burkholderia mallei. PMID:24464461

  1. Global analysis of the Burkholderia thailandensis quorum sensing-controlled regulon.

    Science.gov (United States)

    Majerczyk, Charlotte; Brittnacher, Mitchell; Jacobs, Michael; Armour, Christopher D; Radey, Mathew; Schneider, Emily; Phattarasokul, Somsak; Bunt, Richard; Greenberg, E Peter

    2014-04-01

    Burkholderia thailandensis contains three acyl-homoserine lactone quorum sensing circuits and has two additional LuxR homologs. To identify B. thailandensis quorum sensing-controlled genes, we carried out transcriptome sequencing (RNA-seq) analyses of quorum sensing mutants and their parent. The analyses were grounded in the fact that we identified genes coding for factors shown previously to be regulated by quorum sensing among a larger set of quorum-controlled genes. We also found that genes coding for contact-dependent inhibition were induced by quorum sensing and confirmed that specific quorum sensing mutants had a contact-dependent inhibition defect. Additional quorum-controlled genes included those for the production of numerous secondary metabolites, an uncharacterized exopolysaccharide, and a predicted chitin-binding protein. This study provides insights into the roles of the three quorum sensing circuits in the saprophytic lifestyle of B. thailandensis, and it provides a foundation on which to build an understanding of the roles of quorum sensing in the biology of B. thailandensis and the closely related pathogenic Burkholderia pseudomallei and Burkholderia mallei.

  2. Role of the Fur regulon in iron transport in Bacillus subtilis.

    Science.gov (United States)

    Ollinger, Juliane; Song, Kyung-Bok; Antelmann, Haike; Hecker, Michael; Helmann, John D

    2006-05-01

    The Bacillus subtilis ferric uptake regulator (Fur) protein mediates the iron-dependent repression of at least 20 operons encoding approximately 40 genes. We investigated the physiological roles of Fur-regulated genes by the construction of null mutations in 14 transcription units known or predicted to function in siderophore biosynthesis or iron uptake. We demonstrate that ywbLMN, encoding an elemental iron uptake system orthologous to the copper oxidase-dependent Fe(III) uptake system of Saccharomyces cerevisiae, is essential for growth in low iron minimal medium lacking citric acid. 2,3-Dihydroxybenzoyl-glycine (Itoic acid), the siderophore precursor produced by laboratory strains of B. subtilis, is of secondary importance. In the presence of citrate, the YfmCDEF ABC transporter is required for optimal growth. B. subtilis is unable to grow in minimal medium containing the iron chelator EDDHA unless the ability to synthesize the intact bacillibactin siderophore is restored (by the introduction of a functional sfp gene) or exogenous siderophores are provided. Utilization of the catecholate siderophores bacillibactin and enterobactin requires the FeuABC importer and the YusV ATPase. Utilization of hydroxamate siderophores requires the FhuBGC ABC transporter together with the FhuD (ferrichrome) or YxeB (ferrioxamine) substrate-binding proteins. Growth with schizokinen or arthrobactin is at least partially dependent on the YfhA YfiYZ importer and the YusV ATPase. We have also investigated the effects of a fur mutation on the proteome and documented the derepression of 11 Fur-regulated proteins, including a newly identified thioredoxin reductase homolog, YcgT.

  3. A novel sandwich-type electrochemical aptasensor based on GR-3D Au and aptamer-AuNPs-HRP for sensitive detection of oxytetracycline.

    Science.gov (United States)

    Liu, Su; Wang, Yu; Xu, Wei; Leng, Xueqi; Wang, Hongzhi; Guo, Yuna; Huang, Jiadong

    2017-02-15

    In this paper, a novel sandwich-type electrochemical aptasensor has been fabricated and applied for sensitive and selective detection of antibiotic oxytetracycline (OTC). This sensor was based on graphene-three dimensional nanostructure gold nanocomposite (GR-3D Au) and aptamer-AuNPs-horseradish peroxidase (aptamer-AuNPs-HRP) nanoprobes as signal amplification. Firstly, GR-3D Au film was modified on glassy carbon electrode only by one-step electrochemical coreduction with graphite oxide (GO) and HAuCl 4 at cathodic potentials, which enhanced the electron transfer and loading capacity of biomolecules. Then the aptamer and HRP modified Au nanoparticles provide high affinity and ultrasensitive electrochemical probe with excellent specificity for OTC. Under the optimized conditions, the peak current was linearly proportional to the concentration of OTC in the range of 5×10 -10 -2×10 -3 gL -1 , with a detection limit of 4.98×10 -10 gL -1 . Additionally, this aptasensor had the advantages in high sensitivity, superb specificity and showed good recovery in synthetic samples. Hence, the developed sandwich-type electrochemical aptasensor might provide a useful and practical tool for OTC determination and related food safety analysis and clinical diagnosis. Copyright © 2016 Elsevier B.V. All rights reserved.

  4. A sensitive, colorimetric immunosensor based on Cu-MOFs and HRP for detection of dibutyl phthalate in environmental and food samples.

    Science.gov (United States)

    Zhu, Nuanfei; Zou, Yanmin; Huang, Menglu; Dong, Shuaibing; Wu, Xiangyang; Liang, Guoxi; Han, Zhixiang; Zhang, Zhen

    2018-08-15

    A sensitive and artful colorimetric immunosensor based on horseradish peroxidase (HRP) was designed by labelling metal-organic frameworks (Cu-MOFs) on the second antibody (Cu-MOFs@Ab 2 ) as signal amplification for the detection of trace dibutyl phthalate (DBP). In this system, when Cu-MOFs@Ab 2 was captured by antigen- primary antibody (Ab 1 ) complex, tremendous Cu(II) will be released from Cu-MOFs in the presence of nitric acid (HNO 3 ), and Cu(II) will be further reduced to Cu(I) after the addition of sodium ascorbate (SA), consequently, inhibiting the HRP to catalyse the colorless 3,3',5,5'-tetramethylbenzidine (TMB) into blue oxidized TMB (ox TMB). Under the optimized conditions, the limit of detection (LOD) was 1 μg L -1 , which was almost 60 times lower than that using a conventional ELISA with the same antibody. In addition, our method showed good accuracy and reproducibility (recoveries of 87.73-103.4%; CV values of 1.46-5.95%) through a spike-recovery analysis. The proposed immunosensor indicated great potential for trace DBP determination from environmental and food samples. Copyright © 2018. Published by Elsevier B.V.

  5. Hypothalamic projections to the ventral medulla oblongata in the rat, with special reference to the nucleus raphe pallidus: a study using autoradiographic and HRP techniques

    Energy Technology Data Exchange (ETDEWEB)

    Hosoya, Yasuhiko

    1985-10-07

    Hypothalamic descending projections to the medullary ventral surface were studied autoradiographically in the rat. A small amount of (/sup 3/H)leucine was injected unilaterally into various parts of the hypothalamus by air pressure. Abundant and characteristic terminal labelings were observed bilaterally in the nucleus raphe pallidus, the ventral surface to the pyramidal tract and the nucleus interfascicularis hypoglossi, after injections into the dorsal posterior hypothalamic area caudal to the paraventricular hypothalamic nucleus. Conspicuous, but less numerous labelings were observed in the nucleus raphe obscurus and the ipsilateral raphe magnus. After an injection of (/sup 3/H)leucine into the hypothalamus and injections of horseradish peroxidase (HRP) into the spinal cord in the same animal, silver grains were densely distributed around HRP-labeled neurons in the nucleus raphe pallidus including the nucleus interfascicularis hypoglossi. The present results suggest that the dorsal posterior hypothalamic area projects directly to the spinal-projecting neurons of the nucleus raphe pallidus. 53 refs.; 9 figs.

  6. The Listeria monocytogenes Bile Stimulon under Acidic Conditions Is Characterized by Strain-Specific Patterns and the Upregulation of Motility, Cell Wall Modification Functions, and the PrfA Regulon

    Science.gov (United States)

    Guariglia-Oropeza, Veronica; Orsi, Renato H.; Guldimann, Claudia; Wiedmann, Martin; Boor, Kathryn J.

    2018-01-01

    Listeria monocytogenes uses a variety of transcriptional regulation strategies to adapt to the extra-host environment, the gastrointestinal tract, and the intracellular host environment. While the alternative sigma factor SigB has been proposed to be a key transcriptional regulator that facilitates L. monocytogenes adaptation to the gastrointestinal environment, the L. monocytogenes' transcriptional response to bile exposure is not well-understood. RNA-seq characterization of the bile stimulon was performed in two L. monocytogenes strains representing lineages I and II. Exposure to bile at pH 5.5 elicited a large transcriptomic response with ~16 and 23% of genes showing differential transcription in 10403S and H7858, respectively. The bile stimulon includes genes involved in motility and cell wall modification mechanisms, as well as genes in the PrfA regulon, which likely facilitate survival during the gastrointestinal stages of infection that follow bile exposure. The fact that bile exposure induced the PrfA regulon, but did not induce further upregulation of the SigB regulon (beyond that expected by exposure to pH 5.5), suggests a model where at the earlier stages of gastrointestinal infection (e.g., acid exposure in the stomach), SigB-dependent gene expression plays an important role. Subsequent exposure to bile induces the PrfA regulon, potentially priming L. monocytogenes for subsequent intracellular infection stages. Some members of the bile stimulon showed lineage- or strain-specific distribution when 27 Listeria genomes were analyzed. Even though sigB null mutants showed increased sensitivity to bile, the SigB regulon was not found to be upregulated in response to bile beyond levels expected by exposure to pH 5.5. Comparison of wildtype and corresponding ΔsigB strains newly identified 26 SigB-dependent genes, all with upstream putative SigB-dependent promoters. PMID:29467736

  7. Humoral Responses to Rv1733c, Rv0081, Rv1735c, and Rv1737c DosR Regulon-Encoded Proteins of Mycobacterium tuberculosis in Individuals with Latent Tuberculosis Infection

    Directory of Open Access Journals (Sweden)

    Simon G. Kimuda

    2017-01-01

    Full Text Available Latent tuberculosis infection (LTBI is evidence of immunological control of tuberculosis. Dormancy survival regulator (DosR regulon-encoded proteins may have a role in the maintenance of LTBI. T cell responses to Rv1733c, Rv0081, Rv1735c, and Rv1737c DosR regulon-encoded proteins were found to be most frequent among household contacts of TB cases from Uganda compared to other DosR proteins, but antibody responses were not described. We characterized antibody responses to these proteins in individuals from Uganda. Antibodies to Rv1733c, Rv0081, Rv1735c, and Rv1737c DosR regulon-encoded proteins were measured in 68 uninfected individuals, 62 with LTBI, and 107 with active pulmonary tuberculosis (APTB cases. There were no differences in the concentrations of antibodies to Rv0081, Rv1735c, and Rv1737c DosR regulon-encoded proteins between individuals with LTBI and APTB and those who were uninfected. LTBI was associated with higher concentrations of antibodies to Rv1733c in female participants [adjusted geometric mean ratio: 1.812, 95% confidence interval (CI: 1.105 2.973, and p=0.019] but not in males (p value for interaction = 0.060. Antibodies to the four DosR regulon-encoded proteins investigated may not serve as good biomarkers of LTBI in the general population. More of the M.tb proteome needs to be screened to identify proteins that induce strong antibody responses in LTBI.

  8. Definition of a second Bacillus subtilis pur regulon comprising the pur and xpt-pbuX operons plus pbuG, nupG (yxjA), and pbuE (ydhL)

    DEFF Research Database (Denmark)

    Johansen, L.E.; Nygaard, P.; Lassen, C.

    2003-01-01

    In Bacillus subtilis expression of genes or operons encoding enzymes and other proteins involved in purine synthesis is affected by purine bases and nucleosides in the growth medium. The genes belonging to the PurR regulon (purR, purA, glyA, guaC, pbuO, pbuG, and the pur, yqhZ-folD, and xpt...

  9. Genome-Scale Co-Expression Network Comparison across Escherichia coli and Salmonella enterica Serovar Typhimurium Reveals Significant Conservation at the Regulon Level of Local Regulators Despite Their Dissimilar Lifestyles

    Science.gov (United States)

    Zarrineh, Peyman; Sánchez-Rodríguez, Aminael; Hosseinkhan, Nazanin; Narimani, Zahra; Marchal, Kathleen; Masoudi-Nejad, Ali

    2014-01-01

    Availability of genome-wide gene expression datasets provides the opportunity to study gene expression across different organisms under a plethora of experimental conditions. In our previous work, we developed an algorithm called COMODO (COnserved MODules across Organisms) that identifies conserved expression modules between two species. In the present study, we expanded COMODO to detect the co-expression conservation across three organisms by adapting the statistics behind it. We applied COMODO to study expression conservation/divergence between Escherichia coli, Salmonella enterica, and Bacillus subtilis. We observed that some parts of the regulatory interaction networks were conserved between E. coli and S. enterica especially in the regulon of local regulators. However, such conservation was not observed between the regulatory interaction networks of B. subtilis and the two other species. We found co-expression conservation on a number of genes involved in quorum sensing, but almost no conservation for genes involved in pathogenicity across E. coli and S. enterica which could partially explain their different lifestyles. We concluded that despite their different lifestyles, no significant rewiring have occurred at the level of local regulons involved for instance, and notable conservation can be detected in signaling pathways and stress sensing in the phylogenetically close species S. enterica and E. coli. Moreover, conservation of local regulons seems to depend on the evolutionary time of divergence across species disappearing at larger distances as shown by the comparison with B. subtilis. Global regulons follow a different trend and show major rewiring even at the limited evolutionary distance that separates E. coli and S. enterica. PMID:25101984

  10. Spinal cord projections of the rat main forelimb nerves, studied by transganglionic transport of WGA-HRP and by the disappearance of acid phosphatase.

    Science.gov (United States)

    Castro-Lopes, J M; Coimbra, A

    1991-03-01

    The spinal cord projections of the 3 main forelimb nerves-median, radial and ulnar, were studied in the rat dorsal horn with transganglionic transport of wheat germ agglutinin-horseradish peroxidase (WGA-HRP), or using the disappearance of fluoride resistant acid phosphatase (FRAP) after nerve section. The projection patterns in lamina II were similar following the two procedures. The median and the radial nerve fibers projected to the medial and the intermediate thirds, respectively, of the dorsal horn lamina II in spinal cord segments C4-C8. The ulnar nerve projected to segments C6-C8 between the areas occupied by the other two nerves. The FRAP method also showed that the lateral part of lamina II, which was not filled by radial nerve fibers, received the projections from the dorsal cutaneous branches of cervical spinal nerves. In addition, FRAP disappeared from the medial end of segment T1 after skin incisions extending from the medial brachium to the axilla, which seemed due to severance of the cutaneous branchlets of the lateral anterior thoracic nerve. The FRAP procedure is thus sensitive enough to detect fibers in lamina II arising from small peripheral nerves, and may be used as an alternative to the anterograde tracing methods whenever there are no overlapping projections.

  11. Fabrication and Optimization of ChE/ChO/HRP-AuNPs/c-MWCNTs Based Silver Electrode for Determining Total Cholesterol in Serum

    Directory of Open Access Journals (Sweden)

    Kusum Lata

    2016-01-01

    Full Text Available The developed method used three enzymes comprised of cholesterol esterase, cholesterol oxidase, and peroxidase for fabrication of amperometric biosensor in order to determine total cholesterol in serum samples. Gold nanoparticles (AuNPs and carboxylated multiwall carbon nanotubes (cMWCNTs were used to design core of working electrode, having covalently immobilized ChO, ChE, and HRP. Polyacrylamide layer was finally coated on working electrode in order to prevent enzyme leaching. Chemically synthesised Au nanoparticles were subjected to transmission electron microscopy (TEM for analysing the shape and size of the particles. Working electrode was subjected to FTIR and XRD. The combined action of AuNP and c-MWCNT showed enhancement in electrocatalytic activity at a very low potential of 0.27 V. The pH 7, temperature 40°C, and response time of 20 seconds, respectively, were observed. The biosensor shows a broad linear range from 0.5 mg/dL to 250 mg/dL (0.01 mM–5.83 mM with minimum detection limit being 0.5 mg/dL (0.01 mM. The biosensor showed reusability of more than 45 times and was stable for 60 days. The biosensor was successfully tested for determining total cholesterol in serum samples amperometrically with no significant interference by serum components.

  12. The organization of the fuc regulon specifying L-fucose dissimilation in Escherichia coli K12 as determined by gene cloning.

    Science.gov (United States)

    Chen, Y M; Zhu, Y; Lin, E C

    1987-12-01

    In Escherichia coli the six known genes specifying the utilization of L-fucose as carbon and energy source cluster at 60.2 min and constitute a regulon. These genes include fucP (encoding L-fucose permease), fucI (encoding L-fucose isomerase), fucK (encoding L-fuculose kinase), fucA (encoding L-fuculose 1-phosphate aldolase), fucO (encoding L-1,2-propanediol oxidoreductase), and fucR (encoding the regulatory protein). In this study the fuc genes were cloned and their positions on the chromosome were established by restriction endonuclease and complementation analyses. Clockwise, the gene order is: fucO-fucA-fucP-fucI-fucK-fucR. The operons comprising the structural genes and the direction of transcription were determined by complementation analysis and Southern blot hybridization. The fucPIK and fucA operons are transcribed clockwise. The fucO operon is transcribed counterclockwise. The fucR gene product activates the three structural operons in trans.

  13. HRP2 and pLDH-Based Rapid Diagnostic Tests, Expert Microscopy, and PCR for Detection of Malaria Infection during Pregnancy and at Delivery in Areas of Varied Transmission: A Prospective Cohort Study in Burkina Faso and Uganda.

    Directory of Open Access Journals (Sweden)

    Daniel J Kyabayinze

    Full Text Available Intermittent screening and treatment (IST of malaria during pregnancy has been proposed as an alternative to intermittent preventive treatment in pregnancy (IPTp, where IPTp is failing due to drug resistance. However, the antenatal parasitaemias are frequently very low, and the most appropriate screening test for IST has not been defined.We conducted a multi-center prospective study of 990 HIV-uninfected women attending ANC in two different malaria transmission settings at Tororo District Hospital, eastern Uganda and Colsama Health Center in western Burkina Faso. Women were enrolled in the study in the second or third trimester of pregnancy and followed to delivery, generating 2,597 blood samples for analysis. Screening tests included rapid diagnostic tests (RDTs targeting histidine-rich protein 2 (HRP2 and parasite lactate dehydrogenase (pLDH and microscopy, compared to nPCR as a reference standard. At enrolment, the proportion of pregnant women who were positive for P. falciparum by HRP2/pan pLDH RDT, Pf pLDH/pan pLDH RDT, microscopy and PCR was 38%, 29%, 36% and 44% in Uganda and 21%, 16%, 15% and 35% in Burkina Faso, respectively. All test positivity rates declined during follow-up. In comparison to PCR, the sensitivity of the HRP2/pan pLDH RDT, Pf pLDH/pan pLDH RDT and microscopy was 75.7%, 60.1% and 69.7% in Uganda, 55.8%, 42.6% and 55.8% in Burkina Faso respectively for all antenatal visits. Specificity was greater than 96% for all three tests. Comparison of accuracy using generalized estimating equation revealed that the HRP2- detecting RDT was the most accurate test in both settings.The study suggests that HRP2-based RDTs are the most appropriate point-of-care test currently available for use during pregnancy especially for symptomatic women, but will still miss some PCR-positive women. The clinical significance of these very low density infections needs to be better defined.

  14. The cyclic AMP receptor protein, CRP, is required for both virulence and expression of the minimal CRP regulon in Yersinia pestis biovar microtus.

    Science.gov (United States)

    Zhan, Lingjun; Han, Yanping; Yang, Lei; Geng, Jing; Li, Yingli; Gao, He; Guo, Zhaobiao; Fan, Wei; Li, Gang; Zhang, Lianfeng; Qin, Chuan; Zhou, Dongsheng; Yang, Ruifu

    2008-11-01

    The cyclic AMP receptor protein (CRP) is a bacterial regulator that controls more than 100 promoters, including those involved in catabolite repression. In the present study, a null deletion of the crp gene was constructed for Yersinia pestis bv. microtus strain 201. Microarray expression analysis disclosed that at least 6% of Y. pestis genes were affected by this mutation. Further reverse transcription-PCR and electrophoretic mobility shift assay analyses disclosed a set of 37 genes or putative operons to be the direct targets of CRP, and thus they constitute the minimal CRP regulon in Y. pestis. Subsequent primer extension and DNase I footprinting assays mapped transcriptional start sites, core promoter elements, and CRP binding sites within the DNA regions upstream of pla and pst, revealing positive and direct control of these two laterally acquired plasmid genes by CRP. The crp disruption affected both in vitro and in vivo growth of the mutant and led to a >15,000-fold loss of virulence after subcutaneous infection but a pestis and, particularly, is more important for infection by subcutaneous inoculation. It can further be concluded that the reduced in vivo growth phenotype of the crp mutant should contribute, at least partially, to its attenuation of virulence by both routes of infection. Consistent with a previous study of Y. pestis bv. medievalis, lacZ reporter fusion analysis indicated that the crp deletion resulted in the almost absolute loss of pla promoter activity. The plasminogen activator encoded by pla was previously shown to specifically promote Y. pestis dissemination from peripheral infection routes (subcutaneous infection [flea bite] or inhalation). The above evidence supports the notion that in addition to the reduced in vivo growth phenotype, the defect of pla expression in the crp mutant will greatly contribute to the huge loss of virulence of this mutant strain in subcutaneous infection.

  15. A proteomic analysis of the regulon of the NarP two-component regulatory system response regulator in the bovine pathogen Mannheimia haemolytica A1

    Directory of Open Access Journals (Sweden)

    Inamoto Ichiro

    2011-11-01

    Full Text Available Abstract Background The response of the NarQP two-component signal transduction system regulon in response to the presence of nitrate for the bovine pathogen Mannheimia haemolytica A1 was investigated by proteomic analysis. Total proteins from a narP mutant and the parent SH1217 grown with or without NaNO3 supplement were examined by ISO-DALT 2D electrophoresis and liquid chromatography-mass spectrometry. Results Seventeen proteins were differentially expressed in the parent strain SH1217 in response to the addition of NaNO3 to the growth media. These responses were absent in the narP mutant, indicating that the altered production of these proteins is mediated by NarPMh. Interestingly, NarPMh mediated the increased production of some proteins which are not generally associated with nitrate respiration, such as the iron transporters FbpA and YfeA. The increased production of proteins such as superoxide dismutase, SodA, and GAPDH were also observed. The increased production of these iron-regulated proteins by NarPMh is thought to enhance the swift establishment of the nitrate respiration mechanism of M. haemolytica during pathogenesis. Conclusion The data suggested NarPMh acts as an important regulator which regulates the expression of a small set of proteins in response to nitrate availability. This may contribute to the prevalence of M. haemolytica A1 in its host during pathogenesis of BPP, through enhancing the effectiveness of nitrate respiration either directly or indirectly.

  16. Intracellular Zn(II) Intoxication Leads to Dysregulation of the PerR Regulon Resulting in Heme Toxicity in Bacillus subtilis

    Science.gov (United States)

    2016-01-01

    Transition metal ions (Zn(II), Cu(II)/(I), Fe(III)/(II), Mn(II)) are essential for life and participate in a wide range of biological functions. Cellular Zn(II) levels must be high enough to ensure that it can perform its essential roles. Yet, since Zn(II) binds to ligands with high avidity, excess Zn(II) can lead to protein mismetallation. The major targets of mismetallation, and the underlying causes of Zn(II) intoxication, are not well understood. Here, we use a forward genetic selection to identify targets of Zn(II) toxicity. In wild-type cells, in which Zn(II) efflux prevents intoxication of the cytoplasm, extracellular Zn(II) inhibits the electron transport chain due to the inactivation of the major aerobic cytochrome oxidase. This toxicity can be ameliorated by depression of an alternate oxidase or by mutations that restrict access of Zn(II) to the cell surface. Conversely, efflux deficient cells are sensitive to low levels of Zn(II) that do not inhibit the respiratory chain. Under these conditions, intracellular Zn(II) accumulates and leads to heme toxicity. Heme accumulation results from dysregulation of the regulon controlled by PerR, a metal-dependent repressor of peroxide stress genes. When metallated with Fe(II) or Mn(II), PerR represses both heme biosynthesis (hemAXCDBL operon) and the abundant heme protein catalase (katA). Metallation of PerR with Zn(II) disrupts this coordination, resulting in depression of heme biosynthesis but continued repression of catalase. Our results support a model in which excess heme partitions to the membrane and undergoes redox cycling catalyzed by reduced menaquinone thereby resulting in oxidative stress. PMID:27935957

  17. Characterization of the SigD regulon of C. difficile and its positive control of toxin production through the regulation of tcdR.

    Directory of Open Access Journals (Sweden)

    Imane El Meouche

    Full Text Available Clostridium difficile intestinal disease is mediated largely by the actions of toxins A (TcdA and B (TcdB, whose production occurs after the initial steps of colonization involving different surface or flagellar proteins. In B. subtilis, the sigma factor SigD controls flagellar synthesis, motility, and vegetative autolysins. A homolog of SigD encoding gene is present in the C.difficile 630 genome. We constructed a sigD mutant in C. difficile 630 ∆erm to analyze the regulon of SigD using a global transcriptomic approach. A total of 103 genes were differentially expressed between the wild-type and the sigD mutant, including genes involved in motility, metabolism and regulation. In addition, the sigD mutant displayed decreased expression of genes involved in flagellar biosynthesis, and also of genes encoding TcdA and TcdB as well as TcdR, the positive regulator of the toxins. Genomic analysis and RACE-PCR experiments allowed us to characterize promoter sequences of direct target genes of SigD including tcdR and to identify the SigD consensus. We then established that SigD positively regulates toxin expression via direct control of tcdR transcription. Interestingly, the overexpression of FlgM, a putative anti-SigD factor, inhibited the positive regulation of motility and toxin synthesis by SigD. Thus, SigD appears to be the first positive regulator of the toxin synthesis in C. difficile.

  18. Evolution of the miR5200-FLOWERING LOCUS T flowering time regulon in the temperate grass subfamily Pooideae.

    Science.gov (United States)

    McKeown, Meghan; Schubert, Marian; Preston, Jill C; Fjellheim, Siri

    2017-09-01

    Flowering time is a carefully regulated trait controlled primarily through the action of the central genetic regulator, FLOWERING LOCUS T (FT). Recently it was demonstrated that a microRNA, miR5200, targets the end of the second exon of FT under short-day photoperiods in the grass subfamily Pooideae, thus preventing FT transcripts from reaching threshold levels under non-inductive conditions. Pooideae are an interesting group in that they rapidly diversified from the tropics into the northern temperate region during a major global cooling event spanning the Eocene-Oligocene transition. We hypothesize that miR5200 photoperiod-sensitive regulation of Pooideae flowering time networks assisted their transition into northern seasonal environments. Here, we test predictions derived from this hypothesis that miR5200, originally found in bread wheat and later identified in Brachypodium distachyon, (1) was present in the genome of the Pooideae common ancestor, (2) is transcriptionally regulated by photoperiod, and (3) is negatively correlated with FT transcript abundance, indicative of miR5200 regulating FT. Our results demonstrate that miR5200 did evolve at or around the base of Pooideae, but only acquired photoperiod-regulated transcription within the Brachypodium lineage. Based on expression profiles and previous data, we posit that the progenitor of miR5200 was co-regulated with FT by an unknown mechanism. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  19. The Redox-Sensitive Transcriptional Activator OxyR Regulates the Peroxide Response Regulon in the Obligate Anaerobe Bacteroides fragilis

    Science.gov (United States)

    Rocha, Edson R.; Owens, Gary; Smith, C. Jeffrey

    2000-01-01

    The peroxide response-inducible genes ahpCF, dps, and katB in the obligate anaerobe Bacteroides fragilis are controlled by the redox-sensitive transcriptional activator OxyR. This is the first functional oxidative stress regulator identified and characterized in anaerobic bacteria. oxyR and dps were found to be divergently transcribed, with an overlap in their respective promoter regulatory regions. B. fragilis OxyR and Dps proteins showed high identity to homologues from a closely related anaerobe, Porphyromonas gingivalis. Northern blot analysis revealed that oxyR was expressed as a monocistronic 1-kb mRNA and that dps mRNA was approximately 500 bases in length. dps mRNA was induced over 500-fold by oxidative stress in the parent strain and was constitutively induced in the peroxide-resistant mutant IB263. The constitutive peroxide response in strain IB263 was shown to have resulted from a missense mutation at codon 202 (GAT to GGT) of the oxyR gene [oxyR(Con)] with a predicted D202G substitution in the OxyR protein. Transcriptional fusion analysis revealed that deletion of oxyR abolished the induction of ahpC and katB following treatment with hydrogen peroxide or oxygen exposure. However, dps expression was induced approximately fourfold by oxygen exposure in ΔoxyR strains but not by hydrogen peroxide. This indicates that dps expression is also under the control of an oxygen-dependent OxyR-independent mechanism. Complementation of ΔoxyR mutant strains with wild-type oxyR and oxyR(Con) restored the inducible peroxide response and the constitutive response of the ahpCF, katB, and dps genes, respectively. However, overexpression of OxyR abolished the catalase activity but not katB expression, suggesting that higher levels of intracellular OxyR may be involved in other physiological processes. Analysis of oxyR expression in the parents and in ΔoxyR and overexpressing oxyR strains by Northern blotting and oxyR′::xylB fusions revealed that B. fragilis OxyR does

  20. Listeria-vectored vaccine expressing the Mycobacterium tuberculosis 30 kDa major secretory protein via the constitutively active prfA* regulon boosts BCG efficacy against tuberculosis.

    Science.gov (United States)

    Jia, Qingmei; Dillon, Barbara Jane; Masleša-Galić, Saša; Horwitz, Marcus A

    2017-06-19

    A potent vaccine against tuberculosis, one of the world's deadliest diseases, is needed to enhance the immunity of people worldwide, most of whom have been vaccinated with the partially effective BCG vaccine. Here we investigate novel live attenuated recombinant Listeria monocytogenes (rLm) vaccines expressing the Mycobacterium tuberculosis (Mtb) 30 kDa major secretory protein (r30/Ag85B) (rLm30) as heterologous booster vaccines in animals primed with BCG. Using three attenuated Lm vectors, rLm Δ actA (LmI), rLm Δ actA Δ inlB (LmII), and rLm Δ actA Δ inlB prfA * (LmIII), we constructed five rLm30 vaccine candidates expressing the r30 linked in-frame to the Lm Listeriolycin O signal sequence and driven by the hly promoter (h30) or linked in-frame to the ActA N-terminus and driven by the actA promoter (a30). All five rLm30 vaccines secreted r30 in broth and macrophages; while rLm expressing r30 via a constitutively active prfA * regulon (rLmIII/a30) expressed the greatest amount of r30 in broth culture, all five rLm vaccines expressed equivalent amounts of r30 in infected macrophages. In comparative studies, boosting BCG-immunized mice with rLmIII/a30 induced the strongest antigen-specific T-cell responses, including splenic and lung polyfunctional CD4+ T-cells expressing the three cytokines of interferon-gamma (IFN-γ), tumor necrosis factor-alpha (TNF-α), and interleukin-2 (IL-2) ( P vaccines were generally more potent booster vaccines than r30 in adjuvant and a recombinant adenovirus vaccine expressing r30. In a setting in which BCG alone was highly immunoprotective, boosting mice with rLmIII/a30, the most potent of the vaccines, significantly enhanced protection against aerosolized Mtb ( P <0.01). Copyright © 2017 American Society for Microbiology.

  1. The NifA-RpoN regulon of Mesorhizobium loti strain R7A and its symbiotic activation by a novel LacI/GalR-family regulator.

    Directory of Open Access Journals (Sweden)

    John T Sullivan

    Full Text Available Mesorhizobium loti is the microsymbiont of Lotus species, including the model legume L. japonicus. M. loti differs from other rhizobia in that it contains two copies of the key nitrogen fixation regulatory gene nifA, nifA1 and nifA2, both of which are located on the symbiosis island ICEMlSym(R7A. M. loti R7A also contains two rpoN genes, rpoN1 located on the chromosome outside of ICEMlSym(R7A and rpoN2 that is located on ICEMlSym(R7A. The aims of the current work were to establish how nifA expression was activated in M. loti and to characterise the NifA-RpoN regulon. The nifA2 and rpoN2 genes were essential for nitrogen fixation whereas nifA1 and rpoN1 were dispensable. Expression of nifA2 was activated, possibly in response to an inositol derivative, by a novel regulator of the LacI/GalR family encoded by the fixV gene located upstream of nifA2. Other than the well-characterized nif/fix genes, most NifA2-regulated genes were not required for nitrogen fixation although they were strongly expressed in nodules. The NifA-regulated nifZ and fixU genes, along with nifQ which was not NifA-regulated, were required in M. loti for a fully effective symbiosis although they are not present in some other rhizobia. The NifA-regulated gene msi158 that encodes a porin was also required for a fully effective symbiosis. Several metabolic genes that lacked NifA-regulated promoters were strongly expressed in nodules in a NifA2-dependent manner but again mutants did not have an overt symbiotic phenotype. In summary, many genes encoded on ICEMlSym(R7A were strongly expressed in nodules but not free-living rhizobia, but were not essential for symbiotic nitrogen fixation. It seems likely that some of these genes have functional homologues elsewhere in the genome and that bacteroid metabolism may be sufficiently plastic to adapt to loss of certain enzymatic functions.

  2. The Role of OmpR in the Expression of Genes of the KdgR Regulon Involved in the Uptake and Depolymerization of Oligogalacturonides in Yersinia enterocolitica

    Directory of Open Access Journals (Sweden)

    Marta Nieckarz

    2017-08-01

    Full Text Available Oligogalacturonide (OGA-specific porins of the KdgM family have previously been identified and characterized in enterobacterial plant pathogens. We found that deletion of the gene encoding response regulator OmpR causes the porin KdgM2 to become one of the most abundant proteins in the outer membrane of the human enteropathogen Yersinia enterocolitica. Reporter gene fusion and real-time PCR analysis confirmed that the expression of kdgM2 is repressed by OmpR. We also found that kdgM2 expression is subject to negative regulation by KdgR, a specific repressor of genes involved in the uptake and metabolism of pectin derivatives in plant pathogens. The additive effect of kdgR and ompR mutations suggested that KdgR and OmpR regulate kdgM2 expression independently. We confirmed that kdgM2 occurs in an operon with the pelP gene, encoding the periplasmic pectate lyase PelP. A pectinolytic assay showed strong upregulation of PelP production/activity in a Y. enterocolitica strain lacking OmpR and KdgR, which corroborates the repression exerted by these regulators on kdgM2. In addition, our data showed that OmpR is responsible for up regulation of the kdgM1 gene encoding the second specific oligogalacturonide porin KdgM1. This indicates the involvement of OmpR in the reciprocal regulation of both KdgM1 and KdgM2. Moreover, we demonstrated the negative impact of OmpR on kdgR transcription, which might positively affect the expression of genes of the KdgR regulon. Binding of OmpR to the promoter regions of the kdgM2-pelP-sghX operon, and kdgM1 and kdgR genes was confirmed using the electrophoretic mobility shift assay, suggesting that OmpR can directly regulate their transcription. We also found that the overexpression of porin KdgM2 increases outer membrane permeability. Thus, OmpR-mediated regulation of the KdgM porins may contribute to the fitness of Y. enterocolitica in particular local environments.

  3. Integration of a complex regulatory cascade involving the SirA/BarA and Csr global regulatory systems that controls expression of the Salmonella SPI-1 and SPI-2 virulence regulons through HilD.

    Science.gov (United States)

    Martínez, Luary C; Yakhnin, Helen; Camacho, Martha I; Georgellis, Dimitris; Babitzke, Paul; Puente, José L; Bustamante, Víctor H

    2011-06-01

    Salmonella pathogenicity islands 1 and 2 (SPI-1 and SPI-2) play key roles in the pathogenesis of Salmonella enterica. Previously, we showed that when Salmonella grows in Luria-Bertani medium, HilD, encoded in SPI-1, first induces the expression of hilA, located in SPI-1, and subsequently of the ssrAB operon, located in SPI-2. These genes code for HilA and the SsrA/B two-component system, the positive regulators of the SPI-1 and SPI-2 regulons respectively. In this study, we demonstrate that CsrA, a global regulatory RNA binding protein, post-transcriptionally regulates hilD expression by directly binding near the Shine-Dalgarno and translation initiation codon sequences of the hilD mRNA, preventing its translation and leading to its accelerated turnover. Negative regulation is counteracted by the global SirA/BarA two-component system, which directly activates the expression of CsrB and CsrC, two non-coding regulatory RNAs that sequester CsrA, thereby preventing it from binding to its target mRNAs. Our results illustrate the integration of global and specific regulators into a multifactorial regulatory cascade controlling the expression of virulence genes acquired by horizontal transfer events. © 2011 Blackwell Publishing Ltd.

  4. Predicted RNA Binding Proteins Pes4 and Mip6 Regulate mRNA Levels, Translation, and Localization during Sporulation in Budding Yeast.

    Science.gov (United States)

    Jin, Liang; Zhang, Kai; Sternglanz, Rolf; Neiman, Aaron M

    2017-05-01

    In response to starvation, diploid cells of Saccharomyces cerevisiae undergo meiosis and form haploid spores, a process collectively referred to as sporulation. The differentiation into spores requires extensive changes in gene expression. The transcriptional activator Ndt80 is a central regulator of this process, which controls many genes essential for sporulation. Ndt80 induces ∼300 genes coordinately during meiotic prophase, but different mRNAs within the NDT80 regulon are translated at different times during sporulation. The protein kinase Ime2 and RNA binding protein Rim4 are general regulators of meiotic translational delay, but how differential timing of individual transcripts is achieved was not known. This report describes the characterization of two related NDT80 -induced genes, PES4 and MIP6 , encoding predicted RNA binding proteins. These genes are necessary to regulate the steady-state expression, translational timing, and localization of a set of mRNAs that are transcribed by NDT80 but not translated until the end of meiosis II. Mutations in the predicted RNA binding domains within PES4 alter the stability of target mRNAs. PES4 and MIP6 affect only a small portion of the NDT80 regulon, indicating that they act as modulators of the general Ime2/Rim4 pathway for specific transcripts. Copyright © 2017 American Society for Microbiology.

  5. Structures of the Porphyromonas gingivalis OxyR regulatory domain explain differences in expression of the OxyR regulon in Escherichia coli and P. gingivalis

    International Nuclear Information System (INIS)

    Svintradze, David V.; Peterson, Darrell L.; Collazo-Santiago, Evys A.; Lewis, Janina P.; Wright, H. Tonie

    2013-01-01

    Differences in OxyR regulated expression of oxidative stress genes between Escherichia coli and Porphyromonas gingivalis are explained by very minor differences in structure and amino-acid sequence of the respective oxidized and reduced OxyR regulatory domains. These differences affect OxyR quaternary structures and are predicted from model building of full length OxyR–DNA complexes to confer distinct modes of DNA binding on this transcriptional regulator. OxyR transcriptionally regulates Escherichia coli oxidative stress response genes through a reversibly reducible cysteine disulfide biosensor of cellular redox status. Structural changes induced by redox changes in these cysteines are conformationally transmitted to the dimer subunit interfaces, which alters dimer and tetramer interactions with DNA. In contrast to E. coli OxyR regulatory-domain structures, crystal structures of Porphyromonas gingivalis OxyR regulatory domains show minimal differences in dimer configuration on changes in cysteine disulfide redox status. This locked configuration of the P. gingivalis OxyR regulatory-domain dimer closely resembles the oxidized (activating) form of the E. coli OxyR regulatory-domain dimer. It correlates with the observed constitutive activation of some oxidative stress genes in P. gingivalis and is attributable to a single amino-acid insertion in P. gingivalis OxyR relative to E. coli OxyR. Modelling of full-length P. gingivalis, E. coli and Neisseria meningitidis OxyR–DNA complexes predicts different modes of DNA binding for the reduced and oxidized forms of each

  6. Structures of the Porphyromonas gingivalis OxyR regulatory domain explain differences in expression of the OxyR regulon in Escherichia coli and P. gingivalis

    Energy Technology Data Exchange (ETDEWEB)

    Svintradze, David V. [Virginia Commonwealth University, Richmond, VA 23298-0566 (United States); Virginia Commonwealth University, Richmond, VA 23219-1540 (United States); Peterson, Darrell L. [Virginia Commonwealth University, Richmond, VA 23219-1540 (United States); Virginia Commonwealth University, Richmond, VA 23298-0614 (United States); Collazo-Santiago, Evys A.; Lewis, Janina P. [Virginia Commonwealth University, Richmond, VA 23298-0566 (United States); Wright, H. Tonie, E-mail: xrdproc@vcu.edu [Virginia Commonwealth University, Richmond, VA 23219-1540 (United States); Virginia Commonwealth University, Richmond, VA 23298-0614 (United States); Virginia Commonwealth University, Richmond, VA 23298-0566 (United States)

    2013-10-01

    Differences in OxyR regulated expression of oxidative stress genes between Escherichia coli and Porphyromonas gingivalis are explained by very minor differences in structure and amino-acid sequence of the respective oxidized and reduced OxyR regulatory domains. These differences affect OxyR quaternary structures and are predicted from model building of full length OxyR–DNA complexes to confer distinct modes of DNA binding on this transcriptional regulator. OxyR transcriptionally regulates Escherichia coli oxidative stress response genes through a reversibly reducible cysteine disulfide biosensor of cellular redox status. Structural changes induced by redox changes in these cysteines are conformationally transmitted to the dimer subunit interfaces, which alters dimer and tetramer interactions with DNA. In contrast to E. coli OxyR regulatory-domain structures, crystal structures of Porphyromonas gingivalis OxyR regulatory domains show minimal differences in dimer configuration on changes in cysteine disulfide redox status. This locked configuration of the P. gingivalis OxyR regulatory-domain dimer closely resembles the oxidized (activating) form of the E. coli OxyR regulatory-domain dimer. It correlates with the observed constitutive activation of some oxidative stress genes in P. gingivalis and is attributable to a single amino-acid insertion in P. gingivalis OxyR relative to E. coli OxyR. Modelling of full-length P. gingivalis, E. coli and Neisseria meningitidis OxyR–DNA complexes predicts different modes of DNA binding for the reduced and oxidized forms of each.

  7. Predicting metabolic pathways by sub-network extraction.

    Science.gov (United States)

    Faust, Karoline; van Helden, Jacques

    2012-01-01

    Various methods result in groups of functionally related genes obtained from genomes (operons, regulons, syntheny groups, and phylogenetic profiles), transcriptomes (co-expression groups) and proteomes (modules of interacting proteins). When such groups contain two or more enzyme-coding genes, graph analysis methods can be applied to extract a metabolic pathway that interconnects them. We describe here the way to use the Pathway extraction tool available on the NeAT Web server ( http://rsat.ulb.ac.be/neat/ ) to piece together the metabolic pathway from a group of associated, enzyme-coding genes. The tool identifies the reactions that can be catalyzed by the products of the query genes (seed reactions), and applies sub-graph extraction algorithms to extract from a metabolic network a sub-network that connects the seed reactions. This sub-network represents the predicted metabolic pathway. We describe here the pathway prediction process in a step-by-step way, give hints about the main parametric choices, and illustrate how this tool can be used to extract metabolic pathways from bacterial genomes, on the basis of two study cases: the isoleucine-valine operon in Escherichia coli and a predicted operon in Cupriavidus (Ralstonia) metallidurans.

  8. OECD - HRP Summer School on Nuclear Fuel

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2000-07-01

    In cooperation with the OECD Nuclear Energy Agency (NEA), the Halden Reactor Project organised a Summer School on nuclear fuel in the period August 28 September 1, 2000. The summer school was primarily intended for people who wanted to become acquainted with fuel-related subjects and issues without being experts. It was especially hoped that the summer school would serve to transfer knowledge to the ''young generation'' in the field of nuclear fuel. Experts from Halden Project member organisations gave the following presentations: (1) Overview of the nuclear community, (2) Criteria for safe operation and design of nuclear fuel, (3) Fuel design and fabrication, (4) Cladding Manufacturing, (5) Overview of the Halden Reactor Project, (6) Fuel performance evaluation and modelling, (7) Fission gas release, and (8) Cladding issues. Except for the Overview, which is a written paper, the other contributions are overhead figures from spoken lectures.

  9. OECD - HRP Summer School on Nuclear Fuel

    International Nuclear Information System (INIS)

    2000-01-01

    In cooperation with the OECD Nuclear Energy Agency (NEA), the Halden Reactor Project organised a Summer School on nuclear fuel in the period August 28 September 1, 2000. The summer school was primarily intended for people who wanted to become acquainted with fuel-related subjects and issues without being experts. It was especially hoped that the summer school would serve to transfer knowledge to the ''young generation'' in the field of nuclear fuel. Experts from Halden Project member organisations gave the following presentations: (1) Overview of the nuclear community, (2) Criteria for safe operation and design of nuclear fuel, (3) Fuel design and fabrication, (4) Cladding Manufacturing, (5) Overview of the Halden Reactor Project, (6) Fuel performance evaluation and modelling, (7) Fission gas release, and (8) Cladding issues. Except for the Overview, which is a written paper, the other contributions are overhead figures from spoken lectures

  10. Insights into the Quorum Sensing Regulon of the Acidophilic Acidithiobacillus ferrooxidans Revealed by Transcriptomic in the Presence of an Acyl Homoserine Lactone Superagonist Analogue

    Directory of Open Access Journals (Sweden)

    Sigde Mamani

    2016-09-01

    Full Text Available While a functional quorum sensing system has been identified in the acidophilic chemolithoautotroph Acidithiobacillus ferrooxidans ATCC 23270T and shown to modulate cell adhesion to solid substrates, nothing is known about the genes it regulates. To address the question of how quorum sensing controls biofilm formation in At. ferrooxidansT, the transcriptome of this organism in conditions in which quorum sensing response is stimulated by a synthetic superagonist AHL analogue has been studied. First, the effect on biofilm formation of a synthetic AHL tetrazolic analogue, tetrazole 9c, known for its agonistic QS activity, was assessed by fluorescence and electron microscopy experiments. A faster adherence of At. ferrooxidansT cells on sulfur coupons was observed. Then, tetrazole 9c was used in DNA microarray experiments that allowed the identification of genes regulated by quorum sensing signalling, and more particularly, those involved in early biofilm formation. Interestingly, afeI gene, encoding the AHL synthase, but not the At. ferrooxidans quorum sensing transcriptional regulator AfeR encoding gene, was shown to be regulated by quorum sensing. Data indicated that QS network represents at least 4.5 % (141 genes of the ATCC 23270T genome of which 42.5 % (60 genes are related to biofilm formation. Finally, AfeR was shown to bind specifically to the regulatory region of the afeI gene at the level of the palindromic sequence predicted to be the AfeR binding site. Our results give new insights on the response of At. ferrooxidans to quorum sensing and on biofilm biogenesis, opening new biological/chemical alternatives for bioleaching development and managing acid Mine/Rock drainage environmental damages.

  11. WALS Prediction

    NARCIS (Netherlands)

    Magnus, J.R.; Wang, W.; Zhang, Xinyu

    2012-01-01

    Abstract: Prediction under model uncertainty is an important and difficult issue. Traditional prediction methods (such as pretesting) are based on model selection followed by prediction in the selected model, but the reported prediction and the reported prediction variance ignore the uncertainty

  12. Using sequence-specific chemical and structural properties of DNA to predict transcription factor binding sites.

    Directory of Open Access Journals (Sweden)

    Amy L Bauer

    2010-11-01

    Full Text Available An important step in understanding gene regulation is to identify the DNA binding sites recognized by each transcription factor (TF. Conventional approaches to prediction of TF binding sites involve the definition of consensus sequences or position-specific weight matrices and rely on statistical analysis of DNA sequences of known binding sites. Here, we present a method called SiteSleuth in which DNA structure prediction, computational chemistry, and machine learning are applied to develop models for TF binding sites. In this approach, binary classifiers are trained to discriminate between true and false binding sites based on the sequence-specific chemical and structural features of DNA. These features are determined via molecular dynamics calculations in which we consider each base in different local neighborhoods. For each of 54 TFs in Escherichia coli, for which at least five DNA binding sites are documented in RegulonDB, the TF binding sites and portions of the non-coding genome sequence are mapped to feature vectors and used in training. According to cross-validation analysis and a comparison of computational predictions against ChIP-chip data available for the TF Fis, SiteSleuth outperforms three conventional approaches: Match, MATRIX SEARCH, and the method of Berg and von Hippel. SiteSleuth also outperforms QPMEME, a method similar to SiteSleuth in that it involves a learning algorithm. The main advantage of SiteSleuth is a lower false positive rate.

  13. Climate prediction and predictability

    Science.gov (United States)

    Allen, Myles

    2010-05-01

    Climate prediction is generally accepted to be one of the grand challenges of the Geophysical Sciences. What is less widely acknowledged is that fundamental issues have yet to be resolved concerning the nature of the challenge, even after decades of research in this area. How do we verify or falsify a probabilistic forecast of a singular event such as anthropogenic warming over the 21st century? How do we determine the information content of a climate forecast? What does it mean for a modelling system to be "good enough" to forecast a particular variable? How will we know when models and forecasting systems are "good enough" to provide detailed forecasts of weather at specific locations or, for example, the risks associated with global geo-engineering schemes. This talk will provide an overview of these questions in the light of recent developments in multi-decade climate forecasting, drawing on concepts from information theory, machine learning and statistics. I will draw extensively but not exclusively from the experience of the climateprediction.net project, running multiple versions of climate models on personal computers.

  14. Prediction of transcriptional regulatory sites in the complete genome sequence of Escherichia coli K-12.

    Science.gov (United States)

    Thieffry, D; Salgado, H; Huerta, A M; Collado-Vides, J

    1998-06-01

    As one of the best-characterized free-living organisms, Escherichia coli and its recently completed genomic sequence offer a special opportunity to exploit systematically the variety of regulatory data available in the literature in order to make a comprehensive set of regulatory predictions in the whole genome. The complete genome sequence of E.coli was analyzed for the binding of transcriptional regulators upstream of coding sequences. The biological information contained in RegulonDB (Huerta, A.M. et al., Nucleic Acids Res.,26,55-60, 1998) for 56 different transcriptional proteins was the support to implement a stringent strategy combining string search and weight matrices. We estimate that our search included representatives of 15-25% of the total number of regulatory binding proteins in E.coli. This search was performed on the set of 4288 putative regulatory regions, each 450 bp long. Within the regions with predicted sites, 89% are regulated by one protein and 81% involve only one site. These numbers are reasonably consistent with the distribution of experimental regulatory sites. Regulatory sites are found in 603 regions corresponding to 16% of operon regions and 10% of intra-operonic regions. Additional evidence gives stronger support to some of these predictions, including the position of the site, biological consistency with the function of the downstream gene, as well as genetic evidence for the regulatory interaction. The predictions described here were incorporated into the map presented in the paper describing the complete E.coli genome (Blattner,F.R. et al., Science, 277, 1453-1461, 1997). The complete set of predictions in GenBank format is available at the url: http://www. cifn.unam.mx/Computational_Biology/E.coli-predictions ecoli-reg@cifn.unam.mx, collado@cifn.unam.mx

  15. Earthquake prediction

    International Nuclear Information System (INIS)

    Ward, P.L.

    1978-01-01

    The state of the art of earthquake prediction is summarized, the possible responses to such prediction are examined, and some needs in the present prediction program and in research related to use of this new technology are reviewed. Three basic aspects of earthquake prediction are discussed: location of the areas where large earthquakes are most likely to occur, observation within these areas of measurable changes (earthquake precursors) and determination of the area and time over which the earthquake will occur, and development of models of the earthquake source in order to interpret the precursors reliably. 6 figures

  16. Predictive medicine

    NARCIS (Netherlands)

    Boenink, Marianne; ten Have, Henk

    2015-01-01

    In the last part of the twentieth century, predictive medicine has gained currency as an important ideal in biomedical research and health care. Research in the genetic and molecular basis of disease suggested that the insights gained might be used to develop tests that predict the future health

  17. Prediction Markets

    DEFF Research Database (Denmark)

    Horn, Christian Franz; Ivens, Bjørn Sven; Ohneberg, Michael

    2014-01-01

    In recent years, Prediction Markets gained growing interest as a forecasting tool among researchers as well as practitioners, which resulted in an increasing number of publications. In order to track the latest development of research, comprising the extent and focus of research, this article...... provides a comprehensive review and classification of the literature related to the topic of Prediction Markets. Overall, 316 relevant articles, published in the timeframe from 2007 through 2013, were identified and assigned to a herein presented classification scheme, differentiating between descriptive...... works, articles of theoretical nature, application-oriented studies and articles dealing with the topic of law and policy. The analysis of the research results reveals that more than half of the literature pool deals with the application and actual function tests of Prediction Markets. The results...

  18. Predicting unpredictability

    Science.gov (United States)

    Davis, Steven J.

    2018-04-01

    Analysts and markets have struggled to predict a number of phenomena, such as the rise of natural gas, in US energy markets over the past decade or so. Research shows the challenge may grow because the industry — and consequently the market — is becoming increasingly volatile.

  19. Inference of expanded Lrp-like feast/famine transcription factor targets in a non-model organism using protein structure-based prediction.

    Science.gov (United States)

    Ashworth, Justin; Plaisier, Christopher L; Lo, Fang Yin; Reiss, David J; Baliga, Nitin S

    2014-01-01

    Widespread microbial genome sequencing presents an opportunity to understand the gene regulatory networks of non-model organisms. This requires knowledge of the binding sites for transcription factors whose DNA-binding properties are unknown or difficult to infer. We adapted a protein structure-based method to predict the specificities and putative regulons of homologous transcription factors across diverse species. As a proof-of-concept we predicted the specificities and transcriptional target genes of divergent archaeal feast/famine regulatory proteins, several of which are encoded in the genome of Halobacterium salinarum. This was validated by comparison to experimentally determined specificities for transcription factors in distantly related extremophiles, chromatin immunoprecipitation experiments, and cis-regulatory sequence conservation across eighteen related species of halobacteria. Through this analysis we were able to infer that Halobacterium salinarum employs a divergent local trans-regulatory strategy to regulate genes (carA and carB) involved in arginine and pyrimidine metabolism, whereas Escherichia coli employs an operon. The prediction of gene regulatory binding sites using structure-based methods is useful for the inference of gene regulatory relationships in new species that are otherwise difficult to infer.

  20. Unification predictions

    International Nuclear Information System (INIS)

    Ghilencea, D.; Ross, G.G.; Lanzagorta, M.

    1997-07-01

    The unification of gauge couplings suggests that there is an underlying (supersymmetric) unification of the strong, electromagnetic and weak interactions. The prediction of the unification scale may be the first quantitative indication that this unification may extend to unification with gravity. We make a precise determination of these predictions for a class of models which extend the multiplet structure of the Minimal Supersymmetric Standard Model to include the heavy states expected in many Grand Unified and/or superstring theories. We show that there is a strong cancellation between the 2-loop and threshold effects. As a result the net effect is smaller than previously thought, giving a small increase in both the unification scale and the value of the strong coupling at low energies. (author). 15 refs, 5 figs

  1. Predictable Medea

    Directory of Open Access Journals (Sweden)

    Elisabetta Bertolino

    2010-01-01

    Full Text Available By focusing on the tragedy of the 'unpredictable' infanticide perpetrated by Medea, the paper speculates on the possibility of a non-violent ontological subjectivity for women victims of gendered violence and whether it is possible to respond to violent actions in non-violent ways; it argues that Medea did not act in an unpredictable way, rather through the very predictable subject of resentment and violence. 'Medea' represents the story of all of us who require justice as retribution against any wrong. The presupposition is that the empowered female subjectivity of women’s rights contains the same desire of mastering others of the masculine current legal and philosophical subject. The subject of women’s rights is grounded on the emotions of resentment and retribution and refuses the categories of the private by appropriating those of the righteous, masculine and public subject. The essay opposes the essentialised stereotypes of the feminine and the maternal with an ontological approach of people as singular, corporeal, vulnerable and dependent. There is therefore an emphasis on the excluded categories of the private. Forgiveness is taken into account as a category of the private and a possibility of responding to violence with newness. A violent act is seen in relations to the community of human beings rather than through an isolated setting as in the case of the individual of human rights. In this context, forgiveness allows to risk again and being with. The result is also a rethinking of feminist actions, feminine subjectivity and of the maternal. Overall the paper opens up the Arendtian category of action and forgiveness and the Cavarerian unique and corporeal ontology of the selfhood beyond gendered stereotypes.

  2. Cell individuality: the bistable gene expression of the type III secretion system in Dickeya dadantii 3937.

    Science.gov (United States)

    Zeng, Quan; Laiosa, Michael D; Steeber, Douglas A; Biddle, Eulandria M; Peng, Quan; Yang, Ching-Hong

    2012-01-01

    Dickeya dadantii 3937 is a gram-negative phytopathogenic bacterium that expresses genes encoding a type III secretion system (T3SS) in a bistable pattern when cultured in a homogeneous minimal media. In this work, we further characterized the bistable gene expression of T3SS at the single-cell level. We demonstrated that bistable expression of the HrpL-regulon genes, such as hrpA and hrpN, is controlled by the same regulatory mechanism. We also showed that the expression level of the T3SS master regulatory gene hrpL plays an important role in the development of the bistable expression of hrpA. A high expression level of hrpL is required but unable to guarantee the high-state expression of hrpA in a cell. In addition, bistable expression patterns of T3SS genes in other gram-negative pathogens of the Enterobacteriaceae and Pseudomonadaceae families were also described in this study. This suggests that the T3SS bistability might be a conserved population behavior in several gram-negative bacterial pathogens.

  3. Identification of the ClpX Regulon in Staphylococcus aureus

    DEFF Research Database (Denmark)

    Jelsbak, Lotte; Thomsen, Line Elnif; Ingmer, Hanne

    Staphyloccous aureus is a major human pathogen capable of causing a wide spectrum of infections ranging from superficial wound infections to life-threatening endocarditis and toxic shock syndrome. Essential for S. aureus virulence is a large number of cell-surface-associated proteins and secreted...... we show here that almost 400 genes (15%) are influenced by the clpX deletion. Furthermore, ClpX not only regulates many virulence factors, but rather serves as a global regulator of central functions for S. aureus lifestyle and pathogenicity....

  4. Making detailed predictions makes (some) predictions worse

    Science.gov (United States)

    Kelly, Theresa F.

    In this paper, we investigate whether making detailed predictions about an event makes other predictions worse. Across 19 experiments, 10,895 participants, and 415,960 predictions about 724 professional sports games, we find that people who made detailed predictions about sporting events (e.g., how many hits each baseball team would get) made worse predictions about more general outcomes (e.g., which team would win). We rule out that this effect is caused by inattention or fatigue, thinking too hard, or a differential reliance on holistic information about the teams. Instead, we find that thinking about game-relevant details before predicting winning teams causes people to give less weight to predictive information, presumably because predicting details makes information that is relatively useless for predicting the winning team more readily accessible in memory and therefore incorporated into forecasts. Furthermore, we show that this differential use of information can be used to predict what kinds of games will and will not be susceptible to the negative effect of making detailed predictions.

  5. sigma54-Mediated control of the mannose phosphotransferase sytem in Lactobacillus plantarum impacts on carbohydrate metabolism

    NARCIS (Netherlands)

    Stevens, M.J.A.; Molenaar, D.; Jong, de A.; Vos, de W.M.; Kleerebezem, M.

    2010-01-01

    Sigma factors direct specific binding of the bacterial RNA polymerase to the promoter. Here we present the elucidation of the sigma(54 ) regulon in Lactobacillus plantarum. A sequence-based regulon prediction of sigma(54)-dependent promoters revealed an operon encoding a mannose phosphotransferase

  6. sigma(54)-mediated control of the mannose phosphotransferase sytem in Lactobacillus plantarum impacts on carbohydrate metabolism

    NARCIS (Netherlands)

    Stevens, Marc J. A.; Molenaar, Douwe; de Jong, Anne; De Vos, Willem M.; Kleerebezem, Michiel

    Sigma factors direct specific binding of the bacterial RNA polymerase to the promoter. Here we present the elucidation of the sigma(54) regulon in Lactobacillus plantarum. A sequence-based regulon prediction of sigma(54)-dependent promoters revealed an operon encoding a mannose phosphotransferase

  7. Predictive modeling of complications.

    Science.gov (United States)

    Osorio, Joseph A; Scheer, Justin K; Ames, Christopher P

    2016-09-01

    Predictive analytic algorithms are designed to identify patterns in the data that allow for accurate predictions without the need for a hypothesis. Therefore, predictive modeling can provide detailed and patient-specific information that can be readily applied when discussing the risks of surgery with a patient. There are few studies using predictive modeling techniques in the adult spine surgery literature. These types of studies represent the beginning of the use of predictive analytics in spine surgery outcomes. We will discuss the advancements in the field of spine surgery with respect to predictive analytics, the controversies surrounding the technique, and the future directions.

  8. Predicting outdoor sound

    CERN Document Server

    Attenborough, Keith; Horoshenkov, Kirill

    2014-01-01

    1. Introduction  2. The Propagation of Sound Near Ground Surfaces in a Homogeneous Medium  3. Predicting the Acoustical Properties of Outdoor Ground Surfaces  4. Measurements of the Acoustical Properties of Ground Surfaces and Comparisons with Models  5. Predicting Effects of Source Characteristics on Outdoor Sound  6. Predictions, Approximations and Empirical Results for Ground Effect Excluding Meteorological Effects  7. Influence of Source Motion on Ground Effect and Diffraction  8. Predicting Effects of Mixed Impedance Ground  9. Predicting the Performance of Outdoor Noise Barriers  10. Predicting Effects of Vegetation, Trees and Turbulence  11. Analytical Approximations including Ground Effect, Refraction and Turbulence  12. Prediction Schemes  13. Predicting Sound in an Urban Environment.

  9. Applied predictive control

    CERN Document Server

    Sunan, Huang; Heng, Lee Tong

    2002-01-01

    The presence of considerable time delays in the dynamics of many industrial processes, leading to difficult problems in the associated closed-loop control systems, is a well-recognized phenomenon. The performance achievable in conventional feedback control systems can be significantly degraded if an industrial process has a relatively large time delay compared with the dominant time constant. Under these circumstances, advanced predictive control is necessary to improve the performance of the control system significantly. The book is a focused treatment of the subject matter, including the fundamentals and some state-of-the-art developments in the field of predictive control. Three main schemes for advanced predictive control are addressed in this book: • Smith Predictive Control; • Generalised Predictive Control; • a form of predictive control based on Finite Spectrum Assignment. A substantial part of the book addresses application issues in predictive control, providing several interesting case studie...

  10. Predictable or not predictable? The MOV question

    International Nuclear Information System (INIS)

    Thibault, C.L.; Matzkiw, J.N.; Anderson, J.W.; Kessler, D.W.

    1994-01-01

    Over the past 8 years, the nuclear industry has struggled to understand the dynamic phenomena experienced during motor-operated valve (MOV) operation under differing flow conditions. For some valves and designs, their operational functionality has been found to be predictable; for others, unpredictable. Although much has been accomplished over this period of time, especially on modeling valve dynamics, the unpredictability of many valves and designs still exists. A few valve manufacturers are focusing on improving design and fabrication techniques to enhance product reliability and predictability. However, this approach does not address these issues for installed and inpredictable valves. This paper presents some of the more promising techniques that Wyle Laboratories has explored with potential for transforming unpredictable valves to predictable valves and for retrofitting installed MOVs. These techniques include optimized valve tolerancing, surrogated material evaluation, and enhanced surface treatments

  11. Predictive systems ecology.

    Science.gov (United States)

    Evans, Matthew R; Bithell, Mike; Cornell, Stephen J; Dall, Sasha R X; Díaz, Sandra; Emmott, Stephen; Ernande, Bruno; Grimm, Volker; Hodgson, David J; Lewis, Simon L; Mace, Georgina M; Morecroft, Michael; Moustakas, Aristides; Murphy, Eugene; Newbold, Tim; Norris, K J; Petchey, Owen; Smith, Matthew; Travis, Justin M J; Benton, Tim G

    2013-11-22

    Human societies, and their well-being, depend to a significant extent on the state of the ecosystems that surround them. These ecosystems are changing rapidly usually in response to anthropogenic changes in the environment. To determine the likely impact of environmental change on ecosystems and the best ways to manage them, it would be desirable to be able to predict their future states. We present a proposal to develop the paradigm of predictive systems ecology, explicitly to understand and predict the properties and behaviour of ecological systems. We discuss the necessary and desirable features of predictive systems ecology models. There are places where predictive systems ecology is already being practised and we summarize a range of terrestrial and marine examples. Significant challenges remain but we suggest that ecology would benefit both as a scientific discipline and increase its impact in society if it were to embrace the need to become more predictive.

  12. Seismology for rockburst prediction.

    CSIR Research Space (South Africa)

    De Beer, W

    2000-02-01

    Full Text Available project GAP409 presents a method (SOOTHSAY) for predicting larger mining induced seismic events in gold mines, as well as a pattern recognition algorithm (INDICATOR) for characterising the seismic response of rock to mining and inferring future... State. Defining the time series of a specific function on a catalogue as a prediction strategy, the algorithm currently has a success rate of 53% and 65%, respectively, of large events claimed as being predicted in these two cases, with uncertainties...

  13. Predictability of Conversation Partners

    Science.gov (United States)

    Takaguchi, Taro; Nakamura, Mitsuhiro; Sato, Nobuo; Yano, Kazuo; Masuda, Naoki

    2011-08-01

    Recent developments in sensing technologies have enabled us to examine the nature of human social behavior in greater detail. By applying an information-theoretic method to the spatiotemporal data of cell-phone locations, [C. Song , ScienceSCIEAS0036-8075 327, 1018 (2010)] found that human mobility patterns are remarkably predictable. Inspired by their work, we address a similar predictability question in a different kind of human social activity: conversation events. The predictability in the sequence of one’s conversation partners is defined as the degree to which one’s next conversation partner can be predicted given the current partner. We quantify this predictability by using the mutual information. We examine the predictability of conversation events for each individual using the longitudinal data of face-to-face interactions collected from two company offices in Japan. Each subject wears a name tag equipped with an infrared sensor node, and conversation events are marked when signals are exchanged between sensor nodes in close proximity. We find that the conversation events are predictable to a certain extent; knowing the current partner decreases the uncertainty about the next partner by 28.4% on average. Much of the predictability is explained by long-tailed distributions of interevent intervals. However, a predictability also exists in the data, apart from the contribution of their long-tailed nature. In addition, an individual’s predictability is correlated with the position of the individual in the static social network derived from the data. Individuals confined in a community—in the sense of an abundance of surrounding triangles—tend to have low predictability, and those bridging different communities tend to have high predictability.

  14. Predictability of Conversation Partners

    Directory of Open Access Journals (Sweden)

    Taro Takaguchi

    2011-09-01

    Full Text Available Recent developments in sensing technologies have enabled us to examine the nature of human social behavior in greater detail. By applying an information-theoretic method to the spatiotemporal data of cell-phone locations, [C. Song et al., Science 327, 1018 (2010SCIEAS0036-8075] found that human mobility patterns are remarkably predictable. Inspired by their work, we address a similar predictability question in a different kind of human social activity: conversation events. The predictability in the sequence of one’s conversation partners is defined as the degree to which one’s next conversation partner can be predicted given the current partner. We quantify this predictability by using the mutual information. We examine the predictability of conversation events for each individual using the longitudinal data of face-to-face interactions collected from two company offices in Japan. Each subject wears a name tag equipped with an infrared sensor node, and conversation events are marked when signals are exchanged between sensor nodes in close proximity. We find that the conversation events are predictable to a certain extent; knowing the current partner decreases the uncertainty about the next partner by 28.4% on average. Much of the predictability is explained by long-tailed distributions of interevent intervals. However, a predictability also exists in the data, apart from the contribution of their long-tailed nature. In addition, an individual’s predictability is correlated with the position of the individual in the static social network derived from the data. Individuals confined in a community—in the sense of an abundance of surrounding triangles—tend to have low predictability, and those bridging different communities tend to have high predictability.

  15. Is Time Predictability Quantifiable?

    DEFF Research Database (Denmark)

    Schoeberl, Martin

    2012-01-01

    Computer architects and researchers in the realtime domain start to investigate processors and architectures optimized for real-time systems. Optimized for real-time systems means time predictable, i.e., architectures where it is possible to statically derive a tight bound of the worst......-case execution time. To compare different approaches we would like to quantify time predictability. That means we need to measure time predictability. In this paper we discuss the different approaches for these measurements and conclude that time predictability is practically not quantifiable. We can only...... compare the worst-case execution time bounds of different architectures....

  16. Predicting scholars' scientific impact.

    Directory of Open Access Journals (Sweden)

    Amin Mazloumian

    Full Text Available We tested the underlying assumption that citation counts are reliable predictors of future success, analyzing complete citation data on the careers of ~150,000 scientists. Our results show that i among all citation indicators, the annual citations at the time of prediction is the best predictor of future citations, ii future citations of a scientist's published papers can be predicted accurately (r(2 = 0.80 for a 1-year prediction, P<0.001 but iii future citations of future work are hardly predictable.

  17. Risk Stratification of Stress Fractures and Prediction of Return to Duty

    Science.gov (United States)

    2015-12-01

    SUBJECT TERMS bone microarchitecture, HRpQCT, race, gender , sex, bone mineral density, vBMD, bone geometry, stress fracture 16. SECURITY...are collaborating with local sports medicine physicians, coaches, and athletic trainers to continue recruiting effectively (Task 3, objective 3). We

  18. The Prediction Value

    NARCIS (Netherlands)

    Koster, M.; Kurz, S.; Lindner, I.; Napel, S.

    2013-01-01

    We introduce the prediction value (PV) as a measure of players’ informational importance in probabilistic TU games. The latter combine a standard TU game and a probability distribution over the set of coalitions. Player i’s prediction value equals the difference between the conditional expectations

  19. Predictability of Stock Returns

    Directory of Open Access Journals (Sweden)

    Ahmet Sekreter

    2017-06-01

    Full Text Available Predictability of stock returns has been shown by empirical studies over time. This article collects the most important theories on forecasting stock returns and investigates the factors that affecting behavior of the stocks’ prices and the market as a whole. Estimation of the factors and the way of estimation are the key issues of predictability of stock returns.

  20. Predicting AD conversion

    DEFF Research Database (Denmark)

    Liu, Yawu; Mattila, Jussi; Ruiz, Miguel �ngel Mu�oz

    2013-01-01

    To compare the accuracies of predicting AD conversion by using a decision support system (PredictAD tool) and current research criteria of prodromal AD as identified by combinations of episodic memory impairment of hippocampal type and visual assessment of medial temporal lobe atrophy (MTA) on MRI...

  1. Predicting Free Recalls

    Science.gov (United States)

    Laming, Donald

    2006-01-01

    This article reports some calculations on free-recall data from B. Murdock and J. Metcalfe (1978), with vocal rehearsal during the presentation of a list. Given the sequence of vocalizations, with the stimuli inserted in their proper places, it is possible to predict the subsequent sequence of recalls--the predictions taking the form of a…

  2. Archaeological predictive model set.

    Science.gov (United States)

    2015-03-01

    This report is the documentation for Task 7 of the Statewide Archaeological Predictive Model Set. The goal of this project is to : develop a set of statewide predictive models to assist the planning of transportation projects. PennDOT is developing t...

  3. Evaluating prediction uncertainty

    International Nuclear Information System (INIS)

    McKay, M.D.

    1995-03-01

    The probability distribution of a model prediction is presented as a proper basis for evaluating the uncertainty in a model prediction that arises from uncertainty in input values. Determination of important model inputs and subsets of inputs is made through comparison of the prediction distribution with conditional prediction probability distributions. Replicated Latin hypercube sampling and variance ratios are used in estimation of the distributions and in construction of importance indicators. The assumption of a linear relation between model output and inputs is not necessary for the indicators to be effective. A sequential methodology which includes an independent validation step is applied in two analysis applications to select subsets of input variables which are the dominant causes of uncertainty in the model predictions. Comparison with results from methods which assume linearity shows how those methods may fail. Finally, suggestions for treating structural uncertainty for submodels are presented

  4. Ground motion predictions

    Energy Technology Data Exchange (ETDEWEB)

    Loux, P C [Environmental Research Corporation, Alexandria, VA (United States)

    1969-07-01

    Nuclear generated ground motion is defined and then related to the physical parameters that cause it. Techniques employed for prediction of ground motion peak amplitude, frequency spectra and response spectra are explored, with initial emphasis on the analysis of data collected at the Nevada Test Site (NTS). NTS postshot measurements are compared with pre-shot predictions. Applicability of these techniques to new areas, for example, Plowshare sites, must be questioned. Fortunately, the Atomic Energy Commission is sponsoring complementary studies to improve prediction capabilities primarily in new locations outside the NTS region. Some of these are discussed in the light of anomalous seismic behavior, and comparisons are given showing theoretical versus experimental results. In conclusion, current ground motion prediction techniques are applied to events off the NTS. Predictions are compared with measurements for the event Faultless and for the Plowshare events, Gasbuggy, Cabriolet, and Buggy I. (author)

  5. Ground motion predictions

    International Nuclear Information System (INIS)

    Loux, P.C.

    1969-01-01

    Nuclear generated ground motion is defined and then related to the physical parameters that cause it. Techniques employed for prediction of ground motion peak amplitude, frequency spectra and response spectra are explored, with initial emphasis on the analysis of data collected at the Nevada Test Site (NTS). NTS postshot measurements are compared with pre-shot predictions. Applicability of these techniques to new areas, for example, Plowshare sites, must be questioned. Fortunately, the Atomic Energy Commission is sponsoring complementary studies to improve prediction capabilities primarily in new locations outside the NTS region. Some of these are discussed in the light of anomalous seismic behavior, and comparisons are given showing theoretical versus experimental results. In conclusion, current ground motion prediction techniques are applied to events off the NTS. Predictions are compared with measurements for the event Faultless and for the Plowshare events, Gasbuggy, Cabriolet, and Buggy I. (author)

  6. Structural prediction in aphasia

    Directory of Open Access Journals (Sweden)

    Tessa Warren

    2015-05-01

    Full Text Available There is considerable evidence that young healthy comprehenders predict the structure of upcoming material, and that their processing is facilitated when they encounter material matching those predictions (e.g., Staub & Clifton, 2006; Yoshida, Dickey & Sturt, 2013. However, less is known about structural prediction in aphasia. There is evidence that lexical prediction may be spared in aphasia (Dickey et al., 2014; Love & Webb, 1977; cf. Mack et al, 2013. However, predictive mechanisms supporting facilitated lexical access may not necessarily support structural facilitation. Given that many people with aphasia (PWA exhibit syntactic deficits (e.g. Goodglass, 1993, PWA with such impairments may not engage in structural prediction. However, recent evidence suggests that some PWA may indeed predict upcoming structure (Hanne, Burchert, De Bleser, & Vashishth, 2015. Hanne et al. tracked the eyes of PWA (n=8 with sentence-comprehension deficits while they listened to reversible subject-verb-object (SVO and object-verb-subject (OVS sentences in German, in a sentence-picture matching task. Hanne et al. manipulated case and number marking to disambiguate the sentences’ structure. Gazes to an OVS or SVO picture during the unfolding of a sentence were assumed to indicate prediction of the structure congruent with that picture. According to this measure, the PWA’s structural prediction was impaired compared to controls, but they did successfully predict upcoming structure when morphosyntactic cues were strong and unambiguous. Hanne et al.’s visual-world evidence is suggestive, but their forced-choice sentence-picture matching task places tight constraints on possible structural predictions. Clearer evidence of structural prediction would come from paradigms where the content of upcoming material is not as constrained. The current study used self-paced reading study to examine structural prediction among PWA in less constrained contexts. PWA (n=17 who

  7. Prediction of bull fertility.

    Science.gov (United States)

    Utt, Matthew D

    2016-06-01

    Prediction of male fertility is an often sought-after endeavor for many species of domestic animals. This review will primarily focus on providing some examples of dependent and independent variables to stimulate thought about the approach and methodology of identifying the most appropriate of those variables to predict bull (bovine) fertility. Although the list of variables will continue to grow with advancements in science, the principles behind making predictions will likely not change significantly. The basic principle of prediction requires identifying a dependent variable that is an estimate of fertility and an independent variable or variables that may be useful in predicting the fertility estimate. Fertility estimates vary in which parts of the process leading to conception that they infer about and the amount of variation that influences the estimate and the uncertainty thereof. The list of potential independent variables can be divided into competence of sperm based on their performance in bioassays or direct measurement of sperm attributes. A good prediction will use a sample population of bulls that is representative of the population to which an inference will be made. Both dependent and independent variables should have a dynamic range in their values. Careful selection of independent variables includes reasonable measurement repeatability and minimal correlation among variables. Proper estimation and having an appreciation of the degree of uncertainty of dependent and independent variables are crucial for using predictions to make decisions regarding bull fertility. Copyright © 2016 Elsevier B.V. All rights reserved.

  8. Bootstrap prediction and Bayesian prediction under misspecified models

    OpenAIRE

    Fushiki, Tadayoshi

    2005-01-01

    We consider a statistical prediction problem under misspecified models. In a sense, Bayesian prediction is an optimal prediction method when an assumed model is true. Bootstrap prediction is obtained by applying Breiman's `bagging' method to a plug-in prediction. Bootstrap prediction can be considered to be an approximation to the Bayesian prediction under the assumption that the model is true. However, in applications, there are frequently deviations from the assumed model. In this paper, bo...

  9. Prediction ranges. Annual review

    Energy Technology Data Exchange (ETDEWEB)

    Parker, J.C.; Tharp, W.H.; Spiro, P.S.; Keng, K.; Angastiniotis, M.; Hachey, L.T.

    1988-01-01

    Prediction ranges equip the planner with one more tool for improved assessment of the outcome of a course of action. One of their major uses is in financial evaluations, where corporate policy requires the performance of uncertainty analysis for large projects. This report gives an overview of the uses of prediction ranges, with examples; and risks and uncertainties in growth, inflation, and interest and exchange rates. Prediction ranges and standard deviations of 80% and 50% probability are given for various economic indicators in Ontario, Canada, and the USA, as well as for foreign exchange rates and Ontario Hydro interest rates. An explanatory note on probability is also included. 23 tabs.

  10. Wind power prediction models

    Science.gov (United States)

    Levy, R.; Mcginness, H.

    1976-01-01

    Investigations were performed to predict the power available from the wind at the Goldstone, California, antenna site complex. The background for power prediction was derived from a statistical evaluation of available wind speed data records at this location and at nearby locations similarly situated within the Mojave desert. In addition to a model for power prediction over relatively long periods of time, an interim simulation model that produces sample wind speeds is described. The interim model furnishes uncorrelated sample speeds at hourly intervals that reproduce the statistical wind distribution at Goldstone. A stochastic simulation model to provide speed samples representative of both the statistical speed distributions and correlations is also discussed.

  11. Protein Sorting Prediction

    DEFF Research Database (Denmark)

    Nielsen, Henrik

    2017-01-01

    and drawbacks of each of these approaches is described through many examples of methods that predict secretion, integration into membranes, or subcellular locations in general. The aim of this chapter is to provide a user-level introduction to the field with a minimum of computational theory.......Many computational methods are available for predicting protein sorting in bacteria. When comparing them, it is important to know that they can be grouped into three fundamentally different approaches: signal-based, global-property-based and homology-based prediction. In this chapter, the strengths...

  12. 'Red Flag' Predictions

    DEFF Research Database (Denmark)

    Hallin, Carina Antonia; Andersen, Torben Juul; Tveterås, Sigbjørn

    -generation prediction markets and outline its unique features as a third-generation prediction market. It is argued that frontline employees gain deep insights when they execute operational activities on an ongoing basis in the organization. The experiential learning from close interaction with internal and external......This conceptual article introduces a new way to predict firm performance based on aggregation of sensing among frontline employees about changes in operational capabilities to update strategic action plans and generate innovations. We frame the approach in the context of first- and second...

  13. Towards Predictive Association Theories

    DEFF Research Database (Denmark)

    Kontogeorgis, Georgios; Tsivintzelis, Ioannis; Michelsen, Michael Locht

    2011-01-01

    Association equations of state like SAFT, CPA and NRHB have been previously applied to many complex mixtures. In this work we focus on two of these models, the CPA and the NRHB equations of state and the emphasis is on the analysis of their predictive capabilities for a wide range of applications....... We use the term predictive in two situations: (i) with no use of binary interaction parameters, and (ii) multicomponent calculations using binary interaction parameters based solely on binary data. It is shown that the CPA equation of state can satisfactorily predict CO2–water–glycols–alkanes VLE...

  14. Prediction of intermetallic compounds

    International Nuclear Information System (INIS)

    Burkhanov, Gennady S; Kiselyova, N N

    2009-01-01

    The problems of predicting not yet synthesized intermetallic compounds are discussed. It is noted that the use of classical physicochemical analysis in the study of multicomponent metallic systems is faced with the complexity of presenting multidimensional phase diagrams. One way of predicting new intermetallics with specified properties is the use of modern processing technology with application of teaching of image recognition by the computer. The algorithms used most often in these methods are briefly considered and the efficiency of their use for predicting new compounds is demonstrated.

  15. Filtering and prediction

    CERN Document Server

    Fristedt, B; Krylov, N

    2007-01-01

    Filtering and prediction is about observing moving objects when the observations are corrupted by random errors. The main focus is then on filtering out the errors and extracting from the observations the most precise information about the object, which itself may or may not be moving in a somewhat random fashion. Next comes the prediction step where, using information about the past behavior of the object, one tries to predict its future path. The first three chapters of the book deal with discrete probability spaces, random variables, conditioning, Markov chains, and filtering of discrete Markov chains. The next three chapters deal with the more sophisticated notions of conditioning in nondiscrete situations, filtering of continuous-space Markov chains, and of Wiener process. Filtering and prediction of stationary sequences is discussed in the last two chapters. The authors believe that they have succeeded in presenting necessary ideas in an elementary manner without sacrificing the rigor too much. Such rig...

  16. CMAQ predicted concentration files

    Data.gov (United States)

    U.S. Environmental Protection Agency — CMAQ predicted ozone. This dataset is associated with the following publication: Gantt, B., G. Sarwar, J. Xing, H. Simon, D. Schwede, B. Hutzell, R. Mathur, and A....

  17. Methane prediction in collieries

    CSIR Research Space (South Africa)

    Creedy, DP

    1999-06-01

    Full Text Available The primary aim of the project was to assess the current status of research on methane emission prediction for collieries in South Africa in comparison with methods used and advances achieved elsewhere in the world....

  18. Climate Prediction Center - Outlooks

    Science.gov (United States)

    Weather Service NWS logo - Click to go to the NWS home page Climate Prediction Center Home Site Map News Web resources and services. HOME > Outreach > Publications > Climate Diagnostics Bulletin Climate Diagnostics Bulletin - Tropics Climate Diagnostics Bulletin - Forecast Climate Diagnostics

  19. CMAQ predicted concentration files

    Data.gov (United States)

    U.S. Environmental Protection Agency — model predicted concentrations. This dataset is associated with the following publication: Muñiz-Unamunzaga, M., R. Borge, G. Sarwar, B. Gantt, D. de la Paz, C....

  20. Comparing Spatial Predictions

    KAUST Repository

    Hering, Amanda S.; Genton, Marc G.

    2011-01-01

    Under a general loss function, we develop a hypothesis test to determine whether a significant difference in the spatial predictions produced by two competing models exists on average across the entire spatial domain of interest. The null hypothesis

  1. Genomic prediction using subsampling

    OpenAIRE

    Xavier, Alencar; Xu, Shizhong; Muir, William; Rainey, Katy Martin

    2017-01-01

    Background Genome-wide assisted selection is a critical tool for the?genetic improvement of plants and animals. Whole-genome regression models in Bayesian framework represent the main family of prediction methods. Fitting such models with a large number of observations involves a prohibitive computational burden. We propose the use of subsampling bootstrap Markov chain in genomic prediction. Such method consists of fitting whole-genome regression models by subsampling observations in each rou...

  2. Predicting Online Purchasing Behavior

    OpenAIRE

    W.R BUCKINX; D. VAN DEN POEL

    2003-01-01

    This empirical study investigates the contribution of different types of predictors to the purchasing behaviour at an online store. We use logit modelling to predict whether or not a purchase is made during the next visit to the website using both forward and backward variable-selection techniques, as well as Furnival and Wilson’s global score search algorithm to find the best subset of predictors. We contribute to the literature by using variables from four different categories in predicting...

  3. Empirical Flutter Prediction Method.

    Science.gov (United States)

    1988-03-05

    been used in this way to discover species or subspecies of animals, and to discover different types of voter or comsumer requiring different persuasions...respect to behavior or performance or response variables. Once this were done, corresponding clusters might be sought among descriptive or predictive or...jump in a response. The first sort of usage does not apply to the flutter prediction problem. Here the types of behavior are the different kinds of

  4. Stuck pipe prediction

    KAUST Repository

    Alzahrani, Majed

    2016-03-10

    Disclosed are various embodiments for a prediction application to predict a stuck pipe. A linear regression model is generated from hook load readings at corresponding bit depths. A current hook load reading at a current bit depth is compared with a normal hook load reading from the linear regression model. A current hook load greater than a normal hook load for a given bit depth indicates the likelihood of a stuck pipe.

  5. Stuck pipe prediction

    KAUST Repository

    Alzahrani, Majed; Alsolami, Fawaz; Chikalov, Igor; Algharbi, Salem; Aboudi, Faisal; Khudiri, Musab

    2016-01-01

    Disclosed are various embodiments for a prediction application to predict a stuck pipe. A linear regression model is generated from hook load readings at corresponding bit depths. A current hook load reading at a current bit depth is compared with a normal hook load reading from the linear regression model. A current hook load greater than a normal hook load for a given bit depth indicates the likelihood of a stuck pipe.

  6. Genomic prediction using subsampling.

    Science.gov (United States)

    Xavier, Alencar; Xu, Shizhong; Muir, William; Rainey, Katy Martin

    2017-03-24

    Genome-wide assisted selection is a critical tool for the genetic improvement of plants and animals. Whole-genome regression models in Bayesian framework represent the main family of prediction methods. Fitting such models with a large number of observations involves a prohibitive computational burden. We propose the use of subsampling bootstrap Markov chain in genomic prediction. Such method consists of fitting whole-genome regression models by subsampling observations in each round of a Markov Chain Monte Carlo. We evaluated the effect of subsampling bootstrap on prediction and computational parameters. Across datasets, we observed an optimal subsampling proportion of observations around 50% with replacement, and around 33% without replacement. Subsampling provided a substantial decrease in computation time, reducing the time to fit the model by half. On average, losses on predictive properties imposed by subsampling were negligible, usually below 1%. For each dataset, an optimal subsampling point that improves prediction properties was observed, but the improvements were also negligible. Combining subsampling with Gibbs sampling is an interesting ensemble algorithm. The investigation indicates that the subsampling bootstrap Markov chain algorithm substantially reduces computational burden associated with model fitting, and it may slightly enhance prediction properties.

  7. Deep Visual Attention Prediction

    Science.gov (United States)

    Wang, Wenguan; Shen, Jianbing

    2018-05-01

    In this work, we aim to predict human eye fixation with view-free scenes based on an end-to-end deep learning architecture. Although Convolutional Neural Networks (CNNs) have made substantial improvement on human attention prediction, it is still needed to improve CNN based attention models by efficiently leveraging multi-scale features. Our visual attention network is proposed to capture hierarchical saliency information from deep, coarse layers with global saliency information to shallow, fine layers with local saliency response. Our model is based on a skip-layer network structure, which predicts human attention from multiple convolutional layers with various reception fields. Final saliency prediction is achieved via the cooperation of those global and local predictions. Our model is learned in a deep supervision manner, where supervision is directly fed into multi-level layers, instead of previous approaches of providing supervision only at the output layer and propagating this supervision back to earlier layers. Our model thus incorporates multi-level saliency predictions within a single network, which significantly decreases the redundancy of previous approaches of learning multiple network streams with different input scales. Extensive experimental analysis on various challenging benchmark datasets demonstrate our method yields state-of-the-art performance with competitive inference time.

  8. Candidate Prediction Models and Methods

    DEFF Research Database (Denmark)

    Nielsen, Henrik Aalborg; Nielsen, Torben Skov; Madsen, Henrik

    2005-01-01

    This document lists candidate prediction models for Work Package 3 (WP3) of the PSO-project called ``Intelligent wind power prediction systems'' (FU4101). The main focus is on the models transforming numerical weather predictions into predictions of power production. The document also outlines...... the possibilities w.r.t. different numerical weather predictions actually available to the project....

  9. Nanobody based immunoassay for human soluble epoxide hydrolase detection using polyHRP for signal enhancement—the rediscovery of polyHRP

    Science.gov (United States)

    Soluble epoxide hydrolase (sEH) is a potential pharmacological target for treating hypertension, vascular inflammation, cancer, pain and multiple cardiovascular related diseases. A variable domain of a heavy chain only antibody (termed sdAb, nanobody or VHH) possesses advantages of small size, high ...

  10. Transionospheric propagation predictions

    Science.gov (United States)

    Klobucher, J. A.; Basu, S.; Basu, S.; Bernhardt, P. A.; Davies, K.; Donatelli, D. E.; Fremouw, E. J.; Goodman, J. M.; Hartmann, G. K.; Leitinger, R.

    1979-01-01

    The current status and future prospects of the capability to make transionospheric propagation predictions are addressed, highlighting the effects of the ionized media, which dominate for frequencies below 1 to 3 GHz, depending upon the state of the ionosphere and the elevation angle through the Earth-space path. The primary concerns are the predictions of time delay of signal modulation (group path delay) and of radio wave scintillation. Progress in these areas is strongly tied to knowledge of variable structures in the ionosphere ranging from the large scale (thousands of kilometers in horizontal extent) to the fine scale (kilometer size). Ionospheric variability and the relative importance of various mechanisms responsible for the time histories observed in total electron content (TEC), proportional to signal group delay, and in irregularity formation are discussed in terms of capability to make both short and long term predictions. The data base upon which predictions are made is examined for its adequacy, and the prospects for prediction improvements by more theoretical studies as well as by increasing the available statistical data base are examined.

  11. Predictable grammatical constructions

    DEFF Research Database (Denmark)

    Lucas, Sandra

    2015-01-01

    My aim in this paper is to provide evidence from diachronic linguistics for the view that some predictable units are entrenched in grammar and consequently in human cognition, in a way that makes them functionally and structurally equal to nonpredictable grammatical units, suggesting that these p......My aim in this paper is to provide evidence from diachronic linguistics for the view that some predictable units are entrenched in grammar and consequently in human cognition, in a way that makes them functionally and structurally equal to nonpredictable grammatical units, suggesting...... that these predictable units should be considered grammatical constructions on a par with the nonpredictable constructions. Frequency has usually been seen as the only possible argument speaking in favor of viewing some formally and semantically fully predictable units as grammatical constructions. However, this paper...... semantically and formally predictable. Despite this difference, [méllo INF], like the other future periphrases, seems to be highly entrenched in the cognition (and grammar) of Early Medieval Greek language users, and consequently a grammatical construction. The syntactic evidence speaking in favor of [méllo...

  12. Essays on Earnings Predictability

    DEFF Research Database (Denmark)

    Bruun, Mark

    This dissertation addresses the prediction of corporate earnings. The thesis aims to examine whether the degree of precision in earnings forecasts can be increased by basing them on historical financial ratios. Furthermore, the intent of the dissertation is to analyze whether accounting standards...... forecasts are not more accurate than the simpler forecasts based on a historical timeseries of earnings. Secondly, the dissertation shows how accounting standards affect analysts’ earnings predictions. Accounting conservatism contributes to a more volatile earnings process, which lowers the accuracy...... of analysts’ earnings forecasts. Furthermore, the dissertation shows how the stock market’s reaction to the disclosure of information about corporate earnings depends on how well corporate earnings can be predicted. The dissertation indicates that the stock market’s reaction to the disclosure of earnings...

  13. Pulverized coal devolatilization prediction

    International Nuclear Information System (INIS)

    Rojas, Andres F; Barraza, Juan M

    2008-01-01

    The aim of this study was to predict the two bituminous coals devolatilization at low rate of heating (50 Celsius degrade/min), with program FG-DVC (functional group Depolymerization. Vaporization and crosslinking), and to compare the devolatilization profiles predicted by program FG-DVC, which are obtained in the thermogravimetric analyzer. It was also study the volatile liberation at (10 4 k/s) in a drop-tube furnace. The tar, methane, carbon monoxide, and carbon dioxide, formation rate profiles, and the hydrogen, oxygen, nitrogen and sulphur, elemental distribution in the devolatilization products by FG-DVC program at low rate of heating was obtained; and the liberation volatile and R factor at high rate of heating was calculated. it was found that the program predicts the bituminous coals devolatilization at low rate heating, at high rate heating, a volatile liberation around 30% was obtained

  14. Predicting Ideological Prejudice.

    Science.gov (United States)

    Brandt, Mark J

    2017-06-01

    A major shortcoming of current models of ideological prejudice is that although they can anticipate the direction of the association between participants' ideology and their prejudice against a range of target groups, they cannot predict the size of this association. I developed and tested models that can make specific size predictions for this association. A quantitative model that used the perceived ideology of the target group as the primary predictor of the ideology-prejudice relationship was developed with a representative sample of Americans ( N = 4,940) and tested against models using the perceived status of and choice to belong to the target group as predictors. In four studies (total N = 2,093), ideology-prejudice associations were estimated, and these observed estimates were compared with the models' predictions. The model that was based only on perceived ideology was the most parsimonious with the smallest errors.

  15. Inverse and Predictive Modeling

    Energy Technology Data Exchange (ETDEWEB)

    Syracuse, Ellen Marie [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2017-09-27

    The LANL Seismo-Acoustic team has a strong capability in developing data-driven models that accurately predict a variety of observations. These models range from the simple – one-dimensional models that are constrained by a single dataset and can be used for quick and efficient predictions – to the complex – multidimensional models that are constrained by several types of data and result in more accurate predictions. Team members typically build models of geophysical characteristics of Earth and source distributions at scales of 1 to 1000s of km, the techniques used are applicable for other types of physical characteristics at an even greater range of scales. The following cases provide a snapshot of some of the modeling work done by the Seismo- Acoustic team at LANL.

  16. Tide Predictions, California, 2014, NOAA

    Data.gov (United States)

    U.S. Environmental Protection Agency — The predictions from the web based NOAA Tide Predictions are based upon the latest information available as of the date of the user's request. Tide predictions...

  17. Predictive maintenance primer

    International Nuclear Information System (INIS)

    Flude, J.W.; Nicholas, J.R.

    1991-04-01

    This Predictive Maintenance Primer provides utility plant personnel with a single-source reference to predictive maintenance analysis methods and technologies used successfully by utilities and other industries. It is intended to be a ready reference to personnel considering starting, expanding or improving a predictive maintenance program. This Primer includes a discussion of various analysis methods and how they overlap and interrelate. Additionally, eighteen predictive maintenance technologies are discussed in sufficient detail for the user to evaluate the potential of each technology for specific applications. This document is designed to allow inclusion of additional technologies in the future. To gather the information necessary to create this initial Primer the Nuclear Maintenance Applications Center (NMAC) collected experience data from eighteen utilities plus other industry and government sources. NMAC also contacted equipment manufacturers for information pertaining to equipment utilization, maintenance, and technical specifications. The Primer includes a discussion of six methods used by analysts to study predictive maintenance data. These are: trend analysis; pattern recognition; correlation; test against limits or ranges; relative comparison data; and statistical process analysis. Following the analysis methods discussions are detailed descriptions for eighteen technologies analysts have found useful for predictive maintenance programs at power plants and other industrial facilities. Each technology subchapter has a description of the operating principles involved in the technology, a listing of plant equipment where the technology can be applied, and a general description of the monitoring equipment. Additionally, these descriptions include a discussion of results obtained from actual equipment users and preferred analysis techniques to be used on data obtained from the technology. 5 refs., 30 figs

  18. Predicting tile drainage discharge

    DEFF Research Database (Denmark)

    Iversen, Bo Vangsø; Kjærgaard, Charlotte; Petersen, Rasmus Jes

    used in the analysis. For the dynamic modelling, a simple linear reservoir model was used where different outlets in the model represented tile drain as well as groundwater discharge outputs. This modelling was based on daily measured tile drain discharge values. The statistical predictive model...... was based on a polynomial regression predicting yearly tile drain discharge values using site specific parameters such as soil type, catchment topography, etc. as predictors. Values of calibrated model parameters from the dynamic modelling were compared to the same site specific parameter as used...

  19. Linguistic Structure Prediction

    CERN Document Server

    Smith, Noah A

    2011-01-01

    A major part of natural language processing now depends on the use of text data to build linguistic analyzers. We consider statistical, computational approaches to modeling linguistic structure. We seek to unify across many approaches and many kinds of linguistic structures. Assuming a basic understanding of natural language processing and/or machine learning, we seek to bridge the gap between the two fields. Approaches to decoding (i.e., carrying out linguistic structure prediction) and supervised and unsupervised learning of models that predict discrete structures as outputs are the focus. W

  20. Predicting Anthracycline Benefit

    DEFF Research Database (Denmark)

    Bartlett, John M S; McConkey, Christopher C; Munro, Alison F

    2015-01-01

    PURPOSE: Evidence supporting the clinical utility of predictive biomarkers of anthracycline activity is weak, with a recent meta-analysis failing to provide strong evidence for either HER2 or TOP2A. Having previously shown that duplication of chromosome 17 pericentromeric alpha satellite as measu......PURPOSE: Evidence supporting the clinical utility of predictive biomarkers of anthracycline activity is weak, with a recent meta-analysis failing to provide strong evidence for either HER2 or TOP2A. Having previously shown that duplication of chromosome 17 pericentromeric alpha satellite...

  1. Prediction of Antibody Epitopes

    DEFF Research Database (Denmark)

    Nielsen, Morten; Marcatili, Paolo

    2015-01-01

    Antibodies recognize their cognate antigens in a precise and effective way. In order to do so, they target regions of the antigenic molecules that have specific features such as large exposed areas, presence of charged or polar atoms, specific secondary structure elements, and lack of similarity...... to self-proteins. Given the sequence or the structure of a protein of interest, several methods exploit such features to predict the residues that are more likely to be recognized by an immunoglobulin.Here, we present two methods (BepiPred and DiscoTope) to predict linear and discontinuous antibody...

  2. Basis of predictive mycology.

    Science.gov (United States)

    Dantigny, Philippe; Guilmart, Audrey; Bensoussan, Maurice

    2005-04-15

    For over 20 years, predictive microbiology focused on food-pathogenic bacteria. Few studies concerned modelling fungal development. On one hand, most of food mycologists are not familiar with modelling techniques; on the other hand, people involved in modelling are developing tools dedicated to bacteria. Therefore, there is a tendency to extend the use of models that were developed for bacteria to moulds. However, some mould specificities should be taken into account. The use of specific models for predicting germination and growth of fungi was advocated previously []. This paper provides a short review of fungal modelling studies.

  3. Dopamine reward prediction error coding

    OpenAIRE

    Schultz, Wolfram

    2016-01-01

    Reward prediction errors consist of the differences between received and predicted rewards. They are crucial for basic forms of learning about rewards and make us strive for more rewards?an evolutionary beneficial trait. Most dopamine neurons in the midbrain of humans, monkeys, and rodents signal a reward prediction error; they are activated by more reward than predicted (positive prediction error), remain at baseline activity for fully predicted rewards, and show depressed activity with less...

  4. Steering smog prediction

    NARCIS (Netherlands)

    R. van Liere (Robert); J.J. van Wijk (Jack)

    1997-01-01

    textabstractThe use of computational steering for smog prediction is described. This application is representative for many underlying issues found in steering high performance applications: high computing times, large data sets, and many different input parameters. After a short description of the

  5. Predicting Sustainable Work Behavior

    DEFF Research Database (Denmark)

    Hald, Kim Sundtoft

    2013-01-01

    Sustainable work behavior is an important issue for operations managers – it has implications for most outcomes of OM. This research explores the antecedents of sustainable work behavior. It revisits and extends the sociotechnical model developed by Brown et al. (2000) on predicting safe behavior...

  6. Gate valve performance prediction

    International Nuclear Information System (INIS)

    Harrison, D.H.; Damerell, P.S.; Wang, J.K.; Kalsi, M.S.; Wolfe, K.J.

    1994-01-01

    The Electric Power Research Institute is carrying out a program to improve the performance prediction methods for motor-operated valves. As part of this program, an analytical method to predict the stem thrust required to stroke a gate valve has been developed and has been assessed against data from gate valve tests. The method accounts for the loads applied to the disc by fluid flow and for the detailed mechanical interaction of the stem, disc, guides, and seats. To support development of the method, two separate-effects test programs were carried out. One test program determined friction coefficients for contacts between gate valve parts by using material specimens in controlled environments. The other test program investigated the interaction of the stem, disc, guides, and seat using a special fixture with full-sized gate valve parts. The method has been assessed against flow-loop and in-plant test data. These tests include valve sizes from 3 to 18 in. and cover a considerable range of flow, temperature, and differential pressure. Stem thrust predictions for the method bound measured results. In some cases, the bounding predictions are substantially higher than the stem loads required for valve operation, as a result of the bounding nature of the friction coefficients in the method

  7. Prediction method abstracts

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1994-12-31

    This conference was held December 4--8, 1994 in Asilomar, California. The purpose of this meeting was to provide a forum for exchange of state-of-the-art information concerning the prediction of protein structure. Attention if focused on the following: comparative modeling; sequence to fold assignment; and ab initio folding.

  8. Predicting Intrinsic Motivation

    Science.gov (United States)

    Martens, Rob; Kirschner, Paul A.

    2004-01-01

    Intrinsic motivation can be predicted from participants' perceptions of the social environment and the task environment (Ryan & Deci, 2000)in terms of control, relatedness and competence. To determine the degree of independence of these factors 251 students in higher vocational education (physiotherapy and hotel management) indicated the…

  9. Predicting visibility of aircraft.

    Directory of Open Access Journals (Sweden)

    Andrew Watson

    Full Text Available Visual detection of aircraft by human observers is an important element of aviation safety. To assess and ensure safety, it would be useful to be able to be able to predict the visibility, to a human observer, of an aircraft of specified size, shape, distance, and coloration. Examples include assuring safe separation among aircraft and between aircraft and unmanned vehicles, design of airport control towers, and efforts to enhance or suppress the visibility of military and rescue vehicles. We have recently developed a simple metric of pattern visibility, the Spatial Standard Observer (SSO. In this report we examine whether the SSO can predict visibility of simulated aircraft images. We constructed a set of aircraft images from three-dimensional computer graphic models, and measured the luminance contrast threshold for each image from three human observers. The data were well predicted by the SSO. Finally, we show how to use the SSO to predict visibility range for aircraft of arbitrary size, shape, distance, and coloration.

  10. Climate Prediction Center

    Science.gov (United States)

    Weather Service NWS logo - Click to go to the NWS home page Climate Prediction Center Home Site Map News Organization Enter Search Term(s): Search Search the CPC Go NCEP Quarterly Newsletter Climate Highlights U.S Climate-Weather El Niño/La Niña MJO Blocking AAO, AO, NAO, PNA Climatology Global Monsoons Expert

  11. Predicting Commissary Store Success

    Science.gov (United States)

    2014-12-01

    stores or if it is possible to predict that success. Multiple studies of private commercial grocery consumer preferences , habits and demographics have...appropriate number of competitors due to the nature of international cultures and consumer preferences . 2. Missing Data Four of the remaining stores

  12. Predicting Job Satisfaction.

    Science.gov (United States)

    Blai, Boris, Jr.

    Psychological theories about human motivation and accommodation to environment can be used to achieve a better understanding of the human factors that function in the work environment. Maslow's theory of human motivational behavior provided a theoretical framework for an empirically-derived method to predict job satisfaction and explore the…

  13. Ocean Prediction Center

    Science.gov (United States)

    Social Media Facebook Twitter YouTube Search Search For Go NWS All NOAA Weather Analysis & Forecasts of Commerce Ocean Prediction Center National Oceanic and Atmospheric Administration Analysis & Unified Surface Analysis Ocean Ocean Products Ice & Icebergs NIC Ice Products NAIS Iceberg Analysis

  14. Predicting Reasoning from Memory

    Science.gov (United States)

    Heit, Evan; Hayes, Brett K.

    2011-01-01

    In an effort to assess the relations between reasoning and memory, in 8 experiments, the authors examined how well responses on an inductive reasoning task are predicted from responses on a recognition memory task for the same picture stimuli. Across several experimental manipulations, such as varying study time, presentation frequency, and the…

  15. Predicting coronary heart disease

    DEFF Research Database (Denmark)

    Sillesen, Henrik; Fuster, Valentin

    2012-01-01

    Atherosclerosis is the leading cause of death and disabling disease. Whereas risk factors are well known and constitute therapeutic targets, they are not useful for prediction of risk of future myocardial infarction, stroke, or death. Therefore, methods to identify atherosclerosis itself have bee...

  16. ANTHROPOMETRIC PREDICTIVE EQUATIONS FOR ...

    African Journals Online (AJOL)

    Keywords: Anthropometry, Predictive Equations, Percentage Body Fat, Nigerian Women, Bioelectric Impedance ... such as Asians and Indians (Pranav et al., 2009), ... size (n) of at least 3o is adjudged as sufficient for the ..... of people, gender and age (Vogel eta/., 1984). .... Fish Sold at Ile-Ife Main Market, South West Nigeria.

  17. Predicting Pilot Retention

    Science.gov (United States)

    2012-06-15

    forever… Gig ‘Em! Dale W. Stanley III vii Table of Contents Page Acknowledgments...over the last 20 years. Airbus predicted that these trends would continue as emerging economies , especially in Asia, were creating a fast growing...US economy , pay differential and hiring by the major airlines contributed most to the decision to separate from the Air Force (Fullerton, 2003: 354

  18. Predicting ideological prejudice

    NARCIS (Netherlands)

    Brandt, M.J.

    2018-01-01

    A major shortcoming of current models of ideological prejudice is that although they can anticipate the direction of the association between participants’ ideology and their prejudice against a range of target groups, they cannot predict the size of this association. I developed and tested models

  19. Dopamine reward prediction error coding.

    Science.gov (United States)

    Schultz, Wolfram

    2016-03-01

    Reward prediction errors consist of the differences between received and predicted rewards. They are crucial for basic forms of learning about rewards and make us strive for more rewards-an evolutionary beneficial trait. Most dopamine neurons in the midbrain of humans, monkeys, and rodents signal a reward prediction error; they are activated by more reward than predicted (positive prediction error), remain at baseline activity for fully predicted rewards, and show depressed activity with less reward than predicted (negative prediction error). The dopamine signal increases nonlinearly with reward value and codes formal economic utility. Drugs of addiction generate, hijack, and amplify the dopamine reward signal and induce exaggerated, uncontrolled dopamine effects on neuronal plasticity. The striatum, amygdala, and frontal cortex also show reward prediction error coding, but only in subpopulations of neurons. Thus, the important concept of reward prediction errors is implemented in neuronal hardware.

  20. Urban pluvial flood prediction

    DEFF Research Database (Denmark)

    Thorndahl, Søren Liedtke; Nielsen, Jesper Ellerbæk; Jensen, David Getreuer

    2016-01-01

    Flooding produced by high-intensive local rainfall and drainage system capacity exceedance can have severe impacts in cities. In order to prepare cities for these types of flood events – especially in the future climate – it is valuable to be able to simulate these events numerically both...... historically and in real-time. There is a rather untested potential in real-time prediction of urban floods. In this paper radar data observations with different spatial and temporal resolution, radar nowcasts of 0–2 h lead time, and numerical weather models with lead times up to 24 h are used as inputs...... to an integrated flood and drainage systems model in order to investigate the relative difference between different inputs in predicting future floods. The system is tested on a small town Lystrup in Denmark, which has been flooded in 2012 and 2014. Results show it is possible to generate detailed flood maps...

  1. Predicting Bankruptcy in Pakistan

    Directory of Open Access Journals (Sweden)

    Abdul RASHID

    2011-09-01

    Full Text Available This paper aims to identify the financial ratios that are most significant in bankruptcy prediction for the non-financial sector of Pakistan based on a sample of companies which became bankrupt over the time period 1996-2006. Twenty four financial ratios covering four important financial attributes, namely profitability, liquidity, leverage, and turnover ratios, were examined for a five-year period prior bankruptcy. The discriminant analysis produced a parsimonious model of three variables viz. sales to total assets, EBIT to current liabilities, and cash flow ratio. Our estimates provide evidence that the firms having Z-value below zero fall into the “bankrupt” whereas the firms with Z-value above zero fall into the “non-bankrupt” category. The model achieved 76.9% prediction accuracy when it is applied to forecast bankruptcies on the underlying sample.

  2. Predicting Lotto Numbers

    DEFF Research Database (Denmark)

    Jørgensen, Claus Bjørn; Suetens, Sigrid; Tyran, Jean-Robert

    numbers based on recent drawings. While most players pick the same set of numbers week after week without regards of numbers drawn or anything else, we find that those who do change, act on average in the way predicted by the law of small numbers as formalized in recent behavioral theory. In particular......We investigate the “law of small numbers” using a unique panel data set on lotto gambling. Because we can track individual players over time, we can measure how they react to outcomes of recent lotto drawings. We can therefore test whether they behave as if they believe they can predict lotto......, on average they move away from numbers that have recently been drawn, as suggested by the “gambler’s fallacy”, and move toward numbers that are on streak, i.e. have been drawn several weeks in a row, consistent with the “hot hand fallacy”....

  3. Comparing Spatial Predictions

    KAUST Repository

    Hering, Amanda S.

    2011-11-01

    Under a general loss function, we develop a hypothesis test to determine whether a significant difference in the spatial predictions produced by two competing models exists on average across the entire spatial domain of interest. The null hypothesis is that of no difference, and a spatial loss differential is created based on the observed data, the two sets of predictions, and the loss function chosen by the researcher. The test assumes only isotropy and short-range spatial dependence of the loss differential but does allow it to be non-Gaussian, non-zero-mean, and spatially correlated. Constant and nonconstant spatial trends in the loss differential are treated in two separate cases. Monte Carlo simulations illustrate the size and power properties of this test, and an example based on daily average wind speeds in Oklahoma is used for illustration. Supplemental results are available online. © 2011 American Statistical Association and the American Society for Qualitys.

  4. Chaos detection and predictability

    CERN Document Server

    Gottwald, Georg; Laskar, Jacques

    2016-01-01

    Distinguishing chaoticity from regularity in deterministic dynamical systems and specifying the subspace of the phase space in which instabilities are expected to occur is of utmost importance in as disparate areas as astronomy, particle physics and climate dynamics.   To address these issues there exists a plethora of methods for chaos detection and predictability. The most commonly employed technique for investigating chaotic dynamics, i.e. the computation of Lyapunov exponents, however, may suffer a number of problems and drawbacks, for example when applied to noisy experimental data.   In the last two decades, several novel methods have been developed for the fast and reliable determination of the regular or chaotic nature of orbits, aimed at overcoming the shortcomings of more traditional techniques. This set of lecture notes and tutorial reviews serves as an introduction to and overview of modern chaos detection and predictability techniques for graduate students and non-specialists.   The book cover...

  5. Time-predictable architectures

    CERN Document Server

    Rochange, Christine; Uhrig , Sascha

    2014-01-01

    Building computers that can be used to design embedded real-time systems is the subject of this title. Real-time embedded software requires increasingly higher performances. The authors therefore consider processors that implement advanced mechanisms such as pipelining, out-of-order execution, branch prediction, cache memories, multi-threading, multicorearchitectures, etc. The authors of this book investigate the timepredictability of such schemes.

  6. Cultural Resource Predictive Modeling

    Science.gov (United States)

    2017-10-01

    CR cultural resource CRM cultural resource management CRPM Cultural Resource Predictive Modeling DoD Department of Defense ESTCP Environmental...resource management ( CRM ) legal obligations under NEPA and the NHPA, military installations need to demonstrate that CRM decisions are based on objective...maxim “one size does not fit all,” and demonstrate that DoD installations have many different CRM needs that can and should be met through a variety

  7. Predictive Game Theory

    Science.gov (United States)

    Wolpert, David H.

    2005-01-01

    Probability theory governs the outcome of a game; there is a distribution over mixed strat.'s, not a single "equilibrium". To predict a single mixed strategy must use our loss function (external to the game's players. Provides a quantification of any strategy's rationality. Prove rationality falls as cost of computation rises (for players who have not previously interacted). All extends to games with varying numbers of players.

  8. Predicting appointment breaking.

    Science.gov (United States)

    Bean, A G; Talaga, J

    1995-01-01

    The goal of physician referral services is to schedule appointments, but if too many patients fail to show up, the value of the service will be compromised. The authors found that appointment breaking can be predicted by the number of days to the scheduled appointment, the doctor's specialty, and the patient's age and gender. They also offer specific suggestions for modifying the marketing mix to reduce the incidence of no-shows.

  9. Adjusting estimative prediction limits

    OpenAIRE

    Masao Ueki; Kaoru Fueda

    2007-01-01

    This note presents a direct adjustment of the estimative prediction limit to reduce the coverage error from a target value to third-order accuracy. The adjustment is asymptotically equivalent to those of Barndorff-Nielsen & Cox (1994, 1996) and Vidoni (1998). It has a simpler form with a plug-in estimator of the coverage probability of the estimative limit at the target value. Copyright 2007, Oxford University Press.

  10. Space Weather Prediction

    Science.gov (United States)

    2014-10-31

    prominence eruptions and the ensuing coronal mass ejections. The ProMag is a spectro - polarimeter, consisting of a dual-beam polarization modulation unit...feeding a visible camera and an infrared camera. The instrument is designed to measure magnetic fields in solar prominences by simultaneous spectro ...as a result of coronal hole regions, we expect to improve UV predictions by incorporating an estimate of the Earth-side coronal hole regions. 5

  11. Instrument uncertainty predictions

    International Nuclear Information System (INIS)

    Coutts, D.A.

    1991-07-01

    The accuracy of measurements and correlations should normally be provided for most experimental activities. The uncertainty is a measure of the accuracy of a stated value or equation. The uncertainty term reflects a combination of instrument errors, modeling limitations, and phenomena understanding deficiencies. This report provides several methodologies to estimate an instrument's uncertainty when used in experimental work. Methods are shown to predict both the pretest and post-test uncertainty

  12. Predictive Systems Toxicology

    KAUST Repository

    Kiani, Narsis A.; Shang, Ming-Mei; Zenil, Hector; Tegner, Jesper

    2018-01-01

    In this review we address to what extent computational techniques can augment our ability to predict toxicity. The first section provides a brief history of empirical observations on toxicity dating back to the dawn of Sumerian civilization. Interestingly, the concept of dose emerged very early on, leading up to the modern emphasis on kinetic properties, which in turn encodes the insight that toxicity is not solely a property of a compound but instead depends on the interaction with the host organism. The next logical step is the current conception of evaluating drugs from a personalized medicine point-of-view. We review recent work on integrating what could be referred to as classical pharmacokinetic analysis with emerging systems biology approaches incorporating multiple omics data. These systems approaches employ advanced statistical analytical data processing complemented with machine learning techniques and use both pharmacokinetic and omics data. We find that such integrated approaches not only provide improved predictions of toxicity but also enable mechanistic interpretations of the molecular mechanisms underpinning toxicity and drug resistance. We conclude the chapter by discussing some of the main challenges, such as how to balance the inherent tension between the predictive capacity of models, which in practice amounts to constraining the number of features in the models versus allowing for rich mechanistic interpretability, i.e. equipping models with numerous molecular features. This challenge also requires patient-specific predictions on toxicity, which in turn requires proper stratification of patients as regards how they respond, with or without adverse toxic effects. In summary, the transformation of the ancient concept of dose is currently successfully operationalized using rich integrative data encoded in patient-specific models.

  13. Predictive systems ecology

    OpenAIRE

    Evans, Matthew R.; Bithell, Mike; Cornell, Stephen J.; Dall, Sasha R. X.; D?az, Sandra; Emmott, Stephen; Ernande, Bruno; Grimm, Volker; Hodgson, David J.; Lewis, Simon L.; Mace, Georgina M.; Morecroft, Michael; Moustakas, Aristides; Murphy, Eugene; Newbold, Tim

    2013-01-01

    Human societies, and their well-being, depend to a significant extent on the state of the ecosystems that surround them. These ecosystems are changing rapidly usually in response to anthropogenic changes in the environment. To determine the likely impact of environmental change on ecosystems and the best ways to manage them, it would be desirable to be able to predict their future states. We present a proposal to develop the paradigm of ...

  14. UXO Burial Prediction Fidelity

    Science.gov (United States)

    2017-07-01

    models to capture detailed projectile dynamics during the early phases of water entry are wasted with regard to sediment -penetration depth prediction...ordnance (UXO) migrates and becomes exposed over time in response to water and sediment motion.  Such models need initial sediment penetration estimates...munition’s initial penetration depth into the sediment ,  the velocity of water at the water - sediment boundary (i.e., the bottom water velocity

  15. Predictive Systems Toxicology

    KAUST Repository

    Kiani, Narsis A.

    2018-01-15

    In this review we address to what extent computational techniques can augment our ability to predict toxicity. The first section provides a brief history of empirical observations on toxicity dating back to the dawn of Sumerian civilization. Interestingly, the concept of dose emerged very early on, leading up to the modern emphasis on kinetic properties, which in turn encodes the insight that toxicity is not solely a property of a compound but instead depends on the interaction with the host organism. The next logical step is the current conception of evaluating drugs from a personalized medicine point-of-view. We review recent work on integrating what could be referred to as classical pharmacokinetic analysis with emerging systems biology approaches incorporating multiple omics data. These systems approaches employ advanced statistical analytical data processing complemented with machine learning techniques and use both pharmacokinetic and omics data. We find that such integrated approaches not only provide improved predictions of toxicity but also enable mechanistic interpretations of the molecular mechanisms underpinning toxicity and drug resistance. We conclude the chapter by discussing some of the main challenges, such as how to balance the inherent tension between the predictive capacity of models, which in practice amounts to constraining the number of features in the models versus allowing for rich mechanistic interpretability, i.e. equipping models with numerous molecular features. This challenge also requires patient-specific predictions on toxicity, which in turn requires proper stratification of patients as regards how they respond, with or without adverse toxic effects. In summary, the transformation of the ancient concept of dose is currently successfully operationalized using rich integrative data encoded in patient-specific models.

  16. Predictive Surface Complexation Modeling

    Energy Technology Data Exchange (ETDEWEB)

    Sverjensky, Dimitri A. [Johns Hopkins Univ., Baltimore, MD (United States). Dept. of Earth and Planetary Sciences

    2016-11-29

    Surface complexation plays an important role in the equilibria and kinetics of processes controlling the compositions of soilwaters and groundwaters, the fate of contaminants in groundwaters, and the subsurface storage of CO2 and nuclear waste. Over the last several decades, many dozens of individual experimental studies have addressed aspects of surface complexation that have contributed to an increased understanding of its role in natural systems. However, there has been no previous attempt to develop a model of surface complexation that can be used to link all the experimental studies in order to place them on a predictive basis. Overall, my research has successfully integrated the results of the work of many experimentalists published over several decades. For the first time in studies of the geochemistry of the mineral-water interface, a practical predictive capability for modeling has become available. The predictive correlations developed in my research now enable extrapolations of experimental studies to provide estimates of surface chemistry for systems not yet studied experimentally and for natural and anthropogenically perturbed systems.

  17. Predicting Human Cooperation.

    Directory of Open Access Journals (Sweden)

    John J Nay

    Full Text Available The Prisoner's Dilemma has been a subject of extensive research due to its importance in understanding the ever-present tension between individual self-interest and social benefit. A strictly dominant strategy in a Prisoner's Dilemma (defection, when played by both players, is mutually harmful. Repetition of the Prisoner's Dilemma can give rise to cooperation as an equilibrium, but defection is as well, and this ambiguity is difficult to resolve. The numerous behavioral experiments investigating the Prisoner's Dilemma highlight that players often cooperate, but the level of cooperation varies significantly with the specifics of the experimental predicament. We present the first computational model of human behavior in repeated Prisoner's Dilemma games that unifies the diversity of experimental observations in a systematic and quantitatively reliable manner. Our model relies on data we integrated from many experiments, comprising 168,386 individual decisions. The model is composed of two pieces: the first predicts the first-period action using solely the structural game parameters, while the second predicts dynamic actions using both game parameters and history of play. Our model is successful not merely at fitting the data, but in predicting behavior at multiple scales in experimental designs not used for calibration, using only information about the game structure. We demonstrate the power of our approach through a simulation analysis revealing how to best promote human cooperation.

  18. Predicting big bang deuterium

    Energy Technology Data Exchange (ETDEWEB)

    Hata, N.; Scherrer, R.J.; Steigman, G.; Thomas, D.; Walker, T.P. [Department of Physics, Ohio State University, Columbus, Ohio 43210 (United States)

    1996-02-01

    We present new upper and lower bounds to the primordial abundances of deuterium and {sup 3}He based on observational data from the solar system and the interstellar medium. Independent of any model for the primordial production of the elements we find (at the 95{percent} C.L.): 1.5{times}10{sup {minus}5}{le}(D/H){sub {ital P}}{le}10.0{times}10{sup {minus}5} and ({sup 3}He/H){sub {ital P}}{le}2.6{times}10{sup {minus}5}. When combined with the predictions of standard big bang nucleosynthesis, these constraints lead to a 95{percent} C.L. bound on the primordial abundance deuterium: (D/H){sub best}=(3.5{sup +2.7}{sub {minus}1.8}){times}10{sup {minus}5}. Measurements of deuterium absorption in the spectra of high-redshift QSOs will directly test this prediction. The implications of this prediction for the primordial abundances of {sup 4}He and {sup 7}Li are discussed, as well as those for the universal density of baryons. {copyright} {ital 1996 The American Astronomical Society.}

  19. Disruption prediction at JET

    International Nuclear Information System (INIS)

    Milani, F.

    1998-12-01

    The sudden loss of the plasma magnetic confinement, known as disruption, is one of the major issue in a nuclear fusion machine as JET (Joint European Torus). Disruptions pose very serious problems to the safety of the machine. The energy stored in the plasma is released to the machine structure in few milliseconds resulting in forces that at JET reach several Mega Newtons. The problem is even more severe in the nuclear fusion power station where the forces are in the order of one hundred Mega Newtons. The events that occur during a disruption are still not well understood even if some mechanisms that can lead to a disruption have been identified and can be used to predict them. Unfortunately it is always a combination of these events that generates a disruption and therefore it is not possible to use simple algorithms to predict it. This thesis analyses the possibility of using neural network algorithms to predict plasma disruptions in real time. This involves the determination of plasma parameters every few milliseconds. A plasma boundary reconstruction algorithm, XLOC, has been developed in collaboration with Dr. D. O'Brien and Dr. J. Ellis capable of determining the plasma wall/distance every 2 milliseconds. The XLOC output has been used to develop a multilayer perceptron network to determine plasma parameters as l i and q ψ with which a machine operational space has been experimentally defined. If the limits of this operational space are breached the disruption probability increases considerably. Another approach for prediction disruptions is to use neural network classification methods to define the JET operational space. Two methods have been studied. The first method uses a multilayer perceptron network with softmax activation function for the output layer. This method can be used for classifying the input patterns in various classes. In this case the plasma input patterns have been divided between disrupting and safe patterns, giving the possibility of

  20. Risk Stratification of Stress Fractures and Prediction of Return-to-Duty

    Science.gov (United States)

    2016-12-01

    mgh.harvard.edu; mbouxsei@bidmc.harvard.edu 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) Massachusetts General Hospital AND...ADDRESS(ES) 8. PERFORMING ORGANIZATION REPORT NUMBER Boston, MA 02114-2554 9. SPONSORING / MONITORING AGENCY NAME(S) AND ADDRESS(ES) 10. SPONSOR...with recent stress fracture enrolled. 15. SUBJECT TERMS bone microarchitecture, HRpQCT, race, gender , sex, bone mineral density, vBMD, bone geometry

  1. Genomic Prediction in Barley

    DEFF Research Database (Denmark)

    Edriss, Vahid; Cericola, Fabio; Jensen, Jens D

    2015-01-01

    to next generation. The main goal of this study was to see the potential of using genomic prediction in a commercial Barley breeding program. The data used in this study was from Nordic Seed company which is located in Denmark. Around 350 advanced lines were genotyped with 9K Barely chip from Illumina....... Traits used in this study were grain yield, plant height and heading date. Heading date is number days it takes after 1st June for plant to head. Heritabilities were 0.33, 0.44 and 0.48 for yield, height and heading, respectively for the average of nine plots. The GBLUP model was used for genomic...

  2. Predicting Lotto Numbers

    DEFF Research Database (Denmark)

    Suetens, Sigrid; Galbo-Jørgensen, Claus B.; Tyran, Jean-Robert Karl

    2016-01-01

    We investigate the ‘law of small numbers’ using a data set on lotto gambling that allows us to measure players’ reactions to draws. While most players pick the same set of numbers week after week, we find that those who do change react on average as predicted by the law of small numbers...... as formalized in recent behavioral theory. In particular, players tend to bet less on numbers that have been drawn in the preceding week, as suggested by the ‘gambler’s fallacy’, and bet more on a number if it was frequently drawn in the recent past, consistent with the ‘hot-hand fallacy’....

  3. Predictable return distributions

    DEFF Research Database (Denmark)

    Pedersen, Thomas Quistgaard

    trace out the entire distribution. A univariate quantile regression model is used to examine stock and bond return distributions individually, while a multivariate model is used to capture their joint distribution. An empirical analysis on US data shows that certain parts of the return distributions......-of-sample analyses show that the relative accuracy of the state variables in predicting future returns varies across the distribution. A portfolio study shows that an investor with power utility can obtain economic gains by applying the empirical return distribution in portfolio decisions instead of imposing...

  4. Predicting Ground Illuminance

    Science.gov (United States)

    Lesniak, Michael V.; Tregoning, Brett D.; Hitchens, Alexandra E.

    2015-01-01

    Our Sun outputs 3.85 x 1026 W of radiation, of which roughly 37% is in the visible band. It is directly responsible for nearly all natural illuminance experienced on Earth's surface, either in the form of direct/refracted sunlight or in reflected light bouncing off the surfaces and/or atmospheres of our Moon and the visible planets. Ground illuminance, defined as the amount of visible light intercepting a unit area of surface (from all incident angles), varies over 7 orders of magnitude from day to night. It is highly dependent on well-modeled factors such as the relative positions of the Sun, Earth, and Moon. It is also dependent on less predictable factors such as local atmospheric conditions and weather.Several models have been proposed to predict ground illuminance, including Brown (1952) and Shapiro (1982, 1987). The Brown model is a set of empirical data collected from observation points around the world that has been reduced to a smooth fit of illuminance against a single variable, solar altitude. It provides limited applicability to the Moon and for cloudy conditions via multiplicative reduction factors. The Shapiro model is a theoretical model that treats the atmosphere as a three layer system of light reflectance and transmittance. It has different sets of reflectance and transmittance coefficients for various cloud types.In this paper we compare the models' predictions to ground illuminance data from an observing run at the White Sands missile range (data was obtained from the United Kingdom's Meteorology Office). Continuous illuminance readings were recorded under various cloud conditions, during both daytime and nighttime hours. We find that under clear skies, the Shapiro model tends to better fit the observations during daytime hours with typical discrepancies under 10%. Under cloudy skies, both models tend to poorly predict ground illuminance. However, the Shapiro model, with typical average daytime discrepancies of 25% or less in many cases

  5. Predicting sports betting outcomes

    OpenAIRE

    Flis, Borut

    2014-01-01

    We wish to build a model, which could predict the outcome of basketball games. The goal was to achieve an sufficient enough accuracy to make a profit in sports betting. One learning example is a game in the NBA regular season. Every example has multiple features, which describe the opposing teams. We tried many methods, which return the probability of the home team winning and the probability of the away team winning. These probabilities are used for risk analysis. We used the best model in h...

  6. Predicting chaotic time series

    International Nuclear Information System (INIS)

    Farmer, J.D.; Sidorowich, J.J.

    1987-01-01

    We present a forecasting technique for chaotic data. After embedding a time series in a state space using delay coordinates, we ''learn'' the induced nonlinear mapping using local approximation. This allows us to make short-term predictions of the future behavior of a time series, using information based only on past values. We present an error estimate for this technique, and demonstrate its effectiveness by applying it to several examples, including data from the Mackey-Glass delay differential equation, Rayleigh-Benard convection, and Taylor-Couette flow

  7. Lattice of quantum predictions

    Science.gov (United States)

    Drieschner, Michael

    1993-10-01

    What is the structure of reality? Physics is supposed to answer this question, but a purely empiristic view is not sufficient to explain its ability to do so. Quantum mechanics has forced us to think more deeply about what a physical theory is. There are preconditions every physical theory must fulfill. It has to contain, e.g., rules for empirically testable predictions. Those preconditions give physics a structure that is “a priori” in the Kantian sense. An example is given how the lattice structure of quantum mechanics can be understood along these lines.

  8. Foundations of predictive analytics

    CERN Document Server

    Wu, James

    2012-01-01

    Drawing on the authors' two decades of experience in applied modeling and data mining, Foundations of Predictive Analytics presents the fundamental background required for analyzing data and building models for many practical applications, such as consumer behavior modeling, risk and marketing analytics, and other areas. It also discusses a variety of practical topics that are frequently missing from similar texts. The book begins with the statistical and linear algebra/matrix foundation of modeling methods, from distributions to cumulant and copula functions to Cornish--Fisher expansion and o

  9. Prediction of regulatory elements

    DEFF Research Database (Denmark)

    Sandelin, Albin

    2008-01-01

    Finding the regulatory mechanisms responsible for gene expression remains one of the most important challenges for biomedical research. A major focus in cellular biology is to find functional transcription factor binding sites (TFBS) responsible for the regulation of a downstream gene. As wet......-lab methods are time consuming and expensive, it is not realistic to identify TFBS for all uncharacterized genes in the genome by purely experimental means. Computational methods aimed at predicting potential regulatory regions can increase the efficiency of wet-lab experiments significantly. Here, methods...

  10. Age and Stress Prediction

    Science.gov (United States)

    2000-01-01

    Genoa is a software product that predicts progressive aging and failure in a variety of materials. It is the result of a SBIR contract between the Glenn Research Center and Alpha Star Corporation. Genoa allows designers to determine if the materials they plan on applying to a structure are up to the task or if alternate materials should be considered. Genoa's two feature applications are its progressive failure simulations and its test verification. It allows for a reduction in inspection frequency, rapid design solutions, and manufacturing with low cost materials. It will benefit the aerospace, airline, and automotive industries, with future applications for other uses.

  11. Prediction of Biomolecular Complexes

    KAUST Repository

    Vangone, Anna

    2017-04-12

    Almost all processes in living organisms occur through specific interactions between biomolecules. Any dysfunction of those interactions can lead to pathological events. Understanding such interactions is therefore a crucial step in the investigation of biological systems and a starting point for drug design. In recent years, experimental studies have been devoted to unravel the principles of biomolecular interactions; however, due to experimental difficulties in solving the three-dimensional (3D) structure of biomolecular complexes, the number of available, high-resolution experimental 3D structures does not fulfill the current needs. Therefore, complementary computational approaches to model such interactions are necessary to assist experimentalists since a full understanding of how biomolecules interact (and consequently how they perform their function) only comes from 3D structures which provide crucial atomic details about binding and recognition processes. In this chapter we review approaches to predict biomolecular complexesBiomolecular complexes, introducing the concept of molecular dockingDocking, a technique which uses a combination of geometric, steric and energetics considerations to predict the 3D structure of a biological complex starting from the individual structures of its constituent parts. We provide a mini-guide about docking concepts, its potential and challenges, along with post-docking analysis and a list of related software.

  12. Nuclear criticality predictability

    International Nuclear Information System (INIS)

    Briggs, J.B.

    1999-01-01

    As a result of lots of efforts, a large portion of the tedious and redundant research and processing of critical experiment data has been eliminated. The necessary step in criticality safety analyses of validating computer codes with benchmark critical data is greatly streamlined, and valuable criticality safety experimental data is preserved. Criticality safety personnel in 31 different countries are now using the 'International Handbook of Evaluated Criticality Safety Benchmark Experiments'. Much has been accomplished by the work of the ICSBEP. However, evaluation and documentation represents only one element of a successful Nuclear Criticality Safety Predictability Program and this element only exists as a separate entity, because this work was not completed in conjunction with the experimentation process. I believe; however, that the work of the ICSBEP has also served to unify the other elements of nuclear criticality predictability. All elements are interrelated, but for a time it seemed that communications between these elements was not adequate. The ICSBEP has highlighted gaps in data, has retrieved lost data, has helped to identify errors in cross section processing codes, and has helped bring the international criticality safety community together in a common cause as true friends and colleagues. It has been a privilege to associate with those who work so diligently to make the project a success. (J.P.N.)

  13. Ratchetting strain prediction

    International Nuclear Information System (INIS)

    Noban, Mohammad; Jahed, Hamid

    2007-01-01

    A time-efficient method for predicting ratchetting strain is proposed. The ratchetting strain at any cycle is determined by finding the ratchetting rate at only a few cycles. This determination is done by first defining the trajectory of the origin of stress in the deviatoric stress space and then incorporating this moving origin into a cyclic plasticity model. It is shown that at the beginning of the loading, the starting point of this trajectory coincides with the initial stress origin and approaches the mean stress, displaying a power-law relationship with the number of loading cycles. The method of obtaining this trajectory from a standard uniaxial asymmetric cyclic loading is presented. Ratchetting rates are calculated with the help of this trajectory and through the use of a constitutive cyclic plasticity model which incorporates deviatoric stresses and back stresses that are measured with respect to this moving frame. The proposed model is used to predict the ratchetting strain of two types of steels under single- and multi-step loadings. Results obtained agree well with the available experimental measurements

  14. Predicting space climate change

    Science.gov (United States)

    Balcerak, Ernie

    2011-10-01

    Galactic cosmic rays and solar energetic particles can be hazardous to humans in space, damage spacecraft and satellites, pose threats to aircraft electronics, and expose aircrew and passengers to radiation. A new study shows that these threats are likely to increase in coming years as the Sun approaches the end of the period of high solar activity known as “grand solar maximum,” which has persisted through the past several decades. High solar activity can help protect the Earth by repelling incoming galactic cosmic rays. Understanding the past record can help scientists predict future conditions. Barnard et al. analyzed a 9300-year record of galactic cosmic ray and solar activity based on cosmogenic isotopes in ice cores as well as on neutron monitor data. They used this to predict future variations in galactic cosmic ray flux, near-Earth interplanetary magnetic field, sunspot number, and probability of large solar energetic particle events. The researchers found that the risk of space weather radiation events will likely increase noticeably over the next century compared with recent decades and that lower solar activity will lead to increased galactic cosmic ray levels. (Geophysical Research Letters, doi:10.1029/2011GL048489, 2011)

  15. Prediction of Biomolecular Complexes

    KAUST Repository

    Vangone, Anna; Oliva, Romina; Cavallo, Luigi; Bonvin, Alexandre M. J. J.

    2017-01-01

    Almost all processes in living organisms occur through specific interactions between biomolecules. Any dysfunction of those interactions can lead to pathological events. Understanding such interactions is therefore a crucial step in the investigation of biological systems and a starting point for drug design. In recent years, experimental studies have been devoted to unravel the principles of biomolecular interactions; however, due to experimental difficulties in solving the three-dimensional (3D) structure of biomolecular complexes, the number of available, high-resolution experimental 3D structures does not fulfill the current needs. Therefore, complementary computational approaches to model such interactions are necessary to assist experimentalists since a full understanding of how biomolecules interact (and consequently how they perform their function) only comes from 3D structures which provide crucial atomic details about binding and recognition processes. In this chapter we review approaches to predict biomolecular complexesBiomolecular complexes, introducing the concept of molecular dockingDocking, a technique which uses a combination of geometric, steric and energetics considerations to predict the 3D structure of a biological complex starting from the individual structures of its constituent parts. We provide a mini-guide about docking concepts, its potential and challenges, along with post-docking analysis and a list of related software.

  16. Energy Predictions 2011

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2010-10-15

    Even as the recession begins to subside, the energy sector is still likely to experience challenging conditions as we enter 2011. It should be remembered how very important a role energy plays in driving the global economy. Serving as a simple yet global and unified measure of economic recovery, it is oil's price range and the strength and sustainability of the recovery which will impact the ways in which all forms of energy are produced and consumed. The report aims for a closer insight into these predictions: What will happen with M and A (Mergers and Acquisitions) in the energy industry?; What are the prospects for renewables?; Will the water-energy nexus grow in importance?; How will technological leaps and bounds affect E and P (exploration and production) operations?; What about electric cars? This is the second year Deloitte's Global Energy and Resources Group has published its predictions for the year ahead. The report is based on in-depth interviews with clients, industry analysts, and senior energy practitioners from Deloitte member firms around the world.

  17. Energy Predictions 2011

    International Nuclear Information System (INIS)

    2010-10-01

    Even as the recession begins to subside, the energy sector is still likely to experience challenging conditions as we enter 2011. It should be remembered how very important a role energy plays in driving the global economy. Serving as a simple yet global and unified measure of economic recovery, it is oil's price range and the strength and sustainability of the recovery which will impact the ways in which all forms of energy are produced and consumed. The report aims for a closer insight into these predictions: What will happen with M and A (Mergers and Acquisitions) in the energy industry?; What are the prospects for renewables?; Will the water-energy nexus grow in importance?; How will technological leaps and bounds affect E and P (exploration and production) operations?; What about electric cars? This is the second year Deloitte's Global Energy and Resources Group has published its predictions for the year ahead. The report is based on in-depth interviews with clients, industry analysts, and senior energy practitioners from Deloitte member firms around the world.

  18. Predicting Alloreactivity in Transplantation

    Directory of Open Access Journals (Sweden)

    Kirsten Geneugelijk

    2014-01-01

    Full Text Available Human leukocyte Antigen (HLA mismatching leads to severe complications after solid-organ transplantation and hematopoietic stem-cell transplantation. The alloreactive responses underlying the posttransplantation complications include both direct recognition of allogeneic HLA by HLA-specific alloantibodies and T cells and indirect T-cell recognition. However, the immunogenicity of HLA mismatches is highly variable; some HLA mismatches lead to severe clinical B-cell- and T-cell-mediated alloreactivity, whereas others are well tolerated. Definition of the permissibility of HLA mismatches prior to transplantation allows selection of donor-recipient combinations that will have a reduced chance to develop deleterious host-versus-graft responses after solid-organ transplantation and graft-versus-host responses after hematopoietic stem-cell transplantation. Therefore, several methods have been developed to predict permissible HLA-mismatch combinations. In this review we aim to give a comprehensive overview about the current knowledge regarding HLA-directed alloreactivity and several developed in vitro and in silico tools that aim to predict direct and indirect alloreactivity.

  19. Generalized Predictive Control and Neural Generalized Predictive Control

    Directory of Open Access Journals (Sweden)

    Sadhana CHIDRAWAR

    2008-12-01

    Full Text Available As Model Predictive Control (MPC relies on the predictive Control using a multilayer feed forward network as the plants linear model is presented. In using Newton-Raphson as the optimization algorithm, the number of iterations needed for convergence is significantly reduced from other techniques. This paper presents a detailed derivation of the Generalized Predictive Control and Neural Generalized Predictive Control with Newton-Raphson as minimization algorithm. Taking three separate systems, performances of the system has been tested. Simulation results show the effect of neural network on Generalized Predictive Control. The performance comparison of this three system configurations has been given in terms of ISE and IAE.

  20. Numerical prediction of rose growth

    NARCIS (Netherlands)

    Bernsen, E.; Bokhove, Onno; van der Sar, D.M.

    2006-01-01

    A new mathematical model is presented for the prediction of rose growth in a greenhouse. Given the measured ambient environmental conditions, the model consists of a local photosynthesis model, predicting the photosynthesis per unit leaf area, coupled to a global greenhouse model, which predicts the

  1. Confidence scores for prediction models

    DEFF Research Database (Denmark)

    Gerds, Thomas Alexander; van de Wiel, MA

    2011-01-01

    In medical statistics, many alternative strategies are available for building a prediction model based on training data. Prediction models are routinely compared by means of their prediction performance in independent validation data. If only one data set is available for training and validation,...

  2. Protein docking prediction using predicted protein-protein interface

    Directory of Open Access Journals (Sweden)

    Li Bin

    2012-01-01

    Full Text Available Abstract Background Many important cellular processes are carried out by protein complexes. To provide physical pictures of interacting proteins, many computational protein-protein prediction methods have been developed in the past. However, it is still difficult to identify the correct docking complex structure within top ranks among alternative conformations. Results We present a novel protein docking algorithm that utilizes imperfect protein-protein binding interface prediction for guiding protein docking. Since the accuracy of protein binding site prediction varies depending on cases, the challenge is to develop a method which does not deteriorate but improves docking results by using a binding site prediction which may not be 100% accurate. The algorithm, named PI-LZerD (using Predicted Interface with Local 3D Zernike descriptor-based Docking algorithm, is based on a pair wise protein docking prediction algorithm, LZerD, which we have developed earlier. PI-LZerD starts from performing docking prediction using the provided protein-protein binding interface prediction as constraints, which is followed by the second round of docking with updated docking interface information to further improve docking conformation. Benchmark results on bound and unbound cases show that PI-LZerD consistently improves the docking prediction accuracy as compared with docking without using binding site prediction or using the binding site prediction as post-filtering. Conclusion We have developed PI-LZerD, a pairwise docking algorithm, which uses imperfect protein-protein binding interface prediction to improve docking accuracy. PI-LZerD consistently showed better prediction accuracy over alternative methods in the series of benchmark experiments including docking using actual docking interface site predictions as well as unbound docking cases.

  3. Protein docking prediction using predicted protein-protein interface.

    Science.gov (United States)

    Li, Bin; Kihara, Daisuke

    2012-01-10

    Many important cellular processes are carried out by protein complexes. To provide physical pictures of interacting proteins, many computational protein-protein prediction methods have been developed in the past. However, it is still difficult to identify the correct docking complex structure within top ranks among alternative conformations. We present a novel protein docking algorithm that utilizes imperfect protein-protein binding interface prediction for guiding protein docking. Since the accuracy of protein binding site prediction varies depending on cases, the challenge is to develop a method which does not deteriorate but improves docking results by using a binding site prediction which may not be 100% accurate. The algorithm, named PI-LZerD (using Predicted Interface with Local 3D Zernike descriptor-based Docking algorithm), is based on a pair wise protein docking prediction algorithm, LZerD, which we have developed earlier. PI-LZerD starts from performing docking prediction using the provided protein-protein binding interface prediction as constraints, which is followed by the second round of docking with updated docking interface information to further improve docking conformation. Benchmark results on bound and unbound cases show that PI-LZerD consistently improves the docking prediction accuracy as compared with docking without using binding site prediction or using the binding site prediction as post-filtering. We have developed PI-LZerD, a pairwise docking algorithm, which uses imperfect protein-protein binding interface prediction to improve docking accuracy. PI-LZerD consistently showed better prediction accuracy over alternative methods in the series of benchmark experiments including docking using actual docking interface site predictions as well as unbound docking cases.

  4. Epitope prediction methods

    DEFF Research Database (Denmark)

    Karosiene, Edita

    Analysis. The chapter provides detailed explanations on how to use different methods for T cell epitope discovery research, explaining how input should be given as well as how to interpret the output. In the last chapter, I present the results of a bioinformatics analysis of epitopes from the yellow fever...... peptide-MHC interactions. Furthermore, using yellow fever virus epitopes, we demonstrated the power of the %Rank score when compared with the binding affinity score of MHC prediction methods, suggesting that this score should be considered to be used for selecting potential T cell epitopes. In summary...... immune responses. Therefore, it is of great importance to be able to identify peptides that bind to MHC molecules, in order to understand the nature of immune responses and discover T cell epitopes useful for designing new vaccines and immunotherapies. MHC molecules in humans, referred to as human...

  5. Motor degradation prediction methods

    Energy Technology Data Exchange (ETDEWEB)

    Arnold, J.R.; Kelly, J.F.; Delzingaro, M.J.

    1996-12-01

    Motor Operated Valve (MOV) squirrel cage AC motor rotors are susceptible to degradation under certain conditions. Premature failure can result due to high humidity/temperature environments, high running load conditions, extended periods at locked rotor conditions (i.e. > 15 seconds) or exceeding the motor`s duty cycle by frequent starts or multiple valve stroking. Exposure to high heat and moisture due to packing leaks, pressure seal ring leakage or other causes can significantly accelerate the degradation. ComEd and Liberty Technologies have worked together to provide and validate a non-intrusive method using motor power diagnostics to evaluate MOV rotor condition and predict failure. These techniques have provided a quick, low radiation dose method to evaluate inaccessible motors, identify degradation and allow scheduled replacement of motors prior to catastrophic failures.

  6. Filter replacement lifetime prediction

    Science.gov (United States)

    Hamann, Hendrik F.; Klein, Levente I.; Manzer, Dennis G.; Marianno, Fernando J.

    2017-10-25

    Methods and systems for predicting a filter lifetime include building a filter effectiveness history based on contaminant sensor information associated with a filter; determining a rate of filter consumption with a processor based on the filter effectiveness history; and determining a remaining filter lifetime based on the determined rate of filter consumption. Methods and systems for increasing filter economy include measuring contaminants in an internal and an external environment; determining a cost of a corrosion rate increase if unfiltered external air intake is increased for cooling; determining a cost of increased air pressure to filter external air; and if the cost of filtering external air exceeds the cost of the corrosion rate increase, increasing an intake of unfiltered external air.

  7. Neurological abnormalities predict disability

    DEFF Research Database (Denmark)

    Poggesi, Anna; Gouw, Alida; van der Flier, Wiesje

    2014-01-01

    To investigate the role of neurological abnormalities and magnetic resonance imaging (MRI) lesions in predicting global functional decline in a cohort of initially independent-living elderly subjects. The Leukoaraiosis And DISability (LADIS) Study, involving 11 European centres, was primarily aimed...... at evaluating age-related white matter changes (ARWMC) as an independent predictor of the transition to disability (according to Instrumental Activities of Daily Living scale) or death in independent elderly subjects that were followed up for 3 years. At baseline, a standardized neurological examination.......0 years, 45 % males), 327 (51.7 %) presented at the initial visit with ≥1 neurological abnormality and 242 (38 %) reached the main study outcome. Cox regression analyses, adjusting for MRI features and other determinants of functional decline, showed that the baseline presence of any neurological...

  8. Motor degradation prediction methods

    International Nuclear Information System (INIS)

    Arnold, J.R.; Kelly, J.F.; Delzingaro, M.J.

    1996-01-01

    Motor Operated Valve (MOV) squirrel cage AC motor rotors are susceptible to degradation under certain conditions. Premature failure can result due to high humidity/temperature environments, high running load conditions, extended periods at locked rotor conditions (i.e. > 15 seconds) or exceeding the motor's duty cycle by frequent starts or multiple valve stroking. Exposure to high heat and moisture due to packing leaks, pressure seal ring leakage or other causes can significantly accelerate the degradation. ComEd and Liberty Technologies have worked together to provide and validate a non-intrusive method using motor power diagnostics to evaluate MOV rotor condition and predict failure. These techniques have provided a quick, low radiation dose method to evaluate inaccessible motors, identify degradation and allow scheduled replacement of motors prior to catastrophic failures

  9. Predictability in community dynamics.

    Science.gov (United States)

    Blonder, Benjamin; Moulton, Derek E; Blois, Jessica; Enquist, Brian J; Graae, Bente J; Macias-Fauria, Marc; McGill, Brian; Nogué, Sandra; Ordonez, Alejandro; Sandel, Brody; Svenning, Jens-Christian

    2017-03-01

    The coupling between community composition and climate change spans a gradient from no lags to strong lags. The no-lag hypothesis is the foundation of many ecophysiological models, correlative species distribution modelling and climate reconstruction approaches. Simple lag hypotheses have become prominent in disequilibrium ecology, proposing that communities track climate change following a fixed function or with a time delay. However, more complex dynamics are possible and may lead to memory effects and alternate unstable states. We develop graphical and analytic methods for assessing these scenarios and show that these dynamics can appear in even simple models. The overall implications are that (1) complex community dynamics may be common and (2) detailed knowledge of past climate change and community states will often be necessary yet sometimes insufficient to make predictions of a community's future state. © 2017 John Wiley & Sons Ltd/CNRS.

  10. Neonatal heart rate prediction.

    Science.gov (United States)

    Abdel-Rahman, Yumna; Jeremic, Aleksander; Tan, Kenneth

    2009-01-01

    Technological advances have caused a decrease in the number of infant deaths. Pre-term infants now have a substantially increased chance of survival. One of the mechanisms that is vital to saving the lives of these infants is continuous monitoring and early diagnosis. With continuous monitoring huge amounts of data are collected with so much information embedded in them. By using statistical analysis this information can be extracted and used to aid diagnosis and to understand development. In this study we have a large dataset containing over 180 pre-term infants whose heart rates were recorded over the length of their stay in the Neonatal Intensive Care Unit (NICU). We test two types of models, empirical bayesian and autoregressive moving average. We then attempt to predict future values. The autoregressive moving average model showed better results but required more computation.

  11. Chloride ingress prediction

    DEFF Research Database (Denmark)

    Frederiksen, Jens Mejer; Geiker, Mette Rica

    2008-01-01

    Prediction of chloride ingress into concrete is an important part of durability design of reinforced concrete structures exposed to chloride containing environment. This paper presents experimentally based design parameters for Portland cement concretes with and without silica fume and fly ash...... in marine atmospheric and submersed South Scandinavian environment. The design parameters are based on sequential measurements of 86 chloride profiles taken over ten years from 13 different types of concrete. The design parameters provide the input for an analytical model for chloride profiles as function...... of depth and time, when both the surface chloride concentration and the diffusion coefficient are allowed to vary in time. The model is presented in a companion paper....

  12. Strontium 90 fallout prediction

    International Nuclear Information System (INIS)

    Sarmiento, J.L.; Gwinn, E.

    1986-01-01

    An empirical formula is developed for predicting monthly sea level strontium 90 fallout (F) in the northern hemisphere as a function of time (t), precipitation rate (P), latitude (phi), longitude (lambda), and the sea level concentration of stronium 90 in air (C): F(lambda, phi, t) = C(t, phi)[v /sub d/(phi) + v/sub w/(lambda, phi, t)], where v/sub w/(lambda, phi, t) = a(phi)[P(lambda, phi, t)/P/sub o/]/sup b//sup (//sup phi//sup )/ is the wet removal, v/sub d/(phi) is the dry removal and P 0 is 1 cm/month. The constants v/sub d/, a, and b are determined as functions of latitude by fitting land based observations. The concentration of 90 Sr in air is calculated as a function of the deseasonalized concentration at a reference latitude (C-bar/sub r//sub e//sub f/), the ratio of the observations at the latitude of interest to the reference latitude (R), and a function representing the seasonal trend in the air concentration (1 + g): C-bar(t, phi) = C/sub r//sub e//sub f/(t)R(phi)[1 + g(m, phi)]; m is the month. Zonal trends in C are shown to be relatively small. This formula can be used in conjuction with precipitation observations and/or estimates to predict fallout in the northern hemisphere for any month in the years 1954 to 1974. Error estimates are given; they do not include uncertainty due to errors in precipitation data

  13. Plume rise predictions

    International Nuclear Information System (INIS)

    Briggs, G.A.

    1976-01-01

    Anyone involved with diffusion calculations becomes well aware of the strong dependence of maximum ground concentrations on the effective stack height, h/sub e/. For most conditions chi/sub max/ is approximately proportional to h/sub e/ -2 , as has been recognized at least since 1936 (Bosanquet and Pearson). Making allowance for the gradual decrease in the ratio of vertical to lateral diffusion at increasing heights, the exponent is slightly larger, say chi/sub max/ approximately h/sub e/ - 2 . 3 . In inversion breakup fumigation, the exponent is somewhat smaller; very crudely, chi/sub max/ approximately h/sub e/ -1 . 5 . In any case, for an elevated emission the dependence of chi/sub max/ on h/sub e/ is substantial. It is postulated that a really clever ignorant theoretician can disguise his ignorance with dimensionless constants. For most sources the effective stack height is considerably larger than the actual source height, h/sub s/. For instance, for power plants with no downwash problems, h/sub e/ is more than twice h/sub s/ whenever the wind is less than 10 m/sec, which is most of the time. This is unfortunate for anyone who has to predict ground concentrations, for he is likely to have to calculate the plume rise, Δh. Especially when using h/sub e/ = h/sub s/ + Δh instead of h/sub s/ may reduce chi/sub max/ by a factor of anywhere from 4 to infinity. Factors to be considered in making plume rise predictions are discussed

  14. Predictive coarse-graining

    Energy Technology Data Exchange (ETDEWEB)

    Schöberl, Markus, E-mail: m.schoeberl@tum.de [Continuum Mechanics Group, Technical University of Munich, Boltzmannstraße 15, 85748 Garching (Germany); Zabaras, Nicholas [Institute for Advanced Study, Technical University of Munich, Lichtenbergstraße 2a, 85748 Garching (Germany); Department of Aerospace and Mechanical Engineering, University of Notre Dame, 365 Fitzpatrick Hall, Notre Dame, IN 46556 (United States); Koutsourelakis, Phaedon-Stelios [Continuum Mechanics Group, Technical University of Munich, Boltzmannstraße 15, 85748 Garching (Germany)

    2017-03-15

    We propose a data-driven, coarse-graining formulation in the context of equilibrium statistical mechanics. In contrast to existing techniques which are based on a fine-to-coarse map, we adopt the opposite strategy by prescribing a probabilistic coarse-to-fine map. This corresponds to a directed probabilistic model where the coarse variables play the role of latent generators of the fine scale (all-atom) data. From an information-theoretic perspective, the framework proposed provides an improvement upon the relative entropy method and is capable of quantifying the uncertainty due to the information loss that unavoidably takes place during the coarse-graining process. Furthermore, it can be readily extended to a fully Bayesian model where various sources of uncertainties are reflected in the posterior of the model parameters. The latter can be used to produce not only point estimates of fine-scale reconstructions or macroscopic observables, but more importantly, predictive posterior distributions on these quantities. Predictive posterior distributions reflect the confidence of the model as a function of the amount of data and the level of coarse-graining. The issues of model complexity and model selection are seamlessly addressed by employing a hierarchical prior that favors the discovery of sparse solutions, revealing the most prominent features in the coarse-grained model. A flexible and parallelizable Monte Carlo – Expectation–Maximization (MC-EM) scheme is proposed for carrying out inference and learning tasks. A comparative assessment of the proposed methodology is presented for a lattice spin system and the SPC/E water model.

  15. Data-Based Predictive Control with Multirate Prediction Step

    Science.gov (United States)

    Barlow, Jonathan S.

    2010-01-01

    Data-based predictive control is an emerging control method that stems from Model Predictive Control (MPC). MPC computes current control action based on a prediction of the system output a number of time steps into the future and is generally derived from a known model of the system. Data-based predictive control has the advantage of deriving predictive models and controller gains from input-output data. Thus, a controller can be designed from the outputs of complex simulation code or a physical system where no explicit model exists. If the output data happens to be corrupted by periodic disturbances, the designed controller will also have the built-in ability to reject these disturbances without the need to know them. When data-based predictive control is implemented online, it becomes a version of adaptive control. One challenge of MPC is computational requirements increasing with prediction horizon length. This paper develops a closed-loop dynamic output feedback controller that minimizes a multi-step-ahead receding-horizon cost function with multirate prediction step. One result is a reduced influence of prediction horizon and the number of system outputs on the computational requirements of the controller. Another result is an emphasis on portions of the prediction window that are sampled more frequently. A third result is the ability to include more outputs in the feedback path than in the cost function.

  16. Earthquake prediction with electromagnetic phenomena

    Energy Technology Data Exchange (ETDEWEB)

    Hayakawa, Masashi, E-mail: hayakawa@hi-seismo-em.jp [Hayakawa Institute of Seismo Electomagnetics, Co. Ltd., University of Electro-Communications (UEC) Incubation Center, 1-5-1 Chofugaoka, Chofu Tokyo, 182-8585 (Japan); Advanced Wireless & Communications Research Center, UEC, Chofu Tokyo (Japan); Earthquake Analysis Laboratory, Information Systems Inc., 4-8-15, Minami-aoyama, Minato-ku, Tokyo, 107-0062 (Japan); Fuji Security Systems. Co. Ltd., Iwato-cho 1, Shinjyuku-ku, Tokyo (Japan)

    2016-02-01

    Short-term earthquake (EQ) prediction is defined as prospective prediction with the time scale of about one week, which is considered to be one of the most important and urgent topics for the human beings. If this short-term prediction is realized, casualty will be drastically reduced. Unlike the conventional seismic measurement, we proposed the use of electromagnetic phenomena as precursors to EQs in the prediction, and an extensive amount of progress has been achieved in the field of seismo-electromagnetics during the last two decades. This paper deals with the review on this short-term EQ prediction, including the impossibility myth of EQs prediction by seismometers, the reason why we are interested in electromagnetics, the history of seismo-electromagnetics, the ionospheric perturbation as the most promising candidate of EQ prediction, then the future of EQ predictology from two standpoints of a practical science and a pure science, and finally a brief summary.

  17. OECD - HRP Summer School on Light Water Reactor Structural Materials. August 26th - 30th, 2002

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2002-07-01

    In cooperation with the OECD Nuclear Energy Agency (NEA), the Halden Reactor Project organised a Summer School on Light Water Reactor Structural Materials in the period August 26 - 30, 2002. The summer school was primarily intended for people who wanted to become acquainted with materials-related subjects and issues without being experts. It is especially hoped that the summer school served to transfer knowledge to the ''young generation'' in the field of nuclear. Experts from Halden Project member organisations were solicited for the following programme: (1) Overview of The Nuclear Community and Current Issues, (2) Regulatory Framework for Ensuring Structural Integrity, (3) Non-Destructive Testing for Detection of Cracks, (4) Part I - Basics of Radiation and Radiation Damage, (5) Part II - Radiation Effects on Reactor Internal Materials, (6) Water Chemistry and Radiolysis Effects in LWRs, (7) PWR and Fast Breeder Reactor Internals, (8) PWR and Fast Breeder Reactor Internals, (9) Secondary Side Corrosion Cracking of PWR Steam Generator Tubes, (10) BWR Materials and Their Interaction with the Environment, (11) Radiation Damage in Reactor Pressure Vessels.

  18. OECD - HRP Summer School on Light Water Reactor Structural Materials. August 26th - 30th, 2002

    International Nuclear Information System (INIS)

    2002-01-01

    In cooperation with the OECD Nuclear Energy Agency (NEA), the Halden Reactor Project organised a Summer School on Light Water Reactor Structural Materials in the period August 26 - 30, 2002. The summer school was primarily intended for people who wanted to become acquainted with materials-related subjects and issues without being experts. It is especially hoped that the summer school served to transfer knowledge to the ''young generation'' in the field of nuclear. Experts from Halden Project member organisations were solicited for the following programme: (1) Overview of The Nuclear Community and Current Issues, (2) Regulatory Framework for Ensuring Structural Integrity, (3) Non-Destructive Testing for Detection of Cracks, (4) Part I - Basics of Radiation and Radiation Damage, (5) Part II - Radiation Effects on Reactor Internal Materials, (6) Water Chemistry and Radiolysis Effects in LWRs, (7) PWR and Fast Breeder Reactor Internals, (8) PWR and Fast Breeder Reactor Internals, (9) Secondary Side Corrosion Cracking of PWR Steam Generator Tubes, (10) BWR Materials and Their Interaction with the Environment, (11) Radiation Damage in Reactor Pressure Vessels

  19. Subchronic mild noise stress increases HRP permeability in rat small intestine in vitro

    NARCIS (Netherlands)

    Bijlsma, P. B.; van Raaij, M. T.; Dobbe, C. J.; Timmerman, A.; Kiliaan, A. J.; Taminiau, J. A.; Groot, J. A.

    2001-01-01

    Recently we reported an increased trans- and paracellular protein permeability in rat small intestine after acute cold restraint stress. In the present study, we applied randomized 95- or 105-dB white noise pulses during 45 min/h, 12 h/day, duration 8 days, as a milder, but more chronic stressor to

  20. IFPE/IFA-508 and 515, PCMI Behaviour of Thin Cladding Rods, JAERI and HRP

    International Nuclear Information System (INIS)

    2007-01-01

    Description: To measure the integrated response of UO 2 and its cladding to conditions associated with PCI, the Japan Atomic Energy Research Institute carried out a series of experiments in the Halden BWR. The experiment involved two major objectives. The first was to study the influence of rod design parameters on PCI. Diametral gap, wall cladding thickness, SiO 2 additive, and pellet grain size were used as design parameters. The second objective was to study the influence of pre-irradiation (i.e. burnup) on PCI. The maximum burnup attained in the experiment was 23 MWd/kgU. These research results can be applied to current BWR-type fuel rods. The tests were performed between April 1977 and March 1981

  1. HRP II - The Development of a New Vehicle for Studying Deep Ocean Mixing

    Science.gov (United States)

    2006-02-01

    places them at the center of the sensed volume. The Druck pressure sensor is mounted directly on the lower endcap. The sample rate is 25 Hz, and a...precision 24 bit) pressure Druck (model PDCR 1820-9082) Temperature Thermometrics (model, SP60DA202MAI) with stainless pressure housing Conductivity...1 0.9X41.51 Y-50.15Z40.63*33 $C47.5P-3.6R-1 0.5X41.39Y-49.91 Z40.74* 3D $C47.5P-3.4R-1 0.1 X41.25Y-49.69Z41.09*3A $C47.3P-3.2R-9.6X41.26Y-49.43Z41.37

  2. HrpNEa-induced deterrent effect on phloem feeding of the green ...

    Indian Academy of Sciences (India)

    In response to the phloem-feeding stress, plants defend themselves by .... was quantified as a percentage decrease in the number of feeding aphids .... increased with time during the course of 24 h monitoring ... spent outside the cuticle (nonpenetration; figure 3A, np) ..... R2R3-MYB gene family from Arabidopsis thaliana.

  3. Performance Prediction Toolkit

    Energy Technology Data Exchange (ETDEWEB)

    2017-09-25

    The Performance Prediction Toolkit (PPT), is a scalable co-design tool that contains the hardware and middle-ware models, which accept proxy applications as input in runtime prediction. PPT relies on Simian, a parallel discrete event simulation engine in Python or Lua, that uses the process concept, where each computing unit (host, node, core) is a Simian entity. Processes perform their task through message exchanges to remain active, sleep, wake-up, begin and end. The PPT hardware model of a compute core (such as a Haswell core) consists of a set of parameters, such as clock speed, memory hierarchy levels, their respective sizes, cache-lines, access times for different cache levels, average cycle counts of ALU operations, etc. These parameters are ideally read off a spec sheet or are learned using regression models learned from hardware counters (PAPI) data. The compute core model offers an API to the software model, a function called time_compute(), which takes as input a tasklist. A tasklist is an unordered set of ALU, and other CPU-type operations (in particular virtual memory loads and stores). The PPT application model mimics the loop structure of the application and replaces the computational kernels with a call to the hardware model's time_compute() function giving tasklists as input that model the compute kernel. A PPT application model thus consists of tasklists representing kernels and the high-er level loop structure that we like to think of as pseudo code. The key challenge for the hardware model's time_compute-function is to translate virtual memory accesses into actual cache hierarchy level hits and misses.PPT also contains another CPU core level hardware model, Analytical Memory Model (AMM). The AMM solves this challenge soundly, where our previous alternatives explicitly include the L1,L2,L3 hit-rates as inputs to the tasklists. Explicit hit-rates inevitably only reflect the application modeler's best guess, perhaps informed by a few

  4. Introduction: Long term prediction

    International Nuclear Information System (INIS)

    Beranger, G.

    2003-01-01

    Making a decision upon the right choice of a material appropriate to a given application should be based on taking into account several parameters as follows: cost, standards, regulations, safety, recycling, chemical properties, supplying, transformation, forming, assembly, mechanical and physical properties as well as the behaviour in practical conditions. Data taken from a private communication (J.H.Davidson) are reproduced presenting the life time range of materials from a couple of minutes to half a million hours corresponding to applications from missile technology up to high-temperature nuclear reactors or steam turbines. In the case of deep storage of nuclear waste the time required is completely different from these values since we have to ensure the integrity of the storage system for several thousand years. The vitrified nuclear wastes should be stored in metallic canisters made of iron and carbon steels, stainless steels, copper and copper alloys, nickel alloys or titanium alloys. Some of these materials are passivating metals, i.e. they develop a thin protective film, 2 or 3 nm thick - the so-called passive films. These films prevent general corrosion of the metal in a large range of chemical condition of the environment. In some specific condition, localized corrosion such as the phenomenon of pitting, occurs. Consequently, it is absolutely necessary to determine these chemical condition and their stability in time to understand the behavior of a given material. In other words the corrosion system is constituted by the complex material/surface/medium. For high level nuclear wastes the main features for resolving problem are concerned with: geological disposal; deep storage in clay; waste metallic canister; backfill mixture (clay-gypsum) or concrete; long term behavior; data needed for modelling and for predicting; choice of appropriate solution among several metallic candidates. The analysis of the complex material/surface/medium is of great importance

  5. Predictability of blocking

    International Nuclear Information System (INIS)

    Tosi, E.; Ruti, P.; Tibaldi, S.; D'Andrea, F.

    1994-01-01

    Tibaldi and Molteni (1990, hereafter referred to as TM) had previously investigated operational blocking predictability by the ECMWF model and the possible relationships between model systematic error and blocking in the winter season of the Northern Hemisphere, using seven years of ECMWF operational archives of analyses and day 1 to 10 forecasts. They showed that fewer blocking episodes than in the real atmosphere were generally simulated by the model, and that this deficiency increased with increasing forecast time. As a consequence of this, a major contribution to the systematic error in the winter season was shown to derive from the inability of the model to properly forecast blocking. In this study, the analysis performed in TM for the first seven winter seasons of the ECMWF operational model is extended to the subsequent five winters, during which model development, reflecting both resolution increases and parametrisation modifications, continued unabated. In addition the objective blocking index developed by TM has been applied to the observed data to study the natural low frequency variability of blocking. The ability to simulate blocking of some climate models has also been tested

  6. GABA predicts visual intelligence.

    Science.gov (United States)

    Cook, Emily; Hammett, Stephen T; Larsson, Jonas

    2016-10-06

    Early psychological researchers proposed a link between intelligence and low-level perceptual performance. It was recently suggested that this link is driven by individual variations in the ability to suppress irrelevant information, evidenced by the observation of strong correlations between perceptual surround suppression and cognitive performance. However, the neural mechanisms underlying such a link remain unclear. A candidate mechanism is neural inhibition by gamma-aminobutyric acid (GABA), but direct experimental support for GABA-mediated inhibition underlying suppression is inconsistent. Here we report evidence consistent with a global suppressive mechanism involving GABA underlying the link between sensory performance and intelligence. We measured visual cortical GABA concentration, visuo-spatial intelligence and visual surround suppression in a group of healthy adults. Levels of GABA were strongly predictive of both intelligence and surround suppression, with higher levels of intelligence associated with higher levels of GABA and stronger surround suppression. These results indicate that GABA-mediated neural inhibition may be a key factor determining cognitive performance and suggests a physiological mechanism linking surround suppression and intelligence. Copyright © 2016 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

  7. Predictability in cellular automata.

    Science.gov (United States)

    Agapie, Alexandru; Andreica, Anca; Chira, Camelia; Giuclea, Marius

    2014-01-01

    Modelled as finite homogeneous Markov chains, probabilistic cellular automata with local transition probabilities in (0, 1) always posses a stationary distribution. This result alone is not very helpful when it comes to predicting the final configuration; one needs also a formula connecting the probabilities in the stationary distribution to some intrinsic feature of the lattice configuration. Previous results on the asynchronous cellular automata have showed that such feature really exists. It is the number of zero-one borders within the automaton's binary configuration. An exponential formula in the number of zero-one borders has been proved for the 1-D, 2-D and 3-D asynchronous automata with neighborhood three, five and seven, respectively. We perform computer experiments on a synchronous cellular automaton to check whether the empirical distribution obeys also that theoretical formula. The numerical results indicate a perfect fit for neighbourhood three and five, which opens the way for a rigorous proof of the formula in this new, synchronous case.

  8. Predictive Manufacturing: A Classification Strategy to Predict Product Failures

    DEFF Research Database (Denmark)

    Khan, Abdul Rauf; Schiøler, Henrik; Kulahci, Murat

    2018-01-01

    manufacturing analytics model that employs a big data approach to predicting product failures; third, we illustrate the issue of high dimensionality, along with statistically redundant information; and, finally, our proposed method will be compared against the well-known classification methods (SVM, K......-nearest neighbor, artificial neural networks). The results from real data show that our predictive manufacturing analytics approach, using genetic algorithms and Voronoi tessellations, is capable of predicting product failure with reasonable accuracy. The potential application of this method contributes...... to accurately predicting product failures, which would enable manufacturers to reduce production costs without compromising product quality....

  9. House Price Prediction Using LSTM

    OpenAIRE

    Chen, Xiaochen; Wei, Lai; Xu, Jiaxin

    2017-01-01

    In this paper, we use the house price data ranging from January 2004 to October 2016 to predict the average house price of November and December in 2016 for each district in Beijing, Shanghai, Guangzhou and Shenzhen. We apply Autoregressive Integrated Moving Average model to generate the baseline while LSTM networks to build prediction model. These algorithms are compared in terms of Mean Squared Error. The result shows that the LSTM model has excellent properties with respect to predict time...

  10. Long Range Aircraft Trajectory Prediction

    OpenAIRE

    Magister, Tone

    2009-01-01

    The subject of the paper is the improvement of the aircraft future trajectory prediction accuracy for long-range airborne separation assurance. The strategic planning of safe aircraft flights and effective conflict avoidance tactics demand timely and accurate conflict detection based upon future four–dimensional airborne traffic situation prediction which is as accurate as each aircraft flight trajectory prediction. The improved kinematics model of aircraft relative flight considering flight ...

  11. Review of Nearshore Morphologic Prediction

    Science.gov (United States)

    Plant, N. G.; Dalyander, S.; Long, J.

    2014-12-01

    The evolution of the world's erodible coastlines will determine the balance between the benefits and costs associated with human and ecological utilization of shores, beaches, dunes, barrier islands, wetlands, and estuaries. So, we would like to predict coastal evolution to guide management and planning of human and ecological response to coastal changes. After decades of research investment in data collection, theoretical and statistical analysis, and model development we have a number of empirical, statistical, and deterministic models that can predict the evolution of the shoreline, beaches, dunes, and wetlands over time scales of hours to decades, and even predict the evolution of geologic strata over the course of millennia. Comparisons of predictions to data have demonstrated that these models can have meaningful predictive skill. But these comparisons also highlight the deficiencies in fundamental understanding, formulations, or data that are responsible for prediction errors and uncertainty. Here, we review a subset of predictive models of the nearshore to illustrate tradeoffs in complexity, predictive skill, and sensitivity to input data and parameterization errors. We identify where future improvement in prediction skill will result from improved theoretical understanding, and data collection, and model-data assimilation.

  12. PREDICTED PERCENTAGE DISSATISFIED (PPD) MODEL ...

    African Journals Online (AJOL)

    HOD

    their low power requirements, are relatively cheap and are environment friendly. ... PREDICTED PERCENTAGE DISSATISFIED MODEL EVALUATION OF EVAPORATIVE COOLING ... The performance of direct evaporative coolers is a.

  13. Model Prediction Control For Water Management Using Adaptive Prediction Accuracy

    NARCIS (Netherlands)

    Tian, X.; Negenborn, R.R.; Van Overloop, P.J.A.T.M.; Mostert, E.

    2014-01-01

    In the field of operational water management, Model Predictive Control (MPC) has gained popularity owing to its versatility and flexibility. The MPC controller, which takes predictions, time delay and uncertainties into account, can be designed for multi-objective management problems and for

  14. Predictability and Prediction for an Experimental Cultural Market

    Science.gov (United States)

    Colbaugh, Richard; Glass, Kristin; Ormerod, Paul

    Individuals are often influenced by the behavior of others, for instance because they wish to obtain the benefits of coordinated actions or infer otherwise inaccessible information. In such situations this social influence decreases the ex ante predictability of the ensuing social dynamics. We claim that, interestingly, these same social forces can increase the extent to which the outcome of a social process can be predicted very early in the process. This paper explores this claim through a theoretical and empirical analysis of the experimental music market described and analyzed in [1]. We propose a very simple model for this music market, assess the predictability of market outcomes through formal analysis of the model, and use insights derived through this analysis to develop algorithms for predicting market share winners, and their ultimate market shares, in the very early stages of the market. The utility of these predictive algorithms is illustrated through analysis of the experimental music market data sets [2].

  15. Predicting epileptic seizures in advance.

    Directory of Open Access Journals (Sweden)

    Negin Moghim

    Full Text Available Epilepsy is the second most common neurological disorder, affecting 0.6-0.8% of the world's population. In this neurological disorder, abnormal activity of the brain causes seizures, the nature of which tend to be sudden. Antiepileptic Drugs (AEDs are used as long-term therapeutic solutions that control the condition. Of those treated with AEDs, 35% become resistant to medication. The unpredictable nature of seizures poses risks for the individual with epilepsy. It is clearly desirable to find more effective ways of preventing seizures for such patients. The automatic detection of oncoming seizures, before their actual onset, can facilitate timely intervention and hence minimize these risks. In addition, advance prediction of seizures can enrich our understanding of the epileptic brain. In this study, drawing on the body of work behind automatic seizure detection and prediction from digitised Invasive Electroencephalography (EEG data, a prediction algorithm, ASPPR (Advance Seizure Prediction via Pre-ictal Relabeling, is described. ASPPR facilitates the learning of predictive models targeted at recognizing patterns in EEG activity that are in a specific time window in advance of a seizure. It then exploits advanced machine learning coupled with the design and selection of appropriate features from EEG signals. Results, from evaluating ASPPR independently on 21 different patients, suggest that seizures for many patients can be predicted up to 20 minutes in advance of their onset. Compared to benchmark performance represented by a mean S1-Score (harmonic mean of Sensitivity and Specificity of 90.6% for predicting seizure onset between 0 and 5 minutes in advance, ASPPR achieves mean S1-Scores of: 96.30% for prediction between 1 and 6 minutes in advance, 96.13% for prediction between 8 and 13 minutes in advance, 94.5% for prediction between 14 and 19 minutes in advance, and 94.2% for prediction between 20 and 25 minutes in advance.

  16. Quadratic prediction of factor scores

    NARCIS (Netherlands)

    Wansbeek, T

    1999-01-01

    Factor scores are naturally predicted by means of their conditional expectation given the indicators y. Under normality this expectation is linear in y but in general it is an unknown function of y. II is discussed that under nonnormality factor scores can be more precisely predicted by a quadratic

  17. Predictions for Excited Strange Baryons

    Energy Technology Data Exchange (ETDEWEB)

    Fernando, Ishara P.; Goity, Jose L. [Thomas Jefferson National Accelerator Facility (TJNAF), Newport News, VA (United States)

    2016-04-01

    An assessment is made of predictions for excited hyperon masses which follow from flavor symmetry and consistency with a 1/N c expansion of QCD. Such predictions are based on presently established baryonic resonances. Low lying hyperon resonances which do not seem to fit into the proposed scheme are discussed.

  18. Climate Prediction Center - Seasonal Outlook

    Science.gov (United States)

    Weather Service NWS logo - Click to go to the NWS home page Climate Prediction Center Site Map News Forecast Discussion PROGNOSTIC DISCUSSION FOR MONTHLY OUTLOOK NWS CLIMATE PREDICTION CENTER COLLEGE PARK MD INFLUENCE ON THE MONTHLY-AVERAGED CLIMATE. OUR MID-MONTH ASSESSMENT OF LOW-FREQUENCY CLIMATE VARIABILITY IS

  19. Dividend Predictability Around the World

    DEFF Research Database (Denmark)

    Rangvid, Jesper; Schmeling, Maik; Schrimpf, Andreas

    2014-01-01

    We show that dividend-growth predictability by the dividend yield is the rule rather than the exception in global equity markets. Dividend predictability is weaker, however, in large and developed markets where dividends are smoothed more, the typical firm is large, and volatility is lower. Our f...

  20. Dividend Predictability Around the World

    DEFF Research Database (Denmark)

    Rangvid, Jesper; Schmeling, Maik; Schrimpf, Andreas

    We show that dividend growth predictability by the dividend yield is the rule rather than the exception in global equity markets. Dividend predictability is weaker, however, in large and developed markets where dividends are smoothed more, the typical firm is large, and volatility is lower. Our f...

  1. Decadal climate prediction (project GCEP).

    Science.gov (United States)

    Haines, Keith; Hermanson, Leon; Liu, Chunlei; Putt, Debbie; Sutton, Rowan; Iwi, Alan; Smith, Doug

    2009-03-13

    Decadal prediction uses climate models forced by changing greenhouse gases, as in the International Panel for Climate Change, but unlike longer range predictions they also require initialization with observations of the current climate. In particular, the upper-ocean heat content and circulation have a critical influence. Decadal prediction is still in its infancy and there is an urgent need to understand the important processes that determine predictability on these timescales. We have taken the first Hadley Centre Decadal Prediction System (DePreSys) and implemented it on several NERC institute compute clusters in order to study a wider range of initial condition impacts on decadal forecasting, eventually including the state of the land and cryosphere. The eScience methods are used to manage submission and output from the many ensemble model runs required to assess predictive skill. Early results suggest initial condition skill may extend for several years, even over land areas, but this depends sensitively on the definition used to measure skill, and alternatives are presented. The Grid for Coupled Ensemble Prediction (GCEP) system will allow the UK academic community to contribute to international experiments being planned to explore decadal climate predictability.

  2. Prediction during natural language comprehension

    NARCIS (Netherlands)

    Willems, R.M.; Frank, S.L.; Nijhof, A.D.; Hagoort, P.; Bosch, A.P.J. van den

    2016-01-01

    The notion of prediction is studied in cognitive neuroscience with increasing intensity. We investigated the neural basis of 2 distinct aspects of word prediction, derived from information theory, during story comprehension. We assessed the effect of entropy of next-word probability distributions as

  3. Reliability of windstorm predictions in the ECMWF ensemble prediction system

    Science.gov (United States)

    Becker, Nico; Ulbrich, Uwe

    2016-04-01

    Windstorms caused by extratropical cyclones are one of the most dangerous natural hazards in the European region. Therefore, reliable predictions of such storm events are needed. Case studies have shown that ensemble prediction systems (EPS) are able to provide useful information about windstorms between two and five days prior to the event. In this work, ensemble predictions with the European Centre for Medium-Range Weather Forecasts (ECMWF) EPS are evaluated in a four year period. Within the 50 ensemble members, which are initialized every 12 hours and are run for 10 days, windstorms are identified and tracked in time and space. By using a clustering approach, different predictions of the same storm are identified in the different ensemble members and compared to reanalysis data. The occurrence probability of the predicted storms is estimated by fitting a bivariate normal distribution to the storm track positions. Our results show, for example, that predicted storm clusters with occurrence probabilities of more than 50% have a matching observed storm in 80% of all cases at a lead time of two days. The predicted occurrence probabilities are reliable up to 3 days lead time. At longer lead times the occurrence probabilities are overestimated by the EPS.

  4. Psychometric prediction of penitentiary recidivism.

    Science.gov (United States)

    Medina García, Pedro M; Baños Rivera, Rosa M

    2016-05-01

    Attempts to predict prison recidivism based on the personality have not been very successful. This study aims to provide data on recidivism prediction based on the scores on a personality questionnaire. For this purpose, a predictive model combining the actuarial procedure with a posteriori probability was developed, consisting of the probabilistic calculation of the effective verification of the event once it has already occurred. Cuestionario de Personalidad Situacional (CPS; Fernández, Seisdedos, & Mielgo, 1998) was applied to 978 male inmates classified as recidivists or non-recidivists. High predictive power was achieved, with the area under the curve (AUC) of 0.85 (p <.001; Se = 0.012; 95% CI [0.826, 0.873]. The answers to the CPS items made it possible to properly discriminate 77.3% of the participants. These data indicate the important role of the personality as a key factor in understanding delinquency and predicting recidivism.

  5. Predictive Biomarkers for Asthma Therapy.

    Science.gov (United States)

    Medrek, Sarah K; Parulekar, Amit D; Hanania, Nicola A

    2017-09-19

    Asthma is a heterogeneous disease characterized by multiple phenotypes. Treatment of patients with severe disease can be challenging. Predictive biomarkers are measurable characteristics that reflect the underlying pathophysiology of asthma and can identify patients that are likely to respond to a given therapy. This review discusses current knowledge regarding predictive biomarkers in asthma. Recent trials evaluating biologic therapies targeting IgE, IL-5, IL-13, and IL-4 have utilized predictive biomarkers to identify patients who might benefit from treatment. Other work has suggested that using composite biomarkers may offer enhanced predictive capabilities in tailoring asthma therapy. Multiple biomarkers including sputum eosinophil count, blood eosinophil count, fractional concentration of nitric oxide in exhaled breath (FeNO), and serum periostin have been used to identify which patients will respond to targeted asthma medications. Further work is needed to integrate predictive biomarkers into clinical practice.

  6. Are abrupt climate changes predictable?

    Science.gov (United States)

    Ditlevsen, Peter

    2013-04-01

    It is taken for granted that the limited predictability in the initial value problem, the weather prediction, and the predictability of the statistics are two distinct problems. Lorenz (1975) dubbed this predictability of the first and the second kind respectively. Predictability of the first kind in a chaotic dynamical system is limited due to the well-known critical dependence on initial conditions. Predictability of the second kind is possible in an ergodic system, where either the dynamics is known and the phase space attractor can be characterized by simulation or the system can be observed for such long times that the statistics can be obtained from temporal averaging, assuming that the attractor does not change in time. For the climate system the distinction between predictability of the first and the second kind is fuzzy. This difficulty in distinction between predictability of the first and of the second kind is related to the lack of scale separation between fast and slow components of the climate system. The non-linear nature of the problem furthermore opens the possibility of multiple attractors, or multiple quasi-steady states. As the ice-core records show, the climate has been jumping between different quasi-stationary climates, stadials and interstadials through the Dansgaard-Oechger events. Such a jump happens very fast when a critical tipping point has been reached. The question is: Can such a tipping point be predicted? This is a new kind of predictability: the third kind. If the tipping point is reached through a bifurcation, where the stability of the system is governed by some control parameter, changing in a predictable way to a critical value, the tipping is predictable. If the sudden jump occurs because internal chaotic fluctuations, noise, push the system across a barrier, the tipping is as unpredictable as the triggering noise. In order to hint at an answer to this question, a careful analysis of the high temporal resolution NGRIP isotope

  7. Emerging approaches in predictive toxicology.

    Science.gov (United States)

    Zhang, Luoping; McHale, Cliona M; Greene, Nigel; Snyder, Ronald D; Rich, Ivan N; Aardema, Marilyn J; Roy, Shambhu; Pfuhler, Stefan; Venkatactahalam, Sundaresan

    2014-12-01

    Predictive toxicology plays an important role in the assessment of toxicity of chemicals and the drug development process. While there are several well-established in vitro and in vivo assays that are suitable for predictive toxicology, recent advances in high-throughput analytical technologies and model systems are expected to have a major impact on the field of predictive toxicology. This commentary provides an overview of the state of the current science and a brief discussion on future perspectives for the field of predictive toxicology for human toxicity. Computational models for predictive toxicology, needs for further refinement and obstacles to expand computational models to include additional classes of chemical compounds are highlighted. Functional and comparative genomics approaches in predictive toxicology are discussed with an emphasis on successful utilization of recently developed model systems for high-throughput analysis. The advantages of three-dimensional model systems and stem cells and their use in predictive toxicology testing are also described. © 2014 Wiley Periodicals, Inc.

  8. Earthquake prediction by Kina Method

    International Nuclear Information System (INIS)

    Kianoosh, H.; Keypour, H.; Naderzadeh, A.; Motlagh, H.F.

    2005-01-01

    Earthquake prediction has been one of the earliest desires of the man. Scientists have worked hard to predict earthquakes for a long time. The results of these efforts can generally be divided into two methods of prediction: 1) Statistical Method, and 2) Empirical Method. In the first method, earthquakes are predicted using statistics and probabilities, while the second method utilizes variety of precursors for earthquake prediction. The latter method is time consuming and more costly. However, the result of neither method has fully satisfied the man up to now. In this paper a new method entitled 'Kiana Method' is introduced for earthquake prediction. This method offers more accurate results yet lower cost comparing to other conventional methods. In Kiana method the electrical and magnetic precursors are measured in an area. Then, the time and the magnitude of an earthquake in the future is calculated using electrical, and in particular, electrical capacitors formulas. In this method, by daily measurement of electrical resistance in an area we make clear that the area is capable of earthquake occurrence in the future or not. If the result shows a positive sign, then the occurrence time and the magnitude can be estimated by the measured quantities. This paper explains the procedure and details of this prediction method. (authors)

  9. Collective motion of predictive swarms.

    Directory of Open Access Journals (Sweden)

    Nathaniel Rupprecht

    Full Text Available Theoretical models of populations and swarms typically start with the assumption that the motion of agents is governed by the local stimuli. However, an intelligent agent, with some understanding of the laws that govern its habitat, can anticipate the future, and make predictions to gather resources more efficiently. Here we study a specific model of this kind, where agents aim to maximize their consumption of a diffusing resource, by attempting to predict the future of a resource field and the actions of other agents. Once the agents make a prediction, they are attracted to move towards regions that have, and will have, denser resources. We find that the further the agents attempt to see into the future, the more their attempts at prediction fail, and the less resources they consume. We also study the case where predictive agents compete against non-predictive agents and find the predictors perform better than the non-predictors only when their relative numbers are very small. We conclude that predictivity pays off either when the predictors do not see too far into the future or the number of predictors is small.

  10. Dividend Predictability Around the World

    DEFF Research Database (Denmark)

    Rangvid, Jesper; Schrimpf, Andreas

    The common perception in the literature, mainly based on U.S. data, is that current dividend yields are uninformative about future dividends. We show that this nding changes substantially when looking at a broad international panel of countries, as aggregate dividend growth rates are found...... that in countries where the quality of institutions is high, dividend predictability is weaker. These ndings indicate that the apparent lack of dividend predictability in the U.S. does not, in general, extend to other countries. Rather, dividend predictability is driven by cross-country dierences in rm...

  11. The Theory of Linear Prediction

    CERN Document Server

    Vaidyanathan, PP

    2007-01-01

    Linear prediction theory has had a profound impact in the field of digital signal processing. Although the theory dates back to the early 1940s, its influence can still be seen in applications today. The theory is based on very elegant mathematics and leads to many beautiful insights into statistical signal processing. Although prediction is only a part of the more general topics of linear estimation, filtering, and smoothing, this book focuses on linear prediction. This has enabled detailed discussion of a number of issues that are normally not found in texts. For example, the theory of vecto

  12. Practical aspects of geological prediction

    International Nuclear Information System (INIS)

    Mallio, W.J.; Peck, J.H.

    1981-01-01

    Nuclear waste disposal requires that geology be a predictive science. The prediction of future events rests on (1) recognizing the periodicity of geologic events; (2) defining a critical dimension of effect, such as the area of a drainage basin, the length of a fault trace, etc; and (3) using our understanding of active processes the project the frequency and magnitude of future events in the light of geological principles. Of importance to nuclear waste disposal are longer term processes such as continental denudation and removal of materials by glacial erosion. Constant testing of projections will allow the practical limits of predicting geological events to be defined. 11 refs

  13. Adaptive filtering prediction and control

    CERN Document Server

    Goodwin, Graham C

    2009-01-01

    Preface1. Introduction to Adaptive TechniquesPart 1. Deterministic Systems2. Models for Deterministic Dynamical Systems3. Parameter Estimation for Deterministic Systems4. Deterministic Adaptive Prediction5. Control of Linear Deterministic Systems6. Adaptive Control of Linear Deterministic SystemsPart 2. Stochastic Systems7. Optimal Filtering and Prediction8. Parameter Estimation for Stochastic Dynamic Systems9. Adaptive Filtering and Prediction10. Control of Stochastic Systems11. Adaptive Control of Stochastic SystemsAppendicesA. A Brief Review of Some Results from Systems TheoryB. A Summary o

  14. Predicting emergency diesel starting performance

    International Nuclear Information System (INIS)

    DeBey, T.M.

    1989-01-01

    The US Department of Energy effort to extend the operational lives of commercial nuclear power plants has examined methods for predicting the performance of specific equipment. This effort focuses on performance prediction as a means for reducing equipment surveillance, maintenance, and outages. Realizing these goals will result in nuclear plants that are more reliable, have lower maintenance costs, and have longer lives. This paper describes a monitoring system that has been developed to predict starting performance in emergency diesels. A prototype system has been built and tested on an engine at Sandia National Laboratories. 2 refs

  15. Predictive Models and Computational Embryology

    Science.gov (United States)

    EPA’s ‘virtual embryo’ project is building an integrative systems biology framework for predictive models of developmental toxicity. One schema involves a knowledge-driven adverse outcome pathway (AOP) framework utilizing information from public databases, standardized ontologies...

  16. Fatigue life prediction in composites

    CSIR Research Space (South Africa)

    Huston, RJ

    1994-01-01

    Full Text Available Because of the relatively large number of possible failure mechanisms in fibre reinforced composite materials, the prediction of fatigue life in a component is not a simple process. Several mathematical and statistical models have been proposed...

  17. Trading network predicts stock price.

    Science.gov (United States)

    Sun, Xiao-Qian; Shen, Hua-Wei; Cheng, Xue-Qi

    2014-01-16

    Stock price prediction is an important and challenging problem for studying financial markets. Existing studies are mainly based on the time series of stock price or the operation performance of listed company. In this paper, we propose to predict stock price based on investors' trading behavior. For each stock, we characterize the daily trading relationship among its investors using a trading network. We then classify the nodes of trading network into three roles according to their connectivity pattern. Strong Granger causality is found between stock price and trading relationship indices, i.e., the fraction of trading relationship among nodes with different roles. We further predict stock price by incorporating these trading relationship indices into a neural network based on time series of stock price. Experimental results on 51 stocks in two Chinese Stock Exchanges demonstrate the accuracy of stock price prediction is significantly improved by the inclusion of trading relationship indices.

  18. Prediction based on mean subset

    DEFF Research Database (Denmark)

    Øjelund, Henrik; Brown, P. J.; Madsen, Henrik

    2002-01-01

    , it is found that the proposed mean subset method has superior prediction performance than prediction based on the best subset method, and in some settings also better than the ridge regression and lasso methods. The conclusions drawn from the Monte Carlo study is corroborated in an example in which prediction......Shrinkage methods have traditionally been applied in prediction problems. In this article we develop a shrinkage method (mean subset) that forms an average of regression coefficients from individual subsets of the explanatory variables. A Bayesian approach is taken to derive an expression of how...... the coefficient vectors from each subset should be weighted. It is not computationally feasible to calculate the mean subset coefficient vector for larger problems, and thus we suggest an algorithm to find an approximation to the mean subset coefficient vector. In a comprehensive Monte Carlo simulation study...

  19. EPRI MOV performance prediction program

    International Nuclear Information System (INIS)

    Hosler, J.F.; Damerell, P.S.; Eidson, M.G.; Estep, N.E.

    1994-01-01

    An overview of the EPRI Motor-Operated Valve (MOV) Performance Prediction Program is presented. The objectives of this Program are to better understand the factors affecting the performance of MOVs and to develop and validate methodologies to predict MOV performance. The Program involves valve analytical modeling, separate-effects testing to refine the models, and flow-loop and in-plant MOV testing to provide a basis for model validation. The ultimate product of the Program is an MOV Performance Prediction Methodology applicable to common gate, globe, and butterfly valves. The methodology predicts thrust and torque requirements at design-basis flow and differential pressure conditions, assesses the potential for gate valve internal damage, and provides test methods to quantify potential for gate valve internal damage, and provides test methods to quantify potential variations in actuator output thrust with loading condition. Key findings and their potential impact on MOV design and engineering application are summarized

  20. In silico prediction of genotoxicity.

    Science.gov (United States)

    Wichard, Jörg D

    2017-08-01

    The in silico prediction of genotoxicity has made considerable progress during the last years. The main driver for the pharmaceutical industry is the ICH M7 guideline about the assessment of DNA reactive impurities. An important component of this guideline is the use of in silico models as an alternative approach to experimental testing. The in silico prediction of genotoxicity provides an established and accepted method that defines the first step in the assessment of DNA reactive impurities. This was made possible by the growing amount of reliable Ames screening data, the attempts to understand the activity pathways and the subsequent development of computer-based prediction systems. This paper gives an overview of how the in silico prediction of genotoxicity is performed under the ICH M7 guideline. Copyright © 2016 Elsevier Ltd. All rights reserved.

  1. New Tool to Predict Glaucoma

    Science.gov (United States)

    ... In This Section A New Tool to Predict Glaucoma email Send this article to a friend by ... Close Send Thanks for emailing that article! Tweet Glaucoma can be difficult to detect and diagnose. Measurement ...

  2. Dynamical Predictability of Monthly Means.

    Science.gov (United States)

    Shukla, J.

    1981-12-01

    We have attempted to determine the theoretical upper limit of dynamical predictability of monthly means for prescribed nonfluctuating external forcings. We have extended the concept of `classical' predictability, which primarily refers to the lack of predictability due mainly to the instabilities of synoptic-scale disturbances, to the predictability of time averages, which are determined by the predictability of low-frequency planetary waves. We have carded out 60-day integrations of a global general circulation model with nine different initial conditions but identical boundary conditions of sea surface temperature, snow, sea ice and soil moisture. Three of these initial conditions are the observed atmospheric conditions on 1 January of 1975, 1976 and 1977. The other six initial conditions are obtained by superimposing over the observed initial conditions a random perturbation comparable to the errors of observation. The root-mean-square (rms) error of random perturbations at all the grid points and all the model levels is 3 m s1 in u and v components of wind. The rms vector wind error between the observed initial conditions is >15 m s1.It is hypothesized that for a given averaging period, if the rms error among the time averages predicted from largely different initial conditions becomes comparable to the rms error among the time averages predicted from randomly perturbed initial conditions, the time averages are dynamically unpredictable. We have carried out the analysis of variance to compare the variability, among the three groups, due to largely different initial conditions, and within each group due to random perturbations.It is found that the variances among the first 30-day means, predicted from largely different initial conditions, are significantly different from the variances due to random perturbations in the initial conditions, whereas the variances among 30-day means for days 31-60 are not distinguishable from the variances due to random initial

  3. Predictive coding in Agency Detection

    DEFF Research Database (Denmark)

    Andersen, Marc Malmdorf

    2017-01-01

    Agency detection is a central concept in the cognitive science of religion (CSR). Experimental studies, however, have so far failed to lend support to some of the most common predictions that follow from current theories on agency detection. In this article, I argue that predictive coding, a highly...... promising new framework for understanding perception and action, may solve pending theoretical inconsistencies in agency detection research, account for the puzzling experimental findings mentioned above, and provide hypotheses for future experimental testing. Predictive coding explains how the brain......, unbeknownst to consciousness, engages in sophisticated Bayesian statistics in an effort to constantly predict the hidden causes of sensory input. My fundamental argument is that most false positives in agency detection can be seen as the result of top-down interference in a Bayesian system generating high...

  4. Time-predictable Stack Caching

    DEFF Research Database (Denmark)

    Abbaspourseyedi, Sahar

    completely. Thus, in systems with hard deadlines the worst-case execution time (WCET) of the real-time software running on them needs to be bounded. Modern architectures use features such as pipelining and caches for improving the average performance. These features, however, make the WCET analysis more...... addresses, provides an opportunity to predict and tighten the WCET of accesses to data in caches. In this thesis, we introduce the time-predictable stack cache design and implementation within a time-predictable processor. We introduce several optimizations to our design for tightening the WCET while...... keeping the timepredictability of the design intact. Moreover, we provide a solution for reducing the cost of context switching in a system using the stack cache. In design of these caches, we use custom hardware and compiler support for delivering time-predictable stack data accesses. Furthermore...

  5. NASA/MSFC prediction techniques

    International Nuclear Information System (INIS)

    Smith, R.E.

    1987-01-01

    The NASA/MSFC method of forecasting is more formal than NOAA's. The data are smoothed by the Lagrangian method and linear regression prediction techniques are used. The solar activity period is fixed at 11 years--the mean period of all previous cycles. Interestingly, the present prediction for the time of the next solar minimum is February or March of 1987, which, within the uncertainties of two methods, can be taken to be the same as the NOAA result

  6. Prediction of molecular crystal structures

    International Nuclear Information System (INIS)

    Beyer, Theresa

    2001-01-01

    The ab initio prediction of molecular crystal structures is a scientific challenge. Reliability of first-principle prediction calculations would show a fundamental understanding of crystallisation. Crystal structure prediction is also of considerable practical importance as different crystalline arrangements of the same molecule in the solid state (polymorphs)are likely to have different physical properties. A method of crystal structure prediction based on lattice energy minimisation has been developed in this work. The choice of the intermolecular potential and of the molecular model is crucial for the results of such studies and both of these criteria have been investigated. An empirical atom-atom repulsion-dispersion potential for carboxylic acids has been derived and applied in a crystal structure prediction study of formic, benzoic and the polymorphic system of tetrolic acid. As many experimental crystal structure determinations at different temperatures are available for the polymorphic system of paracetamol (acetaminophen), the influence of the variations of the molecular model on the crystal structure lattice energy minima, has also been studied. The general problem of prediction methods based on the assumption that the experimental thermodynamically stable polymorph corresponds to the global lattice energy minimum, is that more hypothetical low lattice energy structures are found within a few kJ mol -1 of the global minimum than are likely to be experimentally observed polymorphs. This is illustrated by the results for molecule I, 3-oxabicyclo(3.2.0)hepta-1,4-diene, studied for the first international blindtest for small organic crystal structures organised by the Cambridge Crystallographic Data Centre (CCDC) in May 1999. To reduce the number of predicted polymorphs, additional factors to thermodynamic criteria have to be considered. Therefore the elastic constants and vapour growth morphologies have been calculated for the lowest lattice energy

  7. Does Carbon Dioxide Predict Temperature?

    OpenAIRE

    Mytty, Tuukka

    2013-01-01

    Does carbon dioxide predict temperature? No it does not, in the time period of 1880-2004 with the carbon dioxide and temperature data used in this thesis. According to the Inter Governmental Panel on Climate Change(IPCC) carbon dioxide is the most important factor in raising the global temperature. Therefore, it is reasonable to assume that carbon dioxide truly predicts temperature. Because this paper uses observational data it has to be kept in mind that no causality interpretation can be ma...

  8. Prediction of molecular crystal structures

    Energy Technology Data Exchange (ETDEWEB)

    Beyer, Theresa

    2001-07-01

    The ab initio prediction of molecular crystal structures is a scientific challenge. Reliability of first-principle prediction calculations would show a fundamental understanding of crystallisation. Crystal structure prediction is also of considerable practical importance as different crystalline arrangements of the same molecule in the solid state (polymorphs)are likely to have different physical properties. A method of crystal structure prediction based on lattice energy minimisation has been developed in this work. The choice of the intermolecular potential and of the molecular model is crucial for the results of such studies and both of these criteria have been investigated. An empirical atom-atom repulsion-dispersion potential for carboxylic acids has been derived and applied in a crystal structure prediction study of formic, benzoic and the polymorphic system of tetrolic acid. As many experimental crystal structure determinations at different temperatures are available for the polymorphic system of paracetamol (acetaminophen), the influence of the variations of the molecular model on the crystal structure lattice energy minima, has also been studied. The general problem of prediction methods based on the assumption that the experimental thermodynamically stable polymorph corresponds to the global lattice energy minimum, is that more hypothetical low lattice energy structures are found within a few kJ mol{sup -1} of the global minimum than are likely to be experimentally observed polymorphs. This is illustrated by the results for molecule I, 3-oxabicyclo(3.2.0)hepta-1,4-diene, studied for the first international blindtest for small organic crystal structures organised by the Cambridge Crystallographic Data Centre (CCDC) in May 1999. To reduce the number of predicted polymorphs, additional factors to thermodynamic criteria have to be considered. Therefore the elastic constants and vapour growth morphologies have been calculated for the lowest lattice energy

  9. Prediction of interannual climate variations

    International Nuclear Information System (INIS)

    Shukla, J.

    1993-01-01

    It has been known for some time that the behavior of the short-term fluctuations of the earth's atmosphere resembles that of a chaotic non-linear dynamical system, and that the day-to-day weather cannot be predicted beyond a few weeks. However, it has also been found that the interactions of the atmosphere with the underlying oceans and the land surfaces can produce fluctuations whose time scales are much longer than the limits of deterministic prediction of weather. It is, therefore, natural to ask whether it is possible that the seasonal and longer time averages of climate fluctuations can be predicted with sufficient skill to be beneficial for social and economic applications, even though the details of day-to-day weather cannot be predicted beyond a few weeks. The main objective of the workshop was to address this question by assessing the current state of knowledge on predictability of seasonal and interannual climate variability and to investigate various possibilities for its prediction. (orig./KW)

  10. Postprocessing for Air Quality Predictions

    Science.gov (United States)

    Delle Monache, L.

    2017-12-01

    In recent year, air quality (AQ) forecasting has made significant progress towards better predictions with the goal of protecting the public from harmful pollutants. This progress is the results of improvements in weather and chemical transport models, their coupling, and more accurate emission inventories (e.g., with the development of new algorithms to account in near real-time for fires). Nevertheless, AQ predictions are still affected at times by significant biases which stem from limitations in both weather and chemistry transport models. Those are the result of numerical approximations and the poor representation (and understanding) of important physical and chemical process. Moreover, although the quality of emission inventories has been significantly improved, they are still one of the main sources of uncertainties in AQ predictions. For operational real-time AQ forecasting, a significant portion of these biases can be reduced with the implementation of postprocessing methods. We will review some of the techniques that have been proposed to reduce both systematic and random errors of AQ predictions, and improve the correlation between predictions and observations of ground-level ozone and surface particulate matter less than 2.5 µm in diameter (PM2.5). These methods, which can be applied to both deterministic and probabilistic predictions, include simple bias-correction techniques, corrections inspired by the Kalman filter, regression methods, and the more recently developed analog-based algorithms. These approaches will be compared and contrasted, and strength and weaknesses of each will be discussed.

  11. Activation of silent gal genes in the lac-gal regulon of Streptococcus thermophilus

    NARCIS (Netherlands)

    Vaughan, E.E.; Bogaard, van den P.T.C.; Catzeddu, P.; Kuipers, O.P.; Vos, de W.M.

    2001-01-01

    Streptococcus thermophilus strain CNRZ 302 is unable to ferment galactose, neither that generated intracellularly by lactose hydrolysis nor the free sugar. Nevertheless, sequence analysis and complementation studies with Escherichia coli demonstrated that strain CNRZ 302 contained structurally

  12. Novel Members of the Cra Regulon Involved in Carbon Metabolism in Escherichia coli▿ †

    Science.gov (United States)

    Shimada, Tomohiro; Yamamoto, Kaneyoshi; Ishihama, Akira

    2011-01-01

    Cra (catabolite repressor activator) is a global regulator of the genes for carbon metabolism in Escherichia coli. To gain insights into the regulatory roles of Cra, attempts were made to identify the whole set of regulation targets using an improved genomic SELEX (systematic evolution of ligands by exponential enrichment) system. Surprisingly, a total of 164 binding sites were identified for Cra, 144 (88%) of which were newly identified. The majority of known targets were included in the SELEX chip pattern. The promoters examined by the lacZ reporter assay in vivo were all regulated by Cra. These two lines of evidence indicate that a total of as many as 178 promoters are under the control of Cra. The majority of Cra targets are the genes coding for the enzymes involved in central carbon metabolism, covering all the genes for the enzymes involved in glycolysis and metabolism downstream of glycolysis, including the tricarboxylic acid (TCA) cycle and aerobic respiration. Taken together, we propose that Cra plays a key role in balancing the levels of the enzymes for carbon metabolism. PMID:21115656

  13. Novel members of the Cra regulon involved in carbon metabolism in Escherichia coli.

    Science.gov (United States)

    Shimada, Tomohiro; Yamamoto, Kaneyoshi; Ishihama, Akira

    2011-02-01

    Cra (catabolite repressor activator) is a global regulator of the genes for carbon metabolism in Escherichia coli. To gain insights into the regulatory roles of Cra, attempts were made to identify the whole set of regulation targets using an improved genomic SELEX (systematic evolution of ligands by exponential enrichment) system. Surprisingly, a total of 164 binding sites were identified for Cra, 144 (88%) of which were newly identified. The majority of known targets were included in the SELEX chip pattern. The promoters examined by the lacZ reporter assay in vivo were all regulated by Cra. These two lines of evidence indicate that a total of as many as 178 promoters are under the control of Cra. The majority of Cra targets are the genes coding for the enzymes involved in central carbon metabolism, covering all the genes for the enzymes involved in glycolysis and metabolism downstream of glycolysis, including the tricarboxylic acid (TCA) cycle and aerobic respiration. Taken together, we propose that Cra plays a key role in balancing the levels of the enzymes for carbon metabolism.

  14. Global Analysis of the Burkholderia thailandensis Quorum Sensing-Controlled Regulon

    OpenAIRE

    Majerczyk, Charlotte; Brittnacher, Mitchell; Jacobs, Michael; Armour, Christopher D.; Radey, Mathew; Schneider, Emily; Phattarasokul, Somsak; Bunt, Richard; Greenberg, E. Peter

    2014-01-01

    Burkholderia thailandensis contains three acyl-homoserine lactone quorum sensing circuits and has two additional LuxR homologs. To identify B. thailandensis quorum sensing-controlled genes, we carried out transcriptome sequencing (RNA-seq) analyses of quorum sensing mutants and their parent. The analyses were grounded in the fact that we identified genes coding for factors shown previously to be regulated by quorum sensing among a larger set of quorum-controlled genes. We also found that gene...

  15. Predictive value of diminutive colonic adenoma trial: the PREDICT trial.

    Science.gov (United States)

    Schoenfeld, Philip; Shad, Javaid; Ormseth, Eric; Coyle, Walter; Cash, Brooks; Butler, James; Schindler, William; Kikendall, Walter J; Furlong, Christopher; Sobin, Leslie H; Hobbs, Christine M; Cruess, David; Rex, Douglas

    2003-05-01

    Diminutive adenomas (1-9 mm in diameter) are frequently found during colon cancer screening with flexible sigmoidoscopy (FS). This trial assessed the predictive value of these diminutive adenomas for advanced adenomas in the proximal colon. In a multicenter, prospective cohort trial, we matched 200 patients with normal FS and 200 patients with diminutive adenomas on FS for age and gender. All patients underwent colonoscopy. The presence of advanced adenomas (adenoma >or= 10 mm in diameter, villous adenoma, adenoma with high grade dysplasia, and colon cancer) and adenomas (any size) was recorded. Before colonoscopy, patients completed questionnaires about risk factors for adenomas. The prevalence of advanced adenomas in the proximal colon was similar in patients with diminutive adenomas and patients with normal FS (6% vs. 5.5%, respectively) (relative risk, 1.1; 95% confidence interval [CI], 0.5-2.6). Diminutive adenomas on FS did not accurately predict advanced adenomas in the proximal colon: sensitivity, 52% (95% CI, 32%-72%); specificity, 50% (95% CI, 49%-51%); positive predictive value, 6% (95% CI, 4%-8%); and negative predictive value, 95% (95% CI, 92%-97%). Male gender (odds ratio, 1.63; 95% CI, 1.01-2.61) was associated with an increased risk of proximal colon adenomas. Diminutive adenomas on sigmoidoscopy may not accurately predict advanced adenomas in the proximal colon.

  16. Reward positivity: Reward prediction error or salience prediction error?

    Science.gov (United States)

    Heydari, Sepideh; Holroyd, Clay B

    2016-08-01

    The reward positivity is a component of the human ERP elicited by feedback stimuli in trial-and-error learning and guessing tasks. A prominent theory holds that the reward positivity reflects a reward prediction error signal that is sensitive to outcome valence, being larger for unexpected positive events relative to unexpected negative events (Holroyd & Coles, 2002). Although the theory has found substantial empirical support, most of these studies have utilized either monetary or performance feedback to test the hypothesis. However, in apparent contradiction to the theory, a recent study found that unexpected physical punishments also elicit the reward positivity (Talmi, Atkinson, & El-Deredy, 2013). The authors of this report argued that the reward positivity reflects a salience prediction error rather than a reward prediction error. To investigate this finding further, in the present study participants navigated a virtual T maze and received feedback on each trial under two conditions. In a reward condition, the feedback indicated that they would either receive a monetary reward or not and in a punishment condition the feedback indicated that they would receive a small shock or not. We found that the feedback stimuli elicited a typical reward positivity in the reward condition and an apparently delayed reward positivity in the punishment condition. Importantly, this signal was more positive to the stimuli that predicted the omission of a possible punishment relative to stimuli that predicted a forthcoming punishment, which is inconsistent with the salience hypothesis. © 2016 Society for Psychophysiological Research.

  17. Human reliability program: Components and effects

    International Nuclear Information System (INIS)

    Baley-Downes, S.

    1986-01-01

    The term ''Human Reliability Program'' (HRP) is defined as a series of selective controls which are implemented and integrated to identify the ''insider threat'' from current and prospective employees who are dishonest, disloyal and unreliable. The HRP, although not a prediction of human behaviour, is an excellent tool for decision making and should compliment security and improve employee quality. The HRP consists of several component applications such as management evaluation; appropriate background investigative requirements; occupational health examination and laboratory testing; drug/alcohol screening; psychological testing and interviews; polygraph examination; job related aberrant behaviour recognition; on-going education and training; document control; drug/alcohol rehabilitation; periodic HRP audit; and implementation of an onsite central clearing house. The components and effects of HRP are discussed in further detail in this paper

  18. Climate Prediction - NOAA's National Weather Service

    Science.gov (United States)

    Statistical Models... MOS Prod GFS-LAMP Prod Climate Past Weather Predictions Weather Safety Weather Radio National Weather Service on FaceBook NWS on Facebook NWS Director Home > Climate > Predictions Climate Prediction Long range forecasts across the U.S. Climate Prediction Web Sites Climate Prediction

  19. Weighted-Average Least Squares Prediction

    NARCIS (Netherlands)

    Magnus, Jan R.; Wang, Wendun; Zhang, Xinyu

    2016-01-01

    Prediction under model uncertainty is an important and difficult issue. Traditional prediction methods (such as pretesting) are based on model selection followed by prediction in the selected model, but the reported prediction and the reported prediction variance ignore the uncertainty from the

  20. Potential Predictability and Prediction Skill for Southern Peru Summertime Rainfall

    Science.gov (United States)

    WU, S.; Notaro, M.; Vavrus, S. J.; Mortensen, E.; Block, P. J.; Montgomery, R. J.; De Pierola, J. N.; Sanchez, C.

    2016-12-01

    The central Andes receive over 50% of annual climatological rainfall during the short period of January-March. This summertime rainfall exhibits strong interannual and decadal variability, including severe drought events that incur devastating societal impacts and cause agricultural communities and mining facilities to compete for limited water resources. An improved seasonal prediction skill of summertime rainfall would aid in water resource planning and allocation across the water-limited southern Peru. While various underlying mechanisms have been proposed by past studies for the drivers of interannual variability in summertime rainfall across southern Peru, such as the El Niño-Southern Oscillation (ENSO), Madden Julian Oscillation (MJO), and extratropical forcings, operational forecasts continue to be largely based on rudimentary ENSO-based indices, such as NINO3.4, justifying further exploration of predictive skill. In order to bridge this gap between the understanding of driving mechanisms and the operational forecast, we performed systematic studies on the predictability and prediction skill of southern Peru summertime rainfall by constructing statistical forecast models using best available weather station and reanalysis datasets. At first, by assuming the first two empirical orthogonal functions (EOFs) of summertime rainfall are predictable, the potential predictability skill was evaluated for southern Peru. Then, we constructed a simple regression model, based on the time series of tropical Pacific sea-surface temperatures (SSTs), and a more advanced Linear Inverse Model (LIM), based on the EOFs of tropical ocean SSTs and large-scale atmosphere variables from reanalysis. Our results show that the LIM model consistently outperforms the more rudimentary regression models on the forecast skill of domain averaged precipitation index and individual station indices. The improvement of forecast correlation skill ranges from 10% to over 200% for different

  1. Prediction of GNSS satellite clocks

    International Nuclear Information System (INIS)

    Broederbauer, V.

    2010-01-01

    This thesis deals with the characterisation and prediction of GNSS-satellite-clocks. A prerequisite to develop powerful algorithms for the prediction of clock-corrections is the thorough study of the behaviour of the different clock-types of the satellites. In this context the predicted part of the IGU-clock-corrections provided by the Analysis Centers (ACs) of the IGS was compared to the IGS-Rapid-clock solutions to determine reasonable estimates of the quality of already existing well performing predictions. For the shortest investigated interval (three hours) all ACs obtain almost the same accuracy of 0,1 to 0,4 ns. For longer intervals the individual predictions results start to diverge. Thus, for a 12-hours- interval the differences range from nearly 10 ns (GFZ, CODE) until up to some 'tens of ns'. Based on the estimated clock corrections provided via the IGS Rapid products a simple quadratic polynomial turns out to be sufficient to describe the time series of Rubidium-clocks. On the other hand Cesium-clocks show a periodical behaviour (revolution period) with an amplitude of up to 6 ns. A clear correlation between these amplitudes and the Sun elevation angle above the orbital planes can be demonstrated. The variability of the amplitudes is supposed to be caused by temperature-variations affecting the oscillator. To account for this periodical behaviour a quadratic polynomial with an additional sinus-term was finally chosen as prediction model both for the Cesium as well as for the Rubidium clocks. The three polynomial-parameters as well as amplitude and phase shift of the periodic term are estimated within a least-square-adjustment by means of program GNSS-VC/static. Input-data are time series of the observed part of the IGU clock corrections. With the estimated parameters clock-corrections are predicted for various durations. The mean error of the prediction of Rubidium-clock-corrections for an interval of six hours reaches up to 1,5 ns. For the 12-hours

  2. Geophysical Anomalies and Earthquake Prediction

    Science.gov (United States)

    Jackson, D. D.

    2008-12-01

    Finding anomalies is easy. Predicting earthquakes convincingly from such anomalies is far from easy. Why? Why have so many beautiful geophysical abnormalities not led to successful prediction strategies? What is earthquake prediction? By my definition it is convincing information that an earthquake of specified size is temporarily much more likely than usual in a specific region for a specified time interval. We know a lot about normal earthquake behavior, including locations where earthquake rates are higher than elsewhere, with estimable rates and size distributions. We know that earthquakes have power law size distributions over large areas, that they cluster in time and space, and that aftershocks follow with power-law dependence on time. These relationships justify prudent protective measures and scientific investigation. Earthquake prediction would justify exceptional temporary measures well beyond those normal prudent actions. Convincing earthquake prediction would result from methods that have demonstrated many successes with few false alarms. Predicting earthquakes convincingly is difficult for several profound reasons. First, earthquakes start in tiny volumes at inaccessible depth. The power law size dependence means that tiny unobservable ones are frequent almost everywhere and occasionally grow to larger size. Thus prediction of important earthquakes is not about nucleation, but about identifying the conditions for growth. Second, earthquakes are complex. They derive their energy from stress, which is perniciously hard to estimate or model because it is nearly singular at the margins of cracks and faults. Physical properties vary from place to place, so the preparatory processes certainly vary as well. Thus establishing the needed track record for validation is very difficult, especially for large events with immense interval times in any one location. Third, the anomalies are generally complex as well. Electromagnetic anomalies in particular require

  3. Neural Elements for Predictive Coding

    Directory of Open Access Journals (Sweden)

    Stewart SHIPP

    2016-11-01

    Full Text Available Predictive coding theories of sensory brain function interpret the hierarchical construction of the cerebral cortex as a Bayesian, generative model capable of predicting the sensory data consistent with any given percept. Predictions are fed backwards in the hierarchy and reciprocated by prediction error in the forward direction, acting to modify the representation of the outside world at increasing levels of abstraction, and so to optimize the nature of perception over a series of iterations. This accounts for many ‘illusory’ instances of perception where what is seen (heard, etc is unduly influenced by what is expected, based on past experience. This simple conception, the hierarchical exchange of prediction and prediction error, confronts a rich cortical microcircuitry that is yet to be fully documented. This article presents the view that, in the current state of theory and practice, it is profitable to begin a two-way exchange: that predictive coding theory can support an understanding of cortical microcircuit function, and prompt particular aspects of future investigation, whilst existing knowledge of microcircuitry can, in return, influence theoretical development. As an example, a neural inference arising from the earliest formulations of predictive coding is that the source populations of forwards and backwards pathways should be completely separate, given their functional distinction; this aspect of circuitry – that neurons with extrinsically bifurcating axons do not project in both directions – has only recently been confirmed. Here, the computational architecture prescribed by a generalized (free-energy formulation of predictive coding is combined with the classic ‘canonical microcircuit’ and the laminar architecture of hierarchical extrinsic connectivity to produce a template schematic, that is further examined in the light of (a updates in the microcircuitry of primate visual cortex, and (b rapid technical advances made

  4. Neural Elements for Predictive Coding.

    Science.gov (United States)

    Shipp, Stewart

    2016-01-01

    Predictive coding theories of sensory brain function interpret the hierarchical construction of the cerebral cortex as a Bayesian, generative model capable of predicting the sensory data consistent with any given percept. Predictions are fed backward in the hierarchy and reciprocated by prediction error in the forward direction, acting to modify the representation of the outside world at increasing levels of abstraction, and so to optimize the nature of perception over a series of iterations. This accounts for many 'illusory' instances of perception where what is seen (heard, etc.) is unduly influenced by what is expected, based on past experience. This simple conception, the hierarchical exchange of prediction and prediction error, confronts a rich cortical microcircuitry that is yet to be fully documented. This article presents the view that, in the current state of theory and practice, it is profitable to begin a two-way exchange: that predictive coding theory can support an understanding of cortical microcircuit function, and prompt particular aspects of future investigation, whilst existing knowledge of microcircuitry can, in return, influence theoretical development. As an example, a neural inference arising from the earliest formulations of predictive coding is that the source populations of forward and backward pathways should be completely separate, given their functional distinction; this aspect of circuitry - that neurons with extrinsically bifurcating axons do not project in both directions - has only recently been confirmed. Here, the computational architecture prescribed by a generalized (free-energy) formulation of predictive coding is combined with the classic 'canonical microcircuit' and the laminar architecture of hierarchical extrinsic connectivity to produce a template schematic, that is further examined in the light of (a) updates in the microcircuitry of primate visual cortex, and (b) rapid technical advances made possible by transgenic neural

  5. Quantifying prognosis with risk predictions.

    Science.gov (United States)

    Pace, Nathan L; Eberhart, Leopold H J; Kranke, Peter R

    2012-01-01

    Prognosis is a forecast, based on present observations in a patient, of their probable outcome from disease, surgery and so on. Research methods for the development of risk probabilities may not be familiar to some anaesthesiologists. We briefly describe methods for identifying risk factors and risk scores. A probability prediction rule assigns a risk probability to a patient for the occurrence of a specific event. Probability reflects the continuum between absolute certainty (Pi = 1) and certified impossibility (Pi = 0). Biomarkers and clinical covariates that modify risk are known as risk factors. The Pi as modified by risk factors can be estimated by identifying the risk factors and their weighting; these are usually obtained by stepwise logistic regression. The accuracy of probabilistic predictors can be separated into the concepts of 'overall performance', 'discrimination' and 'calibration'. Overall performance is the mathematical distance between predictions and outcomes. Discrimination is the ability of the predictor to rank order observations with different outcomes. Calibration is the correctness of prediction probabilities on an absolute scale. Statistical methods include the Brier score, coefficient of determination (Nagelkerke R2), C-statistic and regression calibration. External validation is the comparison of the actual outcomes to the predicted outcomes in a new and independent patient sample. External validation uses the statistical methods of overall performance, discrimination and calibration and is uniformly recommended before acceptance of the prediction model. Evidence from randomised controlled clinical trials should be obtained to show the effectiveness of risk scores for altering patient management and patient outcomes.

  6. PREDICTING DEMAND FOR COTTON YARNS

    Directory of Open Access Journals (Sweden)

    SALAS-MOLINA Francisco

    2017-05-01

    Full Text Available Predicting demand for fashion products is crucial for textile manufacturers. In an attempt to both avoid out-of-stocks and minimize holding costs, different forecasting techniques are used by production managers. Both linear and non-linear time-series analysis techniques are suitable options for forecasting purposes. However, demand for fashion products presents a number of particular characteristics such as short life-cycles, short selling seasons, high impulse purchasing, high volatility, low predictability, tremendous product variety and a high number of stock-keeping-units. In this paper, we focus on predicting demand for cotton yarns using a non-linear forecasting technique that has been fruitfully used in many areas, namely, random forests. To this end, we first identify a number of explanatory variables to be used as a key input to forecasting using random forests. We consider explanatory variables usually labeled either as causal variables, when some correlation is expected between them and the forecasted variable, or as time-series features, when extracted from time-related attributes such as seasonality. Next, we evaluate the predictive power of each variable by means of out-of-sample accuracy measurement. We experiment on a real data set from a textile company in Spain. The numerical results show that simple time-series features present more predictive ability than other more sophisticated explanatory variables.

  7. Lightning prediction using radiosonde data

    Energy Technology Data Exchange (ETDEWEB)

    Weng, L.Y.; Bin Omar, J.; Siah, Y.K.; Bin Zainal Abidin, I.; Ahmad, S.K. [Univ. Tenaga, Darul Ehsan (Malaysia). College of Engineering

    2008-07-01

    Lightning is a natural phenomenon in tropical regions. Malaysia experiences very high cloud-to-ground lightning density, posing both health and economic concerns to individuals and industries. In the commercial sector, power lines, telecommunication towers and buildings are most frequently hit by lightning. In the event that a power line is hit and the protection system fails, industries which rely on that power line would cease operations temporarily, resulting in significant monetary loss. Current technology is unable to prevent lightning occurrences. However, the ability to predict lightning would significantly reduce damages from direct and indirect lightning strikes. For that reason, this study focused on developing a method to predict lightning with radiosonde data using only a simple back propagation neural network model written in C code. The study was performed at the Kuala Lumpur International Airport (KLIA). In this model, the parameters related to wind were disregarded. Preliminary results indicate that this method shows some positive results in predicting lighting. However, a larger dataset is needed in order to obtain more accurate predictions. It was concluded that future work should include wind parameters to fully capture all properties for lightning formation, subsequently its prediction. 8 refs., 5 figs.

  8. Prediction, Regression and Critical Realism

    DEFF Research Database (Denmark)

    Næss, Petter

    2004-01-01

    This paper considers the possibility of prediction in land use planning, and the use of statistical research methods in analyses of relationships between urban form and travel behaviour. Influential writers within the tradition of critical realism reject the possibility of predicting social...... phenomena. This position is fundamentally problematic to public planning. Without at least some ability to predict the likely consequences of different proposals, the justification for public sector intervention into market mechanisms will be frail. Statistical methods like regression analyses are commonly...... seen as necessary in order to identify aggregate level effects of policy measures, but are questioned by many advocates of critical realist ontology. Using research into the relationship between urban structure and travel as an example, the paper discusses relevant research methods and the kinds...

  9. Intelligent Prediction of Ship Maneuvering

    Directory of Open Access Journals (Sweden)

    Miroslaw Lacki

    2016-09-01

    Full Text Available In this paper the author presents an idea of the intelligent ship maneuvering prediction system with the usage of neuroevolution. This may be also be seen as the ship handling system that simulates a learning process of an autonomous control unit, created with artificial neural network. The control unit observes input signals and calculates the values of required parameters of the vessel maneuvering in confined waters. In neuroevolution such units are treated as individuals in population of artificial neural networks, which through environmental sensing and evolutionary algorithms learn to perform given task efficiently. The main task of the system is to learn continuously and predict the values of a navigational parameters of the vessel after certain amount of time, regarding an influence of its environment. The result of a prediction may occur as a warning to navigator to aware him about incoming threat.

  10. Predictive Modeling in Race Walking

    Directory of Open Access Journals (Sweden)

    Krzysztof Wiktorowicz

    2015-01-01

    Full Text Available This paper presents the use of linear and nonlinear multivariable models as tools to support training process of race walkers. These models are calculated using data collected from race walkers’ training events and they are used to predict the result over a 3 km race based on training loads. The material consists of 122 training plans for 21 athletes. In order to choose the best model leave-one-out cross-validation method is used. The main contribution of the paper is to propose the nonlinear modifications for linear models in order to achieve smaller prediction error. It is shown that the best model is a modified LASSO regression with quadratic terms in the nonlinear part. This model has the smallest prediction error and simplified structure by eliminating some of the predictors.

  11. Sentence-Level Attachment Prediction

    Science.gov (United States)

    Albakour, M.-Dyaa; Kruschwitz, Udo; Lucas, Simon

    Attachment prediction is the task of automatically identifying email messages that should contain an attachment. This can be useful to tackle the problem of sending out emails but forgetting to include the relevant attachment (something that happens all too often). A common Information Retrieval (IR) approach in analyzing documents such as emails is to treat the entire document as a bag of words. Here we propose a finer-grained analysis to address the problem. We aim at identifying individual sentences within an email that refer to an attachment. If we detect any such sentence, we predict that the email should have an attachment. Using part of the Enron corpus for evaluation we find that our finer-grained approach outperforms previously reported document-level attachment prediction in similar evaluation settings.

  12. BBN predictions for 4He

    International Nuclear Information System (INIS)

    Walker, T.P.

    1993-01-01

    The standard model of the hot big bang assumes a homogeneous and isotropic Universe with gravity described by General Relativity and strong and electroweak interactions described by the Standard Model of particle physics. The hot big bang model makes the unavoidable prediction that the production of primordial elements occurred about one minute after the big band (referred to as big bang or primordial nucleosynthesis BBN). This review concerns the range of the primordial abundance of 4 He as predicted by standard BBN (i.e., primordial nucleosynthesis assuming a homogeneous distribution of baryons). In it the author discusses: (1) Uncertainties in the calculation of Y p (the mass fraction of primordial 4 He), (2) The expected range of Y p , (3) How the predictions stack up against the latest observations, and (4) The latest BBN bounds on Ω B h 2 and N ν . 13 refs., 2 figs

  13. Human motion simulation predictive dynamics

    CERN Document Server

    Abdel-Malek, Karim

    2013-01-01

    Simulate realistic human motion in a virtual world with an optimization-based approach to motion prediction. With this approach, motion is governed by human performance measures, such as speed and energy, which act as objective functions to be optimized. Constraints on joint torques and angles are imposed quite easily. Predicting motion in this way allows one to use avatars to study how and why humans move the way they do, given specific scenarios. It also enables avatars to react to infinitely many scenarios with substantial autonomy. With this approach it is possible to predict dynamic motion without having to integrate equations of motion -- rather than solving equations of motion, this approach solves for a continuous time-dependent curve characterizing joint variables (also called joint profiles) for every degree of freedom. Introduces rigorous mathematical methods for digital human modelling and simulation Focuses on understanding and representing spatial relationships (3D) of biomechanics Develops an i...

  14. Model predictive control using fuzzy decision functions

    NARCIS (Netherlands)

    Kaymak, U.; Costa Sousa, da J.M.

    2001-01-01

    Fuzzy predictive control integrates conventional model predictive control with techniques from fuzzy multicriteria decision making, translating the goals and the constraints to predictive control in a transparent way. The information regarding the (fuzzy) goals and the (fuzzy) constraints of the

  15. Evaluating the Predictive Value of Growth Prediction Models

    Science.gov (United States)

    Murphy, Daniel L.; Gaertner, Matthew N.

    2014-01-01

    This study evaluates four growth prediction models--projection, student growth percentile, trajectory, and transition table--commonly used to forecast (and give schools credit for) middle school students' future proficiency. Analyses focused on vertically scaled summative mathematics assessments, and two performance standards conditions (high…

  16. Ensemble method for dengue prediction.

    Science.gov (United States)

    Buczak, Anna L; Baugher, Benjamin; Moniz, Linda J; Bagley, Thomas; Babin, Steven M; Guven, Erhan

    2018-01-01

    In the 2015 NOAA Dengue Challenge, participants made three dengue target predictions for two locations (Iquitos, Peru, and San Juan, Puerto Rico) during four dengue seasons: 1) peak height (i.e., maximum weekly number of cases during a transmission season; 2) peak week (i.e., week in which the maximum weekly number of cases occurred); and 3) total number of cases reported during a transmission season. A dengue transmission season is the 12-month period commencing with the location-specific, historical week with the lowest number of cases. At the beginning of the Dengue Challenge, participants were provided with the same input data for developing the models, with the prediction testing data provided at a later date. Our approach used ensemble models created by combining three disparate types of component models: 1) two-dimensional Method of Analogues models incorporating both dengue and climate data; 2) additive seasonal Holt-Winters models with and without wavelet smoothing; and 3) simple historical models. Of the individual component models created, those with the best performance on the prior four years of data were incorporated into the ensemble models. There were separate ensembles for predicting each of the three targets at each of the two locations. Our ensemble models scored higher for peak height and total dengue case counts reported in a transmission season for Iquitos than all other models submitted to the Dengue Challenge. However, the ensemble models did not do nearly as well when predicting the peak week. The Dengue Challenge organizers scored the dengue predictions of the Challenge participant groups. Our ensemble approach was the best in predicting the total number of dengue cases reported for transmission season and peak height for Iquitos, Peru.

  17. Evoked emotions predict food choice.

    Science.gov (United States)

    Dalenberg, Jelle R; Gutjar, Swetlana; Ter Horst, Gert J; de Graaf, Kees; Renken, Remco J; Jager, Gerry

    2014-01-01

    In the current study we show that non-verbal food-evoked emotion scores significantly improve food choice prediction over merely liking scores. Previous research has shown that liking measures correlate with choice. However, liking is no strong predictor for food choice in real life environments. Therefore, the focus within recent studies shifted towards using emotion-profiling methods that successfully can discriminate between products that are equally liked. However, it is unclear how well scores from emotion-profiling methods predict actual food choice and/or consumption. To test this, we proposed to decompose emotion scores into valence and arousal scores using Principal Component Analysis (PCA) and apply Multinomial Logit Models (MLM) to estimate food choice using liking, valence, and arousal as possible predictors. For this analysis, we used an existing data set comprised of liking and food-evoked emotions scores from 123 participants, who rated 7 unlabeled breakfast drinks. Liking scores were measured using a 100-mm visual analogue scale, while food-evoked emotions were measured using 2 existing emotion-profiling methods: a verbal and a non-verbal method (EsSense Profile and PrEmo, respectively). After 7 days, participants were asked to choose 1 breakfast drink from the experiment to consume during breakfast in a simulated restaurant environment. Cross validation showed that we were able to correctly predict individualized food choice (1 out of 7 products) for over 50% of the participants. This number increased to nearly 80% when looking at the top 2 candidates. Model comparisons showed that evoked emotions better predict food choice than perceived liking alone. However, the strongest predictive strength was achieved by the combination of evoked emotions and liking. Furthermore we showed that non-verbal food-evoked emotion scores more accurately predict food choice than verbal food-evoked emotions scores.

  18. Ensemble method for dengue prediction.

    Directory of Open Access Journals (Sweden)

    Anna L Buczak

    Full Text Available In the 2015 NOAA Dengue Challenge, participants made three dengue target predictions for two locations (Iquitos, Peru, and San Juan, Puerto Rico during four dengue seasons: 1 peak height (i.e., maximum weekly number of cases during a transmission season; 2 peak week (i.e., week in which the maximum weekly number of cases occurred; and 3 total number of cases reported during a transmission season. A dengue transmission season is the 12-month period commencing with the location-specific, historical week with the lowest number of cases. At the beginning of the Dengue Challenge, participants were provided with the same input data for developing the models, with the prediction testing data provided at a later date.Our approach used ensemble models created by combining three disparate types of component models: 1 two-dimensional Method of Analogues models incorporating both dengue and climate data; 2 additive seasonal Holt-Winters models with and without wavelet smoothing; and 3 simple historical models. Of the individual component models created, those with the best performance on the prior four years of data were incorporated into the ensemble models. There were separate ensembles for predicting each of the three targets at each of the two locations.Our ensemble models scored higher for peak height and total dengue case counts reported in a transmission season for Iquitos than all other models submitted to the Dengue Challenge. However, the ensemble models did not do nearly as well when predicting the peak week.The Dengue Challenge organizers scored the dengue predictions of the Challenge participant groups. Our ensemble approach was the best in predicting the total number of dengue cases reported for transmission season and peak height for Iquitos, Peru.

  19. Dinosaur fossils predict body temperatures.

    Directory of Open Access Journals (Sweden)

    James F Gillooly

    2006-07-01

    Full Text Available Perhaps the greatest mystery surrounding dinosaurs concerns whether they were endotherms, ectotherms, or some unique intermediate form. Here we present a model that yields estimates of dinosaur body temperature based on ontogenetic growth trajectories obtained from fossil bones. The model predicts that dinosaur body temperatures increased with body mass from approximately 25 degrees C at 12 kg to approximately 41 degrees C at 13,000 kg. The model also successfully predicts observed increases in body temperature with body mass for extant crocodiles. These results provide direct evidence that dinosaurs were reptiles that exhibited inertial homeothermy.

  20. Calorimetry end-point predictions

    International Nuclear Information System (INIS)

    Fox, M.A.

    1981-01-01

    This paper describes a portion of the work presently in progress at Rocky Flats in the field of calorimetry. In particular, calorimetry end-point predictions are outlined. The problems associated with end-point predictions and the progress made in overcoming these obstacles are discussed. The two major problems, noise and an accurate description of the heat function, are dealt with to obtain the most accurate results. Data are taken from an actual calorimeter and are processed by means of three different noise reduction techniques. The processed data are then utilized by one to four algorithms, depending on the accuracy desired to determined the end-point

  1. Prediction of eyespot infection risks

    Directory of Open Access Journals (Sweden)

    M. Váòová

    2012-12-01

    Full Text Available The objective of the study was to design a prediction model for eyespot (Tapesia yallundae infection based on climatic factors (temperature, precipitation, air humidity. Data from experiment years 1994-2002 were used to study correlations between the eyespot infection index and individual weather characteristics. The model of prediction was constructed using multiple regression when a separate parameter is assigned to each factor, i.e. the frequency of days with optimum temperatures, humidity, and precipitation. The correlation between relative air humidity and precipitation and the infection index is significant.

  2. Can we predict nuclear proliferation

    International Nuclear Information System (INIS)

    Tertrais, Bruno

    2011-01-01

    The author aims at improving nuclear proliferation prediction capacities, i.e. the capacities to identify countries susceptible to acquire nuclear weapons, to interpret sensitive activities, and to assess nuclear program modalities. He first proposes a retrospective assessment of counter-proliferation actions since 1945. Then, based on academic studies, he analyzes what causes and motivates proliferation, with notably the possibility of existence of a chain phenomenon (mechanisms driving from one program to another). He makes recommendations for a global approach to proliferation prediction, and proposes proliferation indices and indicators

  3. CERAPP: Collaborative Estrogen Receptor Activity Prediction Project

    Data.gov (United States)

    U.S. Environmental Protection Agency — Data from a large-scale modeling project called CERAPP (Collaborative Estrogen Receptor Activity Prediction Project) demonstrating using predictive computational...

  4. The Challenge of Weather Prediction

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 2; Issue 3. The Challenge of Weather Prediction Old and Modern Ways of Weather Forecasting. B N Goswami. Series Article Volume 2 Issue 3 March 1997 pp 8-15. Fulltext. Click here to view fulltext PDF. Permanent link:

  5. Predictability of weather and climate

    National Research Council Canada - National Science Library

    Palmer, Tim; Hagedorn, Renate

    2006-01-01

    ... and anthropogenic climate change are among those included. Ensemble systems for forecasting predictability are discussed extensively. Ed Lorenz, father of chaos theory, makes a contribution to theoretical analysis with a previously unpublished paper. This well-balanced volume will be a valuable resource for many years. High-quality chapter autho...

  6. Evaluation of environmental impact predictions

    International Nuclear Information System (INIS)

    Cunningham, P.A.; Adams, S.M.; Kumar, K.D.

    1977-01-01

    An analysis and evaluation of the ecological monitoring program at the Surry Nuclear Power Plant showed that predictions of potential environmental impact made in the Final Environmental Statement (FES), which were based on generally accepted ecological principles, were not completely substantiated by environmental monitoring data. The Surry Nuclear Power Plant (Units 1 and 2) was chosen for study because of the facility's relatively continuous operating history and the availability of environmental data adequate for analysis. Preoperational and operational fish monitoring data were used to assess the validity of the FES prediction that fish would congregate in the thermal plume during winter months and would avoid the plume during summer months. Analysis of monitoring data showed that fish catch per unit effort (CPE) was generally high in the thermal plume during winter months; however, the highest fish catches occurred in the plume during the summer. Possible explanations for differences between the FES prediction and results observed in analysis of monitoring data are discussed, and general recommendations are outlined for improving impact assessment predictions

  7. Using Predictability for Lexical Segmentation.

    Science.gov (United States)

    Çöltekin, Çağrı

    2017-09-01

    This study investigates a strategy based on predictability of consecutive sub-lexical units in learning to segment a continuous speech stream into lexical units using computational modeling and simulations. Lexical segmentation is one of the early challenges during language acquisition, and it has been studied extensively through psycholinguistic experiments as well as computational methods. However, despite strong empirical evidence, the explicit use of predictability of basic sub-lexical units in models of segmentation is underexplored. This paper presents an incremental computational model of lexical segmentation for exploring the usefulness of predictability for lexical segmentation. We show that the predictability cue is a strong cue for segmentation. Contrary to earlier reports in the literature, the strategy yields state-of-the-art segmentation performance with an incremental computational model that uses only this particular cue in a cognitively plausible setting. The paper also reports an in-depth analysis of the model, investigating the conditions affecting the usefulness of the strategy. Copyright © 2016 Cognitive Science Society, Inc.

  8. Solution Patterns Predicting Pythagorean Triples

    Science.gov (United States)

    Ezenweani, Ugwunna Louis

    2013-01-01

    Pythagoras Theorem is an old mathematical treatise that has traversed the school curricula from secondary to tertiary levels. The patterns it produced are quite interesting that many researchers have tried to generate a kind of predictive approach to identifying triples. Two attempts, namely Diophantine equation and Brahmagupta trapezium presented…

  9. Predicting response to epigenetic therapy

    DEFF Research Database (Denmark)

    Treppendahl, Marianne B; Sommer Kristensen, Lasse; Grønbæk, Kirsten

    2014-01-01

    of good pretreatment predictors of response is of great value. Many clinical parameters and molecular targets have been tested in preclinical and clinical studies with varying results, leaving room for optimization. Here we provide an overview of markers that may predict the efficacy of FDA- and EMA...

  10. Predicting Volleyball Serve-Reception

    NARCIS (Netherlands)

    Paulo, Ana; Zaal, Frank T J M; Fonseca, Sofia; Araujo, Duarte

    2016-01-01

    Serve and serve-reception performance have predicted success in volleyball. Given the impact of serve-reception on the game, we aimed at understanding what it is in the serve and receiver's actions that determines the selection of the type of pass used in serve-reception and its efficacy. Four

  11. Prediction of electric vehicle penetration.

    Science.gov (United States)

    2017-05-01

    The object of this report is to present the current market status of plug-in-electric : vehicles (PEVs) and to predict their future penetration within the world and U.S. : markets. The sales values for 2016 show a strong year of PEV sales both in the...

  12. Evoked Emotions Predict Food Choice

    NARCIS (Netherlands)

    Dalenberg, Jelle R.; Gutjar, Swetlana; ter Horst, Gert J.; de Graaf, Kees; Renken, Remco J.; Jager, Gerry

    2014-01-01

    In the current study we show that non-verbal food-evoked emotion scores significantly improve food choice prediction over merely liking scores. Previous research has shown that liking measures correlate with choice. However, liking is no strong predictor for food choice in real life environments.

  13. Framework for Traffic Congestion Prediction

    NARCIS (Netherlands)

    Zaki, J.F.W.; Ali-Eldin, A.M.T.; Hussein, S.E.; Saraya, S.F.; Areed, F.F.

    2016-01-01

    Traffic Congestion is a complex dilemma facing most major cities. It has undergone a lot of research since the early 80s in an attempt to predict traffic in the short-term. Recently, Intelligent Transportation Systems (ITS) became an integral part of traffic research which helped in modeling and

  14. Predicting Character Traits Through Reddit

    Science.gov (United States)

    2015-01-01

    and even employers (Res). Companies like Netflix also use personality classification algorithms in order to provide users with predictions of movies...science behind the netflix algorithms that decide what to watch next, August 2013. Reza Zafarani and Huan Liu. Evaluation without ground truth in social media research. Communications Of The ACM, 58(6):54–60, June 2015. 12

  15. Prediction of natural gas consumption

    International Nuclear Information System (INIS)

    Zhang, R.L.; Walton, D.J.; Hoskins, W.D.

    1993-01-01

    Distributors of natural gas need to predict future consumption in order to purchase a sufficient supply on contract. Distributors that offer their customers equal payment plans need to predict the consumption of each customer 12 months in advance. Estimates of previous consumption are often used for months when meters are inaccessible, or bimonthly-read meters. Existing methods of predicting natural gas consumption, and a proposed new method for each local region are discussed. The proposed model distinguishes the consumption load factors from summer to other seasons by attempting to adjust them by introducing two parameters. The problem is then reduced to a quadratic programming problem. However, since it is not necessary to use both parameters simultaneously, the problem can be solved with a simple iterative procedure. Results show that the new model can improve the two-equation model to a certain scale. The adjustment to heat load factor can reduce the error of prediction markedly while that to base load factor influences the error marginally. 3 refs., 11 figs., 2 tabs

  16. Prediction of Subsidence Depression Development

    Czech Academy of Sciences Publication Activity Database

    Doležalová, Hana; Kajzar, Vlastimil

    2017-01-01

    Roč. 6, č. 4 (2017), s. 208-214 E-ISSN 2391-9361. [Cross-border Exchange of Experience in Production Engineering Using Principles of Mathematics. Rybnik, 07.06.2017-09.06.2017] Institutional support: RVO:68145535 Keywords : undermining * prediction * regression analysis Subject RIV: DH - Mining, incl. Coal Mining OBOR OECD: Mining and mineral processing

  17. Bankruptcy Prediction with Rough Sets

    NARCIS (Netherlands)

    J.C. Bioch (Cor); V. Popova (Viara)

    2001-01-01

    textabstractThe bankruptcy prediction problem can be considered an or dinal classification problem. The classical theory of Rough Sets describes objects by discrete attributes, and does not take into account the order- ing of the attributes values. This paper proposes a modification of the Rough Set

  18. Climate Prediction Center - monthly Outlook

    Science.gov (United States)

    Weather Service NWS logo - Click to go to the NWS home page Climate Prediction Center Site Map News Outlooks monthly Climate Outlooks Banner OFFICIAL Forecasts June 2018 [UPDATED MONTHLY FORECASTS SERVICE ) Canonical Correlation Analysis ECCA - Ensemble Canonical Correlation Analysis Optimal Climate Normals

  19. Climate Prediction Center - Site Index

    Science.gov (United States)

    Weather Service NWS logo - Click to go to the NWS home page Climate Prediction Center Home Site Map News Means Bulletins Annual Winter Stratospheric Ozone Climate Diagnostics Bulletin (Most Recent) Climate (Hazards Outlook) Climate Assessment: Dec. 1999-Feb. 2000 (Seasonal) Climate Assessment: Mar-May 2000

  20. Predictive medical information and underwriting.

    Science.gov (United States)

    Dodge, John H

    2007-01-01

    Medical underwriting involves the application of actuarial science by analyzing medical information to predict the future risk of a claim. The objective is that individuals with like risk are treated in a like manner so that the premium paid is proportional to the risk of future claim.

  1. Can Creativity Predict Cognitive Reserve?

    Science.gov (United States)

    Palmiero, Massimiliano; Di Giacomo, Dina; Passafiume, Domenico

    2016-01-01

    Cognitive reserve relies on the ability to effectively cope with aging and brain damage by using alternate processes to approach tasks when standard approaches are no longer available. In this study, the issue if creativity can predict cognitive reserve has been explored. Forty participants (mean age: 61 years) filled out: the Cognitive Reserve…

  2. A prediction for bubbling geometries

    OpenAIRE

    Okuda, Takuya

    2007-01-01

    We study the supersymmetric circular Wilson loops in N=4 Yang-Mills theory. Their vacuum expectation values are computed in the parameter region that admits smooth bubbling geometry duals. The results are a prediction for the supergravity action evaluated on the bubbling geometries for Wilson loops.

  3. Detecting failure of climate predictions

    Science.gov (United States)

    Runge, Michael C.; Stroeve, Julienne C.; Barrett, Andrew P.; McDonald-Madden, Eve

    2016-01-01

    The practical consequences of climate change challenge society to formulate responses that are more suited to achieving long-term objectives, even if those responses have to be made in the face of uncertainty1, 2. Such a decision-analytic focus uses the products of climate science as probabilistic predictions about the effects of management policies3. Here we present methods to detect when climate predictions are failing to capture the system dynamics. For a single model, we measure goodness of fit based on the empirical distribution function, and define failure when the distribution of observed values significantly diverges from the modelled distribution. For a set of models, the same statistic can be used to provide relative weights for the individual models, and we define failure when there is no linear weighting of the ensemble models that produces a satisfactory match to the observations. Early detection of failure of a set of predictions is important for improving model predictions and the decisions based on them. We show that these methods would have detected a range shift in northern pintail 20 years before it was actually discovered, and are increasingly giving more weight to those climate models that forecast a September ice-free Arctic by 2055.

  4. Predicting severity of paranoid schizophrenia

    OpenAIRE

    Kolesnichenko Elena Vladimirovna

    2015-01-01

    Clinical symptoms, course and outcomes of paranoid schizophrenia are polymorphic. 206 cases of paranoid schizophrenia were investigated. Clinical predictors were collected from hospital records and interviews. Quantitative assessment of the severity of schizophrenia as special indexes was used. Schizoid, epileptoid, psychasthenic and conformal accentuation of personality in the premorbid, early onset of psychosis, paranoid and hallucinatory-paranoid variants of onset predicted more expressed ...

  5. Predictability of Mobile Phone Associations

    DEFF Research Database (Denmark)

    Jensen, Bjørn Sand; Larsen, Jan; Hansen, Lars Kai

    2010-01-01

    Prediction and understanding of human behavior is of high importance in many modern applications and research areas ranging from context-aware services, wireless resource allocation to social sciences. In this study we collect a novel dataset using standard mobile phones and analyze how the predi...... representation, and general behavior. This is of vital interest in the development of context-aware services which rely on forecasting based on mobile phone sensors.......Prediction and understanding of human behavior is of high importance in many modern applications and research areas ranging from context-aware services, wireless resource allocation to social sciences. In this study we collect a novel dataset using standard mobile phones and analyze how...... the predictability of mobile sensors, acting as proxies for humans, change with time scale and sensor type such as GSM and WLAN. Applying recent information theoretic methods, it is demonstrated that an upper bound on predictability is relatively high for all sensors given the complete history (typically above 90...

  6. Numerical prediction of slamming loads

    DEFF Research Database (Denmark)

    Seng, Sopheak; Jensen, Jørgen J; Pedersen, Preben T

    2012-01-01

    It is important to include the contribution of the slamming-induced response in the structural design of large vessels with a significant bow flare. At the same time it is a challenge to develop rational tools to determine the slamming-induced loads and the prediction of their occurrence. Today i...

  7. Predictive models of moth development

    Science.gov (United States)

    Degree-day models link ambient temperature to insect life-stages, making such models valuable tools in integrated pest management. These models increase management efficacy by predicting pest phenology. In Wisconsin, the top insect pest of cranberry production is the cranberry fruitworm, Acrobasis v...

  8. Prediction of Malaysian monthly GDP

    Science.gov (United States)

    Hin, Pooi Ah; Ching, Soo Huei; Yeing, Pan Wei

    2015-12-01

    The paper attempts to use a method based on multivariate power-normal distribution to predict the Malaysian Gross Domestic Product next month. Letting r(t) be the vector consisting of the month-t values on m selected macroeconomic variables, and GDP, we model the month-(t+1) GDP to be dependent on the present and l-1 past values r(t), r(t-1),…,r(t-l+1) via a conditional distribution which is derived from a [(m+1)l+1]-dimensional power-normal distribution. The 100(α/2)% and 100(1-α/2)% points of the conditional distribution may be used to form an out-of sample prediction interval. This interval together with the mean of the conditional distribution may be used to predict the month-(t+1) GDP. The mean absolute percentage error (MAPE), estimated coverage probability and average length of the prediction interval are used as the criterions for selecting the suitable lag value l-1 and the subset from a pool of 17 macroeconomic variables. It is found that the relatively better models would be those of which 2 ≤ l ≤ 3, and involving one or two of the macroeconomic variables given by Market Indicative Yield, Oil Prices, Exchange Rate and Import Trade.

  9. Cast iron - a predictable material

    Directory of Open Access Journals (Sweden)

    Jorg C. Sturm

    2011-02-01

    Full Text Available High strength compacted graphite iron (CGI or alloyed cast iron components are substituting previously used non-ferrous castings in automotive power train applications. The mechanical engineering industry has recognized the value in substituting forged or welded structures with stiff and light-weight cast iron castings. New products such as wind turbines have opened new markets for an entire suite of highly reliable ductile iron cast components. During the last 20 years, casting process simulation has developed from predicting hot spots and solidification to an integral assessment tool for foundries for the entire manufacturing route of castings. The support of the feeding related layout of the casting is still one of the most important duties for casting process simulation. Depending on the alloy poured, different feeding behaviors and self-feeding capabilities need to be considered to provide a defect free casting. Therefore, it is not enough to base the prediction of shrinkage defects solely on hot spots derived from temperature fields. To be able to quantitatively predict these defects, solidification simulation had to be combined with density and mass transport calculations, in order to evaluate the impact of the solidification morphology on the feeding behavior as well as to consider alloy dependent feeding ranges. For cast iron foundries, the use of casting process simulation has become an important instrument to predict the robustness and reliability of their processes, especially since the influence of alloying elements, melting practice and metallurgy need to be considered to quantify the special shrinkage and solidification behavior of cast iron. This allows the prediction of local structures, phases and ultimately the local mechanical properties of cast irons, to asses casting quality in the foundry but also to make use of this quantitative information during design of the casting. Casting quality issues related to thermally driven

  10. HUMAN DECISIONS AND MACHINE PREDICTIONS.

    Science.gov (United States)

    Kleinberg, Jon; Lakkaraju, Himabindu; Leskovec, Jure; Ludwig, Jens; Mullainathan, Sendhil

    2018-02-01

    Can machine learning improve human decision making? Bail decisions provide a good test case. Millions of times each year, judges make jail-or-release decisions that hinge on a prediction of what a defendant would do if released. The concreteness of the prediction task combined with the volume of data available makes this a promising machine-learning application. Yet comparing the algorithm to judges proves complicated. First, the available data are generated by prior judge decisions. We only observe crime outcomes for released defendants, not for those judges detained. This makes it hard to evaluate counterfactual decision rules based on algorithmic predictions. Second, judges may have a broader set of preferences than the variable the algorithm predicts; for instance, judges may care specifically about violent crimes or about racial inequities. We deal with these problems using different econometric strategies, such as quasi-random assignment of cases to judges. Even accounting for these concerns, our results suggest potentially large welfare gains: one policy simulation shows crime reductions up to 24.7% with no change in jailing rates, or jailing rate reductions up to 41.9% with no increase in crime rates. Moreover, all categories of crime, including violent crimes, show reductions; and these gains can be achieved while simultaneously reducing racial disparities. These results suggest that while machine learning can be valuable, realizing this value requires integrating these tools into an economic framework: being clear about the link between predictions and decisions; specifying the scope of payoff functions; and constructing unbiased decision counterfactuals. JEL Codes: C10 (Econometric and statistical methods and methodology), C55 (Large datasets: Modeling and analysis), K40 (Legal procedure, the legal system, and illegal behavior).

  11. Ocean eddies and climate predictability.

    Science.gov (United States)

    Kirtman, Ben P; Perlin, Natalie; Siqueira, Leo

    2017-12-01

    A suite of coupled climate model simulations and experiments are used to examine how resolved mesoscale ocean features affect aspects of climate variability, air-sea interactions, and predictability. In combination with control simulations, experiments with the interactive ensemble coupling strategy are used to further amplify the role of the oceanic mesoscale field and the associated air-sea feedbacks and predictability. The basic intent of the interactive ensemble coupling strategy is to reduce the atmospheric noise at the air-sea interface, allowing an assessment of how noise affects the variability, and in this case, it is also used to diagnose predictability from the perspective of signal-to-noise ratios. The climate variability is assessed from the perspective of sea surface temperature (SST) variance ratios, and it is shown that, unsurprisingly, mesoscale variability significantly increases SST variance. Perhaps surprising is the fact that the presence of mesoscale ocean features even further enhances the SST variance in the interactive ensemble simulation beyond what would be expected from simple linear arguments. Changes in the air-sea coupling between simulations are assessed using pointwise convective rainfall-SST and convective rainfall-SST tendency correlations and again emphasize how the oceanic mesoscale alters the local association between convective rainfall and SST. Understanding the possible relationships between the SST-forced signal and the weather noise is critically important in climate predictability. We use the interactive ensemble simulations to diagnose this relationship, and we find that the presence of mesoscale ocean features significantly enhances this link particularly in ocean eddy rich regions. Finally, we use signal-to-noise ratios to show that the ocean mesoscale activity increases model estimated predictability in terms of convective precipitation and atmospheric upper tropospheric circulation.

  12. Predicting steam generator crevice chemistry

    International Nuclear Information System (INIS)

    Burton, G.; Strati, G.

    2006-01-01

    'Full text:' Corrosion of steam cycle components produces insoluble material, mostly iron oxides, that are transported to the steam generator (SG) via the feedwater and deposited on internal surfaces such as the tubes, tube support plates and the tubesheet. The build up of these corrosion products over time can lead to regions of restricted flow with water chemistry that may be significantly different, and potentially more corrosive to SG tube material, than the bulk steam generator water chemistry. The aim of the present work is to predict SG crevice chemistry using experimentation and modelling as part of AECL's overall strategy for steam generator life management. Hideout-return experiments are performed under CANDU steam generator conditions to assess the accumulation of impurities in hideout, and return from, model crevices. The results are used to validate the ChemSolv model that predicts steam generator crevice impurity concentrations, and high temperature pH, based on process parameters (e.g., heat flux, primary side temperature) and blowdown water chemistry. The model has been incorporated into ChemAND, AECL's system health monitoring software for chemistry monitoring, analysis and diagnostics that has been installed at two domestic and one international CANDU station. ChemAND provides the station chemists with the only method to predict SG crevice chemistry. In one recent application, the software has been used to evaluate the crevice chemistry based on the elevated, but balanced, SG bulk water impurity concentrations present during reactor startup, in order to reduce hold times. The present paper will describe recent hideout-return experiments that are used for the validation of the ChemSolv model, station experience using the software, and improvements to predict the crevice electrochemical potential that will permit station staff to ensure that the SG tubes are in the 'safe operating zone' predicted by Lu (AECL). (author)

  13. Predicting outcome of status epilepticus.

    Science.gov (United States)

    Leitinger, M; Kalss, G; Rohracher, A; Pilz, G; Novak, H; Höfler, J; Deak, I; Kuchukhidze, G; Dobesberger, J; Wakonig, A; Trinka, E

    2015-08-01

    Status epilepticus (SE) is a frequent neurological emergency complicated by high mortality and often poor functional outcome in survivors. The aim of this study was to review available clinical scores to predict outcome. Literature review. PubMed Search terms were "score", "outcome", and "status epilepticus" (April 9th 2015). Publications with abstracts available in English, no other language restrictions, or any restrictions concerning investigated patients were included. Two scores were identified: "Status Epilepticus Severity Score--STESS" and "Epidemiology based Mortality score in SE--EMSE". A comprehensive comparison of test parameters concerning performance, options, and limitations was performed. Epidemiology based Mortality score in SE allows detailed individualization of risk factors and is significantly superior to STESS in a retrospective explorative study. In particular, EMSE is very good at detection of good and bad outcome, whereas STESS detecting bad outcome is limited by a ceiling effect and uncertainty of correct cutoff value. Epidemiology based Mortality score in SE can be adapted to different regions in the world and to advances in medicine, as new data emerge. In addition, we designed a reporting standard for status epilepticus to enhance acquisition and communication of outcome relevant data. A data acquisition sheet used from patient admission in emergency room, from the EEG lab to intensive care unit, is provided for optimized data collection. Status Epilepticus Severity Score is easy to perform and predicts bad outcome, but has a low predictive value for good outcomes. Epidemiology based Mortality score in SE is superior to STESS in predicting good or bad outcome but needs marginally more time to perform. Epidemiology based Mortality score in SE may prove very useful for risk stratification in interventional studies and is recommended for individual outcome prediction. Prospective validation in different cohorts is needed for EMSE, whereas

  14. Multiphase, multicomponent phase behavior prediction

    Science.gov (United States)

    Dadmohammadi, Younas

    Accurate prediction of phase behavior of fluid mixtures in the chemical industry is essential for designing and operating a multitude of processes. Reliable generalized predictions of phase equilibrium properties, such as pressure, temperature, and phase compositions offer an attractive alternative to costly and time consuming experimental measurements. The main purpose of this work was to assess the efficacy of recently generalized activity coefficient models based on binary experimental data to (a) predict binary and ternary vapor-liquid equilibrium systems, and (b) characterize liquid-liquid equilibrium systems. These studies were completed using a diverse binary VLE database consisting of 916 binary and 86 ternary systems involving 140 compounds belonging to 31 chemical classes. Specifically the following tasks were undertaken: First, a comprehensive assessment of the two common approaches (gamma-phi (gamma-ϕ) and phi-phi (ϕ-ϕ)) used for determining the phase behavior of vapor-liquid equilibrium systems is presented. Both the representation and predictive capabilities of these two approaches were examined, as delineated form internal and external consistency tests of 916 binary systems. For the purpose, the universal quasi-chemical (UNIQUAC) model and the Peng-Robinson (PR) equation of state (EOS) were used in this assessment. Second, the efficacy of recently developed generalized UNIQUAC and the nonrandom two-liquid (NRTL) for predicting multicomponent VLE systems were investigated. Third, the abilities of recently modified NRTL model (mNRTL2 and mNRTL1) to characterize liquid-liquid equilibria (LLE) phase conditions and attributes, including phase stability, miscibility, and consolute point coordinates, were assessed. The results of this work indicate that the ϕ-ϕ approach represents the binary VLE systems considered within three times the error of the gamma-ϕ approach. A similar trend was observed for the for the generalized model predictions using

  15. Branch prediction in the pentium family

    DEFF Research Database (Denmark)

    Fog, Agner

    1998-01-01

    How the branch prediction mechanism in the Pentium has been uncovered with all its quirks, and the incredibly more effective branch prediction in the later versions.......How the branch prediction mechanism in the Pentium has been uncovered with all its quirks, and the incredibly more effective branch prediction in the later versions....

  16. Neural Networks for protein Structure Prediction

    DEFF Research Database (Denmark)

    Bohr, Henrik

    1998-01-01

    This is a review about neural network applications in bioinformatics. Especially the applications to protein structure prediction, e.g. prediction of secondary structures, prediction of surface structure, fold class recognition and prediction of the 3-dimensional structure of protein backbones...

  17. Semen analysis and prediction of natural conception

    NARCIS (Netherlands)

    Leushuis, Esther; van der Steeg, Jan Willem; Steures, Pieternel; Repping, Sjoerd; Bossuyt, Patrick M. M.; Mol, Ben Willem J.; Hompes, Peter G. A.; van der Veen, Fulco

    2014-01-01

    Do two semen analyses predict natural conception better than a single semen analysis and will adding the results of repeated semen analyses to a prediction model for natural pregnancy improve predictions? A second semen analysis does not add helpful information for predicting natural conception

  18. Time-Predictable Virtual Memory

    DEFF Research Database (Denmark)

    Puffitsch, Wolfgang; Schoeberl, Martin

    2016-01-01

    Virtual memory is an important feature of modern computer architectures. For hard real-time systems, memory protection is a particularly interesting feature of virtual memory. However, current memory management units are not designed for time-predictability and therefore cannot be used...... in such systems. This paper investigates the requirements on virtual memory from the perspective of hard real-time systems and presents the design of a time-predictable memory management unit. Our evaluation shows that the proposed design can be implemented efficiently. The design allows address translation...... and address range checking in constant time of two clock cycles on a cache miss. This constant time is in strong contrast to the possible cost of a miss in a translation look-aside buffer in traditional virtual memory organizations. Compared to a platform without a memory management unit, these two additional...

  19. Predicting responses from Rasch measures.

    Science.gov (United States)

    Linacre, John M

    2010-01-01

    There is a growing family of Rasch models for polytomous observations. Selecting a suitable model for an existing dataset, estimating its parameters and evaluating its fit is now routine. Problems arise when the model parameters are to be estimated from the current data, but used to predict future data. In particular, ambiguities in the nature of the current data, or overfit of the model to the current dataset, may mean that better fit to the current data may lead to worse fit to future data. The predictive power of several Rasch and Rasch-related models are discussed in the context of the Netflix Prize. Rasch-related models are proposed based on Singular Value Decomposition (SVD) and Boltzmann Machines.

  20. Prediction of dislocation boundary characteristics

    DEFF Research Database (Denmark)

    Winther, Grethe

    Plastic deformation of both fcc and bcc metals of medium to high stacking fault energy is known to result in dislocation patterning in the form of cells and extended planar dislocation boundaries. The latter align with specific crystallographic planes, which depend on the crystallographic......) and it is found that to a large extent the dislocations screen each other’s elastic stress fields [3]. The present contribution aims at advancing the previous theoretical analysis of a boundary on a known crystallographic plane to actual prediction of this plane as well as other boundary characteristics....... Crystal plasticity calculations combined with the hypothesis that these boundaries separate domains with local differences in the slip system activity are introduced to address precise prediction of the experimentally observed boundaries. The presentation will focus on two cases from fcc metals...

  1. Time-Predictable Computer Architecture

    Directory of Open Access Journals (Sweden)

    Schoeberl Martin

    2009-01-01

    Full Text Available Today's general-purpose processors are optimized for maximum throughput. Real-time systems need a processor with both a reasonable and a known worst-case execution time (WCET. Features such as pipelines with instruction dependencies, caches, branch prediction, and out-of-order execution complicate WCET analysis and lead to very conservative estimates. In this paper, we evaluate the issues of current architectures with respect to WCET analysis. Then, we propose solutions for a time-predictable computer architecture. The proposed architecture is evaluated with implementation of some features in a Java processor. The resulting processor is a good target for WCET analysis and still performs well in the average case.

  2. [Predictive factors of anxiety disorders].

    Science.gov (United States)

    Domschke, K

    2014-10-01

    Anxiety disorders are among the most frequent mental disorders in Europe (12-month prevalence 14%) and impose a high socioeconomic burden. The pathogenesis of anxiety disorders is complex with an interaction of biological, environmental and psychosocial factors contributing to the overall disease risk (diathesis-stress model). In this article, risk factors for anxiety disorders will be presented on several levels, e.g. genetic factors, environmental factors, gene-environment interactions, epigenetic mechanisms, neuronal networks ("brain fear circuit"), psychophysiological factors (e.g. startle response and CO2 sensitivity) and dimensional/subclinical phenotypes of anxiety (e.g. anxiety sensitivity and behavioral inhibition), and critically discussed regarding their potential predictive value. The identification of factors predictive of anxiety disorders will possibly allow for effective preventive measures or early treatment interventions, respectively, and reduce the individual patient's suffering as well as the overall socioeconomic burden of anxiety disorders.

  3. Algorithms for Protein Structure Prediction

    DEFF Research Database (Denmark)

    Paluszewski, Martin

    -trace. Here we present three different approaches for reconstruction of C-traces from predictable measures. In our first approach [63, 62], the C-trace is positioned on a lattice and a tabu-search algorithm is applied to find minimum energy structures. The energy function is based on half-sphere-exposure (HSE......) is more robust than standard Monte Carlo search. In the second approach for reconstruction of C-traces, an exact branch and bound algorithm has been developed [67, 65]. The model is discrete and makes use of secondary structure predictions, HSE, CN and radius of gyration. We show how to compute good lower...... bounds for partial structures very fast. Using these lower bounds, we are able to find global minimum structures in a huge conformational space in reasonable time. We show that many of these global minimum structures are of good quality compared to the native structure. Our branch and bound algorithm...

  4. Antipredator defenses predict diversification rates

    Science.gov (United States)

    Arbuckle, Kevin; Speed, Michael P.

    2015-01-01

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

  5. Nonparametric predictive inference in reliability

    International Nuclear Information System (INIS)

    Coolen, F.P.A.; Coolen-Schrijner, P.; Yan, K.J.

    2002-01-01

    We introduce a recently developed statistical approach, called nonparametric predictive inference (NPI), to reliability. Bounds for the survival function for a future observation are presented. We illustrate how NPI can deal with right-censored data, and discuss aspects of competing risks. We present possible applications of NPI for Bernoulli data, and we briefly outline applications of NPI for replacement decisions. The emphasis is on introduction and illustration of NPI in reliability contexts, detailed mathematical justifications are presented elsewhere

  6. Shoulder Dystocia: Prediction and Management

    OpenAIRE

    Hill, Meghan G; Cohen, Wayne R

    2016-01-01

    Shoulder dystocia is a complication of vaginal delivery and the primary factor associated with brachial plexus injury. In this review, we discuss the risk factors for shoulder dystocia and propose a framework for the prediction and prevention of the complication. A recommended approach to management when shoulder dystocia occurs is outlined, with review of the maneuvers used to relieve the obstruction with minimal risk of fetal and maternal injury.

  7. Shoulder dystocia: prediction and management.

    Science.gov (United States)

    Hill, Meghan G; Cohen, Wayne R

    2016-01-01

    Shoulder dystocia is a complication of vaginal delivery and the primary factor associated with brachial plexus injury. In this review, we discuss the risk factors for shoulder dystocia and propose a framework for the prediction and prevention of the complication. A recommended approach to management when shoulder dystocia occurs is outlined, with review of the maneuvers used to relieve the obstruction with minimal risk of fetal and maternal injury.

  8. Black holes, singularities and predictability

    International Nuclear Information System (INIS)

    Wald, R.M.

    1984-01-01

    The paper favours the view that singularities may play a central role in quantum gravity. The author reviews the arguments leading to the conclusion, that in the process of black hole formation and evaporation, an initial pure state evolves to a final density matrix, thus signaling a breakdown in ordinary quantum dynamical evolution. Some related issues dealing with predictability in the dynamical evolution, are also discussed. (U.K.)

  9. Rainfall prediction with backpropagation method

    Science.gov (United States)

    Wahyuni, E. G.; Fauzan, L. M. F.; Abriyani, F.; Muchlis, N. F.; Ulfa, M.

    2018-03-01

    Rainfall is an important factor in many fields, such as aviation and agriculture. Although it has been assisted by technology but the accuracy can not reach 100% and there is still the possibility of error. Though current rainfall prediction information is needed in various fields, such as agriculture and aviation fields. In the field of agriculture, to obtain abundant and quality yields, farmers are very dependent on weather conditions, especially rainfall. Rainfall is one of the factors that affect the safety of aircraft. To overcome the problems above, then it’s required a system that can accurately predict rainfall. In predicting rainfall, artificial neural network modeling is applied in this research. The method used in modeling this artificial neural network is backpropagation method. Backpropagation methods can result in better performance in repetitive exercises. This means that the weight of the ANN interconnection can approach the weight it should be. Another advantage of this method is the ability in the learning process adaptively and multilayer owned on this method there is a process of weight changes so as to minimize error (fault tolerance). Therefore, this method can guarantee good system resilience and consistently work well. The network is designed using 4 input variables, namely air temperature, air humidity, wind speed, and sunshine duration and 3 output variables ie low rainfall, medium rainfall, and high rainfall. Based on the research that has been done, the network can be used properly, as evidenced by the results of the prediction of the system precipitation is the same as the results of manual calculations.

  10. The Clinical Prediction of Dangerousness.

    Science.gov (United States)

    1985-05-01

    8217 8 ings. Szasz (1963) has argued persuasively that clinical predictions of future dangerous behavior are unfairly focused on the mentally ill...Persons labeled paranoid, Szasz states, are readily commitable, while highly dangerous drunken drivers are not. Indeed, dangerousness such as that...Psychology, 31, 492-494. Szasz , T. (1963). Law, liberty and psychiatry. New York: Macmillan. Taft, R. (1955). The ability to judge people. Psychological

  11. Dim prospects for earthquake prediction

    Science.gov (United States)

    Geller, Robert J.

    I was misquoted by C. Lomnitz's [1998] Forum letter (Eos, August 4, 1998, p. 373), which said: [I wonder whether Sasha Gusev [1998] actually believes that branding earthquake prediction a ‘proven nonscience’ [Geller, 1997a] is a paradigm for others to copy.”Readers are invited to verify for themselves that neither “proven nonscience” norv any similar phrase was used by Geller [1997a].

  12. Are Some Semantic Changes Predictable?

    DEFF Research Database (Denmark)

    Schousboe, Steen

    2010-01-01

      Historical linguistics is traditionally concerned with phonology and syntax. With the exception of grammaticalization - the development of auxiliary verbs, the syntactic rather than localistic use of prepositions, etc. - semantic change has usually not been described as a result of regular...... developments, but only as specific meaning changes in individual words. This paper will suggest some regularities in semantic change, regularities which, like sound laws, have predictive power and can be tested against recorded languages....

  13. Butterfly valve torque prediction methodology

    International Nuclear Information System (INIS)

    Eldiwany, B.H.; Sharma, V.; Kalsi, M.S.; Wolfe, K.

    1994-01-01

    As part of the Motor-Operated Valve (MOV) Performance Prediction Program, the Electric Power Research Institute has sponsored the development of methodologies for predicting thrust and torque requirements of gate, globe, and butterfly MOVs. This paper presents the methodology that will be used by utilities to calculate the dynamic torque requirements for butterfly valves. The total dynamic torque at any disc position is the sum of the hydrodynamic torque, bearing torque (which is induced by the hydrodynamic force), as well as other small torque components (such as packing torque). The hydrodynamic torque on the valve disc, caused by the fluid flow through the valve, depends on the disc angle, flow velocity, upstream flow disturbances, disc shape, and the disc aspect ratio. The butterfly valve model provides sets of nondimensional flow and torque coefficients that can be used to predict flow rate and hydrodynamic torque throughout the disc stroke and to calculate the required actuation torque and the maximum transmitted torque throughout the opening and closing stroke. The scope of the model includes symmetric and nonsymmetric discs of different shapes and aspects ratios in compressible and incompressible fluid applications under both choked and nonchoked flow conditions. The model features were validated against test data from a comprehensive flowloop and in situ test program. These tests were designed to systematically address the effect of the following parameters on the required torque: valve size, disc shapes and disc aspect ratios, upstream elbow orientation and its proximity, and flow conditions. The applicability of the nondimensional coefficients to valves of different sizes was validated by performing tests on 42-in. valve and a precisely scaled 6-in. model. The butterfly valve model torque predictions were found to bound test data from the flow-loop and in situ testing, as shown in the examples provided in this paper

  14. Prediction of future asset prices

    Science.gov (United States)

    Seong, Ng Yew; Hin, Pooi Ah; Ching, Soo Huei

    2014-12-01

    This paper attempts to incorporate trading volumes as an additional predictor for predicting asset prices. Denoting r(t) as the vector consisting of the time-t values of the trading volume and price of a given asset, we model the time-(t+1) asset price to be dependent on the present and l-1 past values r(t), r(t-1), ....., r(t-1+1) via a conditional distribution which is derived from a (2l+1)-dimensional power-normal distribution. A prediction interval based on the 100(α/2)% and 100(1-α/2)% points of the conditional distribution is then obtained. By examining the average lengths of the prediction intervals found by using the composite indices of the Malaysia stock market for the period 2008 to 2013, we found that the value 2 appears to be a good choice for l. With the omission of the trading volume in the vector r(t), the corresponding prediction interval exhibits a slightly longer average length, showing that it might be desirable to keep trading volume as a predictor. From the above conditional distribution, the probability that the time-(t+1) asset price will be larger than the time-t asset price is next computed. When the probability differs from 0 (or 1) by less than 0.03, the observed time-(t+1) increase in price tends to be negative (or positive). Thus the above probability has a good potential of being used as a market indicator in technical analysis.

  15. Evoked Emotions Predict Food Choice

    OpenAIRE

    Dalenberg, Jelle R.; Gutjar, Swetlana; ter Horst, Gert J.; de Graaf, Kees; Renken, Remco J.; Jager, Gerry

    2014-01-01

    In the current study we show that non-verbal food-evoked emotion scores significantly improve food choice prediction over merely liking scores. Previous research has shown that liking measures correlate with choice. However, liking is no strong predictor for food choice in real life environments. Therefore, the focus within recent studies shifted towards using emotion-profiling methods that successfully can discriminate between products that are equally liked. However, it is unclear how well ...

  16. Predictive Analytics in Information Systems Research

    OpenAIRE

    Shmueli, Galit; Koppius, Otto

    2011-01-01

    textabstractThis research essay highlights the need to integrate predictive analytics into information systems research and shows several concrete ways in which this goal can be accomplished. Predictive analytics include empirical methods (statistical and other) that generate data predictions as well as methods for assessing predictive power. Predictive analytics not only assist in creating practically useful models, they also play an important role alongside explanatory modeling in theory bu...

  17. Seizure Prediction and its Applications

    Science.gov (United States)

    Iasemidis, Leon D.

    2011-01-01

    Epilepsy is characterized by intermittent, paroxysmal, hypersynchronous electrical activity, that may remain localized and/or spread and severely disrupt the brain’s normal multi-task and multi-processing function. Epileptic seizures are the hallmarks of such activity and had been considered unpredictable. It is only recently that research on the dynamics of seizure generation by analysis of the brain’s electrographic activity (EEG) has shed ample light on the predictability of seizures, and illuminated the way to automatic, prospective, long-term prediction of seizures. The ability to issue warnings in real time of impending seizures (e.g., tens of minutes prior to seizure occurrence in the case of focal epilepsy), may lead to novel diagnostic tools and treatments for epilepsy. Applications may range from a simple warning to the patient, in order to avert seizure-associated injuries, to intervention by automatic timely administration of an appropriate stimulus, for example of a chemical nature like an anti-epileptic drug (AED), electromagnetic nature like vagus nerve stimulation (VNS), deep brain stimulation (DBS), transcranial direct current (TDC) or transcranial magnetic stimulation (TMS), and/or of another nature (e.g., ultrasonic, cryogenic, biofeedback operant conditioning). It is thus expected that seizure prediction could readily become an integral part of the treatment of epilepsy through neuromodulation, especially in the new generation of closed-loop seizure control systems. PMID:21939848

  18. Prediction During Natural Language Comprehension.

    Science.gov (United States)

    Willems, Roel M; Frank, Stefan L; Nijhof, Annabel D; Hagoort, Peter; van den Bosch, Antal

    2016-06-01

    The notion of prediction is studied in cognitive neuroscience with increasing intensity. We investigated the neural basis of 2 distinct aspects of word prediction, derived from information theory, during story comprehension. We assessed the effect of entropy of next-word probability distributions as well as surprisal A computational model determined entropy and surprisal for each word in 3 literary stories. Twenty-four healthy participants listened to the same 3 stories while their brain activation was measured using fMRI. Reversed speech fragments were presented as a control condition. Brain areas sensitive to entropy were left ventral premotor cortex, left middle frontal gyrus, right inferior frontal gyrus, left inferior parietal lobule, and left supplementary motor area. Areas sensitive to surprisal were left inferior temporal sulcus ("visual word form area"), bilateral superior temporal gyrus, right amygdala, bilateral anterior temporal poles, and right inferior frontal sulcus. We conclude that prediction during language comprehension can occur at several levels of processing, including at the level of word form. Our study exemplifies the power of combining computational linguistics with cognitive neuroscience, and additionally underlines the feasibility of studying continuous spoken language materials with fMRI. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  19. Prediction of Chevrel superconducting phases

    International Nuclear Information System (INIS)

    Savitskij, E.M.; Kiseleva, N.N.

    1978-01-01

    Made is an attempt of predicting the possibility of formation of compounds of Mo 3 Se 4 type structure having critical temperatures of transition into superconducting state more than 4.2 K. Cybernetic method of teaching an electronic computer to form notions is used for prediction. Prediction system constructs logic dependence of forming Chevrel superconducting phase of the Asub(x)Bsub(6)Ssub(8) composition (A being an element of the periodic system; B=Cr, Mo, W, Re) and Asub(x)Bsub(6)Ssub(8) compounds having a critical temperature of more than 4.2 K on the properties of A and B elements. A conclusion is made that W, Re, Cr do not form Chevrel phases of the Asub(x)Bsub(6)Ssub(8) composition as B component. Be, Hg, Ra, B, Ac are the reserve for obtaining Asub(x)Mosub(6)Ssub(8) phases. Agsub(x)Mosub(6)Ssub(8) compound may have a high critical temperature. The ways of a critical temperature increase for Chevrel phases are connected with the search of optimal technological conditions for already known superconducting compounds and also with introduction of impurities fixing a distance between sulfur cubes

  20. Childhood asthma-predictive phenotype.

    Science.gov (United States)

    Guilbert, Theresa W; Mauger, David T; Lemanske, Robert F

    2014-01-01

    Wheezing is a fairly common symptom in early childhood, but only some of these toddlers will experience continued wheezing symptoms in later childhood. The definition of the asthma-predictive phenotype is in children with frequent, recurrent wheezing in early life who have risk factors associated with the continuation of asthma symptoms in later life. Several asthma-predictive phenotypes were developed retrospectively based on large, longitudinal cohort studies; however, it can be difficult to differentiate these phenotypes clinically as the expression of symptoms, and risk factors can change with time. Genetic, environmental, developmental, and host factors and their interactions may contribute to the development, severity, and persistence of the asthma phenotype over time. Key characteristics that distinguish the childhood asthma-predictive phenotype include the following: male sex; a history of wheezing, with lower respiratory tract infections; history of parental asthma; history of atopic dermatitis; eosinophilia; early sensitization to food or aeroallergens; or lower lung function in early life. Copyright © 2014 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

  1. Global predictability of temperature extremes

    Science.gov (United States)

    Coughlan de Perez, Erin; van Aalst, Maarten; Bischiniotis, Konstantinos; Mason, Simon; Nissan, Hannah; Pappenberger, Florian; Stephens, Elisabeth; Zsoter, Ervin; van den Hurk, Bart

    2018-05-01

    Extreme temperatures are one of the leading causes of death and disease in both developed and developing countries, and heat extremes are projected to rise in many regions. To reduce risk, heatwave plans and cold weather plans have been effectively implemented around the world. However, much of the world’s population is not yet protected by such systems, including many data-scarce but also highly vulnerable regions. In this study, we assess at a global level where such systems have the potential to be effective at reducing risk from temperature extremes, characterizing (1) long-term average occurrence of heatwaves and coldwaves, (2) seasonality of these extremes, and (3) short-term predictability of these extreme events three to ten days in advance. Using both the NOAA and ECMWF weather forecast models, we develop global maps indicating a first approximation of the locations that are likely to benefit from the development of seasonal preparedness plans and/or short-term early warning systems for extreme temperature. The extratropics generally show both short-term skill as well as strong seasonality; in the tropics, most locations do also demonstrate one or both. In fact, almost 5 billion people live in regions that have seasonality and predictability of heatwaves and/or coldwaves. Climate adaptation investments in these regions can take advantage of seasonality and predictability to reduce risks to vulnerable populations.

  2. Wine Expertise Predicts Taste Phenotype.

    Science.gov (United States)

    Hayes, John E; Pickering, Gary J

    2012-03-01

    Taste phenotypes have long been studied in relation to alcohol intake, dependence, and family history, with contradictory findings. However, on balance - with appropriate caveats about populations tested, outcomes measured and psychophysical methods used - an association between variation in taste responsiveness and some alcohol behaviors is supported. Recent work suggests super-tasting (operationalized via propylthiouracil (PROP) bitterness) not only associates with heightened response but also with more acute discrimination between stimuli. Here, we explore relationships between food and beverage adventurousness and taste phenotype. A convenience sample of wine drinkers (n=330) were recruited in Ontario and phenotyped for PROP bitterness via filter paper disk. They also filled out a short questionnaire regarding willingness to try new foods, alcoholic beverages and wines as well as level of wine involvement, which was used to classify them as a wine expert (n=110) or wine consumer (n=220). In univariate logisitic models, food adventurousness predicted trying new wines and beverages but not expertise. Likewise, wine expertise predicted willingness to try new wines and beverages but not foods. In separate multivariate logistic models, willingness to try new wines and beverages was predicted by expertise and food adventurousness but not PROP. However, mean PROP bitterness was higher among wine experts than wine consumers, and the conditional distribution functions differed between experts and consumers. In contrast, PROP means and distributions did not differ with food adventurousness. These data suggest individuals may self-select for specific professions based on sensory ability (i.e., an active gene-environment correlation) but phenotype does not explain willingness to try new stimuli.

  3. Predicting mortality from human faces.

    Science.gov (United States)

    Dykiert, Dominika; Bates, Timothy C; Gow, Alan J; Penke, Lars; Starr, John M; Deary, Ian J

    2012-01-01

    To investigate whether and to what extent mortality is predictable from facial photographs of older people. High-quality facial photographs of 292 members of the Lothian Birth Cohort 1921, taken at the age of about 83 years, were rated in terms of apparent age, health, attractiveness, facial symmetry, intelligence, and well-being by 12 young-adult raters. Cox proportional hazards regression was used to study associations between these ratings and mortality during a 7-year follow-up period. All ratings had adequate reliability. Concurrent validity was found for facial symmetry and intelligence (as determined by correlations with actual measures of fluctuating asymmetry in the faces and Raven Standard Progressive Matrices score, respectively), but not for the other traits. Age as rated from facial photographs, adjusted for sex and chronological age, was a significant predictor of mortality (hazard ratio = 1.36, 95% confidence interval = 1.12-1.65) and remained significant even after controlling for concurrent, objectively measured health and cognitive ability, and the other ratings. Health as rated from facial photographs, adjusted for sex and chronological age, significantly predicted mortality (hazard ratio = 0.81, 95% confidence interval = 0.67-0.99) but not after adjusting for rated age or objectively measured health and cognition. Rated attractiveness, symmetry, intelligence, and well-being were not significantly associated with mortality risk. Rated age of the face is a significant predictor of mortality risk among older people, with predictive value over and above that of objective or rated health status and cognitive ability.

  4. Developmental dyslexia: predicting individual risk.

    Science.gov (United States)

    Thompson, Paul A; Hulme, Charles; Nash, Hannah M; Gooch, Debbie; Hayiou-Thomas, Emma; Snowling, Margaret J

    2015-09-01

    Causal theories of dyslexia suggest that it is a heritable disorder, which is the outcome of multiple risk factors. However, whether early screening for dyslexia is viable is not yet known. The study followed children at high risk of dyslexia from preschool through the early primary years assessing them from age 3 years and 6 months (T1) at approximately annual intervals on tasks tapping cognitive, language, and executive-motor skills. The children were recruited to three groups: children at family risk of dyslexia, children with concerns regarding speech, and language development at 3;06 years and controls considered to be typically developing. At 8 years, children were classified as 'dyslexic' or not. Logistic regression models were used to predict the individual risk of dyslexia and to investigate how risk factors accumulate to predict poor literacy outcomes. Family-risk status was a stronger predictor of dyslexia at 8 years than low language in preschool. Additional predictors in the preschool years include letter knowledge, phonological awareness, rapid automatized naming, and executive skills. At the time of school entry, language skills become significant predictors, and motor skills add a small but significant increase to the prediction probability. We present classification accuracy using different probability cutoffs for logistic regression models and ROC curves to highlight the accumulation of risk factors at the individual level. Dyslexia is the outcome of multiple risk factors and children with language difficulties at school entry are at high risk. Family history of dyslexia is a predictor of literacy outcome from the preschool years. However, screening does not reach an acceptable clinical level until close to school entry when letter knowledge, phonological awareness, and RAN, rather than family risk, together provide good sensitivity and specificity as a screening battery. © 2015 The Authors. Journal of Child Psychology and Psychiatry published by

  5. Prediction and imitation in speech

    Directory of Open Access Journals (Sweden)

    Chiara eGambi

    2013-06-01

    Full Text Available It has been suggested that intra- and inter-speaker variability in speech are correlated. Interlocutors have been shown to converge on various phonetic dimensions. In addition, speakers imitate the phonetic properties of voices they are exposed to in shadowing, repetition, and even passive listening tasks. We review three theoretical accounts of speech imitation and convergence phenomena: (i the Episodic Theory (ET of speech perception and production (Goldinger, 1998; (ii the Motor Theory (MT of speech perception (Liberman and Whalen, 2000;Galantucci et al., 2006 ; (iii Communication Accommodation Theory (CAT; Giles et al., 1991;Giles and Coupland, 1991. We argue that no account is able to explain all the available evidence. In particular, there is a need to integrate low-level, mechanistic accounts (like ET and MT and higher-level accounts (like CAT. We propose that this is possible within the framework of an integrated theory of production and comprehension (Pickering & Garrod, in press. Similarly to both ET and MT, this theory assumes parity between production and perception. Uniquely, however, it posits that listeners simulate speakers’ utterances by computing forward-model predictions at many different levels, which are then compared to the incoming phonetic input. In our account phonetic imitation can be achieved via the same mechanism that is responsible for sensorimotor adaptation; i.e. the correction of prediction errors. In addition, the model assumes that the degree to which sensory prediction errors lead to motor adjustments is context-dependent. The notion of context subsumes both the preceding linguistic input and non-linguistic attributes of the situation (e.g., the speaker’s and listener’s social identities, their conversational roles, the listener’s intention to imitate.

  6. Comprehensive update of the atomic mass predictions

    International Nuclear Information System (INIS)

    Haustein, P.E.

    1987-01-01

    A project has been completed recently for a comprehensive update of atomic mass predictions. This last occurred in 1976. Over the last 10 years the reliability of these earlier predictions (and others published later) has been analyzed by comparisons of the predictions with new masses from isotopes that were not in the experimental data base when the predictions were prepared. This analysis has highlighted distinct systematic features in various models which frequently result in poor predictions for nuclei that lie far from stability. An overview of the new predictions from models with different theoretical approaches will be presented

  7. Learning to Predict Chemical Reactions

    Science.gov (United States)

    Kayala, Matthew A.; Azencott, Chloé-Agathe; Chen, Jonathan H.

    2011-01-01

    Being able to predict the course of arbitrary chemical reactions is essential to the theory and applications of organic chemistry. Approaches to the reaction prediction problems can be organized around three poles corresponding to: (1) physical laws; (2) rule-based expert systems; and (3) inductive machine learning. Previous approaches at these poles respectively are not high-throughput, are not generalizable or scalable, or lack sufficient data and structure to be implemented. We propose a new approach to reaction prediction utilizing elements from each pole. Using a physically inspired conceptualization, we describe single mechanistic reactions as interactions between coarse approximations of molecular orbitals (MOs) and use topological and physicochemical attributes as descriptors. Using an existing rule-based system (Reaction Explorer), we derive a restricted chemistry dataset consisting of 1630 full multi-step reactions with 2358 distinct starting materials and intermediates, associated with 2989 productive mechanistic steps and 6.14 million unproductive mechanistic steps. And from machine learning, we pose identifying productive mechanistic steps as a statistical ranking, information retrieval, problem: given a set of reactants and a description of conditions, learn a ranking model over potential filled-to-unfilled MO interactions such that the top ranked mechanistic steps yield the major products. The machine learning implementation follows a two-stage approach, in which we first train atom level reactivity filters to prune 94.00% of non-productive reactions with a 0.01% error rate. Then, we train an ensemble of ranking models on pairs of interacting MOs to learn a relative productivity function over mechanistic steps in a given system. Without the use of explicit transformation patterns, the ensemble perfectly ranks the productive mechanism at the top 89.05% of the time, rising to 99.86% of the time when the top four are considered. Furthermore, the system

  8. Learning to predict chemical reactions.

    Science.gov (United States)

    Kayala, Matthew A; Azencott, Chloé-Agathe; Chen, Jonathan H; Baldi, Pierre

    2011-09-26

    Being able to predict the course of arbitrary chemical reactions is essential to the theory and applications of organic chemistry. Approaches to the reaction prediction problems can be organized around three poles corresponding to: (1) physical laws; (2) rule-based expert systems; and (3) inductive machine learning. Previous approaches at these poles, respectively, are not high throughput, are not generalizable or scalable, and lack sufficient data and structure to be implemented. We propose a new approach to reaction prediction utilizing elements from each pole. Using a physically inspired conceptualization, we describe single mechanistic reactions as interactions between coarse approximations of molecular orbitals (MOs) and use topological and physicochemical attributes as descriptors. Using an existing rule-based system (Reaction Explorer), we derive a restricted chemistry data set consisting of 1630 full multistep reactions with 2358 distinct starting materials and intermediates, associated with 2989 productive mechanistic steps and 6.14 million unproductive mechanistic steps. And from machine learning, we pose identifying productive mechanistic steps as a statistical ranking, information retrieval problem: given a set of reactants and a description of conditions, learn a ranking model over potential filled-to-unfilled MO interactions such that the top-ranked mechanistic steps yield the major products. The machine learning implementation follows a two-stage approach, in which we first train atom level reactivity filters to prune 94.00% of nonproductive reactions with a 0.01% error rate. Then, we train an ensemble of ranking models on pairs of interacting MOs to learn a relative productivity function over mechanistic steps in a given system. Without the use of explicit transformation patterns, the ensemble perfectly ranks the productive mechanism at the top 89.05% of the time, rising to 99.86% of the time when the top four are considered. Furthermore, the system

  9. Is quantum theory predictably complete?

    Energy Technology Data Exchange (ETDEWEB)

    Kupczynski, M [Department of Mathematics and Statistics, University of Ottawa, 585 King-Edward Avenue, Ottawa, Ontario K1N 6N5 (Canada); Departement de l' Informatique, UQO, Case postale 1250, succursale Hull, Gatineau, Quebec J8X 3X 7 (Canada)], E-mail: mkupczyn@uottawa.ca

    2009-07-15

    Quantum theory (QT) provides statistical predictions for various physical phenomena. To verify these predictions a considerable amount of data has been accumulated in the 'measurements' performed on the ensembles of identically prepared physical systems or in the repeated 'measurements' on some trapped 'individual physical systems'. The outcomes of these measurements are, in general, some numerical time series registered by some macroscopic instruments. The various empirical probability distributions extracted from these time series were shown to be consistent with the probabilistic predictions of QT. More than 70 years ago the claim was made that QT provided the most complete description of 'individual' physical systems and outcomes of the measurements performed on 'individual' physical systems were obtained in an intrinsically random way. Spin polarization correlation experiments (SPCEs), performed to test the validity of Bell inequalities, clearly demonstrated the existence of strong long-range correlations and confirmed that the beams hitting far away detectors somehow preserve the memory of their common source which would be destroyed if the individual counts of far away detectors were purely random. Since the probabilities describe the random experiments and are not the attributes of the 'individual' physical systems, the claim that QT provides a complete description of 'individual' physical systems seems not only unjustified but also misleading and counter productive. In this paper, we point out that we even do not know whether QT is predictably complete because it has not been tested carefully enough. Namely, it was not proven that the time series of existing experimental data did not contain some stochastic fine structures that could have been averaged out by describing them in terms of the empirical probability distributions. In this paper, we advocate various statistical tests that

  10. Focus on astronomical predictable events

    DEFF Research Database (Denmark)

    Jacobsen, Aase Roland

    2006-01-01

    At the Steno Museum Planetarium we have for many occasions used a countdown clock to get focus om astronomical events. A countdown clock can provide actuality to predictable events, for example The Venus Transit, Opportunity landing on Mars and The Solar Eclipse. The movement of the clock attracs...... the public and makes a point of interest in a small exhibit area. A countdown clock can be simple, but it is possible to expand the concept to an eye-catching part of a museum....

  11. Making predictions in the multiverse

    International Nuclear Information System (INIS)

    Freivogel, Ben

    2011-01-01

    I describe reasons to think we are living in an eternally inflating multiverse where the observable 'constants' of nature vary from place to place. The major obstacle to making predictions in this context is that we must regulate the infinities of eternal inflation. I review a number of proposed regulators, or measures. Recent work has ruled out a number of measures by showing that they conflict with observation, and focused attention on a few proposals. Further, several different measures have been shown to be equivalent. I describe some of the many nontrivial tests these measures will face as we learn more from theory, experiment and observation.

  12. Making predictions in the multiverse

    Energy Technology Data Exchange (ETDEWEB)

    Freivogel, Ben, E-mail: benfreivogel@gmail.com [Center for Theoretical Physics and Laboratory for Nuclear Science, Massachusetts Institute of Technology, Cambridge, MA 02139 (United States)

    2011-10-21

    I describe reasons to think we are living in an eternally inflating multiverse where the observable 'constants' of nature vary from place to place. The major obstacle to making predictions in this context is that we must regulate the infinities of eternal inflation. I review a number of proposed regulators, or measures. Recent work has ruled out a number of measures by showing that they conflict with observation, and focused attention on a few proposals. Further, several different measures have been shown to be equivalent. I describe some of the many nontrivial tests these measures will face as we learn more from theory, experiment and observation.

  13. Flooding Fragility Experiments and Prediction

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Curtis L. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Tahhan, Antonio [Idaho National Lab. (INL), Idaho Falls, ID (United States); Muchmore, Cody [Idaho National Lab. (INL), Idaho Falls, ID (United States); Nichols, Larinda [Idaho National Lab. (INL), Idaho Falls, ID (United States); Bhandari, Bishwo [Idaho National Lab. (INL), Idaho Falls, ID (United States); Pope, Chad [Idaho National Lab. (INL), Idaho Falls, ID (United States)

    2016-09-01

    This report describes the work that has been performed on flooding fragility, both the experimental tests being carried out and the probabilistic fragility predictive models being produced in order to use the text results. Flooding experiments involving full-scale doors have commenced in the Portal Evaluation Tank. The goal of these experiments is to develop a full-scale component flooding experiment protocol and to acquire data that can be used to create Bayesian regression models representing the fragility of these components. This work is in support of the Risk-Informed Safety Margin Characterization (RISMC) Pathway external hazards evaluation research and development.

  14. Mach's predictions and relativistic cosmology

    International Nuclear Information System (INIS)

    Heller, M.

    1989-01-01

    Deep methodological insight of Ernst Mach into the structure of the Newtonian mechanics allowed him to ask questions, the importance of which can be appreciated only today. Three such Mach's ''predictions'' are briefly presented, namely: the possibility of the existence of an allpervading medium which could serve as an universal frame of reference and which has actually been discovered in the form of the microwave background radiation, a certain ''smoothness'' of the Universe which is now recognized as the Robertson-Walker symmetries and the possibility of the experimental verification of the mass anisotropy. 11 refs. (author)

  15. Zephyr - the next generation prediction

    DEFF Research Database (Denmark)

    Giebel, G.; Landberg, L.; Nielsen, Torben Skov

    2001-01-01

    Technical University. This paper will describe a new project funded by the Danish Ministry of Energy where the largest Danish utilities (Elkraft, Elsam, Eltra and SEAS) are participating. Two advantages can be achieved by combining the effort: The software architecture will be state-of-the-art, using...... the Java2TM platform and Enterprise Java Beans technology, and it will ensure that the best forecasts are given on all prediction horizons from the short range (0-9 hours) to the long range (36-48 hours). This is because the IMM approach uses online data and advanced statistical methods, which...

  16. Aviation turbulence processes, detection, prediction

    CERN Document Server

    Lane, Todd

    2016-01-01

    Anyone who has experienced turbulence in flight knows that it is usually not pleasant, and may wonder why this is so difficult to avoid. The book includes papers by various aviation turbulence researchers and provides background into the nature and causes of atmospheric turbulence that affect aircraft motion, and contains surveys of the latest techniques for remote and in situ sensing and forecasting of the turbulence phenomenon. It provides updates on the state-of-the-art research since earlier studies in the 1960s on clear-air turbulence, explains recent new understanding into turbulence generation by thunderstorms, and summarizes future challenges in turbulence prediction and avoidance.

  17. Prediction of burnout. Chapter 14

    International Nuclear Information System (INIS)

    Lee, D.H.

    1977-01-01

    A broad survey is made of the effect on burnout heat flux of various system parameters to give the reader a better initial idea of the significance of changes in individual parameters. A detailed survey is then made of various correlation equations for predicting burnout for steam -water in uniformly heated tubes, annuli, rectangular channels and rod clusters, giving details of recommended equations. Finally comments are made on the influence of heat-flux profile and swirl flow on burnout, and on the definition of dryout margin. (author)

  18. Predicting word sense annotation agreement

    DEFF Research Database (Denmark)

    Martinez Alonso, Hector; Johannsen, Anders Trærup; Lopez de Lacalle, Oier

    2015-01-01

    High agreement is a common objective when annotating data for word senses. However, a number of factors make perfect agreement impossible, e.g. the limitations of the sense inventories, the difficulty of the examples or the interpretation preferences of the annotations. Estimating potential...... agreement is thus a relevant task to supplement the evaluation of sense annotations. In this article we propose two methods to predict agreement on word-annotation instances. We experiment with a continuous representation and a three-way discretization of observed agreement. In spite of the difficulty...

  19. Mechanism and prediction of burnout

    International Nuclear Information System (INIS)

    Hewitt, G.F.

    1977-01-01

    The lecture begins by discussing the definitions of burnout and the various parametric effects as seen from the results for burnout measurements in uniformly heated round tubes. The correlations which are developed from these measurements and their applications to the case of non-uniform axial distribution of heat flux is then discussed in general terms as an illustration of the importance of knowing more about the nature and mechanism of the burnout. The next section of the lecture is concerned with summarizing broadly the various possible mechanisms in both the sub-cooled region and the quality region. It transpires that, for tubes of reasonable length, the normal first occurrence of burnout is in the annular flow regime. A discussion of burnout mechanisms in this regime then follows, with descriptions of the various experimental techniques evolved to study the mechanism. The final section of the lecture is concerned with prediction methods for burnout in annular flow and the application of these methods to prediction of burnout in round tubes, annuli and rod bundles, with a variety of fluids

  20. On predicting monitoring system effectiveness

    Science.gov (United States)

    Cappello, Carlo; Sigurdardottir, Dorotea; Glisic, Branko; Zonta, Daniele; Pozzi, Matteo

    2015-03-01

    While the objective of structural design is to achieve stability with an appropriate level of reliability, the design of systems for structural health monitoring is performed to identify a configuration that enables acquisition of data with an appropriate level of accuracy in order to understand the performance of a structure or its condition state. However, a rational standardized approach for monitoring system design is not fully available. Hence, when engineers design a monitoring system, their approach is often heuristic with performance evaluation based on experience, rather than on quantitative analysis. In this contribution, we propose a probabilistic model for the estimation of monitoring system effectiveness based on information available in prior condition, i.e. before acquiring empirical data. The presented model is developed considering the analogy between structural design and monitoring system design. We assume that the effectiveness can be evaluated based on the prediction of the posterior variance or covariance matrix of the state parameters, which we assume to be defined in a continuous space. Since the empirical measurements are not available in prior condition, the estimation of the posterior variance or covariance matrix is performed considering the measurements as a stochastic variable. Moreover, the model takes into account the effects of nuisance parameters, which are stochastic parameters that affect the observations but cannot be estimated using monitoring data. Finally, we present an application of the proposed model to a real structure. The results show how the model enables engineers to predict whether a sensor configuration satisfies the required performance.

  1. Prediction Reweighting for Domain Adaptation.

    Science.gov (United States)

    Shuang Li; Shiji Song; Gao Huang

    2017-07-01

    There are plenty of classification methods that perform well when training and testing data are drawn from the same distribution. However, in real applications, this condition may be violated, which causes degradation of classification accuracy. Domain adaptation is an effective approach to address this problem. In this paper, we propose a general domain adaptation framework from the perspective of prediction reweighting, from which a novel approach is derived. Different from the major domain adaptation methods, our idea is to reweight predictions of the training classifier on testing data according to their signed distance to the domain separator, which is a classifier that distinguishes training data (from source domain) and testing data (from target domain). We then propagate the labels of target instances with larger weights to ones with smaller weights by introducing a manifold regularization method. It can be proved that our reweighting scheme effectively brings the source and target domains closer to each other in an appropriate sense, such that classification in target domain becomes easier. The proposed method can be implemented efficiently by a simple two-stage algorithm, and the target classifier has a closed-form solution. The effectiveness of our approach is verified by the experiments on artificial datasets and two standard benchmarks, a visual object recognition task and a cross-domain sentiment analysis of text. Experimental results demonstrate that our method is competitive with the state-of-the-art domain adaptation algorithms.

  2. Iowa calibration of MEPDG performance prediction models.

    Science.gov (United States)

    2013-06-01

    This study aims to improve the accuracy of AASHTO Mechanistic-Empirical Pavement Design Guide (MEPDG) pavement : performance predictions for Iowa pavement systems through local calibration of MEPDG prediction models. A total of 130 : representative p...

  3. The Use of Linear Programming for Prediction.

    Science.gov (United States)

    Schnittjer, Carl J.

    The purpose of the study was to develop a linear programming model to be used for prediction, test the accuracy of the predictions, and compare the accuracy with that produced by curvilinear multiple regression analysis. (Author)

  4. Profit Driven Decision Trees for Churn Prediction

    OpenAIRE

    Höppner, Sebastiaan; Stripling, Eugen; Baesens, Bart; Broucke, Seppe vanden; Verdonck, Tim

    2017-01-01

    Customer retention campaigns increasingly rely on predictive models to detect potential churners in a vast customer base. From the perspective of machine learning, the task of predicting customer churn can be presented as a binary classification problem. Using data on historic behavior, classification algorithms are built with the purpose of accurately predicting the probability of a customer defecting. The predictive churn models are then commonly selected based on accuracy related performan...

  5. Robust predictions of the interacting boson model

    International Nuclear Information System (INIS)

    Casten, R.F.; Koeln Univ.

    1994-01-01

    While most recognized for its symmetries and algebraic structure, the IBA model has other less-well-known but equally intrinsic properties which give unavoidable, parameter-free predictions. These predictions concern central aspects of low-energy nuclear collective structure. This paper outlines these ''robust'' predictions and compares them with the data

  6. Phenology prediction component of GypsES

    Science.gov (United States)

    Jesse A. Logan; Lukas P. Schaub; F. William Ravlin

    1991-01-01

    Prediction of phenology is an important component of most pest management programs, and considerable research effort has been expended toward development of predictive tools for gypsy moth phenology. Although phenological prediction is potentially valuable for timing of spray applications (e.g. Bt, or Gypcheck) and other management activities (e.g. placement and...

  7. Climate Prediction Center - The ENSO Cycle

    Science.gov (United States)

    Weather Service NWS logo - Click to go to the NWS home page Climate Prediction Center Home Site Map News Web resources and services. HOME > El Niño/La Niña > The ENSO Cycle ENSO Cycle Banner Climate for Weather and Climate Prediction Climate Prediction Center 5830 University Research Court College

  8. Comparison of Prediction-Error-Modelling Criteria

    DEFF Research Database (Denmark)

    Jørgensen, John Bagterp; Jørgensen, Sten Bay

    2007-01-01

    Single and multi-step prediction-error-methods based on the maximum likelihood and least squares criteria are compared. The prediction-error methods studied are based on predictions using the Kalman filter and Kalman predictors for a linear discrete-time stochastic state space model, which is a r...

  9. Relationship between water temperature predictability and aquatic ...

    African Journals Online (AJOL)

    Macroinvertebrate taxonomic turnover across seasons was higher for sites having lower water temperature predictability values than for sites with higher predictability, while temporal partitioning was greater at sites with greater temperature variability. Macroinvertebrate taxa responded in a predictable manner to changes in ...

  10. Based on BP Neural Network Stock Prediction

    Science.gov (United States)

    Liu, Xiangwei; Ma, Xin

    2012-01-01

    The stock market has a high profit and high risk features, on the stock market analysis and prediction research has been paid attention to by people. Stock price trend is a complex nonlinear function, so the price has certain predictability. This article mainly with improved BP neural network (BPNN) to set up the stock market prediction model, and…

  11. NEURAL METHODS FOR THE FINANCIAL PREDICTION

    OpenAIRE

    Jerzy Balicki; Piotr Dryja; Waldemar Korłub; Piotr Przybyłek; Maciej Tyszka; Marcin Zadroga; Marcin Zakidalski

    2016-01-01

    Artificial neural networks can be used to predict share investment on the stock market, assess the reliability of credit client or predicting banking crises. Moreover, this paper discusses the principles of cooperation neural network algorithms with evolutionary method, and support vector machines. In addition, a reference is made to other methods of artificial intelligence, which are used in finance prediction.

  12. NEURAL METHODS FOR THE FINANCIAL PREDICTION

    Directory of Open Access Journals (Sweden)

    Jerzy Balicki

    2016-06-01

    Full Text Available Artificial neural networks can be used to predict share investment on the stock market, assess the reliability of credit client or predicting banking crises. Moreover, this paper discusses the principles of cooperation neural network algorithms with evolutionary method, and support vector machines. In addition, a reference is made to other methods of artificial intelligence, which are used in finance prediction.

  13. Applications for predictive microbiology to food packaging

    Science.gov (United States)

    Predictive microbiology has been used for several years in the food industry to predict microbial growth, inactivation and survival. Predictive models provide a useful tool in risk assessment, HACCP set-up and GMP for the food industry to enhance microbial food safety. This report introduces the c...

  14. Predictive Analytics in Information Systems Research

    NARCIS (Netherlands)

    G. Shmueli (Galit); O.R. Koppius (Otto)

    2011-01-01

    textabstractThis research essay highlights the need to integrate predictive analytics into information systems research and shows several concrete ways in which this goal can be accomplished. Predictive analytics include empirical methods (statistical and other) that generate data predictions as

  15. Clinical Prediction Models for Cardiovascular Disease: Tufts Predictive Analytics and Comparative Effectiveness Clinical Prediction Model Database.

    Science.gov (United States)

    Wessler, Benjamin S; Lai Yh, Lana; Kramer, Whitney; Cangelosi, Michael; Raman, Gowri; Lutz, Jennifer S; Kent, David M

    2015-07-01

    Clinical prediction models (CPMs) estimate the probability of clinical outcomes and hold the potential to improve decision making and individualize care. For patients with cardiovascular disease, there are numerous CPMs available although the extent of this literature is not well described. We conducted a systematic review for articles containing CPMs for cardiovascular disease published between January 1990 and May 2012. Cardiovascular disease includes coronary heart disease, heart failure, arrhythmias, stroke, venous thromboembolism, and peripheral vascular disease. We created a novel database and characterized CPMs based on the stage of development, population under study, performance, covariates, and predicted outcomes. There are 796 models included in this database. The number of CPMs published each year is increasing steadily over time. Seven hundred seventeen (90%) are de novo CPMs, 21 (3%) are CPM recalibrations, and 58 (7%) are CPM adaptations. This database contains CPMs for 31 index conditions, including 215 CPMs for patients with coronary artery disease, 168 CPMs for population samples, and 79 models for patients with heart failure. There are 77 distinct index/outcome pairings. Of the de novo models in this database, 450 (63%) report a c-statistic and 259 (36%) report some information on calibration. There is an abundance of CPMs available for a wide assortment of cardiovascular disease conditions, with substantial redundancy in the literature. The comparative performance of these models, the consistency of effects and risk estimates across models and the actual and potential clinical impact of this body of literature is poorly understood. © 2015 American Heart Association, Inc.

  16. Pretest Predictions for Ventilation Tests

    International Nuclear Information System (INIS)

    Y. Sun; H. Yang; H.N. Kalia

    2007-01-01

    The objective of this calculation is to predict the temperatures of the ventilating air, waste package surface, concrete pipe walls, and insulation that will be developed during the ventilation tests involving various test conditions. The results will be used as input to the following three areas: (1) Decisions regarding testing set-up and performance. (2) Assessing how best to scale the test phenomena measured. (3) Validating numerical approach for modeling continuous ventilation. The scope of the calculation is to identify the physical mechanisms and parameters related to thermal response in the ventilation tests, and develop and describe numerical methods that can be used to calculate the effects of continuous ventilation. Sensitivity studies to assess the impact of variation of linear power densities (linear heat loads) and ventilation air flow rates are included. The calculation is limited to thermal effect only

  17. The Predictiveness of Achievement Goals

    Directory of Open Access Journals (Sweden)

    Huy P. Phan

    2013-11-01

    Full Text Available Using the Revised Achievement Goal Questionnaire (AGQ-R (Elliot & Murayama, 2008, we explored first-year university students’ achievement goal orientations on the premise of the 2 × 2 model. Similar to recent studies (Elliot & Murayama, 2008; Elliot & Thrash, 2010, we conceptualized a model that included both antecedent (i.e., enactive learning experience and consequence (i.e., intrinsic motivation and academic achievement of achievement goals. Two hundred seventy-seven university students (151 women, 126 men participated in the study. Structural equation modeling procedures yielded evidence that showed the predictive effects of enactive learning experience and mastery goals on intrinsic motivation. Academic achievement was influenced intrinsic motivation, performance-approach goals, and enactive learning experience. Enactive learning experience also served as an antecedent of the four achievement goal types. On the whole, evidence obtained supports the AGQ-R and contributes, theoretically, to 2 × 2 model.

  18. Academic Training: Predicting Natural Catastrophes

    CERN Multimedia

    Françoise Benz

    2005-01-01

    2005-2006 ACADEMIC TRAINING PROGRAMME LECTURE SERIES 12, 13, 14, 15, 16 December from 11:00 to 12:00 - Main Auditorium, bldg. 500 Predicting Natural Catastrophes E. OKAL / Northwestern University, Evanston, USA 1. Tsunamis -- Introduction Definition of phenomenon - basic properties of the waves Propagation and dispersion Interaction with coasts - Geological and societal effects Origin of tsunamis - natural sources Scientific activities in connection with tsunamis. Ideas about simulations 2. Tsunami generation The earthquake source - conventional theory The earthquake source - normal mode theory The landslide source Near-field observation - The Plafker index Far-field observation - Directivity 3. Tsunami warning General ideas - History of efforts Mantle magnitudes and TREMOR algorithms The challenge of 'tsunami earthquakes' Energy-moment ratios and slow earthquakes Implementation and the components of warning centers 4. Tsunami surveys Principles and methodologies Fifteen years of field surveys and re...

  19. The PredictAD project

    DEFF Research Database (Denmark)

    Antila, Kari; Lötjönen, Jyrki; Thurfjell, Lennart

    2013-01-01

    Alzheimer's disease (AD) is the most common cause of dementia affecting 36 million people worldwide. As the demographic transition in the developed countries progresses towards older population, the worsening ratio of workers per retirees and the growing number of patients with age-related illnes...... candidates and implement the framework in software. The results are currently used in several research projects, licensed to commercial use and being tested for clinical use in several trials....... objective of the PredictAD project was to find and integrate efficient biomarkers from heterogeneous patient data to make early diagnosis and to monitor the progress of AD in a more efficient, reliable and objective manner. The project focused on discovering biomarkers from biomolecular data...

  20. Prediction and probability in sciences

    International Nuclear Information System (INIS)

    Klein, E.; Sacquin, Y.

    1998-01-01

    This book reports the 7 presentations made at the third meeting 'physics and fundamental questions' whose theme was probability and prediction. The concept of probability that was invented to apprehend random phenomena has become an important branch of mathematics and its application range spreads from radioactivity to species evolution via cosmology or the management of very weak risks. The notion of probability is the basis of quantum mechanics and then is bound to the very nature of matter. The 7 topics are: - radioactivity and probability, - statistical and quantum fluctuations, - quantum mechanics as a generalized probability theory, - probability and the irrational efficiency of mathematics, - can we foresee the future of the universe?, - chance, eventuality and necessity in biology, - how to manage weak risks? (A.C.)

  1. Meditation experience predicts introspective accuracy.

    Directory of Open Access Journals (Sweden)

    Kieran C R Fox

    Full Text Available The accuracy of subjective reports, especially those involving introspection of one's own internal processes, remains unclear, and research has demonstrated large individual differences in introspective accuracy. It has been hypothesized that introspective accuracy may be heightened in persons who engage in meditation practices, due to the highly introspective nature of such practices. We undertook a preliminary exploration of this hypothesis, examining introspective accuracy in a cross-section of meditation practitioners (1-15,000 hrs experience. Introspective accuracy was assessed by comparing subjective reports of tactile sensitivity for each of 20 body regions during a 'body-scanning' meditation with averaged, objective measures of tactile sensitivity (mean size of body representation area in primary somatosensory cortex; two-point discrimination threshold as reported in prior research. Expert meditators showed significantly better introspective accuracy than novices; overall meditation experience also significantly predicted individual introspective accuracy. These results suggest that long-term meditators provide more accurate introspective reports than novices.

  2. Predicting degradability of organic chemicals

    Energy Technology Data Exchange (ETDEWEB)

    Finizio, A; Vighi, M [Milan Univ. (Italy). Ist. di Entomologia Agraria

    1992-05-01

    Degradability, particularly biodegradability, is one of the most important factors governing the persistence of pollutants in the environment and consequently influencing their behavior and toxicity in aquatic and terrestrial ecosystems. The need for reliable persistence data in order to assess the environmental fate and hazard of chemicals by means of predictive approaches, is evident. Biodegradability tests are requested by the EEC directive on new chemicals. Neverthless, degradation tests are not easy to carry out and data on existing chemicals are very scarce. Therefore, assessing the fate of chemicals in the environment from the simple study of their structure would be a useful tool. Rates of degradation are a function of the rates of a series of processes. Correlation between degradation rates and structural parameters are will be facilitated if one of the processes is rate determining. This review is a survey of studies dealing with relationships between structure and biodegradation of organic chemicals, to identify the value and limitations of this approach.

  3. Unrenormalizable theories can be predictive

    CERN Document Server

    Kubo, J

    2003-01-01

    Unrenormalizable theories contain infinitely many free parameters. Considering these theories in terms of the Wilsonian renormalization group (RG), we suggest a method for removing this large ambiguity. Our basic assumption is the existence of a maximal ultraviolet cutoff in a cutoff theory, and we require that the theory be so fine tuned as to reach the maximal cutoff. The theory so obtained behaves as a local continuum theory to the shortest distance. In concrete examples of the scalar theory we find that at least in a certain approximation to the Wilsonian RG, this requirement enables us to make unique predictions in the infrared regime in terms of a finite number of independent parameters. Therefore, this method might provide a way for calculating quantum corrections in a low-energy effective theory of quantum gravity. (orig.)

  4. Lower-limb growth: how predictable are predictions?

    Science.gov (United States)

    Kelly, Paula M; Diméglio, Alain

    2008-12-01

    The purpose of this review is to clarify the different methods of predictions for growth of the lower limb and to propose a simplified method to calculate the final limb deficit and the correct timing of epiphysiodesis. Lower-limb growth is characterized by four different periods: antenatal growth (exponential); birth to 5 years (rapid growth); 5 years to puberty (stable growth); and puberty, which is the final growth spurt characterized by a rapid acceleration phase lasting 1 year followed by a more gradual deceleration phase lasting 1.5 years. The younger the child, the less precise is the prediction. Repeating measurements can increase the accuracy of predictions and those calculated at the beginning of puberty are the most accurate. The challenge is to reduce the margin of uncertainty. Confrontation of the different parameters-bone age, Tanner signs, annual growth velocity of the standing height, sub-ischial length and sitting height-is the most accurate method. Charts and diagrams are only models and templates. There are many mathematical equations in the literature; we must be able to step back from these rigid calculations because they are a false guarantee. The dynamic of growth needs a flexible approach. There are, however, some rules of thumb that may be helpful for different clinical scenarios. For congenital malformations, at birth the limb length discrepancy must be multiplied by 5 to give the final limb length discrepancy. Multiple by 3 at 1 year of age; by 2 at 3 years in girls and 4 years in boys; by 1.5 at 7 years in girls and boys, by 1.2 at 9 years in girls and 11 years in boys and by 1.1 at the onset of puberty (11 years bone age for girls and 13 years bone age for boys). For the timing of epiphysiodesis, several simple principles must be observed to reduce the margin of error; strict and repeated measurements, rigorous analysis of the data obtained, perfect evaluation of bone age with elbow plus hand radiographs and confirmation with Tanner

  5. Integrated Genome-Based Studies of Shewanella Ecophysiology

    Energy Technology Data Exchange (ETDEWEB)

    Andrei L. Osterman, Ph.D.

    2012-12-17

    Integration of bioinformatics and experimental techniques was applied to mapping and characterization of the key components (pathways, enzymes, transporters, regulators) of the core metabolic machinery in Shewanella oneidensis and related species with main focus was on metabolic and regulatory pathways involved in utilization of various carbon and energy sources. Among the main accomplishments reflected in ten joint publications with other participants of Shewanella Federation are: (i) A systems-level reconstruction of carbohydrate utilization pathways in the genus of Shewanella (19 species). This analysis yielded reconstruction of 18 sugar utilization pathways including 10 novel pathway variants and prediction of > 60 novel protein families of enzymes, transporters and regulators involved in these pathways. Selected functional predictions were verified by focused biochemical and genetic experiments. Observed growth phenotypes were consistent with bioinformatic predictions providing strong validation of the technology and (ii) Global genomic reconstruction of transcriptional regulons in 16 Shewanella genomes. The inferred regulatory network includes 82 transcription factors, 8 riboswitches and 6 translational attenuators. Of those, 45 regulons were inferred directly from the genome context analysis, whereas others were propagated from previously characterized regulons in other species. Selected regulatory predictions were experimentally tested. Integration of this analysis with microarray data revealed overall consistency and provided additional layer of interactions between regulons. All the results were captured in the new database RegPrecise, which is a joint development with the LBNL team. A more detailed analysis of the individual subsystems, pathways and regulons in Shewanella spp included bioinfiormatics-based prediction and experimental characterization of: (i) N-Acetylglucosamine catabolic pathway; (ii)Lactate utilization machinery; (iii) Novel Nrt

  6. PEMS. Advanced predictive emission monitoring

    Energy Technology Data Exchange (ETDEWEB)

    Sandvig Nielsen, J.

    2010-07-15

    In the project PEMS have been developed for boilers, internal combustion engines and gas turbines. The PEMS models have been developed using two principles: The one called ''first principles'' is based on thermo-kinetic modeling of the NO{sub x}-formation by modeling conditions (like temperature, pressure and residence time) in the reaction zones. The other one is data driven using artificial neural network (ANN) and includes no physical properties and no thermo-kinetic formulation. Models of first principles have been developed for gas turbines and gas engines. Data driven models have been developed for gas turbines, gas engines and boilers. The models have been tested on data from sites located in Denmark and the Middle East. Weel and Sandvig has conducted the on-site emission measurements used for development and testing the PEMS models. For gas turbines, both the ''first principles'' and the data driven models have performed excellent considering the ability to reproduce the emission levels of NO{sub x} according to the input variables used for calibration. Data driven models for boilers and gas engines have performed excellent as well. The rather comprehensive first principle model, developed for gas engines, did not perform as well in the prediction of NO{sub x}. Possible a more complex model formulation is required for internal combustion engines. In general, both model types have been validated on data extracted from the data set used for calibration. The data for validation have been selected randomly as individual samplings, and is scattered over the entire measuring campaign. For one natural gas engine a secondary measuring campaign was conducted half a year later than the campaign used for training the data driven model. In the meantime, this engine had been through a refurbishment that included new pistons, piston rings and cylinder linings and cleaning of the cylinder heads. Despite the refurbishment, the

  7. Earthquake predictions using seismic velocity ratios

    Science.gov (United States)

    Sherburne, R. W.

    1979-01-01

    Since the beginning of modern seismology, seismologists have contemplated predicting earthquakes. The usefulness of earthquake predictions to the reduction of human and economic losses and the value of long-range earthquake prediction to planning is obvious. Not as clear are the long-range economic and social impacts of earthquake prediction to a speicifc area. The general consensus of opinion among scientists and government officials, however, is that the quest of earthquake prediction is a worthwhile goal and should be prusued with a sense of urgency. 

  8. Conditional prediction intervals of wind power generation

    DEFF Research Database (Denmark)

    Pinson, Pierre; Kariniotakis, Georges

    2010-01-01

    A generic method for the providing of prediction intervals of wind power generation is described. Prediction intervals complement the more common wind power point forecasts, by giving a range of potential outcomes for a given probability, their so-called nominal coverage rate. Ideally they inform...... on the characteristics of prediction errors for providing conditional interval forecasts. By simultaneously generating prediction intervals with various nominal coverage rates, one obtains full predictive distributions of wind generation. Adapted resampling is applied here to the case of an onshore Danish wind farm...... to the case of a large number of wind farms in Europe and Australia among others is finally discussed....

  9. Sports Tournament Predictions Using Direct Manipulation.

    Science.gov (United States)

    Vuillemot, Romain; Perin, Charles

    2016-01-01

    An advanced interface for sports tournament predictions uses direct manipulation to allow users to make nonlinear predictions. Unlike previous interface designs, the interface helps users focus on their prediction tasks by enabling them to first choose a winner and then fill out the rest of the bracket. In real-world tests of the proposed interface (for the 2014 FIFA World Cup tournament and 2015/2016 UEFA Champions League), the authors validated the use of direct manipulation as an alternative to widgets. Using visitor interaction logs, they were able to determine the strategies people use to perform predictions and identify potential areas of improvement for further prediction interfaces.

  10. The function and failure of sensory predictions.

    Science.gov (United States)

    Bansal, Sonia; Ford, Judith M; Spering, Miriam

    2018-04-23

    Humans and other primates are equipped with neural mechanisms that allow them to automatically make predictions about future events, facilitating processing of expected sensations and actions. Prediction-driven control and monitoring of perceptual and motor acts are vital to normal cognitive functioning. This review provides an overview of corollary discharge mechanisms involved in predictions across sensory modalities and discusses consequences of predictive coding for cognition and behavior. Converging evidence now links impairments in corollary discharge mechanisms to neuropsychiatric symptoms such as hallucinations and delusions. We review studies supporting a prediction-failure hypothesis of perceptual and cognitive disturbances. We also outline neural correlates underlying prediction function and failure, highlighting similarities across the visual, auditory, and somatosensory systems. In linking basic psychophysical and psychophysiological evidence of visual, auditory, and somatosensory prediction failures to neuropsychiatric symptoms, our review furthers our understanding of disease mechanisms. © 2018 New York Academy of Sciences.

  11. Evaluating predictions of critical oxygen desaturation events

    International Nuclear Information System (INIS)

    ElMoaqet, Hisham; Tilbury, Dawn M; Ramachandran, Satya Krishna

    2014-01-01

    This paper presents a new approach for evaluating predictions of oxygen saturation levels in blood ( SpO 2 ). A performance metric based on a threshold is proposed to evaluate  SpO 2 predictions based on whether or not they are able to capture critical desaturations in the  SpO 2 time series of patients. We use linear auto-regressive models built using historical  SpO 2 data to predict critical desaturation events with the proposed metric. In 20 s prediction intervals, 88%–94% of the critical events were captured with positive predictive values (PPVs) between 90% and 99%. Increasing the prediction horizon to 60 s, 46%–71% of the critical events were detected with PPVs between 81% and 97%. In both prediction horizons, more than 97% of the non-critical events were correctly classified. The overall classification capabilities for the developed predictive models were also investigated. The area under ROC curves for 60 s predictions from the developed models are between 0.86 and 0.98. Furthermore, we investigate the effect of including pulse rate (PR) dynamics in the models and predictions. We show no improvement in the percentage of the predicted critical desaturations if PR dynamics are incorporated into the  SpO 2 predictive models (p-value = 0.814). We also show that including the PR dynamics does not improve the earliest time at which critical  SpO 2 levels are predicted (p-value = 0.986). Our results indicate oxygen in blood is an effective input to the PR rather than vice versa. We demonstrate that the combination of predictive models with frequent pulse oximetry measurements can be used as a warning of critical oxygen desaturations that may have adverse effects on the health of patients. (paper)

  12. Potential for western US seasonal snowpack prediction

    Science.gov (United States)

    Kapnick, Sarah B.; Yang, Xiaosong; Vecchi, Gabriel A.; Delworth, Thomas L.; Gudgel, Rich; Malyshev, Sergey; Milly, Paul C. D.; Shevliakova, Elena; Underwood, Seth; Margulis, Steven A.

    2018-01-01

    Western US snowpack—snow that accumulates on the ground in the mountains—plays a critical role in regional hydroclimate and water supply, with 80% of snowmelt runoff being used for agriculture. While climate projections provide estimates of snowpack loss by the end of th ecentury and weather forecasts provide predictions of weather conditions out to 2 weeks, less progress has been made for snow predictions at seasonal timescales (months to 2 years), crucial for regional agricultural decisions (e.g., plant choice and quantity). Seasonal predictions with climate models first took the form of El Niño predictions 3 decades ago, with hydroclimate predictions emerging more recently. While the field has been focused on single-season predictions (3 months or less), we are now poised to advance our predictions beyond this timeframe. Utilizing observations, climate indices, and a suite of global climate models, we demonstrate the feasibility of seasonal snowpack predictions and quantify the limits of predictive skill 8 month sin advance. This physically based dynamic system outperforms observation-based statistical predictions made on July 1 for March snowpack everywhere except the southern Sierra Nevada, a region where prediction skill is nonexistent for every predictor presently tested. Additionally, in the absence of externally forced negative trends in snowpack, narrow maritime mountain ranges with high hydroclimate variability pose a challenge for seasonal prediction in our present system; natural snowpack variability may inherently be unpredictable at this timescale. This work highlights present prediction system successes and gives cause for optimism for developing seasonal predictions for societal needs.

  13. Similarities and Differences Between Warped Linear Prediction and Laguerre Linear Prediction

    NARCIS (Netherlands)

    Brinker, Albertus C. den; Krishnamoorthi, Harish; Verbitskiy, Evgeny A.

    2011-01-01

    Linear prediction has been successfully applied in many speech and audio processing systems. This paper presents the similarities and differences between two classes of linear prediction schemes, namely, Warped Linear Prediction (WLP) and Laguerre Linear Prediction (LLP). It is shown that both

  14. Radon observation for earthquake prediction

    Energy Technology Data Exchange (ETDEWEB)

    Wakita, Hiroshi [Tokyo Univ. (Japan)

    1998-12-31

    Systematic observation of groundwater radon for the purpose of earthquake prediction began in Japan in late 1973. Continuous observations are conducted at fixed stations using deep wells and springs. During the observation period, significant precursory changes including the 1978 Izu-Oshima-kinkai (M7.0) earthquake as well as numerous coseismic changes were observed. At the time of the 1995 Kobe (M7.2) earthquake, significant changes in chemical components, including radon dissolved in groundwater, were observed near the epicentral region. Precursory changes are presumably caused by permeability changes due to micro-fracturing in basement rock or migration of water from different sources during the preparation stage of earthquakes. Coseismic changes may be caused by seismic shaking and by changes in regional stress. Significant drops of radon concentration in groundwater have been observed after earthquakes at the KSM site. The occurrence of such drops appears to be time-dependent, and possibly reflects changes in the regional stress state of the observation area. The absence of radon drops seems to be correlated with periods of reduced regional seismic activity. Experience accumulated over the two past decades allows us to reach some conclusions: 1) changes in groundwater radon do occur prior to large earthquakes; 2) some sites are particularly sensitive to earthquake occurrence; and 3) the sensitivity changes over time. (author)

  15. Solar Flares and Their Prediction

    Science.gov (United States)

    Adams, Mitzi L.

    1999-01-01

    Solar flares and coronal mass ejection's (CMES) can strongly affect the local environment at the Earth. A major challenge for solar physics is to understand the physical mechanisms responsible for the onset of solar flares. Flares, characterized by a sudden release of energy (approx. 10(exp 32) ergs for the largest events) within the solar atmosphere, result in the acceleration of electrons, protons, and heavier ions as well as the production of electromagnetic radiation from hard X-rays to km radio waves (wavelengths approx. = 10(exp -9) cm to 10(exp 6) cm). Observations suggest that solar flares and sunspots are strongly linked. For example, a study of data from 1956-1969, reveals that approx. 93 percent of major flares originate in active regions with spots. Furthermore, the global structure of the sunspot magnetic field can be correlated with flare activity. This talk will review what we know about flare causes and effects and will discuss techniques for quantifying parameters, which may lead to a prediction of solar flares.

  16. Incorrect predictions reduce switch costs.

    Science.gov (United States)

    Kleinsorge, Thomas; Scheil, Juliane

    2015-07-01

    In three experiments, we combined two sources of conflict within a modified task-switching procedure. The first source of conflict was the one inherent in any task switching situation, namely the conflict between a task set activated by the recent performance of another task and the task set needed to perform the actually relevant task. The second source of conflict was induced by requiring participants to guess aspects of the upcoming task (Exps. 1 & 2: task identity; Exp. 3: position of task precue). In case of an incorrect guess, a conflict accrues between the representation of the guessed task and the actually relevant task. In Experiments 1 and 2, incorrect guesses led to an overall increase of reaction times and error rates, but they reduced task switch costs compared to conditions in which participants predicted the correct task. In Experiment 3, incorrect guesses resulted in faster performance overall and to a selective decrease of reaction times in task switch trials when the cue-target interval was long. We interpret these findings in terms of an enhanced level of controlled processing induced by a combination of two sources of conflict converging upon the same target of cognitive control. Copyright © 2015 Elsevier B.V. All rights reserved.

  17. Parallel Prediction of Stock Volatility

    Directory of Open Access Journals (Sweden)

    Priscilla Jenq

    2017-10-01

    Full Text Available Volatility is a measurement of the risk of financial products. A stock will hit new highs and lows over time and if these highs and lows fluctuate wildly, then it is considered a high volatile stock. Such a stock is considered riskier than a stock whose volatility is low. Although highly volatile stocks are riskier, the returns that they generate for investors can be quite high. Of course, with a riskier stock also comes the chance of losing money and yielding negative returns. In this project, we will use historic stock data to help us forecast volatility. Since the financial industry usually uses S&P 500 as the indicator of the market, we will use S&P 500 as a benchmark to compute the risk. We will also use artificial neural networks as a tool to predict volatilities for a specific time frame that will be set when we configure this neural network. There have been reports that neural networks with different numbers of layers and different numbers of hidden nodes may generate varying results. In fact, we may be able to find the best configuration of a neural network to compute volatilities. We will implement this system using the parallel approach. The system can be used as a tool for investors to allocating and hedging assets.

  18. Color prediction in textile application

    Science.gov (United States)

    De Lucia, Maurizio; Buonopane, Massimo

    2004-09-01

    Nowadays production systems of fancy yarns for knits allow the creation of extremely complex products in which many effects are obtained by means of color alteration. Current production technique consists in defining type and quantity of fibers by making preliminary samples. This samples are then compared with a reference one. This comparison is based on operator experience. Many samples are required in order to achieve a sample similar to the reference one. This work requires time and then additional costs for a textile manufacturer. In addition, the methodology is subjective. Nowadays, spectrophotometers are the only devices that seem to be able to provide objective indications. They are based on a spectral analysis of the light reflected by the knit material. In this paper the study of a new method for color evaluation of a mix of wool fibers with different colors is presented. First of all fiber characterization were carried out through scattering and absorption coefficients using the Kubelka-Munk theory. Then the estimated color was compared with a reference item, in order to define conformity by means of objective parameters. Finally, theoretical characterization was compared with the measured quantity. This allowed estimation of prediction quality.

  19. Predictable repair of provisional restorations.

    Science.gov (United States)

    Hammond, Barry D; Cooper, Jeril R; Lazarchik, David A

    2009-01-01

    The importance of provisional restorations is often downplayed, as they are thought of by some as only "temporaries." As a result, a less-than-ideal provisional is sometimes fabricated, in part because of the additional chair time required to make provisional modifications when using traditional techniques. Additionally, in many dental practices, these provisional restorations are often fabricated by auxillary personnel who may not be as well trained in the fabrication process. Because provisionals play an important role in achieving the desired final functional and esthetic result, a high-quality provisional restoration is essential to fabricating a successful definitive restoration. This article describes a method for efficiently and predictably repairing both methacrylate and bis-acryl provisional restorations using flowable composite resin. By use of this relatively simple technique, provisional restorations can now be modified or repaired in a timely and productive manner to yield an exceptional result. Successful execution of esthetic and restorative dentistry requires attention to detail in every aspect of the case. Fabrication of high-quality provisional restorations can, at times, be challenging and time consuming. The techniques for optimizing resin provisional restorations as described in this paper are pragmatic and will enhance the delivery of dental treatment.

  20. Entropy and the Predictability of Online Life

    Directory of Open Access Journals (Sweden)

    Roberta Sinatra

    2014-01-01

    Full Text Available Using mobile phone records and information theory measures, our daily lives have been recently shown to follow strict statistical regularities, and our movement patterns are, to a large extent, predictable. Here, we apply entropy and predictability measures to two datasets of the behavioral actions and the mobility of a large number of players in the virtual universe of a massive multiplayer online game. We find that movements in virtual human lives follow the same high levels of predictability as offline mobility, where future movements can, to some extent, be predicted well if the temporal correlations of visited places are accounted for. Time series of behavioral actions show similar high levels of predictability, even when temporal correlations are neglected. Entropy conditional on specific behavioral actions reveals that in terms of predictability, negative behavior has a wider variety than positive actions. The actions that contain the information to best predict an individual’s subsequent action are negative, such as attacks or enemy markings, while the positive actions of friendship marking, trade and communication contain the least amount of predictive information. These observations show that predicting behavioral actions requires less information than predicting the mobility patterns of humans for which the additional knowledge of past visited locations is crucial and that the type and sign of a social relation has an essential impact on the ability to determine future behavior.