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Sample records for ictaluri identifies virulence-related

  1. Characterization of the RRN Operons in the Channel Catfish Pathogen Edwardsiella ictaluri

    USDA-ARS?s Scientific Manuscript database

    Aims: To advance diagnostics and phylogenetics of Edwardsiella ictaluri by sequencing and characterizing its rrn operons. Methods and Results: The Edw. ictaluri rrn operons were identified from a 5-7 kb insert lambda library and from Edw. ictaluri fosmid clones. We present the complete sequences...

  2. An Automated High-Throughput Cell-Based Multiplexed Flow Cytometry Assay to Identify Novel Compounds to Target Candida albicans Virulence-Related Proteins

    PubMed Central

    Bernardo, Stella M.; Allen, Christopher P.; Waller, Anna; Young, Susan M.; Oprea, Tudor; Sklar, Larry A.; Lee, Samuel A.

    2014-01-01

    Although three major classes of systemic antifungal agents are clinically available, each is characterized by important limitations. Thus, there has been considerable ongoing effort to develop novel and repurposed agents for the therapy of invasive fungal infections. In an effort to address these needs, we developed a novel high-throughput, multiplexed screening method that utilizes small molecules to probe candidate drug targets in the opportunistic fungal pathogen Candida albicans. This method is amenable to high-throughput automated screening and is based upon detection of changes in GFP levels of individually tagged target proteins. We first selected four GFP-tagged membrane-bound proteins associated with virulence or antifungal drug resistance in C. albicans. We demonstrated proof-of-principle that modulation of fluorescence intensity can be used to assay the expression of specific GFP-tagged target proteins to inhibitors (and inducers), and this change is measurable within the HyperCyt automated flow cytometry sampling system. Next, we generated a multiplex of differentially color-coded C. albicans strains bearing C-terminal GFP-tags of each gene encoding candidate drug targets incubated in the presence of small molecules from the Prestwick Chemical Library in 384-well microtiter plate format. Following incubation, cells were sampled through the HyperCyt system and modulation of protein levels, as indicated by changes in GFP-levels of each strain, was used to identify compounds of interest. The hit rate for both inducers and inhibitors identified in the primary screen did not exceed 1% of the total number of compounds in the small-molecule library that was probed, as would be expected from a robust target-specific, high-throughput screening campaign. Secondary assays for virulence characteristics based on null mutant strains were then used to further validate specificity. In all, this study presents a method for the identification and verification of new

  3. Edwardsiella ictaluri infection in Pangasius catfish imported from West Bengal into the Southern Caribbean.

    PubMed

    Phillips, A C N; Reichley, S R; Ware, C; Griffin, M J

    2016-09-05

    In response to a mortality event, seven Pangasius catfish (Pangasianodon hypophthalmus) were submitted to the University of the West Indies, School of Veterinary Medicine, Trinidad and Tobago, for diagnostic evaluation. These fish were part of a consignment that arrived from Kolkata two weeks earlier. Fish presented with perianal haemorrhage and blister-like swellings on the skin which ruptured to leave ulcers. Edwardsiella ictaluri was consistently recovered from the brain and skin. Repetitive sequence-mediated PCR analysis revealed genetic fingerprints consistent with E. ictaluri isolates from farm-raised channel catfish in Mississippi, USA. Plasmid analysis of the case isolates identified two unique plasmids that differ slightly in conformation and content from the pEI1 and pEI2 plasmids described for E. ictaluri from other fish hosts. The case isolates were also PCR negative for several E. ictaluri virulence factors. The biological implications of these genetic differences are unclear and warrant further study. This is the first report and documentation of E. ictaluri infection in Trinidad and Tobago, suggesting the pathogen may have been introduced concurrently with the importation of fish. This report emphasizes the importance of adequate health screenings of imported lots to minimize the threat of introducing E. ictaluri to non-endemic areas.

  4. Edwardsiellosis Caused by Edwardsiella ictaluri in Laboratory Populations of Zebrafish Danio rerio

    PubMed Central

    Hawke, John P.; Kent, Michael; Rogge, Matt; Baumgartner, Wes; Wiles, Judy; Shelley, Johnny; Savolainen, L. Christine; Wagner, Robert; Murray, Katy; Peterson, Tracy S.

    2014-01-01

    We report the first cases of Edwardsiella ictaluri causing epizootics in laboratory populations of Zebrafish Danio rerio. Edwardsiella ictaluri is primarily recognized as a disease of catfish species and is known to cause an economically important bacterial disease of farm-raised catfish in the USA and abroad; however, it has been isolated on occasion from 10 other genera of nonictalurid fishes. We isolated E. ictaluri from moribund Zebrafish held in quarantine at two different universities in two states and from a research facility in a third state between February 23 and December 6, 2011. Edwardsiellosis in Zebrafish can be described as a severe systemic disease characterized by tissue necrosis and the presence of large numbers of extracellular and intracellular bacteria, often within macrophages. The kidneys (pronephros and mesonephros), spleen, nares, and forebrain were the most commonly and severely affected tissues. In outbreaks, mortality was acute and numerous fish died over a 1–2 week period. Mortality continued until the majority of the population was lost, at which time the remaining fish were euthanized. In addition to these cases, four cultures of bacteria isolated from Zebrafish by another diagnostic laboratory were submitted to the Louisiana Aquatic Diagnostic Laboratory for identification and were confirmed as E. ictaluri. In total, eight cultures of E. ictaluri from Zebrafish from Louisiana, Massachusetts, Pennsylvania, and Florida were identified. The isolates were confirmed as E. ictaluri by biochemical phenotype, API 20E (bioMérieux), and amplification and sequencing of a portion of the 16S rRNA gene. Edwardsiella ictaluri isolates from Zebrafish are believed to comprise a unique group and were differentiated from catfish isolates by exhibiting weaker motility, autoaggregation in broth, a different plasmid profile (two plasmids of 4.0 and 3.5 kb), a different API 20E code (4204000), and lack of lipopolysaccharide recognition with Mab Ed9

  5. Identification and Characterization of Putative Translocated Effector Proteins of the Edwardsiella ictaluri Type III Secretion System

    PubMed Central

    Dubytska, Lidiya P.; Rogge, Matthew L.

    2016-01-01

    ABSTRACT Edwardsiella ictaluri, a major pathogen in channel catfish aquaculture, encodes a type III secretion system (T3SS) that is essential for intracellular replication and virulence. Previous work identified three putative T3SS effectors in E. ictaluri, and in silico analysis of the E. ictaluri genome identified six additional putative effectors, all located on the chromosome outside the T3SS pathogenicity island. To establish active translocation by the T3SS, we constructed translational fusions of each effector to the amino-terminal adenylate cyclase (AC) domain of the Bordetella pertussis adenylate cyclase toxin CyaA. When translocated through the membrane of the Edwardsiella-containing vacuole (ECV), the cyclic AMP produced by the AC domain in the presence of calmodulin in the host cell cytoplasm can be measured. Results showed that all nine effectors were translocated from E. ictaluri in the ECV to the cytoplasm of the host cells in the wild-type strain but not in a T3SS mutant, indicating that translocation is dependent on the T3SS machinery. This confirms that the E. ictaluri T3SS is similar to the Salmonella pathogenicity island 2 T3SS in that it translocates effectors through the membrane of the bacterial vacuole directly into the host cell cytoplasm. Additional work demonstrated that both initial acidification and subsequent neutralization of the ECV were necessary for effector translocation, except for two of them that did not require neutralization. Single-gene mutants constructed for seven of the individual effectors were all attenuated for replication in CCO cells, but only three were replication deficient in head kidney-derived macrophages (HKDM). IMPORTANCE The bacterial pathogen Edwardsiella ictaluri causes enteric septicemia of catfish (ESC), an economically significant disease of farm-raised channel catfish. Commercial catfish production accounts for the majority of the total fin fish aquaculture in the United States, with almost 300,000

  6. Experimental challenge studies in Vietnamese catfish, Pangasianodon hypophthalmus (Sauvage), exposed to Edwardsiella ictaluri and Aeromonas hydrophila.

    PubMed

    Crumlish, M; Thanh, P C; Koesling, J; Tung, V T; Gravningen, K

    2010-09-01

    The two main diseases in the pangasius catfish industry are bacillary necrosis of Pangasianodon (BNP) and motile aeromonas septicaemia (MAS), where the aetiological agents have been identified as Edwardsiella ictaluri and Aeromonas hydrophila, respectively. In this study, apparently healthy Pangasianodon hypophthalmus were exposed to E. ictaluri, A. hydrophila or both bacterial species by intraperitoneal injection or immersion. There were 20 fish per treatment group, and the bacterial isolates used for the study were recovered from natural infections of BNP or MAS in farmed Vietnamese P. hypophthalmus. The results of the experimental infections mimicked the natural disease outbreaks reported from these pathogens in P. hypophthalmus. Furthermore, it was clearly demonstrated that E. ictaluri was only recovered from the fish exposed to the bacterium and not recovered from the animals receiving A. hydrophila.

  7. Intraspecific diversity of Edwardsiella ictaluri isolates from diseased freshwater catfish, Pangasianodon hypophthalmus (Sauvage), cultured in the Mekong Delta, Vietnam.

    PubMed

    Bartie, K L; Austin, F W; Diab, A; Dickson, C; Dung, T T; Giacomini, M; Crumlish, M

    2012-09-01

    A molecular epidemiology study was conducted on 90 Edwardsiella ictaluri isolates recovered from diseased farmed freshwater catfish, Pangasianodon hypophthalmus, cultured in the Mekong Delta, Vietnam. Thirteen isolates of E. ictaluri derived from diseased channel catfish, Ictalurus punctatus, cultured in the USA were included for comparison. All the E.ictaluri isolates tested were found to be biochemically indistinguishable. A repetitive (rep)-PCR using the single (GTG)(5) primer was shown to possess limited discriminatory power, yielding two similar DNA profiles categorized as (GTG)(5) -PCR group 1 or 2 among the Vietnam isolates and (GTG)(5) -PCR group 1 within the USA isolates. Macrorestriction analysis identified 14 and 22 unique pulsotypes by XbaI and SpeI, respectively, among a subset of 59 E. ictaluri isolates. Numerical analysis of the combined macrorestriction profiles revealed three main groups: a distinct cluster formed exclusively of the USA isolates, and a major and minor cluster with outliers contained the Vietnam isolates. Antibiotic susceptibility and plasmid profiling supported the existence of the three groups. The results indicate that macrorestriction analysis may be regarded as a suitable typing method among the E. ictaluri species of limited intraspecific diversity. Furthermore, the findings suggest that E. ictaluri originating from Vietnam may constitute a distinct genetic group.

  8. Matrix-assisted laser desorption ionization-time of flight mass spectrometry based identification of Edwardsiella ictaluri isolated from Vietnamese striped catfish (Pangasius hypothalamus)

    PubMed Central

    Nhu, Truong Quynh; Park, Seong Bin; Kim, Si Won; Lee, Jung Seok; Im, Se Pyeong; Lazarte, Jassy Mary S.; Seo, Jong Pyo; Lee, Woo-Jai; Kim, Jae Sung

    2016-01-01

    Edwardsiella (E.) ictaluri is a major bacterial pathogen that affects commercially farmed striped catfish (Pangasius hypothalamus) in Vietnam. In a previous study, 19 strains of E. ictaluri collected from striped catfish were biochemically identified with an API-20E system. Here, the same 19 strains were used to assess the ability of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS; applied using a MALDI Biotyper) to conduct rapid, easy and accurate identification of E. ictaluri. MALDI-TOF MS could directly detect the specific peptide patterns of cultured E. ictaluri colonies with high (> 2.0, indicating species-level identification) scores. MALDI Biotyper 3.0 software revealed that all of the strains examined in this study possessed highly similar peptide peak patterns. In addition, electrophoresis (SDS-PAGE) and subsequent immuno-blotting using a specific chicken antibody (IgY) against E. ictaluri revealed that the isolates had highly similar protein profiles and antigenic banding profiles. The results of this study suggest that E. ictaluri isolated from striped catfish in Vietnam have homologous protein compositions. This is important, because it indicates that MALDI-TOF MS analysis could potentially outperform the conventional methods of identifying E. ictaluri. PMID:26726022

  9. Inflammatory Effects of Edwardsiella ictaluri Lipopolysaccharide Modifications in Catfish Gut

    PubMed Central

    Kilbourne, Jacquelyn; Park, Jie-Yeun; Martin, Taylor; Loh, Amanda; Diaz, Ignacia; Rojas, Robert; Segovia, Cristopher; DeNardo, Dale; Curtiss, Roy

    2014-01-01

    Bacterial lipopolysaccharides (LPS) are structural components of the outer membranes of Gram-negative bacteria and also are potent inducers of inflammation in mammals. Higher vertebrates are extremely sensitive to LPS, but lower vertebrates, like fish, are resistant to their systemic toxic effects. However, the effects of LPS on the fish intestinal mucosa remain unknown. Edwardsiella ictaluri is a primitive member of the Enterobacteriaceae family that causes enteric septicemia in channel catfish (Ictalurus punctatus). E. ictaluri infects and colonizes deep lymphoid tissues upon oral or immersion infection. Both gut and olfactory organs are the primary sites of invasion. At the systemic level, E. ictaluri pathogenesis is relatively well characterized, but our knowledge about E. ictaluri intestinal interaction is limited. Recently, we observed that E. ictaluri oligo-polysaccharide (O-PS) LPS mutants have differential effects on the intestinal epithelia of orally inoculated catfish. Here we evaluate the effects of E. ictaluri O-PS LPS mutants by using a novel catfish intestinal loop model and compare it to the rabbit ileal loop model inoculated with Salmonella enterica serovar Typhimurium LPS. We found evident differences in rabbit ileal loop and catfish ileal loop responses to E. ictaluri and S. Typhimurium LPS. We determined that catfish respond to E. ictaluri LPS but not to S. Typhimurium LPS. We also determined that E. ictaluri inhibits cytokine production and induces disruption of the intestinal fish epithelia in an O-PS-dependent fashion. The E. ictaluri wild type and ΔwibT LPS mutant caused intestinal tissue damage and inhibited proinflammatory cytokine synthesis, in contrast to E. ictaluri Δgne and Δugd LPS mutants. We concluded that the E. ictaluri O-PS subunits play a major role during pathogenesis, since they influence the recognition of the LPS by the intestinal mucosal immune system of the catfish. The LPS structure of E. ictaluri mutants is needed to

  10. Edwardsiella ictaluri as the causative agent of mortality in cultured Nile tilapia.

    PubMed

    Soto, Esteban; Griffin, Matt; Arauz, Maziel; Riofrio, Andres; Martinez, Alexis; Cabrejos, Maria Eugenia

    2012-06-01

    Edwardsiella ictaluri was consistently isolated from the spleens, livers, and head kidneys of diseased Nile tilapia Oreochromis niloticus from a farm experiencing mortality events in several culture ponds. We describe the first published outbreak of E. ictaluri-induced edwardsiellosis in Nile tilapia. Pure cultures of the isolated bacteria were characterized both biochemically and molecularly. Biochemical analysis was performed using the API-20E and RapID One systems, and antimicrobial susceptibility was determined by the broth microdilution method. Molecular analysis involved sequencing of the 16S rRNA gene, species-specific real-time polymerase chain reaction (PCR), and PCR-mediated genomic fingerprinting (rep-PCR). Pairwise sequence analysis of the 16S rRNA gene identified the case isolates to be a 100% match to E. ictaluri cultured from channel catfish in the southeastern United States. However, rep-PCR analysis identified the case isolates to be genetically different from representative strains isolated from disease outbreaks in cultured channel catfish in Mississippi. Infectivity challenges (intraperitoneal injection and immersion) demonstrated that a representative E. ictaluri strain isolated from tilapia was pathogenic to naive tilapia, reproducing clinical signs and mortality, thereby establishing Koch's postulates.

  11. A developing model for Edwardsiella ictaluri pathogenesis

    USDA-ARS?s Scientific Manuscript database

    Edwardsiella ictaluri, the causative agent of Enteric Septicemia of Catfish (ESC), belongs to a rather short list of bacteria known to survive and replicate in macrophages. Macrophages are ameboid-like cells that engulf and then digest cellular debris and pathogens, including bacteria. The process, ...

  12. Urease Activity and Virulence in Edwardsiella ictaluri

    USDA-ARS?s Scientific Manuscript database

    Edwardsiella ictaluri encodes a urease complex that is required for infection of the channel catfish host and for replication in channel catfish macrophages. The complex is comprised of nine genes, including ureA, B and C, which encode the primary enzymatic subunits, ureD, E, F and G, which encode ...

  13. Detection of Quorum Sensing Signal Molecules in Edwardsiella ictaluri Ei-151.

    PubMed

    Yang, Qian; Han, Yin; Tinh, Nguyen Thi Ngoc; Hien, Nguyen Thi; Bossier, Peter

    2012-12-01

    Edwardsiella ictaluri is a Gram-negative pathogenic bacterium in the family Enterobacteriaceae that causes enteric septicemia of catfish, which has become a significant problem in the aquaculture of striped catfish (Pangasianodon hypophthalmus) in Vietnam. In this study, a bacterium designated as Ei-151 was isolated from diseased striped catfish and proved to be virulent. Based on 16S rDNA sequencing and phenotypic tests, the pathogenic bacterium was identified as Edw. ictaluri. The presence of quorum sensing signal molecules in Edw. ictaluri Ei-151 was detected with different biosensor strains. The results showed that Ei-151 produced at least three kinds of acylated homoserine lactone (AHL) signal molecules as detected with the biosensor Agrobacterium tumefaciens KYC55, and the AHLs fingerprint was similar to that of Edw. tarda. During its entire growth, the levels of AHLs and autoinducer-2 produced by Ei-151 peaked at the stationary phase (OD600 1.8), which suggested that both of them may function at the stationary phase. No Cholerae autoinducer-1-like activity (including Edw. ictaluri LMG7860(T)) was detected.

  14. Identification of Differentially Abundant Proteins of Edwardsiella ictaluri during Iron Restriction

    PubMed Central

    Dumpala, Pradeep R.; Peterson, Brian C.; Lawrence, Mark L.; Karsi, Attila

    2015-01-01

    Edwardsiella ictaluri is a Gram-negative facultative anaerobe intracellular bacterium that causes enteric septicemia in channel catfish. Iron is an essential inorganic nutrient of bacteria and is crucial for bacterial invasion. Reduced availability of iron by the host may cause significant stress for bacterial pathogens and is considered a signal that leads to significant alteration in virulence gene expression. However, the precise effect of iron-restriction on E. ictaluri protein abundance is unknown. The purpose of this study was to identify differentially abundant proteins of E. ictaluri during in vitro iron-restricted conditions. We applied two-dimensional difference in gel electrophoresis (2D-DIGE) for determining differentially abundant proteins and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF/TOF MS) for protein identification. Gene ontology and pathway-based functional modeling of differentially abundant proteins was also conducted. A total of 50 unique differentially abundant proteins at a minimum of 2-fold (p ≤ 0.05) difference in abundance due to iron-restriction were detected. The numbers of up- and down-regulated proteins were 37 and 13, respectively. We noted several proteins, including EsrB, LamB, MalM, MalE, FdaA, and TonB-dependent heme/hemoglobin receptor family proteins responded to iron restriction in E. ictaluri. PMID:26168192

  15. Towards the intelligent design of a vaccine against Edwardsiella ictaluri

    USDA-ARS?s Scientific Manuscript database

    Edwardsiella ictaluri is the leading cause of disease loss in the catfish industry in the United States, accounting for an estimated 20.2 % loss in 2009. Previous work to establish live-attenuated vaccines for E. ictaluri demonstrated a relatively weak channel catfish immune response, with better im...

  16. Bacterial distribution and tissue targets following experimental Edwardsiella ictaluri infection in Nile tilapia Oreochromis niloticus.

    PubMed

    Soto, Esteban; Illanes, Oscar; Revan, Floyd; Griffin, Matt; Riofrio, Andrés

    2013-05-27

    Edwardsiella ictaluri, a Gram-negative enteric bacterium, is the known etiological agent of enteric septicemia of catfish. In the last few years, different strains have been implicated as the causative agent of mortality events in cultured fish, including Nile tilapia Oreochromis niloticus L. Due to the emergent nature of edwardsiellosis in non-ictalurid fish, little is known about the dynamics of E. ictaluri infection in tilapia. The purpose of this study was to gain a better understanding of the pathogenesis of edwardsiellosis in tilapia by determining the median lethal and infective doses, tissue targets of infection, rate of bacterial dissemination, and the specific tissue response to E. ictaluri following an immersion challenge with bacterial strains recovered from outbreak events in tilapia. In addition to histopathology assessment, the bacterial burdens in several tissues of infected fish were determined over a 2 wk course of infection using quantitative real-time PCR (qPCR). The collected data suggest the cutaneous and oral routes as the main ports of entry for the organism, which later spreads hematogenously throughout the body. Even though histopathological assessment of infected fish revealed involvement of a wide range of tissues, the severity of the necrotizing and granulomatous lesions in the spleen and head kidney, with concomitant high levels of bacterial DNA in these organs determined by qPCR, identifies them as the main targets of infection.

  17. Mortality and pathology in brown bullheads Amieurus nebulosus associated with a spontaneous Edwardsiella ictaluri outbreak under tank culture conditions

    USGS Publications Warehouse

    Iwanowicz, L.R.; Griffin, A.R.; Cartwright, Deborah D.; Blazer, V.S.

    2006-01-01

    Brown bullheads Amieurus nebulosus (family Ictaluridae) are commonly used as a sentinel of environmental contamination. These fish are not generally cultured under laboratory conditions and little is known about their disease susceptibility. Here we report an outbreak of disease due to Edwardsiella ictaluri in a laboratory population of tank-reared, wild-caught brown bullheads. The isolate was positively identified as E. ictaluri using standard bacteriological substrate utilization tests and a monoclonal antibody specific for this bacterium. This pathogen causes a significant disease in channel catfish Ictalurus punctatus and is associated with disease in other ictalurid and non-ictalurid fishes. It appears that E. ictaluri is also a significant pathogen in brown bullheads and produces clinical signs and lesions similar but not identical to those observed in channel catfish. Since commercial sources of bullheads for laboratory tank studies are not available, precautions should be taken to prevent potential E. ictaluri disease outbreaks from wild-caught bullheads intended for laboratory research. ?? Inter-Research 2006.

  18. Naturally infected catfish concurrently transmit Ichthyophthirius multifiliis and Edwardsiella ictaluri to naive catfish

    USDA-ARS?s Scientific Manuscript database

    Bacterium Edwardsiella ictaluri and parasite Ichthyophthirius multifiliis (Ich) are two common pathogens of channel catfish (Ictalurus punctatus) which cause major losses to catfish aquaculture. There is limited information available whether fish naturally coinfected with Ich and E. ictaluri can con...

  19. Chemical and electroporated transformation of Edwardsiella ictaluri using three different plasmids

    USDA-ARS?s Scientific Manuscript database

    Transfer of DNA by conjugation has been the method generally used for genetic manipulation of Edwardsiella ictaluri because, previously, attempts to transform E. ictaluri by the uptake of naked DNA has apparently failed. We report here the successful transformation of seven strains of E. ictaluri us...

  20. Use of bioluminescence mutant screening for identification of Edwardsiella ictaluri genes involved in channel catfish (Ictalurus punctatus) skin colonization.

    PubMed

    Menanteau-Ledouble, Simon; Lawrence, Mark L

    2013-03-23

    Initial invasion of the host is the first and vital part of any infection process. We have demonstrated that Edwardsiella ictaluri is capable of colonizing and penetrating catfish skin. Therefore, a mutant library was constructed by random insertion of the Mar2xT7 transposon into the chromosome of E. ictaluri harboring the bioluminescence plasmid pAKgfplux1. This library was then screened through a series of three consecutive challenges for mutants showing a decreased ability to colonize the catfish epithelium. Eighteen mutants were identified that have decreased adhesion and virulence. Mutated genes encoded one sensor protein, two transport proteins, five enzymes, two regulatory proteins, and five hypothetical proteins. Among the mutated genes, the first one identified was a gene encoding for RstA/B, which is known to play a role in regulating the expression of invasion genes in Salmonella enterica Typhimurium. Another mutant was lacking a putative ribonuclease similar to a Shigella protein that regulates the expression of adhesin. A third mutant was defective in a protein similar to a Brucella protein that was initially identified as a transporter, but actually is a member of a newly discovered adhesin family. Results from this study could enable development of a new strategy for blocking E. ictaluri invasion at the initial adherence stage. Copyright © 2012 Elsevier B.V. All rights reserved.

  1. Comparison of Vietnamese and US isolates of Edwardsiella ictaluri.

    PubMed

    Rogge, Matthew L; Dubytska, Lidiya; Jung, Tae Sung; Wiles, Judy; Elkamel, Ahmad A; Rennhoff, Amelia; Oanh, Dang Thi; Thune, Ronald L

    2013-09-24

    We compared Edwardsiella ictaluri from striped catfish in Vietnam with US channel catfish isolates. Biochemical analyses and sequencing of the 16S rRNA gene confirmed that the Vietnamese isolates were E. ictaluri. Comparison using rep-PCR fingerprinting demonstrated no significant differences between the isolates, but plasmid analysis indicated that the Vietnamese isolates grouped into 4 plasmid profiles, each different from the typical pEI1 and pEI2 plasmid profile found in the US isolates. Sequencing plasmids representative of the 4 profiles indicated that all contained derivatives of the E. ictaluri plasmid pEI1, whereas only 1 contained a plasmid derivative of the E. ictaluri plasmid pEI2. The pEI2 encoded type III secretion effector, EseI, and its chaperone, EscD, were found to be present on the chromosome in isolates lacking a pEI2 derivative. In addition, 1 isolate carried a 5023 bp plasmid that does not have homology to either pEI1 or pEI2. Furthermore, Vietnamese isolates were PCR positive for the type III and type VI secretion system genes esrC and evpC, respectively, and the urease enzyme, but were PCR-negative for the putative type IV secretion system gene virD4. A monoclonal antibody against the lipopolysaccharide of E. ictaluri ATCC 33202 did not react with the Asian isolates or with the more recent US isolates. Antibiotic resistance patterns were variable and did not correlate to the presence of any particular plasmid profile. Finally, the Vietnamese isolates were avirulent and had a significantly reduced capacity for intracellular replication within head-kidney-derived channel catfish macrophages.

  2. Edwardsiella ictaluri Encodes an Acid Activated Urease that is Required for Intracellular Replication in Channel Catfish Ictalurus punctatus Macrophages

    USDA-ARS?s Scientific Manuscript database

    Genomic analysis indicated that Edwardsiella ictaluri encodes a putative ureasepathogenicity island containing 9 open reading frames, including urea and ammonium transporters. In vitro studies with the wild-type E. ictaluri and a ureG::kan urease mutant strain indicated that E. ictaluri is significa...

  3. Construction and evaluation of an Edwardsiella ictaluri fhuC mutant.

    PubMed

    Abdelhamed, Hossam; Lu, Jingjun; Shaheen, Adel; Abbass, Amany; Lawrence, Mark L; Karsi, Attila

    2013-03-23

    Edwardsiella ictaluri is a Gram-negative facultative intracellular pathogen causing enteric septicemia in channel catfish. Iron is an essential micronutrient needed for bacterial virulence, and to acquire iron, many Gram-negative bacteria secrete ferric iron chelating siderophores. The ferric hydroxamate uptake (Fhu) system consists of four genes (fhuC, fhuD, fhuB, and fhuA), and is involved in the uptake of hydroxamate type siderophores across bacterial membranes. However, the Fhu system and its importance in E. ictaluri virulence have been uninvestigated. Here, we present construction and evaluation of an E. ictaluri ΔfhuC mutant. The E. ictaluri fhuC gene was deleted in-frame by allelic exchange, and the mutant's growth in media and virulence in catfish were determined. Our results indicated that deletion of the E. ictaluri fhuC gene did not affect the growth of E. ictaluri largely in both iron-replete and iron-depleted media. Addition of ferric iron sources into the iron-depleted medium improved the growth of both E. ictaluri ΔfhuC and wild type (WT). Catfish mortalities indicated that E. ictaluri ΔfhuC mutant was attenuated 2.05-fold compared with the parent strain. The catfish immunized with the E. ictaluri ΔfhuC mutant showed a high relative percent survival rate (97.50%) after re-challenge with the WT E. ictaluri strain. Taken together, our data indicates that the fhuC gene contributes to E. ictaluri virulence.

  4. Effects of Bio-Mos on Growth and Survival of Channel Catfish Challenged with Edwardsiella ictaluri

    USDA-ARS?s Scientific Manuscript database

    A major problem in the catfish farming industry has been high disease loss to enteric septicemia of catfish (ESC), caused by the bacterium Edwardsiella ictaluri (E. ictaluri). Methods to control this disease include antibiotic therapy, vaccinations, and management strategies such as taking the fish...

  5. Modified live Edwardsiella ictaluri vaccine, AQUAVAC-ESC, lacks multidrug resistance plasmids

    USDA-ARS?s Scientific Manuscript database

    Plasmid mediated antibiotic resistance was first discovered in Edwardsiella ictaluri in the early 1990’s, and in 2007 an E. ictaluri isolate harboring an IncA/C plasmid was recovered from a moribund channel catfish infected with the bacterium. Due to the identification of multidrug resistance plasm...

  6. Overcoming inconsistencies in mortality rates during winter experimental challenges of channel catfish with Edwardsiella ictaluri

    USDA-ARS?s Scientific Manuscript database

    One of the goals of the ARS Catfish Genetics Research Unit is to incorporate disease resistance to ESC, caused by the bacterium, Edwardsiella ictaluri, into our selective breeding program. Through repeated experiments we have determined an optimal challenge dose of E. ictaluri that produces 50-70% ...

  7. Tricarboxylic acid cycle and one-carbon metabolism pathways are important in Edwardsiella ictaluri virulence.

    PubMed

    Dahal, Neeti; Abdelhamed, Hossam; Lu, Jingjun; Karsi, Attila; Lawrence, Mark L

    2013-01-01

    Edwardsiella ictaluri is a Gram-negative facultative intracellular pathogen causing enteric septicemia of channel catfish (ESC). The disease causes considerable economic losses in the commercial catfish industry in the United States. Although antibiotics are used as feed additive, vaccination is a better alternative for prevention of the disease. Here we report the development and characterization of novel live attenuated E. ictaluri mutants. To accomplish this, several tricarboxylic acid cycle (sdhC, mdh, and frdA) and one-carbon metabolism genes (gcvP and glyA) were deleted in wild type E. ictaluri strain 93-146 by allelic exchange. Following bioluminescence tagging of the E. ictaluri ΔsdhC, Δmdh, ΔfrdA, ΔgcvP, and ΔglyA mutants, their dissemination, attenuation, and vaccine efficacy were determined in catfish fingerlings by in vivo imaging technology. Immunogenicity of each mutant was also determined in catfish fingerlings. Results indicated that all of the E. ictaluri mutants were attenuated significantly in catfish compared to the parent strain as evidenced by 2,265-fold average reduction in bioluminescence signal from all the mutants at 144 h post-infection. Catfish immunized with the E. ictaluri ΔsdhC, Δmdh, ΔfrdA, and ΔglyA mutants had 100% relative percent survival (RPS), while E. ictaluri ΔgcvP vaccinated catfish had 31.23% RPS after re-challenge with the wild type E. ictaluri.

  8. Tricarboxylic Acid Cycle and One-Carbon Metabolism Pathways Are Important in Edwardsiella ictaluri Virulence

    PubMed Central

    Dahal, Neeti; Abdelhamed, Hossam; Lu, Jingjun; Karsi, Attila; Lawrence, Mark L.

    2013-01-01

    Edwardsiella ictaluri is a Gram-negative facultative intracellular pathogen causing enteric septicemia of channel catfish (ESC). The disease causes considerable economic losses in the commercial catfish industry in the United States. Although antibiotics are used as feed additive, vaccination is a better alternative for prevention of the disease. Here we report the development and characterization of novel live attenuated E. ictaluri mutants. To accomplish this, several tricarboxylic acid cycle (sdhC, mdh, and frdA) and one-carbon metabolism genes (gcvP and glyA) were deleted in wild type E. ictaluri strain 93-146 by allelic exchange. Following bioluminescence tagging of the E. ictaluri ΔsdhC, Δmdh, ΔfrdA, ΔgcvP, and ΔglyA mutants, their dissemination, attenuation, and vaccine efficacy were determined in catfish fingerlings by in vivo imaging technology. Immunogenicity of each mutant was also determined in catfish fingerlings. Results indicated that all of the E. ictaluri mutants were attenuated significantly in catfish compared to the parent strain as evidenced by 2,265-fold average reduction in bioluminescence signal from all the mutants at 144 h post-infection. Catfish immunized with the E. ictaluri ΔsdhC, Δmdh, ΔfrdA, and ΔglyA mutants had 100% relative percent survival (RPS), while E. ictaluri ΔgcvP vaccinated catfish had 31.23% RPS after re-challenge with the wild type E. ictaluri. PMID:23762452

  9. [Sodium houttuyfonate inhibits virulence related motility of Pseudomonas aeruginosa].

    PubMed

    Wu, Da-qiang; Huang, Wei-feng; Duan, Qiang-jun; Cheng, Hui-juan; Wang, Chang-zhong

    2015-04-01

    Sodium houttuyfonate (SH) is a derivative of effective component of a Chinese material medica, Houttuynia cordata, which is applied in anti-infection of microorganism. But, the antimicrobial mechanisms of SH still remain unclear. Here, we firstly discovered that SH effectively inhibits the three types of virulence related motility of.Pseudomonas aeruginosa, i.e., swimming, twitching and swarming. The plate assay results showed that the inhibitory action of SH against swimming and twitching in 24 h and swarming in 48 h is dose-dependent; and bacteria nearly lost all of the motile activities under the concentration of 1 x minimum inhibitory concentration (MIC) (512 mg x L(-1) same as azithromycin positive group (1 x MIC, 16 mg x L(-1)). Furthermore, we found that the expression of structural gene flgB and pilG is down-regulated by SH, which implies that inhibitory mechanism of SH against motility of P. aeruginosa may be due to the inhibition of flagella and pili bioformation of P. aeruginosa by SR Therefore, our presented results firstly demonstrate that SH effectively inhibits the motility activities of P. aeruginosa, and suggest that SH could be a promising antipseudomonas agents in clinic.

  10. Comparative genomic analysis of bacteriophages specific to the channel catfish pathogen Edwardsiella ictaluri

    USDA-ARS?s Scientific Manuscript database

    Background: The bacterial pathogen Edwardsiella ictaluri is a primary cause of mortality in channel catfish raised commercially in aquaculture farms. Additional treatment and diagnostic regimes are needed for this enteric pathogen, motivating the discovery and characterization of bacteriophages spe...

  11. Genome sequence of Edwardsiella ictaluri 93-146 a strain associated with a natural channel catfish outbreak of enteric septicemia of catifsh

    USDA-ARS?s Scientific Manuscript database

    Edwardsiella ictaluri is the cause of extensive mortalities and economic losses to the channel catfish industry of the southeast United States. Here we report the complete genome of Edwardsiella ictaluri 93-146. Whole-genome sequence analysis of E. ictaluri provides a tool for understanding the geno...

  12. Attenuation, persistence, and vaccine potential of an Edwardsiella ictaluri purA mutant.

    PubMed Central

    Lawrence, M L; Cooper, R K; Thune, R L

    1997-01-01

    In this study, an adenine-auxotrophic strain of Edwardsiella ictaluri was constructed and its virulence, tissue persistence, and vaccine efficacy were evaluated. A clone containing the purA gene was isolated from an E. ictaluri genomic library, sequenced, and shown to have an overall sequence identity of 79.3% at the nucleotide level and 85.7% at the amino acid level with the Escherichia coli purA gene. The cloned E. ictaluri purA gene was mutated by deleting a 598-bp segment of the gene and inserting the kanamycin resistance gene from Tn903 into the gap. The delta purA::Km(r) gene was subcloned into the suicide plasmid pGP704, and the resulting plasmid was used to deliver the modified gene into a virulent strain of E. ictaluri by conjugation. Homologous recombination replaced the chromosomal purA gene with the mutated gene to create an adenine-auxotrophic strain (LSU-E2). Compared to wild-type E. ictaluri, LSU-E2 was highly attenuated by the injection, immersion, and oral routes of exposure. By the injection route, LSU-E2 had a 50% lethal dose (LD50) that was greater than 5 logs10 higher than the LD50 for wild-type E. ictaluri. In a tissue persistence study, LSU-E2 was able to invade channel catfish by the immersion route and persist in internal organs for at least 48 h. Channel catfish that were vaccinated with a single immersion dose of LSU-E2 had mortality significantly lower (P < 0.01) following a wild-type E. ictaluri challenge than that of nonvaccinated fish. PMID:9353045

  13. Effects of Ichthyophthirius multifiliis parasitism on the survival, hematology and bacterial load in channel catfish previously exposed to Edwardsiella ictaluri

    USDA-ARS?s Scientific Manuscript database

    The effect of Ichthyophthirius multifiliis (Ich) parasitism on survival, hematology and bacterial load in channel catfish, Ictalurus punctatus, previously exposed to Edwardsiella ictaluri was studied. Fish were exposed to E. ictaluri one day prior to Ich in the following treatments: 1)- infected by...

  14. Phenotype, virulence and immunogenicity of Edwardsiella ictaluri cyclic adenosine 3',5'-monophosphate receptor protein (Crp) mutants in catfish host.

    PubMed

    Santander, Javier; Mitra, Arindam; Curtiss, Roy

    2011-12-01

    Edwardsiella ictaluri is an Enterobacteriaceae that causes lethal enteric septicemia in catfish. Being a mucosal facultative intracellular pathogen, this bacterium is an excellent candidate to develop immersion-oral live attenuated vaccines for the catfish aquaculture industry. Deletion of the cyclic 3',5'-adenosine monophosphate (cAMP) receptor protein (crp) gene in several Enterobacteriaceae has been utilized in live attenuated vaccines for mammals and birds. Here we characterize the crp gene and report the effect of a crp deletion in E. ictaluri. The E. ictaluri crp gene and encoded protein are similar to other Enterobacteriaceae family members, complementing Salmonella enterica Δcrp mutants in a cAMP-dependent fashion. The E. ictaluri Δcrp-10 in-frame deletion mutant demonstrated growth defects, loss of maltose utilization, and lack of flagella synthesis. We found that the E. ictaluri Δcrp-10 mutant was attenuated, colonized lymphoid tissues, and conferred immune protection against E. ictaluri infection to zebrafish (Danio rerio) and catfish (Ictalurus punctatus). Evaluation of the IgM titers indicated that bath immunization with the E. ictaluri Δcrp-10 mutant triggered systemic and skin immune responses in catfish. We propose that deletion of the crp gene in E. ictaluri is an effective strategy to develop immersion live attenuated antibiotic-sensitive vaccines for the catfish aquaculture industry.

  15. Comparative genomic analysis of bacteriophages specific to the channel catfish pathogen Edwardsiella ictaluri

    PubMed Central

    2011-01-01

    Background The bacterial pathogen Edwardsiella ictaluri is a primary cause of mortality in channel catfish raised commercially in aquaculture farms. Additional treatment and diagnostic regimes are needed for this enteric pathogen, motivating the discovery and characterization of bacteriophages specific to E. ictaluri. Results The genomes of three Edwardsiella ictaluri-specific bacteriophages isolated from geographically distant aquaculture ponds, at different times, were sequenced and analyzed. The genomes for phages eiAU, eiDWF, and eiMSLS are 42.80 kbp, 42.12 kbp, and 42.69 kbp, respectively, and are greater than 95% identical to each other at the nucleotide level. Nucleotide differences were mostly observed in non-coding regions and in structural proteins, with significant variability in the sequences of putative tail fiber proteins. The genome organization of these phages exhibit a pattern shared by other Siphoviridae. Conclusions These E. ictaluri-specific phage genomes reveal considerable conservation of genomic architecture and sequence identity, even with considerable temporal and spatial divergence in their isolation. Their genomic homogeneity is similarly observed among E. ictaluri bacterial isolates. The genomic analysis of these phages supports the conclusion that these are virulent phages, lacking the capacity for lysogeny or expression of virulence genes. This study contributes to our knowledge of phage genomic diversity and facilitates studies on the diagnostic and therapeutic applications of these phages. PMID:21214923

  16. Transcriptome of intraperitoneal organs of starry flounder Platichthys stellatus challenged by Edwardsiella ictaluri JCM1680

    NASA Astrophysics Data System (ADS)

    Tong, Yanli; Sun, Xiuqin; Wang, Bo; Wang, Ling; Li, Yan; Tian, Jinhu; Zheng, Fengrong; Zheng, Minggang

    2015-01-01

    Platichthys stellatus is an economically important marine bony fish species that is cultured in China on a large scale. However, very little is known about its immune-related genes. In this study, the transcriptome of the immune organs of P. stellatus that were intraperitoneally challenged with the pathogen E dwardsiella ictaluri JCM1680 is analyzed. Total RNA from four tissues (spleen, kidney, liver, and intestine) was mixed equally and then sequenced on an Illumina HiSeq 2000 platform. Overall, 28 465 813 quality reads were generated and assembled into 43 061 unigenes. Similarity searches against public protein sequence databases were used to annotate 28 291 unigenes (65.7% of the total), 368 of which were associated with immunoregulation, including 188 related to immunity response. Additionally, the transcript levels of immunity response unigenes annotated as related to tumor necrosis factor (TNF), TNF receptor, chemokine, major histocompatibility complex, and interleukin-6 were investigated in the different tissues of normal and infected P. stellatus by real-time quantitative PCR. The results confirmed that the unigenes identified in the transcriptome database were indeed expressed and up-regulated in infected P. stellatus. To our knowledge, this is the first report of the sequencing and analysis of the transcriptome of P. stellatus. These findings provide insights into the transcriptomics and immunogenetics of bony fish.

  17. Transcriptome of intraperitoneal organs of starry flounder Platichthys stellatus challenged by Edwardsiella ictaluri JCM1680

    NASA Astrophysics Data System (ADS)

    Tong, Yanli; Sun, Xiuqin; Wang, Bo; Wang, Ling; Li, Yan; Tian, Jinhu; Zheng, Fengrong; Zheng, Minggang

    2014-09-01

    Platichthys stellatus is an economically important marine bony fish species that is cultured in China on a large scale. However, very little is known about its immune-related genes. In this study, the transcriptome of the immune organs of P. stellatus that were intraperitoneally challenged with the pathogen Edwardsiella ictaluri JCM1680 is analyzed. Total RNA from four tissues (spleen, kidney, liver, and intestine) was mixed equally and then sequenced on an Illumina HiSeq 2000 platform. Overall, 28 465 813 quality reads were generated and assembled into 43 061 unigenes. Similarity searches against public protein sequence databases were used to annotate 28 291 unigenes (65.7% of the total), 368 of which were associated with immunoregulation, including 188 related to immunity response. Additionally, the transcript levels of immunity response unigenes annotated as related to tumor necrosis factor (TNF), TNF receptor, chemokine, major histocompatibility complex, and interleukin-6 were investigated in the different tissues of normal and infected P. stellatus by real-time quantitative PCR. The results confirmed that the unigenes identified in the transcriptome database were indeed expressed and up-regulated in infected P. stellatus. To our knowledge, this is the first report of the sequencing and analysis of the transcriptome of P. stellatus. These findings provide insights into the transcriptomics and immunogenetics of bony fish.

  18. Vaccine efficacy of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from Edwardsiella ictaluri against E. tarda in tilapia.

    PubMed

    Trung Cao, Thanh; Tsai, Ming-An; Yang, Chung-Da; Wang, Pei-Chyi; Kuo, Tsun-Yung; Gabriel Chen, Hsu-Chung; Chen, Shih-Chu

    2014-01-01

    Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), derived from the outer-membrane protein (OMP) fraction, has been used as a potential candidate for vaccine development. The gene-encoding 37 kDa GAPDH outer membrane protein (OMP) from Edwardsiella ictaluri was amplified using polymerase chain reaction (PCR) and was cloned and expressed in Escherichia coli BL21 (DE3). Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), Western blotting, and nucleotide and amino acid sequencing were used to analyze the expressed antigenic protein and gene encoding this protein. Comparative DNA and protein sequence analysis of GAPDH from E. ictaluri GAPDHs from several Gram-negative bacterial species within the Enterobacteriaceae family revealed that the GAPDHs within this group are highly conserved and share a sequence similarity of 75-100% with E. ictaluri GDPDH. Rabbit antiserum raised against the E. ictaluri recombinant GAPDH (rGAPDH) protein recognized purified GADPH, indicating that it has a strong immunogenicity. Tilapia fish were intraperitoneally immunized with formalin-killed E. ictaluri whole cells, and rGAPDH (30 μg fish(-1)) from E. ictaluri, both of which were emulsified in ISA 763A adjuvant. At 3 months after immunization, fish were challenged with the E. tarda strain to assess vaccine efficacy; the relative percent survival (RPS) values were found to exceed 71.4%. The specific mean antibody titer log2 level of groups vaccinated with rGAPDH at 3 months was significantly higher than that of non-vaccinated fish (control group). Therefore, this recombinant protein can be considered a multi-purpose candidate vaccine against several pathogenic bacteria.

  19. Influence of Edwardsiella ictaluri Septicemia on nitrite-induced methemoglobinemia in channel catfish (Ictalurus punctatus)

    SciTech Connect

    Tucker, C.S.; MacMillan, J.R.; Schwedler, T.E.

    1984-06-01

    In a previous report, the authors showed that lack of acclimation to nitrite can result in abnormally high levels of methemoglobin in nitrite-exposed channel catfish. They also observed abnormal methemoglobin levels in fish when concurrent bacteremias are present. Enteric Septicemia of Catfish is an acute bacterial disease caused by Edwardsiella ictaluri. Nitrite-induced methemoglobinemia and Enteric Septicemia of Catfish are both economically important diseases of commercially cultured channel catfish. In the present study, the authors investigated the influence of acute infection with E. ictaluri on the level of methemoblobin in nitrite-exposed channel catfish fingerlings.

  20. Modulation of vacuolar pH is required for replication of Edwardsiella ictaluri in channel catfish macrophages.

    PubMed

    Baumgartner, Wes A; Dubytska, Lidiya; Rogge, Matthew L; Mottram, Peter J; Thune, Ronald L

    2014-06-01

    Previous in vitro work demonstrated that Edwardsiella ictaluri produces an acid-activated urease that can modulate environmental pH through the production of ammonia from urea. Additional work revealed that expression of the E. ictaluri type III secretion system (T3SS) is upregulated by acidic pH. Both the urease and the T3SS were previously shown to be essential to intracellular replication. In this work, fluorescence microscopy with LysoTracker Red DND-99 (LTR) indicated that E. ictaluri-containing vacuoles (ECV) became acidified following ingestion by head kidney-derived macrophages (HKDM). In vivo ratiometric imaging demonstrated a lowered ECV pH, which fell to as low as pH 4 but subsequently increased to pH 6 or greater. Inhibition of vacuolar H(+)-ATPases by use of the specific inhibitor bafilomycin A1 abrogated both ECV acidification and intracellular replication in HKDM. Failure of an E. ictaluri urease knockout mutant to increase the ECV pH in the in vivo ratiometric assay suggests that ammonia produced by the urease reaction mediates the pH increase. Additionally, when the specific arginase inhibitor l-norvaline was used to treat E. ictaluri-infected HKDM, the ECV failed to neutralize and E. ictaluri was unable to replicate. This indicates that the HKDM-encoded arginase enzyme produces the urea used by the E. ictaluri urease enzyme. Failure of the ECV to acidify would prevent both upregulation of the T3SS and activation of the urease enzyme, either of which would prevent E. ictaluri from replicating in HKDM. Failure of the ECV to neutralize would result in a vacuolar pH too low to support E. ictaluri replication.

  1. Regulation of the Edwardsiella ictaluri Type III Secretion System by pH and Phosphate Concentration through EsrA, EsrB, and EsrC ▿

    PubMed Central

    Rogge, Matthew L.; Thune, Ronald L.

    2011-01-01

    A recently described Edwardsiella ictaluri type III secretion system (T3SS) with functional similarity to the Salmonella pathogenicity island 2 T3SS is required for replication in channel catfish head-kidney-derived macrophages (HKDM) and virulence in channel catfish. Quantitative PCR and Western blotting identified low pH and phosphate limitation as conducive to expression of the E. ictaluri T3SS, growth conditions that mimic the phagosomal environment. Mutagenesis studies demonstrated that expression is under the control of the EsrAB two-component regulatory system. EsrB also induces upregulation of the AraC-type regulatory protein EsrC, which enhances expression of the EscB/EseG chaperone/effector operon in concert with EsrB and induces expression of the pEI1-encoded effector, EseH. EsrC also induces expression of a putative type VI secretion system translocon protein, EvpC, which is secreted under the same low-pH conditions as the T3SS translocon proteins. The pEI2-encoded effector, EseI, was upregulated under low-pH and low-phosphate conditions but not in an EsrB- or EsrC-dependent manner. Mutations of EsrA and EsrB both resulted in loss of the ability to replicate in HKDM and full attenuation in the channel catfish host. Mutation of EsrC did not affect intracellular replication but did result in attenuation in catfish. Although EsrB is the primary transcriptional regulator for E. ictaluri genes within the T3SS pathogenicity island, EsrC regulates expression of the plasmid-carried effector eseH and appears to mediate coordinated expression of the T6SS with the T3SS. PMID:21551284

  2. Effects of Bio-Mos on growth and survival of channel catfish challenged with Edwardsiella ictaluri

    USDA-ARS?s Scientific Manuscript database

    Research examined the effects of Bio-Mos on growth and disease resistance in channel catfish. Catfish were fed either a Con-Sink (36% crude protein (CP) diet) or Bio-Mos-Sink (36% CP diet with Bio-Mos supplemented at 2 g/kg) sinking pellet for 6 wks. followed by an E. ictaluri challenge. Growth pe...

  3. Comparison of Edwardsiella ictaluri isolates from different hosts and geographic origins

    USDA-ARS?s Scientific Manuscript database

    The intraspecific genetic variability of E. ictaluri isolates from different origins was determined. Isolates were recovered from farm-raised catfish (Ictalurus punctatus) in Mississippi, USA, tilapia cultured in the Western hemisphere, and zebrafish propagated in Florida, USA. These isolates were...

  4. Construction, characterization, expression and immune responses of flagellar proteins of channel catfish, important pathogen Edwardsiella ictaluri

    USDA-ARS?s Scientific Manuscript database

    Background: Edwardsiella ictaluri causes enteric septicemia of catfish, which is the leading disease in channel catfish (Ictalurus punctatus)and is responsible for $50 - 60 million economic losses to catfish producers annually in the southeastern U.S. Bacterial flagella are complex polymeric structu...

  5. Construction, characterization and use of Edwardsiella ictaluri flagella-type three secretion system protein arrays

    USDA-ARS?s Scientific Manuscript database

    Enteric septicemia of catfish, caused by Edwardsiella ictaluri, is the leading disease in channel catfish (Ictalurus punctatus) that is responsible for $50 - 60 million economic losses to catfish producers annually in the Southeastern U.S. The flagella and type three secretion system (TTSS) in Gram...

  6. Bacterial distribution and tissue targets following experimental Edwardsiella ictaluri infection in nile tilapia Oreochromis niloticus

    USDA-ARS?s Scientific Manuscript database

    Edwardsiella ictaluri, a Gram-negative enteric bacterium, is the known etiological agent of enteric septicemia of catfish. In the last few years, different strains have been implicated as the causative agent of mortality events in cultured fish, including Nile tilapia Oreochromis niloticus L. Due to...

  7. Identification of differentially regulated proteins of Edwardsiella ictaluri during iron restriction

    USDA-ARS?s Scientific Manuscript database

    Edwardsiella ictaluri is a Gram-negative facultative anaerobe intracellular bacterium that causes enteric septicemia in channel catfish. Iron is an essential inorganic nutrient of bacteria and is crucial for bacterial invasion. Reduced availability of iron by the host may cause a significant stres...

  8. Specific serum antibody responses in channel catfish (Ictalurus punctatus) provide limited protection against Streptococcus ictaluri challenge

    USDA-ARS?s Scientific Manuscript database

    Passive immunization has been shown to provide a spectrum of protection against certain piscine pathogens, and studies were conducted to determine the role of specific antibodies in immunity to Streptococcus ictaluri. Adult Nile tilapia (Oreochromis niloticus) were injected i.p. with tryptic soy br...

  9. Edwardsiella ictaluri as the causative agent of mortality in cultured Nile tilapia

    USDA-ARS?s Scientific Manuscript database

    Edwardsiella ictaluri was consistently isolated from the spleens, livers, and head kidneys of diseased Nile tilapia Oreochromis niloticus from a farm experiencing mortality events in several culture ponds. We describe the first published outbreak of E. ictaluri–induced Edwardsiellosis in Nile tilapi...

  10. Variation in Susceptibility to Henneguya Ictaluri Infection by Two Species of Catfish and Their Hybrid Cross

    USDA-ARS?s Scientific Manuscript database

    Proliferative gill disease (PGD) in channel catfish Ictalurus punctatus is caused by the myxozoan parasite Henneguya ictaluri. There is no effective treatment for PGD, and mortalities can exceed 50% in severe outbreaks. One approach to controlling losses would be to utilize a less susceptible ictalu...

  11. Global gene expression in channel catfish after vaccination with an attenuated Edwardsiella ictaluri

    USDA-ARS?s Scientific Manuscript database

    To understand the global gene expression in channel catfish after immersion vaccination with an attenuated Edwardsiella ictaluri (AquaVac ESCTM), microarray analysis of 65,182 UniGene transcripts were performed. With a filter of false-discovery rate less than 0.05 and fold change greater than 2, a t...

  12. A Real-Time Polymerase Chain Reaction Assay for the Detection of the Myxozoan Parasite Henneguya Ictaluri in Channel Catfish

    USDA-ARS?s Scientific Manuscript database

    Proliferative gill disease (PGD), caused by the myxozoan parasite Henneguya ictaluri, is the most prevalent parasitic infection affecting commercial channel catfish (Ictalurus punctatus) aquaculture. There are currently no effective chemotherapeutic or biological control measures for PGD, which ofte...

  13. The Aspartate-Semialdehyde Dehydrogenase of Edwardsiella ictaluri and Its Use as Balanced-Lethal System in Fish Vaccinology

    PubMed Central

    Santander, Javier; Xin, Wei; Yang, Zhao; Curtiss, Roy

    2010-01-01

    asdA mutants of Gram-negative bacteria have an obligate requirement for diaminopimelic acid (DAP), which is an essential constituent of the peptidoglycan layer of the cell wall of these organisms. In environments deprived of DAP, i.e., animal tissues, they will undergo lysis. Deletion of the asdA gene has previously been exploited to develop antibiotic-sensitive strains of live attenuated recombinant bacterial vaccines. Introduction of an Asd+ plasmid into a ΔasdA mutant makes the bacterial strain plasmid-dependent. This dependence on the Asd+ plasmid vector creates a balanced-lethal complementation between the bacterial strain and the recombinant plasmid. E. ictaluri is an enteric Gram-negative fish pathogen that causes enteric septicemia in catfish. Because E. ictaluri is a nasal/oral invasive intracellular pathogen, this bacterium is a candidate to develop a bath/oral live recombinant attenuated Edwardsiella vaccine (RAEV) for the catfish aquaculture industry. As a first step to develop an antibiotic-sensitive RAEV strain, we characterized and deleted the E. ictaluri asdA gene. E. ictaluri ΔasdA01 mutants exhibit an absolute requirement for DAP to grow. The asdA gene of E. ictaluri was complemented by the asdA gene from Salmonella. Several Asd+ expression vectors with different origins of replication were transformed into E. ictaluri ΔasdA01. Asd+ vectors were compatible with the pEI1 and pEI2 E. ictaluri native plasmids. The balanced-lethal system was satisfactorily evaluated in vivo. Recombinant GFP, PspA, and LcrV proteins were synthesized by E. ictaluri ΔasdA01 harboring Asd+ plasmids. Here we constructed a balanced-lethal system, which is the first step to develop an antibiotic-sensitive RAEV for the aquaculture industry. PMID:21209920

  14. Fur-Regulated Iron Uptake System of Edwardsiella ictaluri and Its Influence on Pathogenesis and Immunogenicity in the Catfish Host

    PubMed Central

    Golden, Greg; Wanda, Soo-Young; Curtiss, Roy

    2012-01-01

    The ability of bacterial pathogens to take up iron from the host during infection is necessary for their multiplication within the host. However, host high-affinity iron binding proteins limit levels of free iron in fluids and tissues. To overcome this deficiency of iron during infection, bacterial pathogens have developed iron uptake systems that are upregulated in the absence of iron, typically tightly controlled by the ferric uptake regulator (Fur) protein. The iron uptake system of Edwardsiella ictaluri, a host-restricted pathogen of channel catfish (Ictalurus punctatus) and the main pathogen of this fish in aquaculture, is unknown. Here we describe the E. ictaluri Fur protein, the iron uptake machinery controlled by Fur, and the effects of fur gene deletion on virulence and immunogenicity in the fish host. Analysis of the E. ictaluri Fur protein shows that it lacks the N-terminal region found in the majority of pathogen-encoded Fur proteins. However, it is fully functional in regulated genes encoding iron uptake proteins. E. ictaluri grown under iron-limited conditions upregulates an outer membrane protein (HemR) that shows heme-hemoglobin transport activity and is tightly regulated by Fur. In vivo studies showed that an E. ictaluri Δfur mutant is attenuated and immune protective in zebrafish (Danio rerio) and catfish (Ictalurus punctatus), triggering systemic immunity. We conclude that an E. ictaluri Δfur mutant could be an effective component of an immersion-oral vaccine for the catfish industry. PMID:22615248

  15. Fur-regulated iron uptake system of Edwardsiella ictaluri and its influence on pathogenesis and immunogenicity in the catfish host.

    PubMed

    Santander, Javier; Golden, Greg; Wanda, Soo-Young; Curtiss, Roy

    2012-08-01

    The ability of bacterial pathogens to take up iron from the host during infection is necessary for their multiplication within the host. However, host high-affinity iron binding proteins limit levels of free iron in fluids and tissues. To overcome this deficiency of iron during infection, bacterial pathogens have developed iron uptake systems that are upregulated in the absence of iron, typically tightly controlled by the ferric uptake regulator (Fur) protein. The iron uptake system of Edwardsiella ictaluri, a host-restricted pathogen of channel catfish (Ictalurus punctatus) and the main pathogen of this fish in aquaculture, is unknown. Here we describe the E. ictaluri Fur protein, the iron uptake machinery controlled by Fur, and the effects of fur gene deletion on virulence and immunogenicity in the fish host. Analysis of the E. ictaluri Fur protein shows that it lacks the N-terminal region found in the majority of pathogen-encoded Fur proteins. However, it is fully functional in regulated genes encoding iron uptake proteins. E. ictaluri grown under iron-limited conditions upregulates an outer membrane protein (HemR) that shows heme-hemoglobin transport activity and is tightly regulated by Fur. In vivo studies showed that an E. ictaluri Δfur mutant is attenuated and immune protective in zebrafish (Danio rerio) and catfish (Ictalurus punctatus), triggering systemic immunity. We conclude that an E. ictaluri Δfur mutant could be an effective component of an immersion-oral vaccine for the catfish industry.

  16. Probiotics Affect Virulence-Related Gene Expression in Escherichia coli O157:H7▿

    PubMed Central

    Medellin-Peña, Maira Jessica; Wang, Haifeng; Johnson, Roger; Anand, Sanjeev; Griffiths, Mansel W.

    2007-01-01

    The attachment of enterohemorrhagic Escherichia coli O157:H7 (EHEC O157) to host intestinal epithelial cells is essential for the development of hemorrhagic colitis and hemolytic-uremic syndrome in humans. Genes involved in attachment are carried within a pathogenicity island named the locus of enterocyte effacement (LEE), known to be directly activated by quorum sensing (QS). In the present study, we investigated autoinducer-2 (AI-2) production and the expression of several virulence-related genes in EHEC O157 grown in the absence and presence of a Lactobacillus acidophilus-secreted molecule(s). Transcription of important EHEC O157 virulence-related genes was studied by constructing promoter-reporter fusions and reverse transcriptase PCR. Shiga toxin (Stx) production was assayed by an enzyme immunoassay. When EHEC O157 was grown in the presence of chromatographically selected fractions of L. acidophilus La-5 cell-free spent medium, we observed a significant reduction of both extracellular AI-2 concentration and the expression of important virulence-related genes, although no significant difference in Stx production was observed. We show here that L. acidophilus La-5 secretes a molecule(s) that either acts as a QS signal inhibitor or directly interacts with bacterial transcriptional regulators, controlling the transcription of EHEC O157 genes involved in colonization. PMID:17496132

  17. Development of a Defined Minimal Medium for the Growth of Edwardsiella ictaluri

    PubMed Central

    Collins, L. A.; Thune, R. L.

    1996-01-01

    In this report, a complete defined medium and a minimally defined medium are described for Edwardsiella ictaluri. The complete defined medium consists of 46 individual components, including a basal salt solution, glucose, magnesium sulfate, iron sulfate, six trace metals, four nucleotides, 10 vitamins, and 19 amino acids. This medium supports growth in broth and on solid media. Optimal growth at 30(deg)C was obtained at pH 7.0, and at an osmolality of 390 mosmol/kg of H(inf2)O, with a glucose concentration of 4 g/liter. The defined minimal medium reduces the 46 components of the complete medium to eight essential components, including the basal salt solution, glucose, magnesium sulfate, pantothenic acid, and niacinamide. In addition, specific amino acids that depend on the specific requirements of the individual strains of E. ictaluri are added. PMID:16535274

  18. Benign Rabbit Caliciviruses Exhibit Evolutionary Dynamics Similar to Those of Their Virulent Relatives

    PubMed Central

    Mahar, Jackie E.; Nicholson, Leila; Eden, John-Sebastian; Duchêne, Sebastián; Kerr, Peter J.; Duckworth, Janine; Ward, Vernon K.; Holmes, Edward C.

    2016-01-01

    ABSTRACT Two closely related caliciviruses cocirculate in Australia: rabbit hemorrhagic disease virus (RHDV) and rabbit calicivirus Australia 1 (RCV-A1). RCV-A1 causes benign enteric infections in the European rabbit (Oryctolagus cuniculus) in Australia and New Zealand, while its close relative RHDV causes a highly pathogenic infection of the liver in the same host. The comparison of these viruses provides important information on the nature and trajectory of virulence evolution, particularly as highly virulent strains of RHDV may have evolved from nonpathogenic ancestors such as RCV-A1. To determine the evolution of RCV-A1 we sequenced the full-length genomes of 44 RCV-A1 samples isolated from healthy rabbits and compared key evolutionary parameters to those of its virulent relative, RHDV. Despite their marked differences in pathogenicity and tissue tropism, RCV-A1 and RHDV have evolved in a very similar manner. Both viruses have evolved at broadly similar rates, suggesting that their dynamics are largely shaped by high background mutation rates, and both exhibit occasional recombination and an evolutionary environment dominated by purifying selection. In addition, our comparative analysis revealed that there have been multiple changes in both virulence and tissue tropism in the evolutionary history of these and related viruses. Finally, these new genomic data suggest that either RCV-A1 was introduced into Australia after the introduction of myxoma virus as a biocontrol agent in 1950 or there was drastic reduction of the rabbit population, and hence of RCV-A1 genetic diversity, perhaps coincident with the emergence of myxoma virus. IMPORTANCE The comparison of closely related viruses that differ profoundly in propensity to cause disease in their hosts offers a powerful opportunity to reveal the causes of changes in virulence and to study how such changes alter the evolutionary dynamics of these pathogens. Here we describe such a novel comparison involving two

  19. Effects of GH on immune and endocrine responses of channel catfish challenged with Edwardsiella ictaluri.

    PubMed

    Peterson, Brian C; Small, Brian C; Bilodeau, Lanie

    2007-01-01

    The effects of GH on immune and endocrine responses to channel catfish challenged with the bacterium Edwardsiella ictaluri were examined. Catfish (11.7+/-1.0 g) treated with recombinant bovine growth hormone (rbGH) and challenged with E. ictaluri experienced similar mortality as control-exposed fish. Plasma activity of lysozyme was higher (P<0.01) in rbGH-exposed fish. Compared to day 0 controls (non-exposed fish), IGF-I levels decreased (P<0.05) in challenged fish while levels were similar (P>0.10) between treatments. Abundance of GH receptor (GHR) mRNA tended to decrease (P=0.055) in liver of challenged fish while toll like receptor 5 (TLR5) mRNA increased (P<0.05) in liver compared to d 0 controls. An increase in lysozyme may suggest GH enhances a nonspecific immune response. A decrease in GHR mRNA and plasma IGF-I suggests a downregulation of the somatotropic axis in response to disease. The increase in TLR5 mRNA suggests that TLR5 may play a role in host response to bacterial challenge. While exogenous rbGH may play a stimulatory role to increase lysozyme levels, there was no apparent effect of rbGH on mortality to E. ictaluri.

  20. Effects of a phytogenic feed additive on growth and susceptibility of channel catfish to Edwardsiella ictaluri and levels of mannose and rhamnose binding lectin

    USDA-ARS?s Scientific Manuscript database

    A study was conducted to investigate the effect of essential oils (EO) on growth and disease susceptibility to Edwardsiella ictaluri. Weight gain and food conversion ratio were similar. After exposing fish to virulent E. ictaluri, survival was higher (69.5 vs 48.4%) in fish fed EO (P < 0.05). In ...

  1. Effect of multiple mutations in tricarboxylic acid cycle and one-carbon metabolism pathways on Edwardsiella ictaluri pathogenesis.

    PubMed

    Dahal, N; Abdelhamed, H; Lu, J; Karsi, A; Lawrence, M L

    2014-02-21

    Edwardsiella ictaluri is a Gram-negative facultative intracellular pathogen causing enteric septicemia of catfish (ESC). We have shown recently that tricarboxylic acid cycle (TCA) and one-carbon (C1) metabolism are involved in E. ictaluri pathogenesis. However, the effect of multiple mutations in these pathways is unknown. Here, we report four novel E. ictaluri mutants carrying double gene mutations in TCA cycle (EiΔmdhΔsdhC, EiΔfrdAΔsdhC), C1 metabolism (EiΔglyAΔgcvP), and both TCA and C1 metabolism pathways (EiΔgcvPΔsdhC). In-frame gene deletions were constructed by allelic exchange and mutants' virulence and vaccine efficacy were evaluated using in vivo bioluminescence imaging (BLI) as well as end point mortality counts in catfish fingerlings. Results indicated that all the double gene mutants were attenuated compared to wild-type (wt) E. ictaluri. There was a 1.39-fold average reduction in bioluminescence, and hence bacterial numbers, from all the mutants except for EiΔfrdAΔsdhC at 144 h post-infection. Vaccination with mutants was very effective in protecting channel catfish against subsequent infection with virulent E. ictaluri 93-146 strain. In particular, immersion vaccination resulted in complete protection. Our results provide further evidence on the importance of TCA and C1 metabolism pathways in bacterial pathogenesis.

  2. Identification of novel virulence-related genes in Aeromonas hydrophila by screening transposon mutants in a Tetrahymena infection model.

    PubMed

    Pang, Maoda; Xie, Xing; Dong, Yuhao; Du, Hechao; Wang, Nannan; Lu, Chengping; Liu, Yongjie

    2017-02-01

    Outbreaks of motile Aeromonad septicemia (MAS) in fish caused by sequence type (ST) 251 Aeromonas hydrophila have become a prominent problem for the aquaculture industry. The pathogenesis of A. hydrophila is very complicated, and some virulence factors remain to be identified. In this study, to identify novel virulence-related factors, ST251 A. hydrophila strain NJ-35 was used as the parental strain to construct a mutant library comprising 1030 mutant strains by transposon insertion mutagenesis. Subsequently, 33 virulence-attenuated transposon insertion mutants were identified using Tetrahymena and zebrafish as model hosts in sequence. Thermal asymmetric interlaced (Tail)-PCR and Southern blot analysis identified 21 single transposon insertion sites. Seven of the insertion sites are located in non-coding regions, whereas the other 14 insertion sites are located in genes, including aroA, rmlA, rtxA, chiA and plc. All insertion mutants exhibited attenuated virulence in Tetrahymena and zebrafish. Furthermore, the relationship of two genes, chiA and trkH, to virulence was confirmed by gene inactivation and subsequent restoration assays. This study provides new information about the genetic determinants of A. hydrophila pathogenicity and validates the Aeromonas-Tetrahymena co-culture model for high-throughput screening of A. hydrophila virulence factors. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Early interactions of Edwardsiella ictaluri, with Pangasianodon catfish and its invasive ability in cell lines.

    PubMed

    Dung, T T; Chiers, K; Tuan, N A; Sorgeloos, P; Haesebrouck, F; Decostere, A

    2012-06-01

    Commercial Pangasianodon catfish production is heavily impacted by Bacillary Necrosis of Pangasius (BNP) caused by Edwardsiella ictaluri. This study aimed to investigate the early bacterium-host interactions following immersion challenge and to compare the retrieved data with the invasion ability of the used isolates in fish cell lines. Firstly, Pangasianodon hypophthalmus fingerlings were challenged via immersion using E. ictaluri isolate HO2 or 223. At different times post inoculation, fish were sacrificed and gill and internal organ samples were taken for bacteriological, histological and immunohistochemical evaluation. The bacterial load was higher for fish inoculated with isolate HO2 compared with 223. Histological and immunohistochemical analysis revealed multifocal necrotic areas in kidney, spleen and liver of HO2 inoculated fish at 72 h post inoculation with short rod-shaped immunoperoxidase positive bacteria clustered inside cells respectively. Bacteria especially were present in the gills and intestinal tract of HO2 inoculated fish, suggesting the gastrointestinal tract and gills act as portals of entry. Following, the ability of HO2, 223 and four additional isolates to invade a Chinook salmon embryo cell line, a fat head minnow cell line and a rainbow trout liver cell line was tested. All E. ictaluri isolates were invasive in all cell lines albeit at different degrees. Isolate HO2 was highly invasive in all cell lines with a significantly higher invasion capacity than isolate 223 in the Chinook salmon embryo cell line. A correlation between in vivo virulence and in vitro invasiveness hence is suggested although further studies are needed to confirm this hypothesis.

  4. Microevolution of Virulence-Related Genes in Helicobacter pylori Familial Infection

    PubMed Central

    Furuta, Yoshikazu; Konno, Mutsuko; Osaki, Takako; Yonezawa, Hideo; Ishige, Taichiro; Imai, Misaki; Shiwa, Yuh; Shibata-Hatta, Mari; Kanesaki, Yu; Yoshikawa, Hirofumi; Kamiya, Shigeru; Kobayashi, Ichizo

    2015-01-01

    Helicobacter pylori, a bacterial pathogen that can infect human stomach causing gastritis, ulcers and cancer, is known to have a high degree of genome/epigenome diversity as the result of mutation and recombination. The bacteria often infect in childhood and persist for the life of the host. One of the reasons of the rapid evolution of H. pylori is that it changes its genome drastically for adaptation to a new host. To investigate microevolution and adaptation of the H. pylori genome, we undertook whole genome sequencing of the same or very similar sequence type in multi-locus sequence typing (MLST) with seven genes in members of the same family consisting of parents and children in Japan. Detection of nucleotide substitutions revealed likely transmission pathways involving children. Nonsynonymous (amino acid changing) mutations were found in virulence-related genes (cag genes, vacA, hcpDX, tnfα, ggt, htrA and the collagenase gene), outer membrane protein (OMP) genes and other cell surface-related protein genes, signal transduction genes and restriction-modification genes. We reconstructed various pathways by which H. pylori can adapt to a new human host, and our results raised the possibility that the mutational changes in virulence-related genes have a role in adaptation to a child host. Changes in restriction-modification genes might remodel the methylome and transcriptome to help adaptation. This study has provided insights into H. pylori transmission and virulence and has implications for basic research as well as clinical practice. PMID:25978460

  5. Roles for mannose binding lectin and rhamnose binding lectin in channel catfish fed essential oils and challenged with Edwardsiella ictaluri

    USDA-ARS?s Scientific Manuscript database

    A major problem in the catfish farming industry has been high disease loss to enteric septicemia of catfish (ESC), caused by the bacterium Edwardsiella ictaluri. Methods to control this disease include vaccination, antibiotic therapy, and restricted feeding. Another method that has been examined i...

  6. Complete genome sequence of Edwardsiella ictaluri isolate RUSVM-1 recovered from nile tilapia (Oreochromis niloticus) in the Western Hemisphere

    USDA-ARS?s Scientific Manuscript database

    Edwardsiella ictaluri is a Gram-negative, bacillus that has recently been implicated in disease outbreaks in tilapia and zebrafish. We report here the complete and annotated genome of an isolate from a Nile Tilapia (Oreochromis niloticus), which contains a chromosome of 3,630,639 bp and two plasmids...

  7. Changes of serum myeloperoxidase and nitric oxide in the early stage of Edwardsiella ictaluri infection in channel catfish, Ictalurus punctatus

    USDA-ARS?s Scientific Manuscript database

    Enteric septicemia of catfish (ESC), caused by Edwardsiella ictaluri, is an important farm-raised channel catfish, Ictalurus punctatus (Rafinesque), disease. The development of a monitoring system for assessing the catfish health status in hatcheries and ponds is in great demanding. Because of the...

  8. Feeding Lactobacillus spp. and Bacillus spp. Does Not Improve Growth or Survival of Channel Catfish Experimentally Challenged with Edwardsiella ictaluri

    USDA-ARS?s Scientific Manuscript database

    A major problem in the channel catfish industry has been high disease loss to enteric septicemia of catfish, caused by the bacterium Edwardsiella ictaluri. Feeding probiotics may prove beneficial in improving disease resistance. The first study examined the effects of a Lactobacillus probiotic (Flor...

  9. Binding and Phagocytosis by Opsonized and Nonopsonized Channel Catfish Macrophages of Viable DsRed-fluorescent-labeled Edwardsiella ictaluri

    USDA-ARS?s Scientific Manuscript database

    Phagocyte-mediated killing of bacterial pathogens is one of the major defensive mechanisms in fish. The binding, uptake and destruction of recombinant fluorescent protein DsRed transformed Edwardsiella ictaluri by opsonized and nonopsonized channel catfish (Ictalurus punctatus) macrophages was chara...

  10. NRAMP, TNF, TLR5, and Hepcidin Expression in Resistant and Susceptible Families of Channel Catfish Following Challenge With E. ictaluri

    USDA-ARS?s Scientific Manuscript database

    Real-time PCR was used to measure gene expression of Nramp, TNF, TLR5, and Hepcidin, in spleen and liver tissue from two families of channel catfish, one resistant and one susceptible to ESC, following challenge with Edwardsiella ictaluri. There were no significant differences in relative copy numbe...

  11. Application of A Real-Time PCR Assay for The Detection of Henneguya ictaluri In Commercial Channel Catfish Ponds

    USDA-ARS?s Scientific Manuscript database

    Proliferative gill disease (PGD) in channel catfish Ictalurus punctatus is caused by the myxozoan parasite Henneguya ictaluri. Prolonged exposure of channel catfish to the actinospore stage of the parasite results in extensive gill damage, leading to reduced production and significant mortality in ...

  12. Effects of a phytogenic feed additive on susceptibility of channel catfish to Edwardsiella ictaluri and levels of mannose binding lectin

    USDA-ARS?s Scientific Manuscript database

    A study was conducted to investigate the effect of a phytogenic feed additive (Digestarom® P.E.P. MGE) on growth performance and disease susceptibility to Edwardsiella ictaluri. Two hundred and fifty juvenile channel catfish (7.2 ± 0.1 g) were allotted into the following treatments: Control (float...

  13. Identification and characterization of an intervening sequence within the 23S ribosomal RNA genes of Edwardsiella ictaluri

    USDA-ARS?s Scientific Manuscript database

    Comparison of the 23S rRNA gene sequences of Edwardsiella tarda and Edwardsiella ictaluri confirmed a close phylogenetic relationship between these two fish pathogen species and a distant relation with the 'core' members of the Enterobacteriaceae family. Analysis of the rrl gene for 23S rRNA in E. i...

  14. Oral vaccination of channel catfish against enteric septicemia of catfish (ESC) using a live attenuated Edwardsiella ictaluri isolate

    USDA-ARS?s Scientific Manuscript database

    Enteric septicemia of catfish (ESC), caused by Edwardsiella ictaluri, is the most problematic bacterial disease affecting catfish aquaculture in the southeastern United States. Efforts to develop an effective ESC vaccine have had limited industrial success. In commercial settings, ESC vaccines are t...

  15. Oral vaccination of channel catfish against enteric septicemia of catfish using a live attenuated Edwardsiella ictaluri isolate

    USDA-ARS?s Scientific Manuscript database

    Enteric septicemia of catfish (ESC), caused by Edwardsiella ictaluri, is the most problematic bacterial disease affecting catfish aquaculture in the southeastern United States. Efforts to develop an effective ESC vaccine have had limited industrial success. In commercial settings, ESC vaccines are...

  16. Can immunostimulants efficiently replace antibiotic in striped catfish (Pangasianodon hypophthalmus) against bacterial infection by Edwardsiella ictaluri?

    PubMed

    Bich Hang, Bui Thi; Phuong, Nguyen Thanh; Kestemont, Patrick

    2014-10-01

    The present study was performed to determine the efficacy of lipopolysaccharide (LPS) and levamisole on immune response and disease resistance in striped catfish and to compare their respective efficiency with the one of an antibiotic treatment after infection of fish by the bacteria Edwardsiella ictaluri. Fish were divided into 3 groups and each group was injected with LPS (3 mg/kg fish), levamisole (5 mg/kg fish) or phosphate buffer saline as control. At day 21st post immunostimulant injection, fish were bled for assaying immunological variables and then challenged with E. ictaluri. Three days after bacterial infection, an antibiotic treatment was applied into fish subgroups and mortality was compared daily between antibiotic treated and untreated fish until 2 weeks post-challenge. LPS and levamisole significantly enhanced non-specific immune responses such as respiratory burst, lysozyme and complement activity in fish compared with control (p < 0.05). Respiratory burst and complement activity significantly increased in levamisole groups when compared with LPS groups while lysozyme activity did not differ significantly between immunostimulant treatments. Total immunoglobulins significantly increased in levamisole treatment compared with control. After challenge test, accumulated mortality was reduced significantly in both non-antibiotic and antibiotic subgroups of LPS and levamisole compared with control. Moreover, no differences of mortality were observed between fish treated with levamisole or LPS without antibiotics and control fish treated with antibiotics. These results support the possible replacement of antibiotics in striped catfish farming by immunostimulants such as levamisole and LPS.

  17. Mechanisms of intrinsic resistance to antimicrobial peptides of Edwardsiella ictaluri and its influence on fish gut inflammation and virulence

    PubMed Central

    Martin, Taylor; Loh, Amanda; Pohlenz, Camilo; Gatlin, Delbert M.; Curtiss, Roy

    2013-01-01

    The genus Edwardsiella comprises a genetically distinct taxon related to other members of the family Enterobacteriaceae. It consists of bacteria differing strongly in their biochemical and physiological features, natural habitats, and pathogenic properties. Intrinsic resistance to cationic antimicrobial peptides (CAMPs) is a specific property of the genus Edwardsiella. In particular, Edwardsiella ictaluri, an important pathogen of the catfish (Ictalurus punctatus) aquaculture and the causative agent of a fatal systemic infection, is highly resistant to CAMPs. E. ictaluri mechanisms of resistance to CAMPs are unknown. We hypothesized that E. ictaluri lipopolysaccharide (LPS) plays a role in both virulence and resistance to CAMPs. The putative genes related to LPS oligo-polysaccharide (O-PS) synthesis were in-frame deleted. Individual deletions of wibT, gne and ugd eliminated synthesis of the O-PS, causing auto-agglutination, rough colonies, biofilm-like formation and motility defects. Deletion of ugd, the gene that encodes the UDP-glucose dehydrogenase enzyme responsible for synthesis of UDP-glucuronic acid, causes sensitivity to CAMPs, indicating that UDP-glucuronic acid and its derivatives are related to CAMP intrinsic resistance. E. ictaluri OP-S mutants showed different levels of attenuation, colonization of lymphoid tissues and immune protection in zebrafish (Danio rerio) and catfish. Orally inoculated catfish with O-PS mutant strains presented different degrees of gut inflammation and colonization of lymphoid tissues. Here we conclude that intrinsic resistance to CAMPs is mediated by Ugd enzyme, which has a pleiotropic effect in E. ictaluri influencing LPS synthesis, motility, agglutination, fish gut inflammation and virulence. PMID:23676433

  18. Lack of the Delta Subunit of RNA Polymerase Increases Virulence Related Traits of Streptococcus mutans

    PubMed Central

    Xue, Xiaoli; Sztajer, Helena; Buddruhs, Nora; Petersen, Jörn; Rohde, Manfred; Talay, Susanne R.; Wagner-Döbler, Irene

    2011-01-01

    The delta subunit of the RNA polymerase, RpoE, maintains the transcriptional specificity in Gram-positive bacteria. Lack of RpoE results in massive changes in the transcriptome of the human dental caries pathogen Streptococcus mutans. In this study, we analyzed traits of the ΔrpoE mutant which are important for biofilm formation and interaction with oral microorganisms and human cells and performed a global phenotypic analysis of its physiological functions. The ΔrpoE mutant showed higher self-aggregation compared to the wild type and coaggregated with other oral bacteria and Candida albicans. It formed a biofilm with a different matrix structure and an altered surface attachment. The amount of the cell surface antigens I/II SpaP and the glucosyltransferase GtfB was reduced. The ΔrpoE mutant displayed significantly stronger adhesion to human extracellular matrix components, especially to fibronectin, than the wild type. Its adhesion to human epithelial cells HEp-2 was reduced, probably due to the highly aggregated cell mass. The analysis of 1248 physiological traits using phenotype microarrays showed that the ΔrpoE mutant metabolized a wider spectrum of carbon sources than the wild type and had acquired resistance to antibiotics and inhibitory compounds with various modes of action. The reduced antigenicity, increased aggregation, adherence to fibronection, broader substrate spectrum and increased resistance to antibiotics of the ΔrpoE mutant reveal the physiological potential of S. mutans and show that some of its virulence related traits are increased. PMID:21625504

  19. Expression of Streptococcus pneumoniae Virulence-Related Genes in the Nasopharynx of Healthy Children.

    PubMed

    Sakai, Fuminori; Talekar, Sharmila J; Lanata, Claudio F; Grijalva, Carlos G; Klugman, Keith P; Vidal, Jorge E

    2013-01-01

    Colonization and persistence in the human nasopharynx are prerequisites for Streptococcus pneumoniae disease and carriage acquisition, which normally occurs during early childhood. Animal models and in vitro studies (i.e. cell adhesion and cell cytotoxicity assays) have revealed a number of colonization and virulence factors, as well as regulators, implicated in nasopharyngeal colonization and pathogenesis. Expression of genes encoding these factors has never been studied in the human nasopharynx. Therefore, this study analyzed expression of S. pneumoniae virulence-related genes in human nasopharyngeal samples. Our experiments first demonstrate that a density of ≥10(4) CFU/ml of S. pneumoniae cells in the nasopharynx provides enough DNA and RNA to amplify the lytA gene by conventional PCR and to detect the lytA message, respectively. A panel of 21 primers that amplified S. pneumoniae sequences was designed, and their specificity for S. pneumoniae sequences was analyzed in silico and validated against 20 related strains inhabitants of the human upper respiratory tract. These primers were utilized in molecular reactions to find out that all samples contained the genes ply, pavA, lytC, lytA, comD, codY, and mgrA, whereas nanA, nanB, pspA, and rrgB were present in ∼91-98% of the samples. Gene expression studies of these 11 targets revealed that lytC, lytA, pavA and comD were the most highly expressed pneumococcal genes in the nasopharynx whereas the rest showed a moderate to low level of expression. This is the first study to evaluate expression of virulence- and, colonization-related genes in the nasopharynx of healthy children and establishes the foundation for future gene expression studies during human pneumococcal disease.

  20. Combined immersion and oral vaccination of Vietnamese catfish (Pangasianodon hypophthalmus) confers protection against mortality caused by Edwardsiella ictaluri.

    PubMed

    Thinh, N H; Kuo, T Y; Hung, L T; Loc, T H; Chen, S C; Evensen, O; Schuurman, H J

    2009-12-01

    Edwardsiella ictaluri septicemia occurs worldwide and causes high mortality and considerable economic damage to the catfish industry especially in Vietnam and the USA. To control Edwardsiella septicemia farmers extensively use antibiotics and various vaccination methods. Vaccination with inactivated vaccines has come with variable efficacy. In this trial the results of an approach of controlling Edwardsiella septicemia of Tra catfish (Pangasianodon hypophthalmus) in Vietnam through vaccination via mucosal surfaces are presented. The results show that a combination of primary vaccination by immersion with inactivated E. ictaluri followed by an oral boost with a formulated antigen preparation induces a statistically significant level of protection against mortality caused by experimental infection 4 weeks post-boost. Fish immunized by immersion only show significantly lower level of protection but significantly higher than the controls. Repeated boosts result in improved duration of immunity with a relative percent survival (RPS) of 47% at 90% control mortality. The immunization procedure provides an alternative for disease control through vaccination.

  1. The effects of feeding β-glucan to Pangasianodon hypophthalmus on immune gene expression and resistance to Edwardsiella ictaluri.

    PubMed

    Sirimanapong, Wanna; Thompson, Kim D; Ooi, Ei Lin; Bekaert, Michaël; Collet, Bertrand; Taggart, John B; Bron, James E; Green, Darren M; Shinn, Andrew P; Adams, Alexandra; Leaver, Michael J

    2015-11-01

    Pangasianodon hypophthalmus (striped catfish) is an important aquaculture species and intensification of farming has increased disease problems, particularly Edwardsiella ictaluri. The effects of feeding β-glucans on immune gene expression and resistance to E. ictaluri in P. hypophthalmus were explored. Fish were fed 0.1% fungal-derived β-glucan or 0.1% commercial yeast-derived β-glucan or a basal control diet without glucan. After 14 days of feeding, the mRNA expression of immune genes (transferrin, C-reactive protein, precerebellin-like protein, Complement C3 and factor B, 2a MHC class II and interleukin-1 beta) in liver, kidney and spleen were determined. Following this fish from each of the three diet treatment groups were infected with E. ictaluri and further gene expression measured 24 h post-infection (h.p.i.), while the remaining fish were monitored over 2 weeks for mortalities. Cumulative percentage mortality at 14 days post-infection (d.p.i.) was less in β-glucan fed fish compared to controls. There was no difference in gene expression between dietary groups after feeding for 14 days, but there was a clear difference between infected and uninfected fish at 24 h.p.i., and based on principal component analysis β-glucans stimulated the overall expression of immune genes in the liver, kidney and spleen at 24 h.p.i. Copyright © 2015 Elsevier Ltd. All rights reserved.

  2. Tissue persistence and vaccine efficacy of tricarboxylic acid cycle and one-carbon metabolism mutant strains of Edwardsiella ictaluri.

    PubMed

    Dahal, Neeti; Abdelhamed, Hossam; Karsi, Attila; Lawrence, Mark L

    2014-06-30

    Edwardsiella ictaluri causes enteric septicemia in fish. Recently, we reported construction of E. ictaluri mutants with single and double gene deletions in tricarboxylic acid cycle (TCA) and one-carbon (C-1) metabolism. Here, we report the tissue persistence, virulence, and vaccine efficacy of TCA cycle (EiΔsdhC, EiΔfrdA, and EiΔmdh), C-1 metabolism (EiΔgcvP and EiΔglyA), and combination mutants (EiΔfrdAΔsdhC, EiΔgcvPΔsdhC, EiΔmdhΔsdhC, and EiΔgcvPΔglyA) in channel catfish. The tissue persistence study showed that EiΔsdhC, EiΔfrdA, EiΔfrdAΔsdhC, and EiΔgcvPΔsdhC were able to invade catfish and persist until 11 days post-infection. Vaccination of catfish fingerlings with all nine mutants provided significant (P<0.05) protection against subsequent challenge with the virulent parental strain. Vaccinated catfish fingerlings had 100% survival when subsequently challenged by immersion with wild-type E. ictaluri except for EiΔgcvPΔglyA and EiΔgcvP. Mutant EiΔgcvPΔsdhC was found to be very good at protecting catfish fry, as evidenced by 10-fold higher survival compared to non-vaccinated fish.

  3. The two channel catfish intelectin genes exhibit highly differential patterns of tissue expression and regulation after infection with Edwardsiella ictaluri.

    PubMed

    Takano, Tomokazu; Sha, Zhenxia; Peatman, Eric; Terhune, Jeffery; Liu, Hong; Kucuktas, Huseyin; Li, Ping; Edholm, Eva-Stina; Wilson, Melanie; Liu, Zhanjiang

    2008-01-01

    Intelectins (IntL) are Ca(2+)-dependent secretory glycoproteins that play a role in the innate immune response. The mammalian IntL is also known as lactoferrin receptor (LfR) that is involved in iron metabolism. The objective of this study was to characterize the intelectin genes in both channel catfish and blue catfish, to determine their genomic organization and copy numbers, to determine their patterns of tissue expression, and to establish if they are involved in defense responses of catfish after bacterial infection. Two types of IntL genes have been identified from catfish, and IntL2 was completely sequenced. The genomic structure and organization of IntL2 were similar to those of the mammalian species and of zebrafish and grass carp, but orthologies cannot be established with mammalian IntL genes. The IntL genes are highly conserved through evolution. Sequence analysis also indicated the presence of the fibrinogen-related domain in the catfish IntL genes, suggesting their structural conservations. Phylogenetic analysis suggested the presence of at least two prototypes of IntL genes in teleosts, but only one in mammals. The catfish IntL genes exhibited drastically different patterns of expression as compared to those of the mammalian species, or even with the grass carp gene. The catfish IntL1 gene is widely expressed in various tissues, whereas the channel catfish IntL2 gene was mainly expressed in the liver. While the catfish IntL1 is constitutively expressed, the catfish IntL2 was drastically induced by intraperitoneal injection of Edwardsiella ictaluri and/or iron dextran. Such induction was most dramatic when the fish were treated with both the bacteria and iron dextran. While IntL1 was expressed in all leukocyte cell lines, no expression of IntL2 was detected in any of the leukocyte cell lines, suggesting that the up-regulated channel catfish IntL2 expression after bacterial infection may be a consequence of the initial immune response, and/or a

  4. Efficacy of Florfenicol for Control of Mortality Associated with Edwardsiella ictaluri in Three Species of Catfish.

    PubMed

    Gaunt, Patricia S; Chatakondi, Nagaraj; Gao, Dana; Endris, Richard

    2015-03-01

    The efficacy of florfenicol for control of mortality associated with Edwardsiella icatluri was studied in fingerlings of Channel Catfish Ictalurus puntatus (Delta strain), Blue Catfish I. furcatus (D&B strain), and a hybrid catfish (Delta strain Channel Catfish × D&B strain Blue Catfish). On day 0, fish were immersion challenged in 65-L aquaria. For each of the three species of catfish, 10 aquaria were randomly assigned to two treatment groups, either treated with florfenicol at 0 mg/kg of body weight (unmedicated feed) or at 10 mg/kg (medicated feed). Fish were treated for 10 consecutive days, monitored for mortality during this treatment period, and observed for 14 d afterwards. Post observation, all survivors were humanely euthanized in tricaine methanesulfonate, cultured for E. ictaluri, and examined for gross pathology. The mean cumulative percent mortality from enteric septicemia of catfish (ESC) challenge among the three genotypes of catfish did not differ between Blue Catfish, hybrid, and Channel Catfish in treated or control groups. However, the florfenicol-treated fish had a significantly lower mean cumulative mortality (6%) than the controls (78%). All genotypes of catfish tested were responsive to treatment with florfenicol-medicated feed for control of mortality associated with ESC. There were no significant differences in mortality associated with hybrid catfish, blue catfish, and Channel Catfish (Delta strain).

  5. Effects of cortisol and stress on channel catfish (Ictalurus punctatus) pathogen susceptibility and lysozyme activity following exposure to Edwardsiella ictaluri.

    PubMed

    Small, Brian C; Bilodeau, A Lelania

    2005-05-15

    Periods of stress are often associated with disease outbreaks in cultured fish, and stress is often characterized by the secretion of cortisol. Although stress and cortisol secretion are highly correlated in fish, the role of cortisol in affecting channel catfish (Ictalurus punctatus) pathogen susceptibility is unclear. The effects of short-term stress and exogenous cortisol administration on channel catfish susceptibility to Edwardsiella ictaluri, the etiologic agent of enteric septicemia of catfish (ESC), were investigated. Channel catfish were exposed to virulent E. ictaluri following a standardized 30-min low-water stress or administration of dietary cortisol (100 mg/kg feed) and compared to a pathogen-challenged control group of catfish. Pathogen susceptibility increased in stressed catfish (43.3% mortality) when compared to cortisol-fed catfish (26.7%) and controls (26.7%). A greater (P<0.05) percentage of stressed catfish (25.9%) tested positive for E. ictaluri relative to cortisol-fed catfish (13.0%) over the course of the study, however, average levels of circulating bacteria were not different (P>0.05) among the treatments. Catfish challenged by the low-water stress event had elevated (P<0.05) circulating levels of cortisol 1-day post-pathogen exposure and elevated (P<0.05) lysozyme activity 4 and 14 days post-pathogen exposure when compared to cortisol-fed and control-challenged catfish. Cortisol concentrations were not correlated (P>0.05) to either lysozyme activity or bacterial levels; however, lysozyme activity was positively correlated (P=0.0197) to blood bacterial concentrations. These results implicate other stress factors or pathways, separate from or possibly in conjunction with cortisol, in the stress-associated immunosuppression of channel catfish as it relates to ESC susceptibility.

  6. Evaluation of a loop-mediated isothermal amplification method for rapid detection of channel catfish Ictalurus punctatus important bacterial pathogen Edwardsiella ictaluri.

    USDA-ARS?s Scientific Manuscript database

    Channel catfish Ictalurus punctatus infected with Edwardsiella ictaluri results in $40 - 50 million annual losses in profits to catfish producers. Early detection of this pathogen is necessary for disease control and reduction of economic loss. In this communication, the loop-mediated isothermal a...

  7. Growth Performance and Resistance to Edwardsiella ictaluri of Channel Catfish (Ictalurus punctatus)Fed Diets Containing Distiller's Dried Grains with Solubles

    USDA-ARS?s Scientific Manuscript database

    A study was conducted to examine the effect of dietary levels of distiller’s dried grains with solubles (DDGS) on growth, body composition, hematology, immune response and resistance of channel catfish, Ictalurus punctatus, to Edwardsiella ictaluri challenge. Five diets containing 0, 10, 20, 30 and ...

  8. Evaluation of a loop-mediated isothermal amplification method for rapid detection of channel catfish Ictalurus punctatus important bacterial pathogen Edwardsiella ictaluri.

    PubMed

    Yeh, Hung-Yueh; Shoemaker, Craig A; Klesius, Phillip H

    2005-10-01

    Channel catfish Ictalurus punctatus infected with Edwardsiella ictaluri results in 40--50 million dollars annual losses in profits to catfish producers. Early detection of this pathogen is necessary for disease control and reduction of economic loss. In this communication, the loop-mediated isothermal amplification method (LAMP) that amplifies DNA with high specificity and rapidity at an isothermal condition was evaluated for rapid detection of E. ictaluri. A set of four primers, two outer and two inner, was designed specifically to recognize the eip 18 gene of this pathogen. The LAMP reaction mix was optimized. Reaction temperature and time of the LAMP assay for the eip 18 gene were also optimized at 65 degrees C for 60 min, respectively. Our results show that the ladder-like pattern of bands sizes from 234 bp specifically to the E. ictaluri gene was amplified. The detection limit of this LAMP assay was about 20 colony forming units. In addition, this optimized LAMP assay was used to detect the E. ictaluri eip 18 gene in brains of experimentally challenged channel catfish. Thus, we concluded that the LAMP assay can potentially be used for rapid diagnosis in hatcheries and ponds.

  9. Vaccination of full-sib channel catfish families against enteric septicemia of catfish with an oral live attenuated Edwardsiella ictaluri vaccine

    USDA-ARS?s Scientific Manuscript database

    The study evaluated the efficacy of an oral live-attenuated Edwardsiella ictaluri vaccine against enteric septicemia of catfish in 20 full-sib fingerling channel catfish families. Each family was split into vaccinated and non-vaccinated groups. The vaccine was delivered orally by feeding fish diet...

  10. TLR5, NRAMP, TNF, AND Hepcidin Response to Challenge with Edwardsiella ictaluri in Channel Catfish Families with High and Low Susceptibility to Infection

    USDA-ARS?s Scientific Manuscript database

    Responses of toll-like receptor 5 (TLR5), tumor necrosis factor (TNF), natural resistance-associated macrophage protein (Nramp), and hepcidin to experimental challenge with Edwardsiella ictaluri in two families of channel catfish were measured in order to understand the mechanisms through which E. i...

  11. Identification of in vitro upregulated genes in a modified live vaccine strain of Edwardsiella ictaluri compared to a virulent parent strain

    USDA-ARS?s Scientific Manuscript database

    Using PCR-select subtractive cDNA hybridization technique, 41 expressed sequence tags (ESTs) were isolated from a modified live vaccine strain (AQUAVAC-ESC©, formerly RE-33) vs a virulent parent strain (EILO) of Edwardsiella ictaluri. Transcriptional levels of the 41 ESTs in the vaccine strain and t...

  12. Identification of upregulated genes in a modified live vaccine strain of Edwardsiella ictaluri compared to a virulent parent strain and characterization of novel DNA vaccine candidates

    USDA-ARS?s Scientific Manuscript database

    Using PCR-select subtractive cDNA hybridization technique, 41 expressed sequence tags (EST's) were isolated from a modified live vaccine strain (AQUAVAC-ESC formerly RD-33) vs a virulent parent strain (EILO) of Edwardsiella ictaluri. Transcriptional levels of the 41 ESTs in the vaccine strain and th...

  13. Is there a genetic correlation between the resistance of channel catfish to Edwardsiella ictaluri and Flavobacterium columnare, and how do we get there?

    USDA-ARS?s Scientific Manuscript database

    Two major problems in the channel catfish (Ictalurus punctatus) aquaculture industry have been high disease losses to enteric septicemia of catfish (ESC), caused by Edwardsiella ictaluri and columnaris disease, caused by Flavobacterium columnare. Methods to control and prevent these diseases includ...

  14. A real time polymerase chain reaction assay for quantification of Edwardsiella ictaluri in catfish pond water and genetic homogeneity of diagnostic case isolates from Mississippi

    USDA-ARS?s Scientific Manuscript database

    A quantitative polymerase chain reaction (qPCR) assay was developed for the detection and quantification of Edwardsiella ictaluri in channel catfish Ictalurus punctatus pond water using modifications to a published E. ictaluri–specific qPCR assay and previously established protocols for the molecula...

  15. In vitro and in vivo interaction of macrophages from vaccinated and non-vaccinated channel catfish (Ictalurus punctatus) to Edwardsiella ictaluri

    USDA-ARS?s Scientific Manuscript database

    Macrophages from modified live vaccinated and non-vaccinated catfish were used in in vitro and in vivo studies with red fluorescent Edwardsiella ictaluri to assess phagocytic ability, reactive oxygen and nitric oxide production and bactericidal activity. In the in vitro experiment, macrophages were...

  16. Antimicrobial resistance and virulence-related genes of Streptococcus obtained from dairy cows with mastitis in Inner Mongolia, China.

    PubMed

    Ding, Yuexia; Zhao, Junli; He, Xiuling; Li, Man; Guan, Hong; Zhang, Ziying; Li, Peifeng

    2016-01-01

    Mastitis is the most expensive disease in the dairy cattle industry and results in decreased reproductive performance. Streptococcus, especially Streptococcus agalactiae, possesses a variety of virulence factors that contribute to pathogenicity. Streptococcus isolated from mastitis was tested to assess the prevalence of antimicrobial resistance and distribution of antibiotic resistance- and virulence-related genes. Eighty-one Streptococcus isolates were phenotypically characterized for antimicrobial resistance against 15 antibiotics by determining minimum inhibitory concentrations (MIC) using a micro-dilution method. Resistance- and virulence-related genes were detected by PCR. High percentage of resistance to β-lactams, along with tetracycline and erythromycin, was found. Resistance to three or more of seven antimicrobial agents was observed at 88.9%, with penicillin-tetracycline-erythromycin-clindamycin as the major profile in Streptococcus isolates. Resistant genes were detected by PCR, the result showed that 86.4, 86.4, 81.5, and 38.3% of isolates were mainly carrying the pbp2b, tetL, tetM, and ermB genes, respectively. Nine virulence genes were investigated. Genes cyl, glnA, cfb, hylB, and scaA were found to be in 50% of isolates, while 3.7, 21, and 4.9% of isolates were positive for bca, lmb, and scpB, genes, respectively. None of the isolates carried the bac gene. This study suggests the need for prudent use of antimicrobial agents in veterinary clinical medicine to avoid the increase and dissemination of antimicrobial resistance arising from the use of antimicrobial drugs in animals.

  17. Growth temperature alters Salmonella Enteritidis heat/acid resistance, membrane lipid composition and stress/virulence related gene expression.

    PubMed

    Yang, Yishan; Khoo, Wei Jie; Zheng, Qianwang; Chung, Hyun-Jung; Yuk, Hyun-Gyun

    2014-02-17

    The influence of growth temperature (10, 25, 37, and 42 °C) on the survival of Salmonella Enteritidis in simulated gastric fluid (SGF; pH=2.0) and during heat treatment (54, 56, 58, and 60 °C), on the membrane fatty acid composition, as well as on stress-/virulence-related gene expression was studied. Cells incubated at temperatures lower or higher than 37 °C did not increase their acid resistance, with the maximum D-value of 3.07 min in cells grown at 37 °C; while those incubated at higher temperature increased their heat resistance, with the maximum D60 °C-values of 1.4 min in cells grown at 42 °C. A decrease in the ratio of unsaturated to saturated fatty acids was observed as the growth temperature increased. Compared to the control cells grown at 37 °C, the expression of rpoS was 16.5- and 14.4-fold higher in cells cultivated at 10 and 25 °C, respectively; while the expression of rpoH was 2.9-fold higher in those cultivated at 42 °C. The increased expression of stress response gene rpoH and the decreased ratio of unsaturated to saturated fatty acids correlated with the greater heat resistance of bacteria grown at 42 °C; while the decreased expression of stress response gene rpoS at 42 °C might contribute to the decrease in acid resistance. Virulence related genes-spvR, hilA, avrA-were induced in cells cultivated at 42 °C, except sefA which was induced in the control cells. This study indicates that environmental temperature may affect the virulence potential of S. Enteritidis, thus temperature should be well controlled during food storage.

  18. Virulence-related genes, adhesion and invasion of some Yersinia enterocolitica-like strains suggests its pathogenic potential.

    PubMed

    Imori, Priscilla F M; Passaglia, Jaqueline; Souza, Roberto A; Rocha, Lenaldo B; Falcão, Juliana P

    2017-03-01

    Yersina enterocolitica-like species have not been extensively studied regarding its pathogenic potential. This work aimed to assess the pathogenic potential of some Y. enterocolitica-like strains by evaluating the presence of virulence-related genes by PCR and their ability to adhere to and invade Caco-2 and HEp-2 cells. A total of 50 Y. frederiksenii, 55 Y. intermedia and 13 Y. kristensenii strains were studied. The strains contained the following genes: Y. frederiksenii, fepA(44%), fes(44%) and ystB(18%); Y. intermedia, ail(53%), fepA (35%), fepD(2%), fes(97%), hreP(2%), ystB(2%) and tccC(35%); Y. kristensenii, ail(62%), ystB(23%), fepA(77%), fepD(54%), fes(54%) and hreP(77%). Generally, the Y. enterocolitica-like strains had a reduced ability to adhere to and invade mammalian cells compared to the highly pathogenic Y. enterocolitica 8081. However, Y. kristensenii FCF410 and Y. frederiksenii FCF461 presented high invasion potentials in Caco-2 cells after five days of pre-incubation increased by 45- and 7.2-fold compared to Y. enterocolitica 8081, respectively; but, the ail gene was not detected in these strains. The presence of virulence-related genes in some of the Y. enterocolitica-like strains indicated their possible pathogenic potential. Moreover, the results suggest the existence of alternative virulence mechanisms and that the pathogenicity of Y. kristensenii and Y. frederiksenii may be strain-dependent.

  19. Identification of QTLs Associated with Virulence Related Traits and Drug Resistance in Cryptococcus neoformans

    PubMed Central

    Vogan, Aaron A.; Khankhet, Jordan; Samarasinghe, Himeshi; Xu, Jianping

    2016-01-01

    Cryptococcus neoformans is a basidiomycete fungus capable of causing deadly meningoenchephilitis, primarily in immunocompromised individuals. Formerly, C. neoformans was composed of two divergent lineages, but these have recently been elevated to species status, now C. neoformans (formerly C. neoformans var. grubii) and C. deneoformans (formerly C. neoformans var. neoformans). While both species can cause deadly infections in humans, C. neoformans is much more prevalent in clinical settings than C. deneoformans. However, the genetic factors contributing to their significant differences in virulence remain largely unknown. Quantitative trait locus (QTL) mapping is a powerful tool that can be used to identify genomic regions associated with phenotypic differences between strains. Here, we analyzed a hybrid cross between these two species and identified a total of 23 QTL, including five for melanin production, six for cell size, one for cell wall thickness, five for the frequency of capsule production, three for minimal inhibitory concentration (MIC) of fluconazole in broth, and three for MIC on solid medium. For the fluconazole resistance-associated QTL, three showed environment and/or concentration-specific effects. Our results provide a large number of candidate gene regions from which to explore the molecular bases for phenotypic differences between C. neoformans and C. deneoformans. PMID:27371951

  20. Identification of QTLs Associated with Virulence Related Traits and Drug Resistance in Cryptococcus neoformans.

    PubMed

    Vogan, Aaron A; Khankhet, Jordan; Samarasinghe, Himeshi; Xu, Jianping

    2016-09-08

    Cryptococcus neoformans is a basidiomycete fungus capable of causing deadly meningoenchephilitis, primarily in immunocompromised individuals. Formerly, C. neoformans was composed of two divergent lineages, but these have recently been elevated to species status, now C. neoformans (formerly C. neoformans var. grubii) and C. deneoformans (formerly C. neoformans var. neoformans). While both species can cause deadly infections in humans, C. neoformans is much more prevalent in clinical settings than C. deneoformans However, the genetic factors contributing to their significant differences in virulence remain largely unknown. Quantitative trait locus (QTL) mapping is a powerful tool that can be used to identify genomic regions associated with phenotypic differences between strains. Here, we analyzed a hybrid cross between these two species and identified a total of 23 QTL, including five for melanin production, six for cell size, one for cell wall thickness, five for the frequency of capsule production, three for minimal inhibitory concentration (MIC) of fluconazole in broth, and three for MIC on solid medium. For the fluconazole resistance-associated QTL, three showed environment and/or concentration-specific effects. Our results provide a large number of candidate gene regions from which to explore the molecular bases for phenotypic differences between C. neoformans and C. deneoformans.

  1. Prevalence of Virulence-Related Determinants in Clinical Isolates of Staphylococcus epidermidis

    PubMed Central

    Najar Peerayeh, Shahin; Jazayeri Moghadas, Ali; Behmanesh, Mehrdad

    2016-01-01

    Background Staphylococcus epidermidis, a member of the human flora, is recognized as an opportunistic pathogen and cause of nosocomial infections. Staphylococcus epidermidis surface components are able to establish bacteria on the host surface, and cause infection. Objectives The frequency of icaA, IS256, aap, fbe and bhp in clinical isolates of S. epidermidis were investigated in this study. Materials and Methods Fifty-nine S. epidermidis isolates were collected from blood (50), wound (1), urine (4) and tracheal (4) samples (Tehran, Iran). Staphylococcus epidermidis isolates were identified with conventional bacteriological tests. Virulence-associated genes were detected by specific polymerase chain reactions (PCRs). Results Of the 59 S. epidermidis, fbe was found in 89.8%, while aap and bhp were observed in 64.4% and 15.3% of the samples, respectively. Coexistence of aap and fbe was found in 32 isolates, while coexistence of bhp and fbe was observed in five isolates. Two isolates were negative for the investigated genes. Conclusions Prevalence of fbe and aap was significantly different from similar studies, yet frequency of bhp was in accordance with other studies. Prevalence of icaA and IS256 was not significantly different from some studies while a significant difference was observed when results were compared with some other studies. PMID:27800129

  2. Phosphate Limitation Induces Drastic Physiological Changes, Virulence-Related Gene Expression, and Secondary Metabolite Production in Pseudovibrio sp. Strain FO-BEG1

    PubMed Central

    González, José M.; Bondarev, Vladimir

    2015-01-01

    Phosphorus is a vital nutrient for living organisms and is obtained by bacteria primarily via phosphate uptake. However, phosphate is often scarcely accessible in nature, and there is evidence that in many areas of the ocean, its concentration limits bacterial growth. Surprisingly, the phosphate starvation response has been extensively investigated in different model organisms (e.g., Escherichia coli), but there is a dearth of studies on heterotrophic marine bacteria. In this work, we describe the response of Pseudovibrio sp. strain FO-BEG1, a metabolically versatile alphaproteobacterium and potential symbiont of marine sponges, to phosphate limitation. We compared the physiology, protein expression, and secondary metabolite production under phosphate-limited conditions to those under phosphate surplus conditions. We observed that phosphate limitation had a pleiotropic effect on the physiology of the strain, triggering cell elongation, the accumulation of polyhydroxyalkanoate, the degradation of polyphosphate, and the exchange of membrane lipids in favor of phosphorus-free lipids such as sulfoquinovosyl diacylglycerols. Many proteins involved in the uptake and degradation of phospho-organic compounds were upregulated, together with subunits of the ABC transport system for phosphate. Under conditions of phosphate limitation, FO-BEG1 secreted compounds into the medium that conferred an intense yellow coloration to the cultures. Among these compounds, we identified the potent antibiotic tropodithietic acid. Finally, toxin-like proteins and other proteins likely involved in the interaction with the eukaryotic host were also upregulated. Altogether, our data suggest that phosphate limitation leads to a pronounced reorganization of FO-BEG1 physiology, involving phosphorus, carbon, and sulfur metabolism; cell morphology; secondary metabolite production; and the expression of virulence-related genes. PMID:25769826

  3. The Extra-Cytoplasmic Function Sigma Factor SigX Modulates Biofilm and Virulence-Related Properties in Pseudomonas aeruginosa

    PubMed Central

    Gicquel, Gwendoline; Bouffartigues, Emeline; Bains, Manjeet; Oxaran, Virginie; Rosay, Thibaut; Lesouhaitier, Olivier; Connil, Nathalie; Bazire, Alexis; Maillot, Olivier; Bénard, Magalie; Cornelis, Pierre; Hancock, Robert E. W.; Dufour, Alain; Feuilloley, Marc G. J.; Orange, Nicole; Déziel, Eric; Chevalier, Sylvie

    2013-01-01

    SigX, one of the 19 extra-cytoplasmic function sigma factors of P. aeruginosa, was only known to be involved in transcription of the gene encoding the major outer membrane protein OprF. We conducted a comparative transcriptomic study between the wildtype H103 strain and its sigX mutant PAOSX, which revealed a total of 307 differentially expressed genes that differed by more than 2 fold. Most dysregulated genes belonged to six functional classes, including the “chaperones and heat shock proteins”, “antibiotic resistance and susceptibility”, “energy metabolism”, “protein secretion/export apparatus”, and “secreted factors”, and “motility and attachment” classes. In this latter class, the large majority of the affected genes were down-regulated in the sigX mutant. In agreement with the array data, the sigX mutant was shown to demonstrate substantially reduced motility, attachment to biotic and abiotic surfaces, and biofilm formation. In addition, virulence towards the nematode Caenorhabditis elegans was reduced in the sigX mutant, suggesting that SigX is involved in virulence-related phenotypes. PMID:24260387

  4. Comparative analysis of the genomes of clinical isolates of Mycobacterium avium subsp. hominissuis regarding virulence-related genes.

    PubMed

    Jeffrey, Brendan; Rose, Sasha J; Gilbert, Kerrigan; Lewis, Matthew; Bermudez, Luiz E

    2017-07-01

    Mycobacterium avium subsp. hominissuis is a member of the M. avium complex, a heterogeneous group of bacteria that cause lung infection in immunocompetent patients or disseminated infection in patients with immunosuppression. The bacteria belonging to this complex have variable virulence, depending on the strain considered, and therefore a representative of the most common clinical phenotype was analysed. The genomic sequences of four M. avium subsp. hominissuis isolates obtained from clinical specimens were completed. Mav101, Mav100 and MavA5 were isolated from the blood of patients with AIDS. MavA5 was disseminated from the lung, while Mav3388 was isolated from the lungs of a patient with chronic lung disease. The sequences were annotated using the published Mav104 genome as a blueprint. Functional and virulence analyses of the sequences were carried out. Mice studies comparing the virulence of the strains were performed. Findings showed that while Mav101 was very similar to Mav104, there were numerous differences between Mav104 and the remaining strains at nucleotide and predicted protein levels. The presence of genes associated with biofilm formation and several known virulence-related genes were sometimes differentially present among the isolates, suggesting overlapping functions by different genetic determinants. The sequences provided important information about M. avium heterogenicity and evolution as a pathogen. The limitation is the lack of understanding on possible overlapping functions of genes/proteins.

  5. Effects of a phytogenic feed additive on growth performance, susceptibility of channel catfish to Edwardsiella ictaluri and levels of mannose binding lectin.

    PubMed

    Peterson, Brian C; Peatman, E; Ourth, D D; Waldbieser, G C

    2015-05-01

    A study was conducted to investigate the effect of a phytogenic feed additive (Digestarom® P.E.P. MGE; containing the essential oils carvacrol, thymol, anethol, and limonene) on growth performance and disease susceptibility to Edwardsiella ictaluri. Two hundred and fifty juvenile channel catfish, Ictalurus punctatus (7.2 ± 0.1 g) were allotted into the following treatments: Control (floating diet) and EO (floating diet supplemented with essential oils). The fish were fed their respective diets for 6 weeks. At the end of the study, all fish were exposed to virulent E. ictaluri by bath immersion (1.9 × 10(7) cfu/mL; final concentration). Plasma and tissue samples were taken to quantify protein and mRNA expression levels of mannose binding lectin (MBL). Weight gain and food conversion ratio were similar between treatments. After exposing fish to virulent E. ictaluri and monitoring mortality for 21 days, survival was 43% higher (69.5 vs 48.4%) in fish fed EO compared to fish not treated with EO (P < 0.05). One day after challenge, plasma MBL levels were down-regulated in the non-treated fish compared to non-challenged fish. In the EO fish, MBL levels were similar to non-challenged fish but significantly higher than non-treated fed fish (P < 0.001). By d 7, plasma MBL levels increased in non-treated fed fish to levels observed in the EO and non-challenged fish. On d 14, MBL mRNA levels were upregulated 15-fold in fish fed EO compared to non-treated fed fish and non-challenged fish (P < 0.001). The results demonstrate that essential oils improved survival of channel catfish challenged with E. ictaluri. Mechanisms through which essential oils improve survival may involve MBL.

  6. Genome-Wide Identification of Pseudomonas aeruginosa Virulence-Related Genes Using a Caenorhabditis elegans Infection Model

    PubMed Central

    Feinbaum, Rhonda L.; Urbach, Jonathan M.; Liberati, Nicole T.; Djonovic, Slavica; Adonizio, Allison; Carvunis, Anne-Ruxandra; Ausubel, Frederick M.

    2012-01-01

    Pseudomonas aeruginosa strain PA14 is an opportunistic human pathogen capable of infecting a wide range of organisms including the nematode Caenorhabditis elegans. We used a non-redundant transposon mutant library consisting of 5,850 clones corresponding to 75% of the total and approximately 80% of the non-essential PA14 ORFs to carry out a genome-wide screen for attenuation of PA14 virulence in C. elegans. We defined a functionally diverse 180 mutant set (representing 170 unique genes) necessary for normal levels of virulence that included both known and novel virulence factors. Seven previously uncharacterized virulence genes (ABC transporters PchH and PchI, aminopeptidase PepP, ATPase/molecular chaperone ClpA, cold shock domain protein PA0456, putative enoyl-CoA hydratase/isomerase PA0745, and putative transcriptional regulator PA14_27700) were characterized with respect to pigment production and motility and all but one of these mutants exhibited pleiotropic defects in addition to their avirulent phenotype. We examined the collection of genes required for normal levels of PA14 virulence with respect to occurrence in P. aeruginosa strain-specific genomic regions, location on putative and known genomic islands, and phylogenetic distribution across prokaryotes. Genes predominantly contributing to virulence in C. elegans showed neither a bias for strain-specific regions of the P. aeruginosa genome nor for putatively horizontally transferred genomic islands. Instead, within the collection of virulence-related PA14 genes, there was an overrepresentation of genes with a broad phylogenetic distribution that also occur with high frequency in many prokaryotic clades, suggesting that in aggregate the genes required for PA14 virulence in C. elegans are biased towards evolutionarily conserved genes. PMID:22911607

  7. A real-time polymerase chain reaction assay for quantification of Edwardsiella ictaluri in catfish pond water and genetic homogeneity of diagnostic case isolates from Mississippi.

    PubMed

    Griffin, Matt J; Mauel, Michael J; Greenway, Terrence E; Khoo, Lester H; Wise, David J

    2011-12-01

    A quantitative polymerase chain reaction (qPCR) assay was developed for the detection and quantification of Edwardsiella ictaluri in channel catfish Ictalurus punctatus pond water using modifications to a published E. ictaluri-specific qPCR assay and previously established protocols for the molecular detection of myxozoan parasites in catfish ponds. Genomic DNA equivalents indicative of the number of bacteria in a sample were determined and standard curves correlating to bacterial numbers were established. The assay was found to be highly repeatable and reproducible, with a linear dynamic range of five orders of magnitude. There was no interference of the assay from the presence of large quantities of nontarget DNA. Known quantities of bacteria were added to sample volumes of 40 or 500 mL of pond water collected from several different ponds. The minimum level of detection was approximately 100 cell equivalents (CE) in 40 (2.5 CE/mL) or 500 mL of pond water (0.2 CE/mL). Sample volumes of 40 mL yielded the most consistent results, which were not significantly different from those obtained from broth culture alone. Cell equivalents determined by qPCR in 40-mL pond water samples spiked with known quantities of bacteria were within one order of magnitude of the actual number of cells added. Repetitive element-based polymerase chain reaction analysis of archived isolates demonstrated the genetic homogeneity of E. ictaluri, and consistent amplification of these isolates by qPCR analysis demonstrated the stability of the PCR target. The assay described here provides a reliable method for the detection and quantification of E. ictaluri in pond water and will be an invaluable tool in epidemiological studies. Additionally, the assay provides a way to evaluate the effects that vaccination, antibiotic treatments, and restricted feeding practices have on E. ictaluri populations during an outbreak. Information obtained with these tools will aid in optimizing disease management

  8. Antimicrobial susceptibility pattern of Edwardsiella ictaluri isolates from natural outbreaks of bacillary necrosis of Pangasianodon hypophthalmus in Vietnam.

    PubMed

    Tu, Thanh Dung; Haesebrouck, Freddy; Nguyen, Anh Tuan; Sorgeloos, Patrick; Baele, Margo; Decostere, Annemie

    2008-12-01

    The purpose of this study was to assess the in vitro susceptibility of 64 Vietnamese isolates of Edwardsiella ictaluri, the causal agent of the infectious disease Bacillus Necrosis Pangasius in Pangasianodon hypophthalmus, using the agar dilution technique. All isolates originated from different farms and were collected between 2002 and 2005. None of the isolates displayed acquired resistance to amoxicillin, amoxicillin-clavulanic acid, chloramphenicol, florfenicol, gentamicin, kanamycin, neomycin, and nitrofurantoin. Acquired resistance to streptomycin was detected in 83%, to oxytetracycline in 81%, and to trimethoprim in 71% of the isolates, as indicated by a bimodal distribution of the minimal inhibitory concentrations (MICs) of these antimicrobials. The MICs of enrofloxacin displayed a monomodal distribution with tailing toward the higher MIC values, possibly indicating reduced susceptibility of a minority of isolates (3 out of the 64). For the quinolone antimicrobial agents flumequin and oxolinic acid, acquired resistance was encountered in 8% and 6% of the strains, respectively. All strains were intrinsically resistant to the polypeptide antimicrobial agent colistin. Seventy-three percent of the isolates were shown to have acquired resistance to at least three antimicrobial agents. The results of this study emphasize the strict need to control both the prophylactic and curative use of antimicrobial agents in Vietnamese aquaculture.

  9. Effects of ammonia stress, dietary linseed oil and Edwardsiella ictaluri challenge on juvenile darkbarbel catfish Pelteobagrus vachelli.

    PubMed

    Li, Ming; Yu, Na; Qin, Jian G; Li, Erchao; Du, Zhenyu; Chen, Liqiao

    2014-05-01

    A two-stage study was carried out to test the response of juvenile darkbarbel catfish Pelteobagrus vachelli to ammonia stress, dietary lipid and bacterial challenge. At stage 1, the catfish (0.99 ± 0.01 g) fed a commercial diet were exposed to 0.01 and 5.70 mg L(-1) total ammonia nitrogen in nine replicates for 14 days. At stage 2, all fish previously exposed to either low or high ammonia were separately transferred into low ammonia (<0.01 mg L(-1)), and divided into three feeding groups. Fish were then fed three levels of linseed oil (0, 2 and 4%) in triplicate for 46 days. Fish growth performance and immune response were low in high ammonia at stage 1. At stage 2, fish growth and immune response were not significantly different between fish previously exposed to low and high ammonia in all diets. Fish fed 4% linseed oil showed the greatest weight gain, feed efficiency ratio, red blood cells, hemoglobin and hematocrit, and achieved higher lysozyme activity, phagocytic index, respiratory burst and total immunoglobulin than fish fed 0% linseed oil, but did not differ from fish fed 2% linseed oil regardless of previous ammonia exposure. After 14-day infection of Edwardsiella ictaluri, cumulative mortality of fish previously exposed to low ammonia was lower than that of fish exposed to high ammonia in all diets. Cumulative mortality of fish fed 0% linseed oil was highest, but the antibody titer of fish fed 4% linseed oil was highest regardless of previous ammonia treatments. This study indicates that ammonia stress has a lasting effect even after ammonia is lowed, but the adverse effect on fish can be mitigated through manipulation of dietary oil inclusion, especially under the challenge of pathogenic bacteria. Copyright © 2014 Elsevier Ltd. All rights reserved.

  10. Genes Similar to the Vibrio parahaemolyticus Virulence-Related Genes tdh, tlh, and vscC2 Occur in Other Vibrionaceae Species Isolated from a Pristine Estuary

    PubMed Central

    Klein, Savannah L.; Gutierrez West, Casandra K.; Mejia, Diana M.

    2014-01-01

    Detection of the human pathogen Vibrio parahaemolyticus often relies on molecular biological analysis of species-specific virulence factor genes. These genes have been employed in determinations of V. parahaemolyticus population numbers and the prevalence of pathogenic V. parahaemolyticus strains. Strains of the Vibrionaceae species Photobacterium damselae, Vibrio diabolicus, Vibrio harveyi, and Vibrio natriegens, as well as strains similar to Vibrio tubiashii, were isolated from a pristine salt marsh estuary. These strains were examined for the V. parahaemolyticus hemolysin genes tdh, trh, and tlh and for the V. parahaemolyticus type III secretion system 2α gene vscC2 using established PCR primers and protocols. Virulence-related genes occurred at high frequencies in non-V. parahaemolyticus Vibrionaceae species. V. diabolicus was of particular interest, as several strains were recovered, and the large majority (>83%) contained virulence-related genes. It is clear that detection of these genes does not ensure correct identification of virulent V. parahaemolyticus. Further, the occurrence of V. parahaemolyticus-like virulence factors in other vibrios potentially complicates tracking of outbreaks of V. parahaemolyticus infections. PMID:24212573

  11. Genes similar to the Vibrio parahaemolyticus virulence-related genes tdh, tlh, and vscC2 occur in other vibrionaceae species isolated from a pristine estuary.

    PubMed

    Klein, Savannah L; Gutierrez West, Casandra K; Mejia, Diana M; Lovell, Charles R

    2014-01-01

    Detection of the human pathogen Vibrio parahaemolyticus often relies on molecular biological analysis of species-specific virulence factor genes. These genes have been employed in determinations of V. parahaemolyticus population numbers and the prevalence of pathogenic V. parahaemolyticus strains. Strains of the Vibrionaceae species Photobacterium damselae, Vibrio diabolicus, Vibrio harveyi, and Vibrio natriegens, as well as strains similar to Vibrio tubiashii, were isolated from a pristine salt marsh estuary. These strains were examined for the V. parahaemolyticus hemolysin genes tdh, trh, and tlh and for the V. parahaemolyticus type III secretion system 2α gene vscC2 using established PCR primers and protocols. Virulence-related genes occurred at high frequencies in non-V. parahaemolyticus Vibrionaceae species. V. diabolicus was of particular interest, as several strains were recovered, and the large majority (>83%) contained virulence-related genes. It is clear that detection of these genes does not ensure correct identification of virulent V. parahaemolyticus. Further, the occurrence of V. parahaemolyticus-like virulence factors in other vibrios potentially complicates tracking of outbreaks of V. parahaemolyticus infections.

  12. Insights into the virulence-related genes of Edwardsiella tarda isolated from turbot in Europe: genetic homogeneity and evidence for vibrioferrin production.

    PubMed

    Castro, N; Osorio, C R; Buján, N; Fuentes, J C; Rodríguez, J; Romero, M; Jiménez, C; Toranzo, A E; Magariños, B

    2016-05-01

    Edwardsiella tarda has long been known as a pathogen that causes severe economic losses in aquaculture industry. Insights gained on E. tarda pathogenesis may prove useful in the development of new methods for the treatment of infections as well as preventive measures against future outbreaks. In this report, we have established the correlation between the presence of virulence genes, related with three aspects typically involved in bacterial pathogenesis (chondroitinase activity, quorum sensing and siderophore-mediated ferric uptake systems), in the genome of E. tarda strains isolated from turbot in Europe and their phenotypic traits. A total of 8 genes were tested by PCR for their presence in 73 E. tarda isolates. High homogeneity was observed in the presence/absence pattern of all the strains. Positive results in the amplification of virulence-related genes were correlated with the detection of chondroitinase activity in agar plates, in vivo AHL production during fish infection and determination of type of siderophore produced by E. tarda. To the best of our knowledge, this is the first study carried out with European strains on potential virulence factors. Furthermore, we demonstrated for the first time that E. tarda produces the siderophore vibrioferrin. © 2015 John Wiley & Sons Ltd.

  13. Virulence-related traits of epidemic Acinetobacter baumannii strains belonging to the international clonal lineages I-III and to the emerging genotypes ST25 and ST78

    PubMed Central

    2013-01-01

    Background Acinetobacter baumannii is responsible for large epidemics in hospitals, where it can persist for long time on abiotic surfaces. This study investigated some virulence-related traits of epidemic A. baumannii strains assigned to distinct MLST genotypes, including those corresponding to the international clones I-III as well as emerging genotypes responsible for recent epidemics. Methods Genotyping of bacteria was performed by PFGE analysis and MLST according to the Pasteur’s scheme. Biofilm formation on polystyrene plates was assessed by crystal violet staining; resistance to desiccation was evaluated on glass cover-slips when kept at room-temperature and 31% relative humidity; adherence to and invasion of A549 human alveolar epithelial cells were determined by the analysis of viable bacteria associated with or internalized by A549 human alveolar epithelial cells; Galleria mellonella killing assays were used to analyze the virulence of A. baumannii in vivo. Results The ability to form biofilm was significantly higher for A. baumannnii strains assigned to ST2 (international clone II), ST25 and ST78 compared to other STs. All A. baumannii strains survived on dry surfaces for over 16 days, and strains assigned to ST1 (international clone I) and ST78 survived for up to 89 and 96 days, respectively. Adherence to A549 pneumocytes was higher for strains assigned to ST2, ST25 and ST78 than other genotypes; a positive correlation exists between adherence and biofilm formation. Strains assigned to ST78 also showed significantly higher ability to invade A549 cells. No significant differences in the killing of G. mellonella worms were found among strains. Conclusions Elevated resistance to desiccation, high biofilm-forming capacity on abiotic surfaces and adherence to A549 cells might have favoured the spread and persistence in the hospital environment of A. baumannii strains assigned to the international clones I and II and to the emerging genotypes ST25 and ST78

  14. Presence of T3SS2 and other virulence-related genes in tdh-negative Vibrio parahaemolyticus environmental strains isolated from marine samples in the area of the Venetian Lagoon, Italy.

    PubMed

    Caburlotto, Greta; Gennari, Micol; Ghidini, Valentina; Tafi, Mariacarla; Lleo, Maria M

    2009-12-01

    Vibrio parahaemolyticus-mediated disease has traditionally been associated with two virulence factors, thermostable direct haemolysin (TDH) and TDH-related haemolysin (TRH), which are present in most clinical isolates. Recently, it has been suggested that other virulence-related factors, such as some type III secretion system (T3SS) proteins, urease and DNA-methyltransferase, among others, might also play a role in disease caused by this bacterial species and have been shown to be carried by clinical, but not by environmental strains. Screening for a number of virulence and virulence-related genes in a collection of V. parahaemolyticus strains isolated from the Italian Adriatic coast indicates that in addition to the trh-positive strains isolated (6%), a significant percentage (18%) of these strains contain one or more genes with a possible role in pathogenicity. Specifically, some of the V. parahaemolyticus strains described in this study are the first environmental strains ever detected carrying T3SS2 genes. Data obtained by reverse transcription-PCR on environmental strain RNA indicate that at least some of these genes are functional. On the basis of the results obtained, it is suggested that such strains might constitute an environmental reservoir of genes possibly contributing to V. parahaemolyticus pathogenicity and to the spread, in the marine environment, of virulence-related genes usually found in clinical strains.

  15. A conserved two-component regulatory system, PidS/PidR, globally regulates pigmentation and virulence-related phenotypes of Burkholderia glumae.

    PubMed

    Karki, Hari Sharan; Barphagha, Inderjit Kaur; Ham, Jong Hyun

    2012-09-01

    Burkholderia glumae is a rice pathogenic bacterium that causes bacterial panicle blight. Some strains of this pathogen produce dark brown pigments when grown on casamino-acid peptone glucose (CPG) agar medium. A pigment-positive and highly virulent strain of B. glumae, 411gr-6, was randomly mutagenized with mini-Tn5gus, and the resulting mini-Tn5gus derivatives showing altered pigmentation phenotypes were screened on CPG agar plates to identify the genetic elements governing the pigmentation of B. glumae. In this study, a novel two-component regulatory system (TCRS) composed of the PidS sensor histidine kinase and the PidR response regulator was identified as an essential regulatory factor for pigmentation. Notably, the PidS/PidR TCRS was also required for the elicitation of the hypersensitive response on tobacco leaves, indicating the dependence of the hypersensitive response and pathogenicity (Hrp) type III secretion system of B. glumae on this regulatory factor. In addition, B. glumae mutants defective in the PidS/PidR TCRS showed less production of the phytotoxin, toxoflavin, and less virulence on rice panicles and onion bulbs relative to the parental strain, 411gr-6. The presence of highly homologous PidS and PidR orthologues in other Burkholderia species suggests that PidS/PidR-family TCRSs may exert the same or similar functions in different Burkholderia species, including both plant and animal pathogens.

  16. The novel virulence-related gene stp of Streptococcus suis serotype 9 strain contributes to a significant reduction in mouse mortality.

    PubMed

    Zhu, Haodan; Huang, Dongyan; Zhang, Wei; Wu, Zongfu; Lu, Yan; Jia, Hongying; Wang, Ming; Lu, Chengping

    2011-12-01

    Streptococcus suis is an important swine pathogen responsible for a diverse range of diseases. S. suis serotype 2 (SS2) and S. suis serotype 9 (SS9) are the prevalent serotypes in diseased Chinese pigs. Little is known about SS9 virulence factors. Two strains, GZ0565 and SH040917, were isolated from a diseased pig and a healthy pig, respectively. Suppression subtractive hybridization (SSH) was used to identify SS9 virulence genes associated with pathogenicity. We identified 30 gene fragments unique to GZ0565, including stp which encodes a serine/threonine protein phosphatase known to affect the virulence and morphology of bacteria. To investigate the role of stp in pathogenesis of SS9, an isogenic stp mutant (Δstp) and a complementation strain (CΔstp) were constructed. The results demonstrated that the stp affected the expression of a few genes involving in adhesion and virulence for bacteria. The Δstp exhibited a significant decrease in HEp-2 cell adherence, compared with the wild type, and a reduced survival ratio in whole blood. The Δstp was attenuated in a CD1 murine model of infection and its LD50 values was seven-fold higher than the wild type. Our data suggest that stp is involved in the pathogenesis of SS9. Copyright © 2011 Elsevier Ltd. All rights reserved.

  17. Large-scale identification of small noncoding RNA with strand-specific deep sequencing and characterization of a novel virulence-related sRNA in Brucella melitensis

    PubMed Central

    Zhong, Zhijun; Xu, Xiaoyang; Li, Xinran; Liu, Shiwei; Lei, Shuangshuang; Yang, Mingjuan; Yu, Jiuxuan; Yuan, Jiuyun; Ke, Yuehua; Du, Xinying; Wang, Zhoujia; Ren, Zhihua; Peng, Guangneng; Wang, Yufei; Chen, Zeliang

    2016-01-01

    Brucella is the causative agent of brucellosis, a worldwide epidemic zoonosis. Small noncoding RNAs (sRNAs) are important modulators of gene expression and involved in pathogenesis and stress adaptation of Brucella. In this study, using a strand-specific RNA deep-sequencing approach, we identified a global set of sRNAs expressed by B. melitensis 16M. In total, 1321 sRNAs were identified, ranging from 100 to 600 nucleotides. These sRNAs differ in their expression levels and strand and chromosomal distributions. The role of BSR0441, one of these sRNAs, in the virulence of B. melitensis 16M was further characterized. BSR0441 was highly induced during the infection of macrophages and mice. The deletion mutant of BSR0441 showed significantly reduced spleen colonization in the middle and late phases of infection. The expression of the BSR0441 target mRNA genes was also altered in the BSR0441 mutant strain during macrophage and mice infection, which is consistent with its reduced intracellular survival capacity. In summary, Brucella encodes a large number of sRNAs, which may be involved in the stress adaptation and virulence of Brucella. Further investigation of these regulators will extend our understanding of the Brucella pathogenesis mechanism and the interactions between Brucella and its hosts. PMID:27112796

  18. Identification of the putative protein phosphatase gene PTC1 as a virulence-related gene using a silkworm model of Candida albicans infection.

    PubMed

    Hanaoka, Nozomu; Takano, Yukie; Shibuya, Kazutoshi; Fugo, Hajime; Uehara, Yoshimasa; Niimi, Masakazu

    2008-10-01

    Protein phosphatases are critical for the regulation of many cellular processes. Null mutants of 21 putative protein phosphatases of Candida albicans were constructed by consecutive allele replacement using the URA3 and ARG4 marker genes. A simple silkworm model of C. albicans infection was used to screen the panel of mutants. Four null mutant (cmp1Delta, yvh1Delta, sit4Delta, and ptc1Delta) strains showed attenuated virulence in the silkworm model relative to that of control and parental strains. Three of the mutants, the cmp1Delta, yvh1Delta, and sit4Delta mutants, had previously been identified as affecting virulence in a conventional mouse model, indicating the validity of the silkworm model screen. Disruption of the putative protein phosphatase gene PTC1 of C. albicans, which has 52% identity to the Saccharomyces cerevisiae type 2C protein phosphatase PTC1, significantly reduced virulence in the silkworm model. The mutant was also avirulent in a mouse model of disseminated candidiasis. Reintroducing either of the C. albicans PTC1 alleles into the disruptant strain, using a cassette containing either allele under the control of a constitutive ACT1 promoter, restored virulence in both infection models. Characterization of ptc1Delta revealed other phenotypic traits, including reduced hyphal growth in vitro and in vivo, and reduced extracellular proteolytic activity. We conclude that PTC1 may contribute to pathogenicity in C. albicans.

  19. Enteroaggregative Escherichia coli in Venda, South Africa: distribution of virulence-related genes by multiplex polymerase chain reaction in stool samples of human immunodeficiency virus (HIV)-positive and HIV-negative individuals and primary school children.

    PubMed

    Samie, Amidou; Obi, Chikwelu Larry; Dillingham, Rebecca; Pinkerton, Relana C; Guerrant, Richard L

    2007-07-01

    We used a multiplex polymerase chain reaction (PCR) and a quantitative real-time PCR to determine the distribution of three enteroaggregative Escherichia coli (EAEC) virulence-related genes in stool samples from hospital patients and school children in the Venda region of South Africa. At least one gene was found in 52 (16.5%) samples, 50 (19.6%) from hospitals and 2 (3%) from schools. The AA probe was found in 36 (69%), the aggR gene was found in 41 (79%), and the aap gene was found in 49 (94%) of all positive samples. EAEC was significantly associated with diarrhea and intestinal inflammation and was significantly higher (chi(2) = 5.360, P = 0.021) in human immunodeficiency virus (HIV)-positive persons (29.5%) than in HIV-negative persons (13.7%). The presence of EAEC genes was significantly associated with occult blood (chi(2) = 30.543, P < 0.0001) in the stool samples. This study suggests that the clinical presentation of EAEC infection may be directly related to the bacterial load as well as to the genetic characteristics of the strains involved.

  20. Membrane lipid composition and stress/virulence related gene expression of Salmonella Enteritidis cells adapted to lactic acid and trisodium phosphate and their resistance to lethal heat and acid stress.

    PubMed

    Yang, Yishan; Kadim, Mellissa Irlianti; Khoo, Wei Jie; Zheng, Qianwang; Setyawati, Magdiel Inggrid; Shin, Yu-Jin; Lee, Seung-Cheol; Yuk, Hyun-Gyun

    2014-11-17

    This study evaluated the acid and heat resistance of Salmonella Enteritidis in simulated gastric fluid (pH 2.0) and during thermal treatment (54-60 °C), respectively, after adaptation to lactic acid (LA) or trisodium phosphate (TSP) at various pHs (pH 5.3-9.0). The changes in membrane lipid composition and expression levels of RpoS and RpoH were examined to elucidate their roles in bacterial stress resistance. Transcriptional profile of several virulence-related genes was also analyzed. Results showed that LA-adapted cells at pH 5.3 and 6.3 had higher acid and heat resistance than control cells and cells adapted to TSP at pH 8.3 and 9.0. LA-adapted cells had the lowest ratio of unsaturated to saturated fatty acids, indicating that they might possess a less fluid membrane. It was observed that the expression levels of RpoH and RpoS were upregulated in TSP-adapted cells but not in LA-adapted cells. Thus, these results indicate that the increased acid and heat resistance of LA-adapted S. Enteritidis was possibly due to the decreased membrane fluidity instead of the upregulation of RpoS and RpoH. About 6.0, 2.1, and 2.46-fold upregulation of spvR, avrA, and hilA were observed in cells adapted to TSP at pH 9.0, except sefA that had its highest expression level in the control cells, indicating that the expression of these virulence genes highly depends on environmental conditions. This is the first study to show that the alteration in the cytoplasmic membrane rather than RpoS and RpoH plays a more crucial role in conferring greater acid and heat resistance on LA-adapted S. Enteritidis, thus providing a better understanding on the bacterial stress response to acidic conditions.

  1. Comparative analysis of Edwardsiella isolates from fish in the eastern United States identifies two distinct genetic taxa amongst organisms phenotypically classified as E. tarda

    USGS Publications Warehouse

    Griffin, Matt J.; Quiniou, Sylvie M.; Cody, Theresa; Tabuchi, Maki; Ware, Cynthia; Cipriano, Rocco C.; Mauel, Michael J.; Soto, Esteban

    2013-01-01

    Edwardsiella tarda, a Gram-negative member of the family Enterobacteriaceae, has been implicated in significant losses in aquaculture facilities worldwide. Here, we assessed the intra-specific variability of E. tarda isolates from 4 different fish species in the eastern United States. Repetitive sequence mediated PCR (rep-PCR) using 4 different primer sets (ERIC I & II, ERIC II, BOX, and GTG5) and multi-locus sequence analysis of 16S SSU rDNA, groEl, gyrA, gyrB, pho, pgi, pgm, and rpoA gene fragments identified two distinct genotypes of E. tarda (DNA group I; DNA group II). Isolates that fell into DNA group II demonstrated more similarity to E. ictaluri than DNA group I, which contained the reference E. tarda strain (ATCC #15947). Conventional PCR analysis using published E. tarda-specific primer sets yielded variable results, with several primer sets producing no observable amplification of target DNA from some isolates. Fluorometric determination of G + C content demonstrated 56.4% G + C content for DNA group I, 60.2% for DNA group II, and 58.4% for E. ictaluri. Surprisingly, these isolates were indistinguishable using conventional biochemical techniques, with all isolates demonstrating phenotypic characteristics consistent with E. tarda. Analysis using two commercial test kits identified multiple phenotypes, although no single metabolic characteristic could reliably discriminate between genetic groups. Additionally, anti-microbial susceptibility and fatty acid profiles did not demonstrate remarkable differences between groups. The significant genetic variation (<90% similarity at gyrA, gyrB, pho, phi and pgm; <40% similarity by rep-PCR) between these groups suggests organisms from DNA group II may represent an unrecognized, genetically distinct taxa of Edwardsiella that is phenotypically indistinguishable from E. tarda.

  2. Identifying Hazards

    EPA Pesticide Factsheets

    The federal government has established a system of labeling hazardous materials to help identify the type of material and threat posed. Summaries of information on over 300 chemicals are maintained in the Envirofacts Master Chemical Integrator.

  3. Characterization of group A Streptococcus strains recovered from Mexican children with pharyngitis by automated DNA sequencing of virulence-related genes: unexpectedly large variation in the gene (sic) encoding a complement-inhibiting protein.

    PubMed Central

    Mejia, L M; Stockbauer, K E; Pan, X; Cravioto, A; Musser, J M

    1997-01-01

    Sequence variation was studied in several target genes in 54 strains of group A Streptococcus (GAS) cultured from children with pharyngitis in Mexico City. Although 16 distinct emm alleles were identified, only 4 had not been previously described. Virtually all bacteria (31 of 33 [94%] with the streptococcal pyrogenic exotoxin gene (speA) had emm1-related, emm3, or emm6 alleles. The gene (sic) encoding an extracellular GAS protein that inhibits complement function was unusually variable among isolates with the emm1 family of alleles, with a total of seven variants identified. The data suggest that many GAS strains infecting Mexican children are genetically similar to organisms commonly encountered in the United States and western Europe. Sequence variation in the sic gene is useful for rapid differentiation among GAS isolates with the emm1 family of alleles. PMID:9399523

  4. Identifying Development Needs

    ERIC Educational Resources Information Center

    Clark, R. J.; Turner, T. S.

    1976-01-01

    To identify management development needs some organizations have adopted the assessment center method, using simulations of work situations performed before and evaluated by specially trained observers (assessors). (MF)

  5. Gang Identifiers and Terminology.

    ERIC Educational Resources Information Center

    Cantrell, Mary Lynn

    1992-01-01

    Provides lists of gang identifiers and terminology. Suggests that, to find out names and associated identifiers of local gangs, readers should talk to their local police. Included in listing are descriptions of gang-related symbols, physical signals, graffiti, slogans, right-left rules, colors, clothing, jewelry, hair styles, and fingernails. Also…

  6. Metal alloy identifier

    DOEpatents

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

    1987-01-01

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

  7. Identifying learning styles.

    PubMed

    Hughes, Grace

    2016-12-14

    What was the nature of the CPD activity, practice-related feedback and/or event and/or experience in your practice? The article explored different learning styles and outlined some of the models that can be used to identify them. It discussed the limitations of these models, indicating that although they can be helpful in identifying a student's preferred learning style, this is not 'fixed' and might change over time. Learning is also influenced by other factors, such as culture and age.

  8. Identifying Technical Vocabulary

    ERIC Educational Resources Information Center

    Chung, Teresa Mihwa; Nation, Paul

    2004-01-01

    This study compared four different approaches to identifying technical words in an anatomy text. The first approach used a four step rating scale, and was used as the comparison for evaluating the other three approaches. It had a high degree of reliability. The least successful approach was that using clues provided by the writer such as labels in…

  9. Identifying Early School Leaving

    ERIC Educational Resources Information Center

    Poole, Millicent E.

    1978-01-01

    Using a matched sample of students who stay in school and those who drop out, or leave early, an attempt was made, via multiple discriminant analysis, to identify the significant characteristics which distinguish "drop outs" from their peers who remain at school. Results indicated that both types of students have similar value orientations and…

  10. Understanding and identifying variability

    USDA-ARS?s Scientific Manuscript database

    Variability is the quality of being uneven or lacking uniformity. Understanding the causes, magnitude, and strategies to manage variability within crop production settings can be used to directly improve agricultural production systems. Identifying when the magnitude of variability is high enough to...

  11. Identifying Nursing's Future Leaders.

    ERIC Educational Resources Information Center

    Gunning, Carolyn S.; Hawken, Patty L.

    1990-01-01

    A study determined that encouraging and supporting students in professional activities while they were still in school would lead those students to participate in professional nursing organizations after they graduated. Organized nursing needs to identify the factors that influence nurses to join organizations and concentrate on these factors to…

  12. Detection of Edwardsiella ictaluri in frozen catfish: Epidemiological application

    USDA-ARS?s Scientific Manuscript database

    Sampling large numbers of pond-cultured fish species for population studies will most likely occur in a hot ambient environment without immediate access to laboratory facilities. One solution to maintain sample integrity may be to place fish on dry ice and then transfer them to storage at -80ºC for...

  13. Identifying Marine Phytoplankton

    NASA Astrophysics Data System (ADS)

    Hargraves, Paul E.

    Until recently, anyone who needed to accurately identify marine phytoplankton had one of four choices: use the outdated Englishlanguage volumes by E. E. Cupp and N. I. Hendey plus the more recent book by J. Dodge, acquire a working knowledge of German and use the old volumes by Schiller and Hustedt, spend huge amounts of time in an exceedingly well-equipped marine science library trying in vain to keep up with the rapidly evolving field of phytoplankton systematics and taxonomy, or track down one of the rarest of endangered species—a phytoplankton taxonomist—and beg for help.To these unfortunate choices is added one considerably more hopeful: Identifying Marine Phytoplankton. This volume, which has seven contributing authors, contains most of the taxonomic groups that make up the planktonic autotrophs and some heterotrophs of the seas, coasts, and estuaries of the world (missing are cyanobacteria and some of the picoplankton groups).

  14. Oil Shale Identifier

    NASA Astrophysics Data System (ADS)

    Rocha, J.; Santacruz, J.; Randall, S.; McRae Alvarado, B.

    2016-12-01

    The main objective of our project was to identify which type of rock and where certain resources were positioned based on their properties, from well log data. During our research, we created best estimates of ranges for selected sedimentary rocks, by researching the properties of every rock. Although there are over a 1,000 different types of rocks and materials, each one has its own classifications, unique to it. When unearthing for resources, it is important to have knowledge of what type it is you are going for. These classifications are determined from logging tools, and are stored in charts called "Well Log Data". These Well Log Data charts are used to identify and determine what rock is underground in the reservoirs. Knowing what kind of rock is underneath would make the process of oil drilling both time and cost efficient. This project is a plug-in created in Petrel and Ocean to be able to identify the type of rock or mineral, specifically oil shale, based on its qualifications.

  15. On identified predictive control

    NASA Technical Reports Server (NTRS)

    Bialasiewicz, Jan T.

    1993-01-01

    Self-tuning control algorithms are potential successors to manually tuned PID controllers traditionally used in process control applications. A very attractive design method for self-tuning controllers, which has been developed over recent years, is the long-range predictive control (LRPC). The success of LRPC is due to its effectiveness with plants of unknown order and dead-time which may be simultaneously nonminimum phase and unstable or have multiple lightly damped poles (as in the case of flexible structures or flexible robot arms). LRPC is a receding horizon strategy and can be, in general terms, summarized as follows. Using assumed long-range (or multi-step) cost function the optimal control law is found in terms of unknown parameters of the predictor model of the process, current input-output sequence, and future reference signal sequence. The common approach is to assume that the input-output process model is known or separately identified and then to find the parameters of the predictor model. Once these are known, the optimal control law determines control signal at the current time t which is applied at the process input and the whole procedure is repeated at the next time instant. Most of the recent research in this field is apparently centered around the LRPC formulation developed by Clarke et al., known as generalized predictive control (GPC). GPC uses ARIMAX/CARIMA model of the process in its input-output formulation. In this paper, the GPC formulation is used but the process predictor model is derived from the state space formulation of the ARIMAX model and is directly identified over the receding horizon, i.e., using current input-output sequence. The underlying technique in the design of identified predictive control (IPC) algorithm is the identification algorithm of observer/Kalman filter Markov parameters developed by Juang et al. at NASA Langley Research Center and successfully applied to identification of flexible structures.

  16. Identifying Distant AGNs

    NASA Astrophysics Data System (ADS)

    Trouille, Laura; Barger, Amy; Tremonti, Christy

    2014-07-01

    The Baldwin, Phillips, and Terlevich emission-line ratio diagnostic ([OIII]/Hβ versus [NII]/Hα, hereafter BPT diagram) efficiently separates galaxies whose signal is dominated by star formation (BPT-SF) from those dominated by AGN activity (BPT-AGN). Yet the BPT diagram is limited to z<0.5, the redshift at which [NII]λ6584 leaves the optical spectral window. Using the Sloan Digital Sky Survey (SDSS), we construct a new diagnostic, or TBT diagram, that is based on rest-frame g-z color, [NeIII]λ3869, and [OII]λλ3726+3729 and can be used for galaxies out to z<1.4. The TBT diagram identifies 98.7% of the SDSS BPT-AGN as TBT-AGN and 97% of the SDSS BPT-SF as TBT-SF. Furthermore, it identifies 97% of the OPTX Chandra X-ray selected AGNs as TBT-AGN. This is in contrast to the BPT diagram, which misidentifies 20% of X-ray selected AGNs as BPT-SF.

  17. Isolation and identification of flavobacterium columnare and Steptococcus iniae antibacterial compounds from the terrestrial plant Atraphaxis laetevirens

    USDA-ARS?s Scientific Manuscript database

    Columnaris disease, enteric septicemia of catfish, and streptococcosis are common bacterial diseases of certain freshwater fish and are caused by Flavobacterium columnare, Edwardsiella ictaluri, and Streptococcus iniae, respectively. Various plants were selected to evaluate, isolate, and identify co...

  18. Encrypting personal identifiers.

    PubMed Central

    Meux, E

    1994-01-01

    STUDY SETTING. A statewide patient discharge database contained only one unique identifier: the social security number (SSN). A method was developed to transform (encrypt) the SSN so that it could be made publicly available, for purposes of linking discharge records, without revealing the SSN itself. The method of encrypting the SSN into a Record Linkage Number (RLN) is described. PRINCIPAL FINDINGS. The same RLN will always result from the same SSN; it is highly improbable that the same RLN would be produced by two different SSNs; the SSN cannot be derived from the RLN, even given access to the encryption program; the encryption method cannot be determined through knowledge of a number of SSN/RLN combinations; and the method can be described, evaluated, and adapted for use by other researchers without compromising confidentiality of the RLNs resulting from the method. PMID:8005792

  19. List identifies threatened ecosystems

    NASA Astrophysics Data System (ADS)

    Showstack, Randy

    2012-09-01

    The International Union for Conservation of Nature (IUCN) announced on 9 September that it will develop a new Red List of Ecosystems that will identify which ecosystems are vulnerable or endangered. The list, which is modeled on the group's Red List of Threatened Species™, could help to guide conservation activities and influence policy processes such as the Convention on Biological Diversity, according to the group. “We will assess the status of marine, terrestrial, freshwater, and subterranean ecosystems at local, regional, and global levels,” stated Jon Paul Rodriguez, leader of IUCN's Ecosystems Red List Thematic Group. “The assessment can then form the basis for concerted implementation action so that we can manage them sustainably if their risk of collapse is low or restore them if they are threatened and then monitor their recovery.”

  20. Identifying potential academic leaders

    PubMed Central

    White, David; Krueger, Paul; Meaney, Christopher; Antao, Viola; Kim, Florence; Kwong, Jeffrey C.

    2016-01-01

    Objective To identify variables associated with willingness to undertake leadership roles among academic family medicine faculty. Design Web-based survey. Bivariate and multivariable analyses (logistic regression) were used to identify variables associated with willingness to undertake leadership roles. Setting Department of Family and Community Medicine at the University of Toronto in Ontario. Participants A total of 687 faculty members. Main outcome measures Variables related to respondents’ willingness to take on various academic leadership roles. Results Of all 1029 faculty members invited to participate in the survey, 687 (66.8%) members responded. Of the respondents, 596 (86.8%) indicated their level of willingness to take on various academic leadership roles. Multivariable analysis revealed that the predictors associated with willingness to take on leadership roles were as follows: pursuit of professional development opportunities (odds ratio [OR] 3.79, 95% CI 2.29 to 6.27); currently holding at least 1 leadership role (OR 5.37, 95% CI 3.38 to 8.53); a history of leadership training (OR 1.86, 95% CI 1.25 to 2.78); the perception that mentorship is important for one’s current role (OR 2.25, 95% CI 1.40 to 3.60); and younger age (OR 0.97, 95% CI 0.95 to 0.99). Conclusion Willingness to undertake new or additional leadership roles was associated with 2 variables related to leadership experiences, 2 variables related to perceptions of mentorship and professional development, and 1 demographic variable (younger age). Interventions that support opportunities in these areas might expand the pool and strengthen the academic leadership potential of faculty members. PMID:27331226

  1. A hypervariable genomic island identified in clinical and environmental Mycobacterium avium subsp. hominissuis isolates from Germany.

    PubMed

    Sanchini, Andrea; Semmler, Torsten; Mao, Lei; Kumar, Narender; Dematheis, Flavia; Tandon, Kshitij; Peddireddy, Vidyullatha; Ahmed, Niyaz; Lewin, Astrid

    2016-11-01

    Mycobacterium avium subsp. hominissuis (MAH) is an opportunistic human pathogen widespread in the environment. Genomic islands (GI)s represent a part of the accessory genome of bacteria and influence virulence, drug-resistance or fitness and trigger bacterial evolution. We previously identified a novel GI in four MAH genomes. Here, we further explored this GI in a larger collection of MAH isolates from Germany (n=41), including 20 clinical and 21 environmental isolates. Based on comparative whole genome analysis, we detected this GI in 39/41 (95.1%) isolates. Although all these GIs integrated in the same insertion hotspot, there is high variability in the genetic structure of this GI: eight different types of GI have been identified, designated A-H (sized 6.2-73.3kb). These GIs were arranged as single GI (23/41, 56.1%), combination of two different GIs (14/41, 34.1%) or combination of three different GIs (2/41, 4.9%) in the insertion hotspot. Moreover, two GI types shared more than 80% sequence identity with sequences of M. canettii, responsible for Tuberculosis. A total of 253 different genes were identified in all GIs, among which the previously documented virulence-related genes mmpL10 and mce. The diversity of the GI and the sequence similarity with other mycobacteria suggests cross-species transfer, involving also highly pathogenic species. Shuffling of potential virulence genes such as mmpL10 via this GI may create new pathogens that can cause future outbreaks. Copyright © 2016 Elsevier GmbH. All rights reserved.

  2. Identifying Phronotypes in Psychiatry

    PubMed Central

    Kozel, F. Andrew

    2010-01-01

    Refinements in the methods of diagnosis for psychiatric disorders are critically needed. These new methods should be based on objectively measured brain characteristics that provide clinically useful information. Studying the brain with respect to psychiatric disorders, however, faces numerous challenges. Utilizing techniques learned in other areas of medicine to deal with symptoms that lead to complex disorders can provide insight into improving diagnostic models in psychiatry. Specifically, many areas of medicine use objective measures of an organ's function or characteristic to guide clinical management of particular subjective complaints. In psychiatry, an objectively measured brain characteristic that provides clinically useful information is proposed to be that person's “phronotype.” Important requirements to developing phronotypes are discussed. Identifying phronotypes in psychiatry will require a specific investigative approach that must be grounded in rigorous scientific methodology. Successfully developing such markers will have a profound impact on clinical care, clinical research, basic science research, and most importantly the lives of those suffering from these illnesses. PMID:21423450

  3. Identifying Adolescent Sleep Problems

    PubMed Central

    Short, Michelle A.; Gradisar, Michael; Gill, Jason; Camfferman, Danny

    2013-01-01

    Objectives To examine the efficacy of self-report and parental report of adolescent sleep problems and compare these findings to the incidence of adolescents who fulfill clinical criteria for a sleep problem. Sleep and daytime functioning factors that predict adolescents’ self-identification of a sleep problem will also be examined. Method 308 adolescents (aged 13–17 years) from eight socioeconomically diverse South Australian high schools participated in this study. Participants completed a survey battery during class time, followed by a 7-day Sleep Diary and the Flinders Fatigue Scale completed on the final day of the study. Parents completed a Sleep, Medical, Education and Family History Survey. Results The percentage of adolescents fulfilling one or more of the criteria for a sleep problem was inordinately high at 66%. Adolescent self-reporting a sleep problem was significantly lower than the adolescents who had one or more of the clinical criteria for a sleep problem (23.1% vs. 66.6%; χ2 = 17.46, p<.001). Parental report of their adolescent having a sleep problem was significantly lower than adolescent self-report (14.3% vs. 21.1%, p<.001). Adolescents who reported unrefreshing sleep were 4.81 times more likely to report a sleep problem. For every hour that bedtime was delayed, the odds of self-reporting a sleep problem increased by 1.91 times, while each additional 10 minutes taken to fall asleep increased the odds 1.40 times. Conclusion While many adolescents were found to have sleep patterns indicative of a sleep problem, only a third of this number self-identify having a sleep problem, while only a sixth of this number are indicated by parental report. This study highlights important features to target in future sleep education and intervention strategies for both adolescents and parents. PMID:24086501

  4. Virulence-related physiological changes and antigenic variation in populations of Streptococcus mutans colonizing gnotobiotic rats.

    PubMed

    Gibbons, R J; Qureshi, J V

    1980-09-01

    The purpose of this study was to determine if populations of Streptococcus mutans which were undergoing antigenic variation while colonizing gnotobiotic rats concomitantly became altered in physiological characteristics which affected their virulence. S. mutans strain JBP (serotype c), which was freshly isolated from a carious lesion in a 6-year old child, was used to inoculate gnotobiotic rats; uninfected animals served as controls. Substrains were isolated from animals 1, 2, 3, 4, and 12 weeks after infection; samples of pilocarpine-stimulated saliva were also obtained from representative animals for antibody analyses. Isolates derived from stock cultures of strain JBP proved to be homogeneous with respect to all of the physiological characteristics monitored. However, substrains isolated from the animals within 4 weeks after infection were altered with respect to their ability to agglutinate in the presence of sucrose, their ability to form adherent growth in sucrose broth, and the terminal pH attained in glucose broth. Some isolates obtained 12 weeks after infection no longer synthesized detectable levels of c antigen or intracellular glycogen, and they formed atypical smooth colonies on mitis salivarius agar. With an enzyme-linked immunosorbent assay, low levels of immunoglobulin A (IgA) antibodies reactive with whole JBP cells were detected in saliva samples of uninfected control animals at each sampling period; these evidently were induced to antigens contained in the diet of the animals. Significantly higher levels of IgA antibodies were present in saliva samples from animals infected with strain JBP for 3 weeks or longer. Thus, the emergence of antigenic and physiological variants of S. mutans in the animals was paralleled by increased levels of salivary IgA antibodies. The reactivity of salivary IgG with JBP cells was low, and it fluctuated in both groups of animals. No antibodies of the IgM class were detected. When tested in gnotobiotic rats, several variants, including strains which no longer formed typical rough colonies or adherent growth in sucrose broth, proved much less virulent than parental strain JBP in inducing carious lesions. Prior oral immunization, which resulted in higher levels of salivary and serum IgA antibodies reactive with strain JBP, was found to accelerate the emergence of smooth-colony variants in the animals; it was also associated with decreased streptococcal population levels on the teeth and in feces of the rats. It is suggested that part of the mechanism by which artificial immunization leads to a reduction in dental caries development in experimental animals is due to the earlier selection of less virulent streptococcal populations.

  5. A Network Inference Workflow Applied to Virulence-Related Processes in Salmonella typhimurium

    SciTech Connect

    Taylor, Ronald C.; Singhal, Mudita; Weller, Jennifer B.; Khoshnevis, Saeed; Shi, Liang; McDermott, Jason E.

    2009-04-20

    Inference of the structure of mRNA transcriptional regulatory networks, protein regulatory or interaction networks, and protein activation/inactivation-based signal transduction networks are critical tasks in systems biology. In this article we discuss a workflow for the reconstruction of parts of the transcriptional regulatory network of the pathogenic bacterium Salmonella typhimurium based on the information contained in sets of microarray gene expression data now available for that organism, and describe our results obtained by following this workflow. The primary tool is one of the network inference algorithms deployed in the Software Environment for BIological Network Inference (SEBINI). Specifically, we selected the algorithm called Context Likelihood of Relatedness (CLR), which uses the mutual information contained in the gene expression data to infer regulatory connections. The associated analysis pipeline automatically stores the inferred edges from the CLR runs within SEBINI and, upon request, transfers the inferred edges into either Cytoscape or the plug-in Collective Analysis of Biological of Biological Interaction Networks (CABIN) tool for further post-analysis of the inferred regulatory edges. The following article presents the outcome of this workflow, as well as the protocols followed for microarray data collection, data cleansing, and network inference. Our analysis revealed several interesting interactions, functional groups, metabolic pathways, and regulons in S. typhimurium.

  6. Characterization of Virulence-Related Phenotypes in Candida Species of the CUG Clade

    PubMed Central

    Priest, Shelby J.

    2015-01-01

    Candida species cause a variety of mucosal and invasive infections and are, collectively, the most important human fungal pathogens in the developed world. The majority of these infections result from a few related species within the “CUG clade,” so named because they use a nonstandard translation for that codon. Some members of the CUG clade, such as Candida albicans, present significant clinical problems, whereas others, such as Candida (Meyerozyma) guilliermondii, are uncommon in patients. The differences in incidence rates are imperfectly correlated with virulence in animal models of infection, but comparative analyses that might provide an explanation for why some species are effective pathogens and others are not have been rare or incomplete. To better understand the phenotypic basis for these differences, we characterized eight CUG clade species—C. albicans, C. dubliniensis, C. tropicalis, C. parapsilosis, Clavispora lusitaniae, M. guilliermondii, Debaryomyces hansenii, and Lodderomyces elongisporus—for host-relevant phenotypes, including nutrient utilization, stress tolerance, morphogenesis, interactions with phagocytes, and biofilm formation. Two species deviated from expectations based on animal studies and human incidence. C. dubliniensis was quite robust, grouping in nearly all assays with the most virulent species, C. albicans and C. tropicalis, whereas C. parapsilosis was substantially less fit than might be expected from its clinical importance. These findings confirm the utility of in vitro measures of virulence and provide insight into the evolution of virulence in the CUG clade. PMID:26150417

  7. Subinhibitory concentrations of punicalagin reduces expression of virulence-related exoproteins by Staphylococcus aureus.

    PubMed

    Mun, Su-Hyun; Kong, Ryong; Seo, Yun-Soo; Zhou, Tian; Kang, Ok-Hwa; Shin, Dong-Won; Kwon, Dong-Yeul

    2016-11-01

    Staphylococcus aureus produces a number of virulence factors. The major virulence factors exhibited by S aureus include various antigens, enzymes, cytotoxins and exotoxins (e.g. hemolysins, enterotoxins and toxic shock syndrome toxin). In this report, we show the influence of punicalagin on the secretion of exoprotein from S aureus by western blotting, tumor necrosis factor (TNF) release assay and quantitative RT-PCR. When added to S aureus cultures at an OD600 of 0.9, graded subinhibitory concentrations of punicalagin reduced the production of α-toxin, SEA and SEB in methicillin-resistant Staphylococcus aureus in a dose-dependent manner. Consistently, punicalagin reduced TNF-inducing activity by S aureus culture supernatants. Here, the transcriptional level of agr (accessory gene regulator) in S aureus was inhibited by punicalagin, suggesting that the reduced transcription may affect the secretion of exotoxins. These findings suggest that the expression of α-toxin and enterotoxins in S aureus is sensitive to the action of punicalagin, which may be an advantageous candidate in the treatment of toxigenic staphylococcal disease.

  8. Stochastic control system parameter identifiability

    NASA Technical Reports Server (NTRS)

    Lee, C. H.; Herget, C. J.

    1975-01-01

    The parameter identification problem of general discrete time, nonlinear, multiple input/multiple output dynamic systems with Gaussian white distributed measurement errors is considered. The knowledge of the system parameterization was assumed to be known. Concepts of local parameter identifiability and local constrained maximum likelihood parameter identifiability were established. A set of sufficient conditions for the existence of a region of parameter identifiability was derived. A computation procedure employing interval arithmetic was provided for finding the regions of parameter identifiability. If the vector of the true parameters is locally constrained maximum likelihood (CML) identifiable, then with probability one, the vector of true parameters is a unique maximal point of the maximum likelihood function in the region of parameter identifiability and the constrained maximum likelihood estimation sequence will converge to the vector of true parameters.

  9. Identifying the Emergency Management Profession.

    ERIC Educational Resources Information Center

    Chiesa, Adele M.

    1987-01-01

    In building an emergency management library collection within a training institution, technical data become secondary to identifying common goals, methods, and systems found at the federal, state, and local levels for responding to and planning for disasters and crises. These goals help identify emergency management skills public officials should…

  10. Identifying Context Variables in Research.

    ERIC Educational Resources Information Center

    Piazza, Carolyn L.

    1987-01-01

    Identifies context variables in written composition from theoretical perspectives in cognitive psychology, sociology, and anthropology. Considers how multiple views of context from across the disciplines can build toward a broader definition of writing. (JD)

  11. Identifying Occupationally Specific Affective Behaviors.

    ERIC Educational Resources Information Center

    Pucel, David J.

    1993-01-01

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

  12. Identifying Context Variables in Research.

    ERIC Educational Resources Information Center

    Piazza, Carolyn L.

    1987-01-01

    Identifies context variables in written composition from theoretical perspectives in cognitive psychology, sociology, and anthropology. Considers how multiple views of context from across the disciplines can build toward a broader definition of writing. (JD)

  13. Methods for identifying translational researchers.

    PubMed

    Feeney, Mary K; Johnson, Timothy; Welch, Eric W

    2014-03-01

    There is currently no generally accepted method for identifying the community of translational researchers when evaluating Clinical and Translational Science Centers. We use data from the multiyear evaluation of the University of Illinois at Chicago Center for Clinical and Translational Science (CCTS) to investigate the complexities of reliably identifying translational researchers. We use three methods to identify translational researchers: (1) participating in CCTS services and programs; (2) self-identifying as a translational researcher; and (3) engaging in activities that are characteristic of translational science. We find little overlap of these differently defined research groups. We conclude with a discussion of how the findings suggest challenges for evaluating translational science programs and the need for better definition, communication, and demonstration of translational science for scientists and evaluators.

  14. Identifying Occupationally Specific Affective Behaviors.

    ERIC Educational Resources Information Center

    Pucel, David J.

    1993-01-01

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

  15. Identifying Clients Predisposed To Failure

    ERIC Educational Resources Information Center

    Carnes, G. D.

    1973-01-01

    Studies are reviewed that report the prediction of rehabilitation failure from personality measures. Related research is discussed that suggest the dynamics underlying a key concept, the "hypochondriacally organized personality" which is identifiable from the Rorschach anatomy response percentage. (Author)

  16. Identifying discharge practice training needs.

    PubMed

    Lees, L; Emmerson, K

    A training needs analysis tool was developed to identify nurses' discharge training needs and to improve discharge practice. The tool includes 49 elements of discharge practice subdivided into four areas: corporate, operational, clinical and nurse-led discharge. The tool was disseminated to 15 wards on two hospital sites with assistance from the practice development team. Analysis of discharge training is important to assess discharge training needs and to identify staff who may assist with training.

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

    PubMed

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

    2016-04-04

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

  18. Analysis of the Protein Kinase A-Regulated Proteome of Cryptococcus neoformans Identifies a Role for the Ubiquitin-Proteasome Pathway in Capsule Formation

    PubMed Central

    Geddes, J. M. H.; Caza, M.; Croll, D.; Stoynov, N.; Foster, L. J.

    2016-01-01

    ABSTRACT The opportunistic fungal pathogen Cryptococcus neoformans causes life-threatening meningitis in immunocompromised individuals. The expression of virulence factors, including capsule and melanin, is in part regulated by the cyclic-AMP/protein kinase A (cAMP/PKA) signal transduction pathway. In this study, we investigated the influence of PKA on the composition of the intracellular proteome to obtain a comprehensive understanding of the regulation that underpins virulence. Through quantitative proteomics, enrichment and bioinformatic analyses, and an interactome study, we uncovered a pattern of PKA regulation for proteins associated with translation, the proteasome, metabolism, amino acid biosynthesis, and virulence-related functions. PKA regulation of the ubiquitin-proteasome pathway in C. neoformans showed a striking parallel with connections between PKA and protein degradation in chronic neurodegenerative disorders and other human diseases. Further investigation of proteasome function with the inhibitor bortezomib revealed an impact on capsule production as well as hypersusceptibility for strains with altered expression or activity of PKA. Parallel studies with tunicamycin also linked endoplasmic reticulum stress with capsule production and PKA. Taken together, the data suggest a model whereby expression of PKA regulatory and catalytic subunits and the activation of PKA influence proteostasis and the function of the endoplasmic reticulum to control the elaboration of the polysaccharide capsule. Overall, this study revealed both broad and conserved influences of the cAMP/PKA pathway on the proteome and identified proteostasis as a potential therapeutic target for the treatment of cryptococcosis. PMID:26758180

  19. Identifying tier one key suppliers.

    PubMed

    Wicks, Steve

    2013-01-01

    In today's global marketplace, businesses are becoming increasingly reliant on suppliers for the provision of key processes, activities, products and services in support of their strategic business goals. The result is that now, more than ever, the failure of a key supplier has potential to damage reputation, productivity, compliance and financial performance seriously. Yet despite this, there is no recognised standard or guidance for identifying a tier one key supplier base and, up to now, there has been little or no research on how to do so effectively. This paper outlines the key findings of a BCI-sponsored research project to investigate good practice in identifying tier one key suppliers, and suggests a scalable framework process model and risk matrix tool to help businesses effectively identify their tier one key supplier base.

  20. Persistent Identifiers Implementation in EOSDIS

    NASA Technical Reports Server (NTRS)

    Ramapriyan, H. K. " Rama"

    2016-01-01

    This presentation provides the motivation for and status of implementation of persistent identifiers in NASA's Earth Observation System Data and Information System (EOSDIS). The motivation is provided from the point of view of long-term preservation of datasets such that a number of questions raised by current and future users can be answered easily and precisely. A number of artifacts need to be preserved along with datasets to make this possible, especially when the authors of datasets are no longer available to address users questions. The artifacts and datasets need to be uniquely and persistently identified and linked with each other for full traceability, understandability and scientific reproducibility. Current work in the Earth Science Data and Information System (ESDIS) Project and the Distributed Active Archive Centers (DAACs) in assigning Digital Object Identifiers (DOI) is discussed as well as challenges that remain to be addressed in the future.

  1. [Advances in recently identified coronaviruses].

    PubMed

    Geng, He-Yuan; Tan, Wen-Jie

    2013-01-01

    Coronaviruses are a large family of viruses which include viruses that cause the common cold and severe acute respiratory syndrome (SARS) in humans and other diseases in animals. There are considerable genetic diversities within coronaviruses due to their wide rang hosts and their special gene replication and transcription mechanisms. During this process, gene recombinations often occur, resulting in novel subtype or coronavirus emerge constantly. Of note are SARS-like-CoVs and novel HCoV-EMC identified in 2012. This minireview summarized major advances of recently identified coronaviruses, focusing on the genome structures and interspecies jumping mechanism of coronavirus.

  2. Testing times: identifying puberty in an identified skeletal sample.

    PubMed

    Henderson, Charlotte Y; Padez, Cristina

    2017-06-01

    Identifying the onset of puberty in skeletal remains can provide evidence of social changes associated with the onset of adulthood. This paper presents the first test of a skeletal method for identifying stages of development associated with the onset of puberty in a skeletal sample of known age and cause of death. Skeletal methods for assessing skeletal development associated with changes associated with puberty were recorded in the identified skeletal collection in Coimbra, Portugal. Historical data on the onset of menarche in this country are used to test the method. As expected, females mature faster than their male counterparts. There is some side asymmetry in development. Menarche was found to have been achieved by an average age of 15. Asymmetry must be taken into account when dealing with partially preserved skeletons. Age of menarche is consistent, although marginally higher, than the age expected based on historical data for this time and location. Skeletal development in males could not be tested against historical data, due to the lack of counterpart historical data. The ill health known to be present in this prematurely deceased population may have delayed skeletal development and the onset of puberty.

  3. Identifying Pilots with Parkinson's Disease.

    PubMed

    Clem, Peter A; Navathe, Pooshan D; Drane, Michael A

    2016-06-01

    In 2012 the Australian Institute of Health and Welfare produced a report titled 'Dementia in Australia.'(2) The report noted that the number of people with dementia in Australia would reach almost 400,000 by 2020. Australia is a jurisdiction which does not impose a mandatory retirement age for pilots. With an aging population it was hypothesized that conditions such as Parkinson's disease (PD) were likely to be seen more commonly by the Civil Aviation Safety Authority (CASA). It was decided that this was an appropriate time to retrospectively study the data held by CASA. An interrogation of CASA databases was undertaken. Data was produced comparing percentage of Class 1 certificate holders over 60 yr of age against time. A cohort of pilots and controllers with PD was identified. The history of the cases was reviewed. The study confirms that the pilot population is aging in line with population trends. Over a period from 1992 to 2012, 22 cases of pilots and controllers with PD were identified. The study confirmed that PD will be of increased relevance over the next decade. Gaps between policy and practice managing past cases were identified. Updated guidelines have been published aiming to address the deficiencies identified in the study. Historically pilots and controllers have been able to maintain certification for an average of 3.75 yr. This information should be of benefit to clinicians, pilots, and controllers when considering occupation and treatment options.

  4. "Geriatricizing" Hospitalists: Identifying Educational Opportunities

    ERIC Educational Resources Information Center

    Friedman, Susan M.; Gillespie, Suzanne M.; Medina-Walpole, Annette M.; Caprio, Thomas V.; Karuza, Jurgis; McCann, Robert M.

    2013-01-01

    The objective of this study was to identify differences between geriatricians and hospitalists in caring for hospitalized older adults, so as to inform faculty development programs that have the goal of improving older patient care. Eleven hospitalists and 13 geriatricians were surveyed regarding knowledge, confidence, and practice patterns in…

  5. SOCIODEMOGRAPHIC DATA USED FOR IDENTIFYING ...

    EPA Pesticide Factsheets

    Due to unique social and demographic characteristics, various segments of the population may experience exposures different from those of the general population, which, in many cases, may be greater. When risk assessments do not characterize subsets of the general population, the populations that may experience the greatest risk remain unidentified. When such populations are not identified, the social and demographic data relevant to these populations is not considered when preparing exposure estimates, which can underestimate exposure and risk estimates for at-risk populations. Thus, it is necessary for risk or exposure assessors characterizing a diverse population, to first identify and then enumerate certain groups within the general population who are at risk for greater contaminant exposures. The document entitled Sociodemographic Data Used for Identifying Potentially Highly Exposed Populations (also referred to as the Highly Exposed Populations document), assists assessors in identifying and enumerating potentially highly exposed populations. This document presents data relating to factors which potentially impact an individual or group's exposure to environmental contaminants based on activity patterns (how time is spent), microenvironments (locations where time is spent), and other socio-demographic data such as age, gender, race and economic status. Populations potentially more exposed to various chemicals of concern, relative to the general population

  6. "Geriatricizing" Hospitalists: Identifying Educational Opportunities

    ERIC Educational Resources Information Center

    Friedman, Susan M.; Gillespie, Suzanne M.; Medina-Walpole, Annette M.; Caprio, Thomas V.; Karuza, Jurgis; McCann, Robert M.

    2013-01-01

    The objective of this study was to identify differences between geriatricians and hospitalists in caring for hospitalized older adults, so as to inform faculty development programs that have the goal of improving older patient care. Eleven hospitalists and 13 geriatricians were surveyed regarding knowledge, confidence, and practice patterns in…

  7. Identifying the Gifted Child Humorist.

    ERIC Educational Resources Information Center

    Fern, Tami L.

    1991-01-01

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

  8. Identifying Innovative Agricultural Education Programs

    ERIC Educational Resources Information Center

    Rayfield, John; Murphy, Tim; Briers, Gary; Lewis, Lauren

    2012-01-01

    Researchers identified innovative agricultural education programs across the United States. A Delphi study was conducted with the teachers in innovative programs. According to the teachers, innovative programs in 2020 will use hands-on activities and will be run by highly motivated teachers. The purpose of innovative programs in the future will be…

  9. Identifiability, exchangeability and confounding revisited

    PubMed Central

    Greenland, Sander; Robins, James M

    2009-01-01

    In 1986 the International Journal of Epidemiology published "Identifiability, Exchangeability and Epidemiological Confounding". We review the article from the perspective of a quarter century after it was first drafted and relate it to subsequent developments on confounding, ignorability, and collapsibility. PMID:19732410

  10. Methods of Identifying Marketing Competencies

    ERIC Educational Resources Information Center

    Crawford, Lucy C.; Ertel, Kenneth A.

    1970-01-01

    The competency pattern and the task analysis are two approaches used to identify content that affects the distributive education curriculum. These and other research tools provide essential information about capabilities required for entrance into and persistence in careers at prescribed levels of distributive jobs. (Author)

  11. Identifying predictors of treatment response.

    PubMed

    Yoder, Paul; Compton, Don

    2004-01-01

    This article provides a rationale for considering predictors of growth in a treatment group as inadequate to identifying predictors of treatment response. When we interpret predictors of growth in a treatment group as synonymous with predictors of treatment response, we implicitly attribute all of the treated children's growth to the treatment, an untenable assumption under most conditions. We also contend that the use of standard scores in predictors of growth studies does not allow us to differentiate growth from treatment, from growth from other factors. We present two research methodologies that are appropriate methods of identifying predictors of treatment response: (a) single-subject experimental logic utilized to identify the specific participants in which treatment responses (not just growth) were found, combined with follow-up group comparison logic to identify the characteristics on which responders and nonresponders differ, and (b) statistical interactions among child/family/context characteristics and randomly assigned group membership. Principles for selecting potential predictors of treatment response are provided.

  12. Identified Sins in Teaching Reading.

    ERIC Educational Resources Information Center

    Ediger, Marlow

    This paper cites as selected taboos in teaching reading (identified by educators very frequently) the following: (1) homogeneous grouping; (2) round robin reading; (3) use of textbooks and workbooks in the curriculum; (4) individual endeavors in school work; (5) memorization of content; and (6) the controlled vocabulary in reading. The paper…

  13. Metadata, Identifiers, and Physical Samples

    NASA Astrophysics Data System (ADS)

    Arctur, D. K.; Lenhardt, W. C.; Hills, D. J.; Jenkyns, R.; Stroker, K. J.; Todd, N. S.; Dassie, E. P.; Bowring, J. F.

    2016-12-01

    Physical samples are integral to much of the research conducted by geoscientists. The samples used in this research are often obtained at significant cost and represent an important investment for future research. However, making information about samples - whether considered data or metadata - available for researchers to enable discovery is difficult: a number of key elements related to samples are difficult to characterize in common ways, such as classification, location, sample type, sampling method, repository information, subsample distribution, and instrumentation, because these differ from one domain to the next. Unifying these elements or developing metadata crosswalks is needed. The iSamples (Internet of Samples) NSF-funded Research Coordination Network (RCN) is investigating ways to develop these types of interoperability and crosswalks. Within the iSamples RCN, one of its working groups, WG1, has focused on the metadata related to physical samples. This includes identifying existing metadata standards and systems, and how they might interoperate with the International Geo Sample Number (IGSN) schema (schema.igsn.org) in order to help inform leading practices for metadata. For example, we are examining lifecycle metadata beyond the IGSN `birth certificate.' As a first step, this working group is developing a list of relevant standards and comparing their various attributes. In addition, the working group is looking toward technical solutions to facilitate developing a linked set of registries to build the web of samples. Finally, the group is also developing a comparison of sample identifiers and locators. This paper will provide an overview and comparison of the standards identified thus far, as well as an update on the technical solutions examined for integration. We will discuss how various sample identifiers might work in complementary fashion with the IGSN to more completely describe samples, facilitate retrieval of contextual information, and

  14. Identifying the potential rural optometrist.

    PubMed

    Kegel-Flom, P

    1976-09-01

    Rural optometrists were found to differ from urban optometrists in background, environmental attitude, and interest patterns. Attitude toward the urban environment and place of origin were the best predictors of an optometrist's practice location. When "urbanism" and "origin" were scaled and placed in a multiple regression equation to predict practice location, identification of an optometrist's location as rural or urban was highly accurate. Most importantly, scores on the equation were predictive of optometry students' future practice locations. A single cut-off point on the equation correctly identified 79% of students who entered rural or isolated small city practice and 81% of those who entered urban practice. The findings suggest that optometry students most likely to enter rural (or indeed urban) practice can be objectively identified early in, or even prior to, training. Such identification may assist educators in selecting and training optometrists who will deliver vision care to people in areas of greatest need.

  15. Identifying and managing problem drinkers.

    PubMed Central

    Kahan, M.

    1996-01-01

    Problem drinking is far more common than severe alcohol dependence and is associated with considerable morbidity and health care costs. Whereas patients with alcohol dependence respond best to intensive treatment, one or more brief sessions of physician advice and counseling reduces alcohol consumption among problem drinkers. The two most useful tools to identify problem drinkers are the CAGE and the drinking problem question. PMID:8653034

  16. Identifying Targets from Filtering Effects

    DTIC Science & Technology

    2012-10-24

    Introduction Considering a radar (or sonar) target as more than a simple point scatterer brings up the possibility of identifying the target based on the...2000. [8] M. Vespe, C. J. Baker, and H. D. Griffiths , "Automatic target regognition using multi-diversity radar," Radar, Sonar \\& Navigation, IET, vol...A. Taflove and S. C. Hagness, Computational Electrodynamics : The Finite Difference Time Domain Method. Norwood, MA: Artech House, 2005.

  17. Identifying Network Perturbation in Cancer

    PubMed Central

    Logsdon, Benjamin A.; Gentles, Andrew J.; Lee, Su-In

    2016-01-01

    We present a computational framework, called DISCERN (DIfferential SparsE Regulatory Network), to identify informative topological changes in gene-regulator dependence networks inferred on the basis of mRNA expression datasets within distinct biological states. DISCERN takes two expression datasets as input: an expression dataset of diseased tissues from patients with a disease of interest and another expression dataset from matching normal tissues. DISCERN estimates the extent to which each gene is perturbed—having distinct regulator connectivity in the inferred gene-regulator dependencies between the disease and normal conditions. This approach has distinct advantages over existing methods. First, DISCERN infers conditional dependencies between candidate regulators and genes, where conditional dependence relationships discriminate the evidence for direct interactions from indirect interactions more precisely than pairwise correlation. Second, DISCERN uses a new likelihood-based scoring function to alleviate concerns about accuracy of the specific edges inferred in a particular network. DISCERN identifies perturbed genes more accurately in synthetic data than existing methods to identify perturbed genes between distinct states. In expression datasets from patients with acute myeloid leukemia (AML), breast cancer and lung cancer, genes with high DISCERN scores in each cancer are enriched for known tumor drivers, genes associated with the biological processes known to be important in the disease, and genes associated with patient prognosis, in the respective cancer. Finally, we show that DISCERN can uncover potential mechanisms underlying network perturbation by explaining observed epigenomic activity patterns in cancer and normal tissue types more accurately than alternative methods, based on the available epigenomic data from the ENCODE project. PMID:27145341

  18. Identifying crash patterns on roundabouts.

    PubMed

    Polders, Evelien; Daniels, Stijn; Casters, Winfried; Brijs, Tom

    2015-01-01

    Roundabouts are a type of circular intersection control generally associated with a favorable influence on traffic safety. International studies of intersections converted to roundabouts indicate a strong reduction in injury crashes, particularly for crashes with fatal or serious injuries. Nevertheless, some crashes still occur at roundabouts. The present study aims to improve the understanding of roundabout safety by identifying crash types, locations, and factors that are associated with roundabout crashes. An analysis of 399 crashes on 28 roundabouts in Flanders, Belgium, was carried out based on detailed crash descriptions; that is, crash data and collision diagrams. The crashes are sampled from police-reported crashes at roundabouts in the region of Flanders, Belgium. Collision diagrams of the registered crashes were used to distinguish 8 different crash types. The roundabout itself is divided into 11 detailed and different typical segments, according to previously established knowledge on the occurrence of crashes at roundabouts. The 8 roundabout crash types are examined by injury severity, crash location within the roundabout, type of roundabout, type of cycle facility, and type of involved road user. Four dominant crash types are identified: rear-end crashes, collisions with vulnerable road users, entering-circulating crashes, and single-vehicle collisions with the central island. Crashes with vulnerable road users and collisions with the central island are characterized by significantly higher proportions of injury crashes. About 80% of the crashes occurred on the entry lanes and the circulatory road (segments 1-4). Road users who are the most at risk to be involved in serious injury crashes at roundabouts are cyclists and moped riders. The main goal of this study was to identify and analyze dominant crash types at roundabouts by taking into account detailed information on the crash location. Some connections between certain roundabout crash types, their

  19. Identifying the health conscious consumer.

    PubMed

    Kraft, F B; Goodell, P W

    1993-01-01

    Individuals who lead a "wellness-oriented" lifestyle are concerned with nutrition, fitness, stress, and their environment. They accept responsibility for their health and are excellent customers for health-related products and services. Those who lack a wellness orientation are identified as higher health risks and become candidates for health promotion program intervention. The authors report a new scale by which to measure the wellness-oriented lifestyle. Scale development procedures are detailed, followed by information from five studies that support its validity. The authors suggest ways health care marketers may use the Wellness Scale to segment and target potential customers and position their products and services.

  20. Featured Image: Identifying Weird Galaxies

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2017-08-01

    Hoags Object, an example of a ring galaxy. [NASA/Hubble Heritage Team/Ray A. Lucas (STScI/AURA)]The above image (click for the full view) shows PanSTARRSobservationsof some of the 185 galaxies identified in a recent study as ring galaxies bizarre and rare irregular galaxies that exhibit stars and gas in a ring around a central nucleus. Ring galaxies could be formed in a number of ways; one theory is that some might form in a galaxy collision when a smaller galaxy punches through the center of a larger one, triggering star formation around the center. In a recent study, Ian Timmis and Lior Shamir of Lawrence Technological University in Michigan explore ways that we may be able to identify ring galaxies in the overwhelming number of images expected from large upcoming surveys. They develop a computer analysis method that automatically finds ring galaxy candidates based on their visual appearance, and they test their approach on the 3 million galaxy images from the first PanSTARRS data release. To see more of the remarkable galaxies the authors found and to learn more about their identification method, check out the paper below.CitationIan Timmis and Lior Shamir 2017 ApJS 231 2. doi:10.3847/1538-4365/aa78a3

  1. Detecting and identifying offset gaze.

    PubMed

    Balsdon, Tarryn; Clifford, Colin W G

    2017-06-14

    A number of experiments have demonstrated that observers can accurately identify stimuli that they fail to detect (Rollman and Nachmias, 1972; Harris and Fahle, 1995; Allik et al. 1982, 2014). Using a 2x2AFC double judgements procedure, we demonstrated an analogous pattern of performance in making judgements about the direction of eye gaze. Participants were shown two faces in succession: one with direct gaze and one with gaze offset to the left or right. We found that they could identify the direction of gaze offset (left/right) better than they could detect which face contained the offset gaze. A simple Thurstonian model, under which the detection judgement is shown to be more computationally complex, was found to explain the empirical data. A further experiment incorporated metacognitive ratings into the double judgements procedure to measure observers' metacognitive awareness (Meta-d') across the two judgements and to assess whether observers were aware of the evidence for offset gaze when detection performance was at and below threshold. Results suggest that metacognitive awareness is tied to performance, with approximately equal Meta-d' across the two judgements, when sensitivity is taken into account. These results show that both performance and metacognitive awareness rely not only on the strength of sensory evidence but also on the computational complexity of the decision, which determines the relative distance of that evidence from the decision axes.

  2. Identifying teaching in wild animals.

    PubMed

    Thornton, Alex; Raihani, Nichola J

    2010-08-01

    After a long period of neglect, the study of teaching in nonhuman animals is beginning to take a more prominent role in research on social learning. Unlike other forms of social learning, teaching requires knowledgeable individuals to play an active role in facilitating learning by the naive. Casting aside anthropocentric requirements for cognitive mechanisms assumed to underpin teaching in our own species, researchers are now beginning to discover evidence for teaching across a wide range of taxa. Nevertheless, unequivocal evidence for teaching remains scarce, with convincing experimental data limited to meerkats, pied babblers, and tandem-running ants. In this review, our aim is to stimulate further research in different species and contexts by providing conceptual and methodological guidelines for identifying teaching, with a focus on natural populations. We begin by highlighting the fact that teaching is a form of cooperative behavior that functions to promote learning in others and show that consideration of these key characteristics is critical in helping to identify suitable targets for future research. We then go on to discuss potential observational, experimental, and statistical techniques that may assist researchers in providing evidence that the criteria that make up the accepted operational definition of teaching have been met. Supplemental materials for this article may be downloaded from http://lb.psychonomic-journals.org/content/supplemental.

  3. Identifying future zoonotic disease threats

    PubMed Central

    Cooper, Natalie; Nunn, Charles L.

    2013-01-01

    Background and objectives: Emerging infectious diseases often originate in wildlife, making it important to identify infectious agents in wild populations. It is widely acknowledged that wild animals are incompletely sampled for infectious agents, especially in developing countries, but it is unclear how much more sampling is needed, and where that effort should focus in terms of host species and geographic locations. Here, we identify these gaps in primate parasites, many of which have already emerged as threats to human health. Methodology: We obtained primate host–parasite records and other variables from existing databases. We then investigated sampling effort within primates relative to their geographic range size, and within countries relative to their primate species richness. We used generalized linear models, controlling for phylogenetic or spatial autocorrelation, to model variation in sampling effort across primates and countries. Finally, we used species richness estimators to extrapolate parasite species richness. Results: We found uneven sampling effort within all primate groups and continents. Sampling effort among primates was influenced by their geographic range size and substrate use, with terrestrial species receiving more sampling. Our parasite species richness estimates suggested that, among the best sampled primates and countries, almost half of primate parasites remain to be sampled; for most primate hosts, the situation is much worse. Conclusions and implications: Sampling effort for primate parasites is uneven and low. The sobering message is that we know little about even the best studied primates, and even less regarding the spatial and temporal distribution of parasitism within species. PMID:24481184

  4. Identifying infection hotspots early on.

    PubMed

    Shabha, Ghasson

    2012-04-01

    According to many published studies, 'ducting in ventilation and air-conditioning are largely overlooked and ignored, as they are out of sight and out of mind', despite mounting evidence indicating a higher risk in spreading airborne infections'. So says Ghasson Shabha BSc (Arch) MSc, PhD (Arch), MBIFM, Associate CIBSE, PG Cert Ed, of the Faculty of Technology, Engineering and the Environment (TEE), at the Birmingham School of the Built Environment (BSBE) at Birmingham City University, who adds that CIBSE estimates that fewer than 5% of buildings with air-conditioning systems above 12 kW have been inspected so far. Here he argues that incorporating 3D building information modelling software into existing computer-aided facilities management software systems will enable hospitals' 'infection hotspots' to be far more quickly identified, and subsequently monitored, to prevent future problems.

  5. Identifying and mapping community vulnerability.

    PubMed

    Morrow, B H

    1999-03-01

    Disaster vulnerability is socially constructed, i.e., it arises out of the social and economic circumstances of everyday living. Most often discussed from the perspective of developing nations, this article extends the argument using American demographic trends. Examples from recent disasters, Hurricane Andrew in particular, illustrate how certain categories of people, such as the poor, the elderly, women-headed households and recent residents, are at greater risk throughout the disaster response process. Knowledge of where these groups are concentrated within communities and the general nature of their circumstances is an important step towards effective emergency management. Emergency planners, policy-makers and responding organisations are encouraged to identify and locate high-risk sectors on Community Vulnerability Maps, integrating this information into GIS systems where feasible. Effective disaster management calls for aggressively involving these neighbourhoods and groups at all levels of planning and response, as well as mitigation efforts that address the root causes of vulnerability.

  6. Identifying methamphetamine exposure in children

    PubMed Central

    Castaneto, Marisol S.; Barnes, Allan J.; Scheidweiler, Karl B.; Schaffer, Michael; Rogers, Kristen K.; Stewart, Deborah; Huestis, Marilyn A.

    2013-01-01

    Introduction Methamphetamine (MAMP) use, distribution and manufacture remain a serious public health and safety problem in the United States, and children environmentally exposed to MAMP face a myriad of developmental, social and health risks, including severe abuse and neglect necessitating child protection involvement. It is recommended that drug-endangered children receive medical evaluation and care with documentation of overall physical and mental conditions and have urine drug testing.1 The primary aim of this study was to determine the best biological matrix to detect MAMP, amphetamine (AMP), methylenedioxymethamphetamine (MDMA), methylenedioxyamphetamine (MDA) and methylenedioxyethylamphetamine (MDEA) in environmentally exposed children. Method 91 children, environmentally exposed to household MAMP intake, were medically evaluated at the Child and Adolescent Abuse Resource and Evaluation (CAARE) Diagnostic and Treatment Center at the University of California, Davis (UCD) Children's Hospital. MAMP, AMP, MDMA, MDA and MDEA were quantified in urine and oral fluid (OF) by gas chromatography mass spectrometry (GCMS) and in hair by liquid chromatography tandem mass spectrometry (LCMSMS). Results Overall drug detection rates in OF, urine and hair were 6.9%, 22.1% and 77.8%, respectively. Seventy children (79%) tested positive for 1 or more drugs in 1 or more matrices. MAMP was the primary analyte detected in all 3 biological matrices. All positive OF (n=5) and 18 of 19 positive urine specimens also had a positive hair test. Conclusion Hair analysis offered a more sensitive tool for identifying MAMP, AMP and MDMA environmental exposure in children than urine or OF testing. A negative urine, or hair test does not exclude the possibility of drug exposure, but hair testing provided the greatest sensitivity for identifying drug-exposed children. PMID:24263642

  7. Identifying problem and compulsive gamblers.

    PubMed Central

    van Es, R.

    2000-01-01

    OBJECTIVE: To present a meta-analysis of current research on the prevalence, identification, and treatment of problem and compulsive gamblers. QUALITY OF EVIDENCE: Problem and compulsive gambling was not a socio-scientific concern until the last two decades. Hence research on this topic is limited. The summary and analysis for this paper relied on computer searches of journal and news abstracts in addition to direct contact with organizations addressing the identification and treatment of compulsive gamblers. MAIN MESSAGE: An estimated 5% of those who gamble run into problems. About 1% of those who gamble are predicted to experience serious problems. Successful treatment of problem and compulsive gambling continues to be a challenge. Although cognitive therapy has been the favoured approach, a combination of several therapeutic approaches is advocated. CONCLUSIONS: Problem and compulsive gambling can present a real health threat. As with other addictions, treatment strategies continue to be a baffling social problem. Aware and informed physicians can have a pivotal role in the difficult process of identifying, acknowledging, and remediating problem and compulsive gambling. PMID:10907572

  8. Identifying and Bounding Ethnic Neighborhoods

    PubMed Central

    Logan, John R.; Spielman, Seth; Xu, Hongwei; Klein, Philip N.

    2013-01-01

    This study presents three novel approaches to the question of how best to identify ethnic neighborhoods (or more generally, neighborhoods defined any aspect of their population composition) and to define their boundaries. It takes advantage of unusual data on the residential locations of all residents of Newark, NJ, in 1880 to avoid having to accept arbitrary administrative units (like census tracts) as the building blocks of neighborhoods. For theoretical reasons the street segment is chosen as the basic unit of analysis. All three methods use information on the ethnic composition of buildings or street segments and the ethnicity of their neighbors. One approach is a variation of k-functions calculated for each adult resident, which are then subjected to a cluster analysis to detect discrete patterns. The second is an application of an energy minimization algorithm commonly used to enhance digital images. The third is a Bayesian approach previously used to study county-level disability data. Results of all three methods depend on decisions about technical procedures and criteria that are made by the investigator. Resulting maps are roughly similar, but there is no one best solution. We conclude that researchers should continue to seek alternative methods, and that the preferred method depends on how one’s conceptualization of neighborhoods matches the empirical approach. PMID:24039327

  9. RECOVIR Software for Identifying Viruses

    NASA Technical Reports Server (NTRS)

    Chakravarty, Sugoto; Fox, George E.; Zhu, Dianhui

    2013-01-01

    Most single-stranded RNA (ssRNA) viruses mutate rapidly to generate a large number of strains with highly divergent capsid sequences. Determining the capsid residues or nucleotides that uniquely characterize these strains is critical in understanding the strain diversity of these viruses. RECOVIR (an acronym for "recognize viruses") software predicts the strains of some ssRNA viruses from their limited sequence data. Novel phylogenetic-tree-based databases of protein or nucleic acid residues that uniquely characterize these virus strains are created. Strains of input virus sequences (partial or complete) are predicted through residue-wise comparisons with the databases. RECOVIR uses unique characterizing residues to identify automatically strains of partial or complete capsid sequences of picorna and caliciviruses, two of the most highly diverse ssRNA virus families. Partition-wise comparisons of the database residues with the corresponding residues of more than 300 complete and partial sequences of these viruses resulted in correct strain identification for all of these sequences. This study shows the feasibility of creating databases of hitherto unknown residues uniquely characterizing the capsid sequences of two of the most highly divergent ssRNA virus families. These databases enable automated strain identification from partial or complete capsid sequences of these human and animal pathogens.

  10. Identifying Chemical Groups for Biomonitoring

    PubMed Central

    Krowech, Gail; Hoover, Sara; Plummer, Laurel; Sandy, Martha; Zeise, Lauren; Solomon, Gina

    2016-01-01

    Summary: Regulatory agencies face daunting challenges identifying emerging chemical hazards because of the large number of chemicals in commerce and limited data on exposure and toxicology. Evaluating one chemical at a time is inefficient and can lead to replacement with uncharacterized chemicals or chemicals with structural features already linked to toxicity. The Office of Environmental Health Hazard Assessment (OEHHA) has developed a process for constructing and assessing chemical groups for potential biomonitoring in California. We screen for chemicals with significant exposure potential and propose possible chemical groups, based on structure and function. To support formal consideration of these groups by Biomonitoring California’s Scientific Guidance Panel, we conduct a detailed review of exposure and toxicity data and examine the likelihood of detection in biological samples. To date, 12 chemical groups have been constructed and added to the pool of chemicals that can be selected for Biomonitoring California studies, including p,p´-bisphenols, brominated and chlorinated organic compounds used as flame retardants, non-halogenated aromatic phosphates, and synthetic polycyclic musks. Evaluating chemical groups, rather than individual chemicals, is an efficient way to respond to shifts in chemical use and the emergence of new chemicals. This strategy can enable earlier identification of important chemicals for monitoring and intervention. PMID:27905275

  11. Identifying acid salts of magnesium

    SciTech Connect

    Plumb, R.; Thivierge, R.F. Jr.; Xu, W.W.

    1987-11-05

    In preliminary work they found that significant quantities of certain nitrogen oxides and of sulfuric acid were absorbed by lower hydrates of magnesium sulfate. It appeared that acid salts were being formed but the known chemistry of group IIA (group 2) sulfates and acid sulfates which was worked out many years ago did not provide an explanation of their observations. They developed a new technique for delineating the solidus boundary of ternary mixtures using friability tests and applied it to the systems of interest. Magnesium acid salt hydrates with compositions on the solidus boundary could be readily identified. X-ray powder patterns confirmed the existence of two previously unknown ternary compounds, Mg/sub 2/(HSO/sub 4/)/sub 2/SO/sub 4/ x 4H/sub 2/O and Mg(HSO/sub 4/)/sub 2/ x H/sub 2/SO/sub 4/ x 3H/sub 2/O. Mixed acid sulfate-nitrate-hydrates could be detected but fuming at room temperatures interfered with quantitative determinations of the solidus boundary and X-ray measurements.

  12. Identifying and Inactivating Bacterial Spores

    NASA Technical Reports Server (NTRS)

    Newcombe, David; Dekas, Anne; Venkateswaran, Kasthuri

    2009-01-01

    Problems associated with, and new strategies for, inactivating resistant organisms like Bacillus canaveralius (found at Kennedy Space Center during a survey of three NASA cleanrooms) have been defined. Identifying the particular component of the spore that allows its heightened resistance can guide the development of sterilization procedures that are targeted to the specific molecules responsible for resistance, while avoiding using unduly harsh methods that jeopardize equipment. The key element of spore resistance is a multilayered protein shell that encases the spore called the spore coat. The coat of the best-studied spore-forming microbe, B. subtilis, consists of at least 45 proteins, most of which are poorly characterized. Several protective roles for the coat are well characterized including resistance to desiccation, large toxic molecules, ortho-phthalaldehyde, and ultraviolet (UV) radiation. One important long-term specific goal is an improved sterilization procedure that will enable NASA to meet planetary protection requirements without a terminal heat sterilization step. This would support the implementation of planetary protection policies for life-detection missions. Typically, hospitals and government agencies use biological indicators to ensure the quality control of sterilization processes. The spores of B. canaveralius that are more resistant to osmotic stress would serve as a better biological indicator for potential survival than those in use currently.

  13. Priority Planetary Science Missions Identified

    NASA Astrophysics Data System (ADS)

    Showstack, Randy

    2011-03-01

    The U.S. National Research Council's (NRC) planetary science decadal survey report, released on 7 March, lays out a grand vision for priority planetary science missions for 2013-2022 within a tightly constrained fiscal environment. The cost-conscious report, issued by NRC's Committee on the Planetary Science Decadal Survey, identifies high-priority flagship missions, recommends a number of potential midsized missions, and indicates support for some smaller missions. The report states that the highest-priority flagship mission for the decade is the Mars Astrobiology Explorer-Cacher (MAX-C)—the first of three components of a NASA/European Space Agency Mars sample return campaign—provided that the mission scope can be reduced so that MAX-C costs no more than $2.5 billion. The currently estimated mission cost of $3.5 billion “would take up a disproportionate near-term share of the overall budget for NASA's Planetary Science Division,” the report notes.

  14. Identifying ELIXIR Core Data Resources

    PubMed Central

    Durinx, Christine; McEntyre, Jo; Appel, Ron; Apweiler, Rolf; Barlow, Mary; Blomberg, Niklas; Cook, Chuck; Gasteiger, Elisabeth; Kim, Jee-Hyub; Lopez, Rodrigo; Redaschi, Nicole; Stockinger, Heinz; Teixeira, Daniel; Valencia, Alfonso

    2017-01-01

    The core mission of ELIXIR is to build a stable and sustainable infrastructure for biological information across Europe. At the heart of this are the data resources, tools and services that ELIXIR offers to the life-sciences community, providing stable and sustainable access to biological data. ELIXIR aims to ensure that these resources are available long-term and that the life-cycles of these resources are managed such that they support the scientific needs of the life-sciences, including biological research. ELIXIR Core Data Resources are defined as a set of European data resources that are of fundamental importance to the wider life-science community and the long-term preservation of biological data. They are complete collections of generic value to life-science, are considered an authority in their field with respect to one or more characteristics, and show high levels of scientific quality and service. Thus, ELIXIR Core Data Resources are of wide applicability and usage. This paper describes the structures, governance and processes that support the identification and evaluation of ELIXIR Core Data Resources. It identifies key indicators which reflect the essence of the definition of an ELIXIR Core Data Resource and support the promotion of excellence in resource development and operation. It describes the specific indicators in more detail and explains their application within ELIXIR’s sustainability strategy and science policy actions, and in capacity building, life-cycle management and technical actions. The identification process is currently being implemented and tested for the first time. The findings and outcome will be evaluated by the ELIXIR Scientific Advisory Board in March 2017. Establishing the portfolio of ELIXIR Core Data Resources and ELIXIR Services is a key priority for ELIXIR and publicly marks the transition towards a cohesive infrastructure. PMID:27803796

  15. Identifying ELIXIR Core Data Resources.

    PubMed

    Durinx, Christine; McEntyre, Jo; Appel, Ron; Apweiler, Rolf; Barlow, Mary; Blomberg, Niklas; Cook, Chuck; Gasteiger, Elisabeth; Kim, Jee-Hyub; Lopez, Rodrigo; Redaschi, Nicole; Stockinger, Heinz; Teixeira, Daniel; Valencia, Alfonso

    2016-01-01

    The core mission of ELIXIR is to build a stable and sustainable infrastructure for biological information across Europe. At the heart of this are the data resources, tools and services that ELIXIR offers to the life-sciences community, providing stable and sustainable access to biological data. ELIXIR aims to ensure that these resources are available long-term and that the life-cycles of these resources are managed such that they support the scientific needs of the life-sciences, including biological research. ELIXIR Core Data Resources are defined as a set of European data resources that are of fundamental importance to the wider life-science community and the long-term preservation of biological data. They are complete collections of generic value to life-science, are considered an authority in their field with respect to one or more characteristics, and show high levels of scientific quality and service. Thus, ELIXIR Core Data Resources are of wide applicability and usage. This paper describes the structures, governance and processes that support the identification and evaluation of ELIXIR Core Data Resources. It identifies key indicators which reflect the essence of the definition of an ELIXIR Core Data Resource and support the promotion of excellence in resource development and operation. It describes the specific indicators in more detail and explains their application within ELIXIR's sustainability strategy and science policy actions, and in capacity building, life-cycle management and technical actions. The identification process is currently being implemented and tested for the first time. The findings and outcome will be evaluated by the ELIXIR Scientific Advisory Board in March 2017. Establishing the portfolio of ELIXIR Core Data Resources and ELIXIR Services is a key priority for ELIXIR and publicly marks the transition towards a cohesive infrastructure.

  16. Experimental methods for identifying failure mechanisms

    NASA Technical Reports Server (NTRS)

    Daniel, I. M.

    1983-01-01

    Experimental methods for identifying failure mechanisms in fibrous composites are studied. Methods to identify failure in composite materials includes interferometry, holography, fractography and ultrasonics.

  17. 10 Ways to Identify Hearing Loss

    MedlinePlus

    Skip Navigation Bar Home Current Issue Past Issues 10 Ways to Identify Hearing Loss Past Issues / Spring ... due to excessive noise exposure and other causes. 10 Ways to Identify Hearing Loss Take the following ...

  18. 10 Ways to Identify Hearing Loss

    MedlinePlus

    ... page please turn JavaScript on. Feature: Hearing Loss 10 Ways to Identify Hearing Loss Past Issues / Spring ... Research / Screening Newborns / How Loud Is Too Loud? / 10 Ways to Identify Hearing Loss Spring 2015 Issue: ...

  19. Structural Identifiability of Viscoelastic Mechanical Systems

    PubMed Central

    2014-01-01

    We solve the local and global structural identifiability problems for viscoelastic mechanical models represented by networks of springs and dashpots. We propose a very simple characterization of both local and global structural identifiability based on identifiability tables, with the purpose of providing a guideline for constructing arbitrarily complex, identifiable spring-dashpot networks. We illustrate how to use our results in a number of examples and point to some applications in cardiovascular modeling. PMID:24523860

  20. Method of identifying plant pathogen tolerance

    DOEpatents

    Ecker, Joseph R.; Staskawicz, Brian J.; Bent, Andrew F.; Innes, Roger W.

    1997-10-07

    A process for identifying a plant having disease tolerance comprising administering to a plant an inhibitory amount of ethylene and screening for ethylene insensitivity, thereby identifying a disease tolerant plant, is described. Plants identified by the foregoing process are also described.

  1. 29 CFR 4010.7 - Identifying information.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

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

  2. 29 CFR 4010.7 - Identifying information.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 29 Labor 9 2012-07-01 2012-07-01 false Identifying information. 4010.7 Section 4010.7 Labor... DISCLOSURE REQUIREMENTS ANNUAL FINANCIAL AND ACTUARIAL INFORMATION REPORTING § 4010.7 Identifying information..., http://www.pbgc.gov, the following identifying information with respect to each member of the filer's...

  3. 29 CFR 4010.7 - Identifying information.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 29 Labor 9 2013-07-01 2013-07-01 false Identifying information. 4010.7 Section 4010.7 Labor... DISCLOSURE REQUIREMENTS ANNUAL FINANCIAL AND ACTUARIAL INFORMATION REPORTING § 4010.7 Identifying information..., http://www.pbgc.gov, the following identifying information with respect to each member of the filer's...

  4. Ability of Slovakian Pupils to Identify Birds

    ERIC Educational Resources Information Center

    Prokop, Pavol; Rodak, Rastislav

    2009-01-01

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

  5. Method of identifying plant pathogen tolerance

    DOEpatents

    Ecker, J.R.; Staskawicz, B.J.; Bent, A.F.; Innes, R.W.

    1997-10-07

    A process for identifying a plant having disease tolerance comprising administering to a plant an inhibitory amount of ethylene and screening for ethylene insensitivity, thereby identifying a disease tolerant plant, is described. Plants identified by the foregoing process are also described. 7 figs.

  6. Ability of Slovakian Pupils to Identify Birds

    ERIC Educational Resources Information Center

    Prokop, Pavol; Rodak, Rastislav

    2009-01-01

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

  7. A Small Secreted Virulence-Related Protein Is Essential for the Necrotrophic Interactions of Sclerotinia sclerotiorum with Its Host Plants

    PubMed Central

    Lyu, Xueliang; Shen, Cuicui; Fu, Yanping; Xie, Jiatao; Jiang, Daohong; Li, Guoqing; Cheng, Jiasen

    2016-01-01

    Small, secreted proteins have been found to play crucial roles in interactions between biotrophic/hemi-biotrophic pathogens and plants. However, little is known about the roles of these proteins produced by broad host-range necrotrophic phytopathogens during infection. Here, we report that a cysteine-rich, small protein SsSSVP1 in the necrotrophic phytopathogen Sclerotinia sclerotiorum was experimentally confirmed to be a secreted protein, and the secretion of SsSSVP1 from hyphae was followed by internalization and cell-to-cell movement independent of a pathogen in host cells. SsSSVP1∆SP could induce significant plant cell death and targeted silencing of SsSSVP1 resulted in a significant reduction in virulence. Through yeast two-hybrid (Y2H), coimmunoprecipitation (co-IP) and bimolecular fluorescence complementation (BiFC) assays, we demonstrated that SsSSVP1∆SP interacted with QCR8, a subunit of the cytochrome b-c1 complex of mitochondrial respiratory chain in plants. Double site-directed mutagenesis of two cysteine residues (C38 and C44) in SsSSVP1∆SP had significant effects on its homo-dimer formation, SsSSVP1∆SP-QCR8 interaction and plant cell death induction, indicating that partial cysteine residues surely play crucial roles in maintaining the structure and function of SsSSVP1. Co-localization and BiFC assays showed that SsSSVP1∆SP might hijack QCR8 to cytoplasm before QCR8 targeting into mitochondria, thereby disturbing its subcellular localization in plant cells. Furthermore, virus induced gene silencing (VIGS) of QCR8 in tobacco caused plant abnormal development and cell death, indicating the cell death induced by SsSSVP1∆SP might be caused by the SsSSVP1∆SP-QCR8 interaction, which had disturbed the QCR8 subcellular localization and hence disabled its biological functions. These results suggest that SsSSVP1 is a potential effector which may manipulate plant energy metabolism to facilitate the infection of S. sclerotiorum. Our findings indicate novel roles of small secreted proteins in the interactions between host-non-specific necrotrophic fungi and plants, and highlight the significance to illuminate the pathogenic mechanisms of this type of interaction. PMID:26828434

  8. Structural and mutational analyses of the Leptospira interrogans virulence-related heme oxygenase provide insights into its catalytic mechanism

    PubMed Central

    Soldano, Anabel; Klinke, Sebastián; Otero, Lisandro H.; Rivera, Mario; Catalano-Dupuy, Daniela L.

    2017-01-01

    Heme oxygenase from Leptospira interrogans is an important virulence factor. During catalysis, redox equivalents are provided to this enzyme by the plastidic-type ferredoxin-NADP+ reductase also found in L. interrogans. This process may have evolved to aid this bacterial pathogen to obtain heme-iron from their host and enable successful colonization. Herein we report the crystal structure of the heme oxygenase-heme complex at 1.73 Å resolution. The structure reveals several distinctive features related to its function. A hydrogen bonded network of structural water molecules that extends from the catalytic site to the protein surface was cleared observed. A depression on the surface appears to be the H+ network entrance from the aqueous environment to the catalytic site for O2 activation, a key step in the heme oxygenase reaction. We have performed a mutational analysis of the F157, located at the above-mentioned depression. The mutant enzymes were unable to carry out the complete degradation of heme to biliverdin since the reaction was arrested at the verdoheme stage. We also observed that the stability of the oxyferrous complex, the efficiency of heme hydroxylation and the subsequent conversion to verdoheme was adversely affected. These findings underscore a long-range communication between the outer fringes of the hydrogen-bonded network of structural waters and the heme active site during catalysis. Finally, by analyzing the crystal structures of ferredoxin-NADP+ reductase and heme oxygenase, we propose a model for the productive association of these proteins. PMID:28771589

  9. Resistance to amoxicillin-clavulanate and its relation to virulence-related factors in Yersinia enterocolitica biovar 1A.

    PubMed

    Singhal, N; Kumar, M; Virdi, J S

    2016-01-01

    Recent studies have reported that the virulence factors (VFs) were detected more frequently in amoxicillin-clavulanate (AMC) susceptible clinical isolates of Escherichia coli. Here, we have evaluated the relationship between VFs and AMC-resistance phenotype in clinical isolates of Y. enterocolitica biovar 1A. The presence/absence of VFs was compared with their minimum inhibitory concentrations for AMC in strains of two serovars. We observed that the strains of the serovar O: 6, 30-6, 31 showed a similar relationship between the number of VFs and resistance to clavulanic acid as in E. coli but not of serovar O: 6, 30. Variations in the promoters/complete coding sequences (CCDSs) of β-lactamase gene (bla A) or the serological characteristics could not account for unusual susceptibility to AMC displayed by the strains of the serovar O: 6, 30. Therefore, we speculate that since the clinical strains of serovar O: 6, 30-6, 31 originated from the environment they were less exposed to antibiotics compared to clinical strains of serovar O: 6, 30. Thus, AMC susceptibility seems to be influenced by factors other than serotypes or promoters/CCDS of β-lactamase genes.

  10. Intragenic Recombination Has a Critical Role on the Evolution of Legionella pneumophila Virulence-Related Effector sidJ

    PubMed Central

    Costa, Joana; Teixeira, Paulo Gonçalves; d'Avó, Ana Filipa; Júnior, Célio Santos; Veríssimo, António

    2014-01-01

    SidJ is a Dot/Icm effector involved in the trafficking or retention of ER-derived vesicles to Legionella pneumophila vacuoles whose mutation causes an observable growth defect, both in macrophage and amoeba hosts. Given the crucial role of this effector in L. pneumophila virulence we investigated the mechanisms shaping its molecular evolution. The alignment of SidJ sequences revealed several alleles with amino acid variations that may influence the protein properties. The identification of HGT events and the detection of balancing selection operating on sidJ evolution emerge as a clear result. Evidence suggests that intragenic recombination is an important strategy in the evolutionary adaptive process playing an active role on sidJ genetic plasticity. This pattern of evolution is in accordance with the life style of L. pneumophila as a broad host-range pathogen by preventing host-specialization and contributing to the resilience of the species. PMID:25299187

  11. Virulence-related Mycobacterium avium subsp hominissuis MAV_2928 gene is associated with vacuole remodeling in macrophages

    PubMed Central

    2010-01-01

    Background Mycobacterium avium subsp hominissuis (previously Mycobacterium avium subsp avium) is an environmental organism associated with opportunistic infections in humans. Mycobacterium hominissuis infects and replicates within mononuclear phagocytes. Previous study characterized an attenuated mutant in which the PPE gene (MAV_2928) homologous to Rv1787 was inactivated. This mutant, in contrast to the wild-type bacterium, was shown both to have impaired the ability to replicate within macrophages and to have prevented phagosome/lysosome fusion. Results MAV_2928 gene is primarily upregulated upon phagocytosis. The transcriptional profile of macrophages infected with the wild-type bacterium and the mutant were examined using DNA microarray, which showed that the two bacteria interact uniquely with mononuclear phagocytes. Based on the results, it was hypothesized that the phagosome environment and vacuole membrane of the wild-type bacterium might differ from the mutant. Wild-type bacterium phagosomes expressed a number of proteins different from those infected with the mutant. Proteins on the phagosomes were confirmed by fluorescence microscopy and Western blot. The environment in the phagosome of macrophages infected with the mutant differed from the environment of vacuoles with M. hominissuis wild-type in the concentration of zinc, manganese, calcium and potassium. Conclusion The results suggest that the MAV_2928 gene/operon might participate in the establishment of bacterial intracellular environment in macrophages. PMID:20359357

  12. Differential expression of pathogenicity- and virulence-related genes of Xanthomonas axonopodis pv. citri under copper stress.

    PubMed

    Palmieri, Ana Carolina Basílio; do Amaral, Alexandre Morais; Homem, Rafael Augusto; Machado, Marcos Antonio

    2010-04-01

    In this study, we used real-time quantitative PCR (RT-qPCR) to evaluate the expression of 32 genes of Xanthomonas axonopodis pv. citri related to pathogenicity and virulence that are also involved in copper detoxification. Nearly all of the genes were up-regulated, including copA and copB. Two genes homologous to members of the type II secretion system (xcsH and xcsC) and two involved in the degradation of plant cell wall components (pglA and pel) were the most expressed in response to an elevated copper concentration. The type II secretion system (xcs operon) and a few homologues of proteins putatively secreted by this system showed enhanced expression when the bacteria were exposed to a high concentration of copper sulfate. The enhanced expression of the genes of secretion II system during copper stress suggests that this pathway may have an important role in the adaptative response of X. axonopodis pv. citri to toxic compounds. These findings highlight the potential role of these genes in attenuating the toxicity of certain metals and could represent an important means of bacterial resistance against chemicals used to control diseases.

  13. Sequence variation in virulence-related genes of Bordetella pertussis isolates from Poland in the period 1959-2013.

    PubMed

    Mosiej, E; Zawadka, M; Krysztopa-Grzybowska, K; Polak, M; Augustynowicz, E; Piekarska, K; Lutyńska, A

    2015-01-01

    This study aimed to characterise Bordetella pertussis isolates circulating in Poland since 1959. Sequence analysis of ptxA, ptxC, prn, tcfA, fim2, fim3 and ptxP for 175 clinical isolates and currently and previously used vaccine strains was performed. Clinical isolates from the period 1995-2013 were found to be different to three currently used vaccine strains harbouring the allelic combination ptxA2-ptxC1-ptxP1-prn1-tcfA2-fim2-1-fim3-1, seen frequently in Poland in the early pertussis vaccination period but not found after 1995. Generally, among B. pertussis isolates from the period 2000-2013, two genotypes predominated, ptxA1-ptxC1-ptxP1-prn1-tcfA2-fim2-2-fim3-1 and ptxA1-ptxC1-ptxP1-prn2-tcfA2-fim2-1-fim3-1, with frequencies of 45% and 32.5%, respectively. The isolates harbouring ptxA1-ptxC2-ptxP3-prn2-tcfA2-fim2-1-fim3-2 and ptxA1-ptxC2-ptxP3-prn2-tcfA2-fim2-1-fim3-1 profiles, currently highly prevalent within other European Union (EU) countries, were rarely found in Poland, as they circulated in the period 2000-2013 with frequencies of 10% and 5%, respectively. We hypothesise that several previous changes of strain composition in whole-cell pertussis vaccine produced locally and used since 1960 in Poland resulted in a more diverse immune pressure in the population, resulting in different prevalence of alleles compared to elsewhere.

  14. Efficacy of florfenicol for control of mortality associated with Edwardsiella ictaluri in three species of catfish

    USDA-ARS?s Scientific Manuscript database

    The efficacy of florfenicol against Edwardsiella icatluri infection was studied in channel catfish (Ictalurus puntatus (Delta strain)), hybrid catfish (Ictalurus punctatus (Delta strain) x Ictalurus furcatus (D&B strain)), and blue catfish (Ictalurus furcatus (D&B strain) fingerlings in 65L aquaria....

  15. Gender nor sex hormones alter the disease susceptibility of channel catfish to Edwardsiella ictaluri

    USDA-ARS?s Scientific Manuscript database

    The use of monosex populations for aquaculture is becoming widely used for several species. Monosex populations are not in wide use in the catfish industry but techniques to develop all male populations have been developed. These studies were conducted to determine if there were any differences be...

  16. Plasma cortisol stress response in channel catfish, Ictalurus punctatus influences susceptibility to Edwardeseilla ictaluri

    USDA-ARS?s Scientific Manuscript database

    Cortisol is a primary stress hormone in fish as its plasma variations correlate with the occurrence of various stressful situations. Past studies have demonstrated that fish subjected to handling stress or poor water quality had a reduced ability to resist pathogens. Channel catfish fingerlings th...

  17. Expression profiles of seven channel catfish antimicrobial peptides in response to Edwardsiella ictaluri infection

    USDA-ARS?s Scientific Manuscript database

    Using quantitative PCR technique, the relative transcriptional levels of seven channel catfish antimicrobial peptide (AMP) genes [NK-lysin type 1, NK-lysin type 2, NK-lysin type 3, bactericidal permeability-increasing protein (BPI), cathepsin D, hepcidin, and liver-expressed antimicrobial peptide 2 ...

  18. Identifying Candidate Chemical-Disease Linkages ...

    EPA Pesticide Factsheets

    Presentation at meeting on Environmental and Epigenetic Determinants of IBD in New York, NY on identifying candidate chemical-disease linkages by using AOPs to identify molecular initiating events and using relevant high throughput assays to screen for candidate chemicals. This hazard information is combined with exposure models to inform risk assessment. Presentation at meeting on Environmental and Epigenetic Determinants of IBD in New York, NY on identifying candidate chemical-disease linkages by using AOPs to identify molecular initiating events and using relevant high throughput assays to screen for candidate chemicals. This hazard information is combined with exposure models to inform risk assessment.

  19. On the identifiability of metabolic network models.

    PubMed

    Berthoumieux, Sara; Brilli, Matteo; Kahn, Daniel; de Jong, Hidde; Cinquemani, Eugenio

    2013-12-01

    A major problem for the identification of metabolic network models is parameter identifiability, that is, the possibility to unambiguously infer the parameter values from the data. Identifiability problems may be due to the structure of the model, in particular implicit dependencies between the parameters, or to limitations in the quantity and quality of the available data. We address the detection and resolution of identifiability problems for a class of pseudo-linear models of metabolism, so-called linlog models. Linlog models have the advantage that parameter estimation reduces to linear or orthogonal regression, which facilitates the analysis of identifiability. We develop precise definitions of structural and practical identifiability, and clarify the fundamental relations between these concepts. In addition, we use singular value decomposition to detect identifiability problems and reduce the model to an identifiable approximation by a principal component analysis approach. The criterion is adapted to real data, which are frequently scarce, incomplete, and noisy. The test of the criterion on a model with simulated data shows that it is capable of correctly identifying the principal components of the data vector. The application to a state-of-the-art dataset on central carbon metabolism in Escherichia coli yields the surprising result that only 4 out of 31 reactions, and 37 out of 100 parameters, are identifiable. This underlines the practical importance of identifiability analysis and model reduction in the modeling of large-scale metabolic networks. Although our approach has been developed in the context of linlog models, it carries over to other pseudo-linear models, such as generalized mass-action (power-law) models. Moreover, it provides useful hints for the identifiability analysis of more general classes of nonlinear models of metabolism.

  20. Portable Radiometer Identifies Minerals in the Field

    NASA Technical Reports Server (NTRS)

    Goetz, A. F. H.; Machida, R. A.

    1982-01-01

    Hand-held optical instrument aids in identifying minerals in field. Can be used in exploration for minerals on foot or by aircraft. The radiometer is especially suitable for identifying clay and carbonate minerals. Radiometer measures reflectances of mineral at two wavelengths, computes ratio of reflectances, and displays ratio to user.

  1. Identifying Bilingual Semantic Neural Representations across Languages

    ERIC Educational Resources Information Center

    Buchweitz, Augusto; Shinkareva, Svetlana V.; Mason, Robert A.; Mitchell, Tom M.; Just, Marcel Adam

    2012-01-01

    The goal of the study was to identify the neural representation of a noun's meaning in one language based on the neural representation of that same noun in another language. Machine learning methods were used to train classifiers to identify which individual noun bilingual participants were thinking about in one language based solely on their…

  2. Healthcare Identifiers legislation: a whiff of fourberie.

    PubMed

    Mendelson, Danuta

    2010-05-01

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

  3. Self-Identifying Emergency Radio Beacons

    NASA Technical Reports Server (NTRS)

    Friedman, Morton L.

    1987-01-01

    Rescue teams aided by knowledge of vehicle in distress. Similar to conventional emergency transmitters except contains additional timing and modulating circuits. Additions to standard emergency transmitter enable transmitter to send rescuers identifying signal in addition to conventional distress signal created by sweep generator. Data generator contains identifying code.

  4. Identifying Bilingual Semantic Neural Representations across Languages

    ERIC Educational Resources Information Center

    Buchweitz, Augusto; Shinkareva, Svetlana V.; Mason, Robert A.; Mitchell, Tom M.; Just, Marcel Adam

    2012-01-01

    The goal of the study was to identify the neural representation of a noun's meaning in one language based on the neural representation of that same noun in another language. Machine learning methods were used to train classifiers to identify which individual noun bilingual participants were thinking about in one language based solely on their…

  5. Identifying Opinion Leaders to Promote Behavior Change

    ERIC Educational Resources Information Center

    Valente, Thomas W.; Pumpuang, Patchareeya

    2007-01-01

    This article reviews 10 techniques used to identify opinion leaders to promote behavior change. Opinion leaders can act as gatekeepers for interventions, help change social norms, and accelerate behavior change. Few studies document the manner in which opinion leaders are identified, recruited, and trained to promote health. The authors categorize…

  6. Marking Identifiable Scripts: Following up Student Concerns

    ERIC Educational Resources Information Center

    Owen, Cathy; Stefaniak, John; Corrigan, Gerry

    2010-01-01

    Introduction: Medical student concern that the submission of named examination scripts to examiners could cause bias initiated a study on the effect of identified and de-identified scripts on assessment outcome. Methods: Data were collected from a convenience examination sample of Year 1 (n = 88 students; n = 29 questions) and Year 2 scripts (n =…

  7. Parameter Identifiability of Fundamental Pharmacodynamic Models

    PubMed Central

    Janzén, David L. I.; Bergenholm, Linnéa; Jirstrand, Mats; Parkinson, Joanna; Yates, James; Evans, Neil D.; Chappell, Michael J.

    2016-01-01

    Issues of parameter identifiability of routinely used pharmacodynamics models are considered in this paper. The structural identifiability of 16 commonly applied pharmacodynamic model structures was analyzed analytically, using the input-output approach. Both fixed-effects versions (non-population, no between-subject variability) and mixed-effects versions (population, including between-subject variability) of each model structure were analyzed. All models were found to be structurally globally identifiable under conditions of fixing either one of two particular parameters. Furthermore, an example was constructed to illustrate the importance of sufficient data quality and show that structural identifiability is a prerequisite, but not a guarantee, for successful parameter estimation and practical parameter identifiability. This analysis was performed by generating artificial data of varying quality to a structurally identifiable model with known true parameter values, followed by re-estimation of the parameter values. In addition, to show the benefit of including structural identifiability as part of model development, a case study was performed applying an unidentifiable model to real experimental data. This case study shows how performing such an analysis prior to parameter estimation can improve the parameter estimation process and model performance. Finally, an unidentifiable model was fitted to simulated data using multiple initial parameter values, resulting in highly different estimated uncertainties. This example shows that although the standard errors of the parameter estimates often indicate a structural identifiability issue, reasonably “good” standard errors may sometimes mask unidentifiability issues. PMID:27994553

  8. Marking Identifiable Scripts: Following up Student Concerns

    ERIC Educational Resources Information Center

    Owen, Cathy; Stefaniak, John; Corrigan, Gerry

    2010-01-01

    Introduction: Medical student concern that the submission of named examination scripts to examiners could cause bias initiated a study on the effect of identified and de-identified scripts on assessment outcome. Methods: Data were collected from a convenience examination sample of Year 1 (n = 88 students; n = 29 questions) and Year 2 scripts (n =…

  9. Identifying Information Focuses in Listening Comprehension

    ERIC Educational Resources Information Center

    Zhang, Hong-yan

    2011-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Starr, J.

    2013-12-01

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

  11. Structural Identifiability of Dynamic Systems Biology Models

    PubMed Central

    Villaverde, Alejandro F.

    2016-01-01

    A powerful way of gaining insight into biological systems is by creating a nonlinear differential equation model, which usually contains many unknown parameters. Such a model is called structurally identifiable if it is possible to determine the values of its parameters from measurements of the model outputs. Structural identifiability is a prerequisite for parameter estimation, and should be assessed before exploiting a model. However, this analysis is seldom performed due to the high computational cost involved in the necessary symbolic calculations, which quickly becomes prohibitive as the problem size increases. In this paper we show how to analyse the structural identifiability of a very general class of nonlinear models by extending methods originally developed for studying observability. We present results about models whose identifiability had not been previously determined, report unidentifiabilities that had not been found before, and show how to modify those unidentifiable models to make them identifiable. This method helps prevent problems caused by lack of identifiability analysis, which can compromise the success of tasks such as experiment design, parameter estimation, and model-based optimization. The procedure is called STRIKE-GOLDD (STRuctural Identifiability taKen as Extended-Generalized Observability with Lie Derivatives and Decomposition), and it is implemented in a MATLAB toolbox which is available as open source software. The broad applicability of this approach facilitates the analysis of the increasingly complex models used in systems biology and other areas. PMID:27792726

  12. Identifiability of PBPK Models with Applications to ...

    EPA Pesticide Factsheets

    Any statistical model should be identifiable in order for estimates and tests using it to be meaningful. We consider statistical analysis of physiologically-based pharmacokinetic (PBPK) models in which parameters cannot be estimated precisely from available data, and discuss different types of identifiability that occur in PBPK models and give reasons why they occur. We particularly focus on how the mathematical structure of a PBPK model and lack of appropriate data can lead to statistical models in which it is impossible to estimate at least some parameters precisely. Methods are reviewed which can determine whether a purely linear PBPK model is globally identifiable. We propose a theorem which determines when identifiability at a set of finite and specific values of the mathematical PBPK model (global discrete identifiability) implies identifiability of the statistical model. However, we are unable to establish conditions that imply global discrete identifiability, and conclude that the only safe approach to analysis of PBPK models involves Bayesian analysis with truncated priors. Finally, computational issues regarding posterior simulations of PBPK models are discussed. The methodology is very general and can be applied to numerous PBPK models which can be expressed as linear time-invariant systems. A real data set of a PBPK model for exposure to dimethyl arsinic acid (DMA(V)) is presented to illustrate the proposed methodology. We consider statistical analy

  13. Structural Identifiability of Dynamic Systems Biology Models.

    PubMed

    Villaverde, Alejandro F; Barreiro, Antonio; Papachristodoulou, Antonis

    2016-10-01

    A powerful way of gaining insight into biological systems is by creating a nonlinear differential equation model, which usually contains many unknown parameters. Such a model is called structurally identifiable if it is possible to determine the values of its parameters from measurements of the model outputs. Structural identifiability is a prerequisite for parameter estimation, and should be assessed before exploiting a model. However, this analysis is seldom performed due to the high computational cost involved in the necessary symbolic calculations, which quickly becomes prohibitive as the problem size increases. In this paper we show how to analyse the structural identifiability of a very general class of nonlinear models by extending methods originally developed for studying observability. We present results about models whose identifiability had not been previously determined, report unidentifiabilities that had not been found before, and show how to modify those unidentifiable models to make them identifiable. This method helps prevent problems caused by lack of identifiability analysis, which can compromise the success of tasks such as experiment design, parameter estimation, and model-based optimization. The procedure is called STRIKE-GOLDD (STRuctural Identifiability taKen as Extended-Generalized Observability with Lie Derivatives and Decomposition), and it is implemented in a MATLAB toolbox which is available as open source software. The broad applicability of this approach facilitates the analysis of the increasingly complex models used in systems biology and other areas.

  14. Identifying Codes on Directed De Bruijn Graphs

    DTIC Science & Technology

    2014-12-19

    ar X iv :1 41 2. 58 42 v1 [ m at h. C O ] 1 8 D ec 2 01 4 Identifying Codes on Directed De Bruijn Graphs Debra Boutin ∗ Department of...Mathematics Hamilton College Victoria Horan † Air Force Research Laboratory Information Directorate December 19, 2014 Abstract For a directed graph G, a t...length at most t is both non-empty and unique. A graph is called t-identifiable if there exists a t-identifying code. This paper shows that the de

  15. Helping You Identify Quality Laboratory Services

    MedlinePlus

    Helping You Identify Quality Laboratory Services Selecting quality health care services for yourself, a relative or friend requires special thought and attention. The Joint Commission has prepared this information ...

  16. Study Identifies New Lymphoma Treatment Target

    Cancer.gov

    NCI researchers have identified new therapeutic targets for diffuse large B-cell lymphoma. Drugs that hit these targets are under clinical development and the researchers hope to begin testing them in clinical trials of patients with DLBCL.

  17. Identifying associations between genomic alterations in tumors.

    PubMed

    George, Joshy; Gorringe, Kylie L; Smyth, Gordon K; Bowtell, David D L

    2013-01-01

    Single-nucleotide polymorphism (SNP) mapping arrays are a reliable method for identifying somatic copy number alterations in cancer samples. Though this is immensely useful to identify potential driver genes, it is not sufficient to identify genes acting in a concerted manner. In cancer cells, co-amplified genes have been shown to provide synergistic effects, and genomic alterations targeting a pathway have been shown to occur in a mutually exclusive manner. We therefore developed a bioinformatic method for detecting such gene pairs using an integrated analysis of genomic copy number and gene expression data. This approach allowed us to identify a gene pair that is co-amplified and co-expressed in high-grade serous ovarian cancer. This finding provided information about the interaction of specific genetic events that contribute to the development and progression of this disease.

  18. Determining the identifiability of DNA database entries.

    PubMed Central

    Malin, B.; Sweeney, L.

    2000-01-01

    CleanGene is a software program that helps determine the identifiability of sequenced DNA, independent of any explicit demographics or identifiers maintained with the DNA. The program computes the likelihood that the release of DNA database entries could be related to specific individuals that are the subjects of the data. The engine within CleanGene relies on publicly available health care data and on knowledge of particular diseases to help relate identified individuals to DNA entries. Over 20 diseases, ranging over ataxias, blood diseases, and sex-linked mutations are accounted for, with 98-100% of individuals found identifiable. We assume the genetic material is released in a linear sequencing format from an individual's genome. CleanGene and its related experiments are useful tools for any institution seeking to provide anonymous genetic material for research purposes. PMID:11079941

  19. Identifying Consumer Education Content for Industrial Arts.

    ERIC Educational Resources Information Center

    Sharpe, Dennis B.; Baker, Glenn E.

    1982-01-01

    The survey described here identified suitable consumer topics which can be infused into industrial courses at all grade levels. The survey reinforced the development of sound consumer skills as an important objective of industrial arts education. (SK)

  20. Asteroid Redirect Mission: Identify, Redirect, Explore

    NASA Image and Video Library

    NASA is developing a first-ever mission to identify, capture and redirect a near-Earth asteroid to a stable orbit around the moon, where astronauts will explore it in the 2020s, returning with samp...

  1. Identifying regional opportunities for accelerated timber managemnet

    Treesearch

    David A. Gansner; Joseph E. Barnard; Samuel F. Gingrich; Samuel F. Gingrich

    1973-01-01

    Describes a procedure for identifying regional opportunities for accelerated timber management and demonstrates its application. Results provide a basis for rational choices among alternative management strategies and permit meaningful micro- and macro-evaluations of treatment response.

  2. Identifying signs of intimate partner violence.

    PubMed

    Ali, Parveen; McGarry, Julie; Dhingra, Katie

    2016-02-01

    Intimate partner violence is a major public health and social problem that affects people everywhere. Nurses can play an important role in identifying victims who present to healthcare settings with domestic abuse-related health issues. Evidence suggests that most women who present to emergency departments have experienced domestic abuse at some point in their lives, but that only 5% are identified by healthcare professionals. To identify and respond to victims effectively, emergency nurses must understand domestic abuse and its associated complexities. This article provides an overview of these issues, including the different types of abuse, and their prevalence, causes and effects on health. The article also explores how emergency nurses can identify and manage the effects of violence at work.

  3. IDENTIFYING KEY CONTRIBUTIONS TO INFORMATION SCIENCE,

    DTIC Science & Technology

    Several alternative approaches were examined to determine how one might identify some of the key (written) contributions to ’ information science ’. The...references. The unclear selective patterns in current bibliographies in the information science field also present problems. It is suggested that in...identifying key contributions we are far from common agreement on the conceptual, methodological or practical contributions to the information science field

  4. Identifying ECM Mediators of Tumor Cell Dormancy

    DTIC Science & Technology

    2008-05-01

    proliferating cells. f) At time of euthanasia, stage of estrous will be determined by vaginal smear so that inter- animal variation due to estrous...ratio of the number of distinct peptides identified for each protein divided by the total number of peptides identified in the two hour run are...displayed as the peptide count ratio. Using this peptide counting label-free quantification approach, surprisingly, suggested that the three fibrillar

  5. Identifying ECM Mediators of Tumor Cell Dormancy

    DTIC Science & Technology

    2009-05-01

    determined by vaginal smear so that inter- animal variation due to estrous can be controlled for across groups. Further, cervical samples will be... peptides identified for each protein divided by the total number of peptides identified in the two hour run are displayed as the peptide count ratio...Using this peptide counting label-free quantification approach, surprisingly, suggested that the three fibrillar collagen chains were at lower levels in

  6. Newly identified YSO candidates towards LDN 1188

    NASA Astrophysics Data System (ADS)

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

    2013-11-01

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

  7. ORCID Author Identifiers: A Primer for Librarians.

    PubMed

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

    2016-01-01

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

  8. Identifying Codes on Directed De Bruijn Graphs

    DTIC Science & Technology

    2015-08-27

    2. 15. SUBJECT TERMS Identifying Code; De Bruijn Network; Graph Theory 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT UU 18. NUMBER...in graphs . IEEE Trans. Inform. Theory , 44(2):599–611, 1998. 1 [10] Samir Khuller, Balaji Raghavachari, and Azriel Rosenfeld. Landmarks in graphs ...JOURNAL ARTICLE (POST PRINT) 3. DATES COVERED (From - To) JUN 2013 – AUG 2015 4. TITLE AND SUBTITLE IDENTIFYING CODES ON DIRECTED DE BRUIJN GRAPHS 5a

  9. Exploiting intrinsic fluctuations to identify model parameters.

    PubMed

    Zimmer, Christoph; Sahle, Sven; Pahle, Jürgen

    2015-04-01

    Parameterisation of kinetic models plays a central role in computational systems biology. Besides the lack of experimental data of high enough quality, some of the biggest challenges here are identification issues. Model parameters can be structurally non-identifiable because of functional relationships. Noise in measured data is usually considered to be a nuisance for parameter estimation. However, it turns out that intrinsic fluctuations in particle numbers can make parameters identifiable that were previously non-identifiable. The authors present a method to identify model parameters that are structurally non-identifiable in a deterministic framework. The method takes time course recordings of biochemical systems in steady state or transient state as input. Often a functional relationship between parameters presents itself by a one-dimensional manifold in parameter space containing parameter sets of optimal goodness. Although the system's behaviour cannot be distinguished on this manifold in a deterministic framework it might be distinguishable in a stochastic modelling framework. Their method exploits this by using an objective function that includes a measure for fluctuations in particle numbers. They show on three example models, immigration-death, gene expression and Epo-EpoReceptor interaction, that this resolves the non-identifiability even in the case of measurement noise with known amplitude. The method is applied to partially observed recordings of biochemical systems with measurement noise. It is simple to implement and it is usually very fast to compute. This optimisation can be realised in a classical or Bayesian fashion.

  10. IDENTIFYING COLLISIONAL FAMILIES IN THE KUIPER BELT

    SciTech Connect

    Marcus, Robert A.; Ragozzine, Darin; Murray-Clay, Ruth A.; Holman, Matthew J.

    2011-05-20

    The identification and characterization of numerous collisional families-clusters of bodies with a common collisional origin-in the asteroid belt has added greatly to the understanding of asteroid belt formation and evolution. More recent study has also led to an appreciation of physical processes that had previously been neglected (e.g., the Yarkovsky effect). Collisions have certainly played an important role in the evolution of the Kuiper Belt as well, though only one collisional family has been identified in that region to date, around the dwarf planet Haumea. In this paper, we combine insights into collisional families from numerical simulations with the current observational constraints on the dynamical structure of the Kuiper Belt to investigate the ideal sizes and locations for identifying collisional families. We find that larger progenitors (r {approx} 500 km) result in more easily identifiable families, given the difficulty in identifying fragments of smaller progenitors in magnitude-limited surveys, despite their larger spread and less frequent occurrence. However, even these families do not stand out well from the background. Identifying families as statistical overdensities is much easier than characterizing families by distinguishing individual members from interlopers. Such identification seems promising, provided the background population is well known. In either case, families will also be much easier to study where the background population is small, i.e., at high inclinations. Overall, our results indicate that entirely different techniques for identifying families will be needed for the Kuiper Belt, and we provide some suggestions.

  11. Identifying nineteenth century genealogical links from genotypes.

    PubMed

    Stankovich, Jim; Bahlo, Melanie; Rubio, Justin P; Wilkinson, Christopher R; Thomson, Russell; Banks, Annette; Ring, Maree; Foote, Simon J; Speed, Terence P

    2005-07-01

    We have developed a likelihood method to identify moderately distant genealogical relationships from genomewide scan data. The aim is to compare the genotypes of many pairs of people and identify those pairs most likely to be related to one another. We have tested the algorithm using the genotypes of 170 Tasmanians with multiple sclerosis recruited into a haplotype association study. It is estimated from genealogical records that approximately 65% of Tasmania's current population of 470,000 are direct descendants of the 13,000 female founders living in this island state of Australia in the mid-nineteenth century. All cases and four to five relatives of each case have been genotyped with microsatellite markers at a genomewide average density of 4 cM. Previous genealogical research has identified 51 pairwise relationships linking 56 of the 170 cases. Testing the likelihood calculation on these known relative pairs, we have good power to identify relationships up to degree eight (e.g. third cousins once removed). Applying the algorithm to all other pairs of cases, we have identified a further 61 putative relative pairs, with an estimated false discovery rate of 10%. The power to identify genealogical links should increase when the new, denser sets of SNP markers are used. Except in populations where there is a searchable electronic database containing virtually all genealogical links in the past six generations, the algorithm should be a useful aid for genealogists working on gene-mapping projects, both linkage studies and association studies.

  12. Distributed design approach in persistent identifiers systems

    NASA Astrophysics Data System (ADS)

    Golodoniuc, Pavel; Car, Nicholas; Klump, Jens

    2017-04-01

    The need to identify both digital and physical objects is ubiquitous in our society. Past and present persistent identifier (PID) systems, of which there is a great variety in terms of technical and social implementations, have evolved with the advent of the Internet, which has allowed for globally unique and globally resolvable identifiers. PID systems have catered for identifier uniqueness, integrity, persistence, and trustworthiness, regardless of the identifier's application domain, the scope of which has expanded significantly in the past two decades. Since many PID systems have been largely conceived and developed by small communities, or even a single organisation, they have faced challenges in gaining widespread adoption and, most importantly, the ability to survive change of technology. This has left a legacy of identifiers that still exist and are being used but which have lost their resolution service. We believe that one of the causes of once successful PID systems fading is their reliance on a centralised technical infrastructure or a governing authority. Golodoniuc et al. (2016) proposed an approach to the development of PID systems that combines the use of (a) the Handle system, as a distributed system for the registration and first-degree resolution of persistent identifiers, and (b) the PID Service (Golodoniuc et al., 2015), to enable fine-grained resolution to different information object representations. The proposed approach solved the problem of guaranteed first-degree resolution of identifiers, but left fine-grained resolution and information delivery under the control of a single authoritative source, posing risk to the long-term availability of information resources. Herein, we develop these approaches further and explore the potential of large-scale decentralisation at all levels: (i) persistent identifiers and information resources registration; (ii) identifier resolution; and (iii) data delivery. To achieve large-scale decentralisation

  13. Scalable persistent identifier systems for dynamic datasets

    NASA Astrophysics Data System (ADS)

    Golodoniuc, P.; Cox, S. J. D.; Klump, J. F.

    2016-12-01

    Reliable and persistent identification of objects, whether tangible or not, is essential in information management. Many Internet-based systems have been developed to identify digital data objects, e.g., PURL, LSID, Handle, ARK. These were largely designed for identification of static digital objects. The amount of data made available online has grown exponentially over the last two decades and fine-grained identification of dynamically generated data objects within large datasets using conventional systems (e.g., PURL) has become impractical. We have compared capabilities of various technological solutions to enable resolvability of data objects in dynamic datasets, and developed a dataset-centric approach to resolution of identifiers. This is particularly important in Semantic Linked Data environments where dynamic frequently changing data is delivered live via web services, so registration of individual data objects to obtain identifiers is impractical. We use identifier patterns and pattern hierarchies for identification of data objects, which allows relationships between identifiers to be expressed, and also provides means for resolving a single identifier into multiple forms (i.e. views or representations of an object). The latter can be implemented through (a) HTTP content negotiation, or (b) use of URI querystring parameters. The pattern and hierarchy approach has been implemented in the Linked Data API supporting the United Nations Spatial Data Infrastructure (UNSDI) initiative and later in the implementation of geoscientific data delivery for the Capricorn Distal Footprints project using International Geo Sample Numbers (IGSN). This enables flexible resolution of multi-view persistent identifiers and provides a scalable solution for large heterogeneous datasets.

  14. On the relationship between sloppiness and identifiability.

    PubMed

    Chis, Oana-Teodora; Villaverde, Alejandro F; Banga, Julio R; Balsa-Canto, Eva

    2016-12-01

    Dynamic models of biochemical networks are often formulated as sets of non-linear ordinary differential equations, whose states are the concentrations or abundances of the network components. They typically have a large number of kinetic parameters, which must be determined by calibrating the model with experimental data. In recent years it has been suggested that dynamic systems biology models are universally sloppy, meaning that the values of some parameters can be perturbed by several orders of magnitude without causing significant changes in the model output. This observation has prompted calls for focusing on model predictions rather than on parameters. In this work we examine the concept of sloppiness, investigating its links with the long-established notions of structural and practical identifiability. By analysing a set of case studies we show that sloppiness is not equivalent to lack of identifiability, and that sloppy models can be identifiable. Thus, using sloppiness to draw conclusions about the possibility of estimating parameter values can be misleading. Instead, structural and practical identifiability analyses are better tools for assessing the confidence in parameter estimates. Furthermore, we show that, when designing new experiments to decrease parametric uncertainty, designs that optimize practical identifiability criteria are more informative than those that minimize sloppiness. Copyright © 2016 Elsevier Inc. All rights reserved.

  15. Identifying Surfaces on the Pale Blue Dot

    NASA Astrophysics Data System (ADS)

    Cowan, Nicolas B.; Strait, T. E.

    2013-01-01

    The changing color of an unresolved planet hint at its cloud structure and surface features. Principal component analysis has previously been shown to robustly identify the number of surfaces contributing to disk-integrated observations. We have taken an important next step by showing that one can identify the reflectance spectra of unknown surface types, based solely on time-resolved, disk-integrated multi-band photometry. We test our method on disk-integrated observations of Earth taken by the Deep Impact spacecraft as part of the EPOXI mission. Critically, we borrow analysis tools from the remote sensing community, where spatially-resolved spectral data are routinely analyzed in an automated way to identify known (eg. boreal forest) as well as unknown surfaces (eg. military bunkers). Our study indicates that planned missions like the Terrestrial Planet Finder (TPF) will be able to identify new surfaces on exoplanets, and also offers a relatively model-independent avenue to identifying surface liquid water on other worlds.

  16. Identifying Turbulent Structures through Topological Segmentation

    SciTech Connect

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

    2016-01-01

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

  17. Scientometric methods for identifying emerging technologies

    DOEpatents

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

    2015-11-03

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

  18. Identifying non-resonant Kepler planetary systems

    NASA Astrophysics Data System (ADS)

    Veras, Dimitri; Ford, Eric B.

    2012-02-01

    The Kepler mission has discovered a plethora of multiple transiting planet candidate exosystems, many of which feature putative pairs of planets near mean motion resonance commensurabilities. Identifying potentially resonant systems could help guide future observations and enhance our understanding of planetary formation scenarios. We develop and apply an algebraic method to determine which Kepler two-planet systems cannot be in a first-fourth order resonance, given the current, publicly available data. This method identifies when any potentially resonant angle of a system must circulate. We identify and list 70 near-resonant systems which cannot actually reside in resonance, assuming a widely used formulation for deriving planetary masses from their observed radii and that these systems do not contain unseen bodies that affect the interactions of the observed planets. This work strengthens the argument that a high fraction of exoplanetary systems may be near resonance but not actually in resonance.

  19. Bayesian inference to identify parameters in viscoelasticity

    NASA Astrophysics Data System (ADS)

    Rappel, Hussein; Beex, Lars A. A.; Bordas, Stéphane P. A.

    2017-08-01

    This contribution discusses Bayesian inference (BI) as an approach to identify parameters in viscoelasticity. The aims are: (i) to show that the prior has a substantial influence for viscoelasticity, (ii) to show that this influence decreases for an increasing number of measurements and (iii) to show how different types of experiments influence the identified parameters and their uncertainties. The standard linear solid model is the material description of interest and a relaxation test, a constant strain-rate test and a creep test are the tensile experiments focused on. The experimental data are artificially created, allowing us to make a one-to-one comparison between the input parameters and the identified parameter values. Besides dealing with the aforementioned issues, we believe that this contribution forms a comprehensible start for those interested in applying BI in viscoelasticity.

  20. Photoacoustic tomography to identify inflammatory arthritis

    NASA Astrophysics Data System (ADS)

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

    2012-09-01

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

  1. Computational methods to identify new antibacterial targets.

    PubMed

    McPhillie, Martin J; Cain, Ricky M; Narramore, Sarah; Fishwick, Colin W G; Simmons, Katie J

    2015-01-01

    The development of resistance to all current antibiotics in the clinic means there is an urgent unmet need for novel antibacterial agents with new modes of action. One of the best ways of finding these is to identify new essential bacterial enzymes to target. The advent of a number of in silico tools has aided classical methods of discovering new antibacterial targets, and these programs are the subject of this review. Many of these tools apply a cheminformatic approach, utilizing the structural information of either ligand or protein, chemogenomic databases, and docking algorithms to identify putative antibacterial targets. Considering the wealth of potential drug targets identified from genomic research, these approaches are perfectly placed to mine this rich resource and complement drug discovery programs.

  2. Psychosocial counselling of identifiable sperm donors.

    PubMed

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

    2016-05-01

    What do identifiable sperm donors feel about psychosocial counselling? Identifiable sperm donors found it important that psychosocial counselling focused on emotional consequences and on rules and regulations and they expected to have access to psychosocial counselling at the time that donor-offspring actually sought contact. Most studies on sperm donors are on anonymous donors and focus on recruitment, financial compensation, anonymity and motivations. There is limited knowledge on the value that identifiable sperm donors place on psychosocial counselling and what their needs are in this respect. We performed a qualitative study from March until June 2014 with 25 identifiable sperm donors, who were or had been a donor at the Centre for Reproductive Medicine of the Academic Medical Centre in Amsterdam any time between 1989 and 2014. We held semi-structured in-depth interviews with identifiable sperm donors with an average age of 44 years. The interviews were fully transcribed and analysed using the constant comparative method of grounded theory. Twelve out of 15 donors (former donors ITALIC! n = 8, active donors ITALIC! n = 7) who had received a counselling session during their intake procedure found it important that they had been able to talk about issues such as the emotional consequences of donation, disclosure to their own children, family and friends, future contact with donor-offspring and rules and regulations. Of the 10 former donors who had received no counselling session, 8 had regretted the lack of intensive counselling. In the years following their donation, most donors simply wanted to know how many offspring had been born using their sperm and had no need for further counselling. Nevertheless, they frequently mentioned that they were concerned about the well-being of 'their' offspring. In addition, they would value the availability of psychosocial counselling in the event that donor-offspring actually sought contact. A limitation of our study is its

  3. On identifiability of flexible structure parameters

    NASA Technical Reports Server (NTRS)

    Joshi, S. M.; Goglia, G. L.

    1983-01-01

    This report investigates the identifiability of modal parameters of flexible structures. Expressions are derived for Cramer-Rao lower bounds for the modal parameters, that is, frequencies, damping ratios and mode shapes or slopes. The optimal initial state, which maximizes the trace of the Fisher information matrix in the absence of persistent input, is obtained. The concepts discussed are applied to a finite-element model of the 122 meter hoop/column antenna. The numerical results show that the identifiability of the structural frequencies is excellent, followed by that of the damping ratios and the mode-slopes.

  4. Identifying gaps in international food safety regulation.

    PubMed

    McGrady, Benn; Ho, Christina S

    2011-01-01

    The rise in food importation in countries such as the United States, coupled with food safety incidents, has led to increased concern with the safety of imported food. This concern has prompted discussion of how international law and governance mechanisms might enhance food safety. This paper identifies the objectives underlying multilateral approaches to food safety such as raising food safety standards abroad, information sharing and ensuring market access. The paper then explores how these objectives are integrated into the international system and identifies how the current state of the law creates imbalances in the pursuit of these objectives.

  5. Molecular Fingerprints to Identify Candida Species

    PubMed Central

    Spampinato, Claudia

    2013-01-01

    A wide range of molecular techniques have been developed for genotyping Candida species. Among them, multilocus sequence typing (MLST) and microsatellite length polymorphisms (MLP) analysis have recently emerged. MLST relies on DNA sequences of internal regions of various independent housekeeping genes, while MLP identifies microsatellite instability. Both methods generate unambiguous and highly reproducible data. Here, we review the results achieved by using these two techniques and also provide a brief overview of a new method based on high-resolution DNA melting (HRM). This method identifies sequence differences by subtle deviations in sample melting profiles in the presence of saturating fluorescent DNA binding dyes. PMID:23844370

  6. Identifying the substance abuser in clinical practice.

    PubMed

    Bell, K

    1992-01-01

    Illicit drugs are used regularly by 14.5 million Americans. By identifying patients who abuse substances, the nurse will be better able to provide for the treatment interventions needed and omit ineffective treatment interventions. The patient will benefit by receiving timely and appropriate care. To identify substance abusers, the nurse must know effects of commonly abused drugs, their routes of administration, withdrawal signs, and the physical assessments that should be performed. The most common drugs abused are narcotics, depressants, antidepressants, anti-anxiety drugs, stimulants, hallucinogens, and marijuana.

  7. Minimal covariant observables identifying all pure states

    NASA Astrophysics Data System (ADS)

    Carmeli, Claudio; Heinosaari, Teiko; Toigo, Alessandro

    2013-09-01

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

  8. Identifying node importance in complex networks

    NASA Astrophysics Data System (ADS)

    Hu, Ping; Fan, Wenli; Mei, Shengwei

    2015-07-01

    In this paper, we propose a novel node importance evaluation method from the perspective of the existence of mutual dependence among nodes. The node importance comprises its initial importance and the importance contributions from both the adjacent and non-adjacent nodes according to the dependence strength between them. From the simulation analyses on an example network and the ARPA network, we observe that our method can well identify the node importance. Then, the cascading failures on the Netscience and E-mail networks demonstrate that the networks are more vulnerable when continuously removing the important nodes identified by our method, which further proves the accuracy of our method.

  9. Field guide for identifying fuel loading models

    Treesearch

    Pamela G. Sikkink; Duncan C. Lutes; Robert E. Keane

    2009-01-01

    This report details a procedure for identifying fuel loading models (FLMs) in the field. FLMs are a new classification system for predicting fire effects from on-site fuels. Each FLM class represents fuel beds that have similar fuel loadings and produce similar emissions and soil surface heating when burned using computer simulations. We describe how to estimate fuel...

  10. Problems Identifying Independent and Dependent Variables

    ERIC Educational Resources Information Center

    Leatham, Keith R.

    2012-01-01

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

  11. [Identifying Gifted American Indian Students.] What Works.

    ERIC Educational Resources Information Center

    Davidson, Karen

    1997-01-01

    In Hardin (Montana) schools, where 55% of students are American Indians, the same identification methods are used to identify gifted students among all cultural groups. These methods include nonverbal standardized tests and subjective recommendations based on the Frasier Talent Assessment Profile. Other equitable practices include equal…

  12. Identifying Concrete and Formal Operational Children.

    ERIC Educational Resources Information Center

    Docherty, Edward M.

    This paper presents a study designed to determine if groups of concrete and formal operational children can be identified through the technique of cluster analysis, using a battery of Piagetian tasks. A Total of 64 subjects, 8 boys and 8 girls from each of the second, fourth, sixth, and eighth grade levels, were selected from a public elementary…

  13. International Team Identifies Biomarker for Scleroderma

    MedlinePlus

    ... that are under development for this disease," said study author Robert Lafyatis, M.D., of the Boston University School of Medicine. "This would enable us to more rapidly identify new therapies in early clinical trials." With this goal in mind, Dr. Lafyatis helped form an international network of ...

  14. Professional Development: Identifying Effective Instructional Coaching Activities

    ERIC Educational Resources Information Center

    Mannino, Gina

    2014-01-01

    The purpose of this study was to identify the instructional coaching activities most used by instructional coaches in southeast Texas school districts and to test if there was a relationship between the use of instructional coaching and perceived improvement in the instructional practices of teachers and student achievement. The participants for…

  15. Methods for Identifying Versioned and Plagiarized Documents.

    ERIC Educational Resources Information Center

    Hoad, Timothy C.; Zobel, Justin

    2003-01-01

    Describes research that was conducted to develop and evaluate techniques for identifying plagiarism, revisions, and different versions of online documents. Highlights include ranking; parsing; similarity measures; identity measures; fingerprinting documents; measuring effectiveness via recall and precision; and experiments on two document…

  16. Identifying Depression in Students with Mental Retardation.

    ERIC Educational Resources Information Center

    Stough, Laura M.; Baker, Lynn

    1999-01-01

    Offers guidelines to teachers for identifying depression in students with mental retardation. Discusses prevalence and symptoms of depression, causes of depression, difficulty of diagnosis in students with mental retardation, detecting symptoms in the classroom, treatment of depression, and psychological services. Inserts list ideas for helping…

  17. Identify, Organize, and Retrieve Items Using Zotero

    ERIC Educational Resources Information Center

    Clark, Brian; Stierman, John

    2009-01-01

    Librarians build collections. To do this they use tools that help them identify, organize, and retrieve items for the collection. Zotero (zoh-TAIR-oh) is such a tool that helps the user build a library of useful books, articles, web sites, blogs, etc., discovered while surfing online. A visit to Zotero's homepage, www.zotero.org, shows a number of…

  18. National Board Certification Identifies Strong Teachers

    ERIC Educational Resources Information Center

    Education Digest: Essential Readings Condensed for Quick Review, 2009

    2009-01-01

    Advanced certification through the National Board for Professional Teaching Standards (NBPTS) is an effective way to identify highly skilled teachers, according to a congressionally mandated report from the National Research Council. Students taught by NBPTS-certified teachers make greater gains on achievement tests than students taught by…

  19. Identifying Ethical Hypernorms for Accounting Educators

    ERIC Educational Resources Information Center

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

    2012-01-01

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

  20. Identifying the Context of Postsecondary Instructional Programs.

    ERIC Educational Resources Information Center

    Levinson-Rose, Judith; Menges, Robert J.

    A framework for articulating postsecondary instructional programs is described. The framework identifies two important sources of influence on programs: the type of institution within which the program operates and the program objectives. These factors influence both program components and how these components are linked and processes that are…

  1. How to Identify High-Growth Schools

    ERIC Educational Resources Information Center

    Pfeiffer, Linda E.

    2015-01-01

    When researching school options, parents may want to look for schools with high-growth scores which, according to research, may be indicators of other characteristics such as programming, leadership, culture, and size. This quick guide offers parents tips on how to identify high-growth schools and what to ask when evaluating school options. An…

  2. Ideas Identified and Distributed through Project IDEA.

    ERIC Educational Resources Information Center

    American Alliance for Health, Physical Education, and Recreation, Washington, DC.

    This document contains ideas on a variety of subjects directed at the physical educator. The work was compiled by Project IDEA (Identify, Distribute, Exchange for Action). Topics include the following: (a) scheduling, (b) curriculum, (c) games, (d) specific courses, (e) life sports, (f) fitness, (g) adaptive Physical education, (h) course methods,…

  3. Sputum induction problems identified through genetic fingerprinting.

    PubMed

    Nivin, Beth; O'Flaherty, Tholief; Leibert, Eric; Zhao, Ben Yang; Driscoll, Jeffrey

    2002-10-01

    To identify the contamination source of a cluster of eight positive Mycobacterium tuberculosis isolates from one laboratory session. Spoligotyping was performed on M. tuberculosis isolates processed during one laboratory session. Laboratory and sputum induction protocols and records were reviewed. Sputum induction staff were interviewed. An environmental assessment of the sputum induction booth was performed. Spoligotyping identified a unique strain of susceptible M. tuberculosis from five induced sputa collected at Clinic A on the same day. Three specimens processed concurrently from other clinics had spoligotypes different from each other and from the cluster strain. A laboratory investigation revealed no procedural lapses. Sputum induction records from Clinic A indicated that patient 1 in the sputum induction booth had prior culture-confirmed tuberculosis. Patient 2 had a history of a drug-resistant strain. Patient 3 had completed tuberculosis treatment, with positive cultures 7 months earlier. Patients 4 and 5 were new to the clinic and had no subsequent positive M. tuberculosis specimens. The sputum induction booth was working within normal parameters. Sputum induction that day was overseen by a new employee with limited training and no supervision. A review of the sputum induction protocol identified ambiguity regarding care of the ultrasonic nebulizer between patients, which may have led to reuse of the discarded nebulizer solution from patient 1. A break in the sputum induction protocol may have contributed to contamination of patient specimens. Sputum induction is complicated, mandating adequate staff training and supervision and patient preparation. Spoligotyping identified a potential source of M. tuberculosis contamination.

  4. Techniques for identifying predators of goose nests

    USGS Publications Warehouse

    Anthony, R. Michael; Grand, J.B.; Fondell, T.F.; Miller, David A.

    2006-01-01

    We used cameras and artificial eggs to identify nest predators of dusky Canada goose Branta canadensis occidentalis nests during 1997-2000. Cameras were set up at 195 occupied goose nests and 60 artificial nests. We placed wooden eggs and domestic goose eggs that were emptied and then filled with wax or foam in an additional 263 natural goose nests to identify predators from marks in the artificial eggs. All techniques had limitations, but each correctly identified predators and estimated their relative importance. Nests with cameras had higher rates of abandonment than natural nests, especially during laying. Abandonment rates were reduced by deploying artificial eggs late in laying and reducing time at nests. Predation rates for nests with cameras were slightly lower than for nests without cameras. Wax-filled artificial eggs caused mortality of embryos in natural nests, but were better for identifying predator marks at artificial nests. Use of foam-filled artificial eggs in natural nests was the most cost effective means of monitoring nest predation. ?? Wildlife Biology (2006).

  5. Identifying the Multiple Intelligences of Your Students

    ERIC Educational Resources Information Center

    McClellan, Joyce A.; Conti, Gary J.

    2008-01-01

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

  6. Identifying Fallacies of Reference in Argumentation

    ERIC Educational Resources Information Center

    Gough, Jim

    2009-01-01

    The experience of teaching informal logic (sometimes called practical logic) at the introductory level over the last fifteen years has allowed the author the opportunity to identify some interesting problems. These problems have been encountered by students attempting to understand some of the ideas presented in the informal logic course and by…

  7. Student Success Factors: Identifying Key Predictors

    ERIC Educational Resources Information Center

    Sulaiman, Ainin; Mohezar, Suhana

    2006-01-01

    The authors' main aim in this study was to identify key predictors of Master of Business Administration (MBA) students' academic performance. The authors measured performance by the students' cumulative grade point average achieved, using data from the Students Information Systems and Application database. The authors found that a student's…

  8. Identifying the Rhetoric of Uncertainty Reduction.

    ERIC Educational Resources Information Center

    Williams, David E.

    Offering a rhetorical perspective of uncertainty reduction, this paper (1) discusses uncertainty reduction theory and dramatism; (2) identifies rhetorical strategies inherent in C. W. Berger and R. J. Calabrese's theory; (3) extends predicted outcome value to influenced outcome value; and (4) argues that the goal of uncertainty reduction and…

  9. National Board Certification Identifies Strong Teachers

    ERIC Educational Resources Information Center

    Education Digest: Essential Readings Condensed for Quick Review, 2009

    2009-01-01

    Advanced certification through the National Board for Professional Teaching Standards (NBPTS) is an effective way to identify highly skilled teachers, according to a congressionally mandated report from the National Research Council. Students taught by NBPTS-certified teachers make greater gains on achievement tests than students taught by…

  10. Identifiability and Equivalence of GLLIRM Models

    ERIC Educational Resources Information Center

    Revuelta, Javier

    2009-01-01

    The generalized logit-linear item response model (GLLIRM) is a linearly constrained nominal categories model (NCM) that computes the scale and intercept parameters for categories as a weighted sum of basic parameters. This paper addresses the problems of the identifiability of the basic parameters and the equivalence between different GLLIRM…

  11. Biogeographic methods identify gymnosperm biodiversity hotspots

    NASA Astrophysics Data System (ADS)

    Contreras-Medina, Raúl; Morrone, Juan J.; Luna Vega, Isolda

    2001-10-01

    A remarkable congruence among areas of endemism, panbiogeographic nodes, and refugia in western North America, Japan, south-western China, Tasmania, and New Caledonia indicates that these areas deserve special status for conservation. Here we propose that areas identified by different biogeographic methods are significant candidates for designation as hotspots.

  12. Problems Identifying Independent and Dependent Variables

    ERIC Educational Resources Information Center

    Leatham, Keith R.

    2012-01-01

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

  13. Identifying Advanced Technologies for Education's Future.

    ERIC Educational Resources Information Center

    Moore, Gwendolyn B.; Yin, Robert K.

    A study to determine how three advanced technologies might be applied to the needs of special education students helped inspire the development of a new method for identifying such applications. This new method, named the "Hybrid Approach," combines features of the two traditional methods: technology-push and demand-pull. Technology-push involves…

  14. Identifying Mentors for Student Employees on Campus

    ERIC Educational Resources Information Center

    Frock, David

    2015-01-01

    Purpose: This exploratory research project aims to seek an effective process for identifying supervisors of part-time student employees who also serve in a mentoring capacity. Design/methodology/approach: This paper is based on a review of literature and an evaluation process focused on established traits and functions of mentoring as applied to…

  15. Using lice to identify cowbird hosts

    USGS Publications Warehouse

    Hahn, D.C.; Osenton, P.C.; Price, R.W.

    1995-01-01

    Avian lice may link fledgling Brown-headed Cowbirds to the host species that raised them. Lice, if host-specific and transferred to nestling cowbirds, could serve to identify the principal host species raising cowbirds in a local area. This approach of trapping cowbird fledglings in a feeding flock, then collecting and identifying the lice they carry is economical. The alternative requires a team of people to locate large numbers of parasitized host nests. We trapped 250 cowbird fledglings during June-August 1994 on Patuxent Research Center, and from them we collected 426 lice identified as representing 6 genera and 12 species. We. also collected and identified 347 lice from 30 known host species that were mist-netted on our Center. The lice found on cowbird fledglings in this population can be linked to Wood Thrush, Red-eyed Vireo, Common Yellowthroat, Rufous-sided Towhee, Red-winged Blackbird, Common Grackle, Song Sparrow, Field Sparrow, and Tree sparrow, based on this study and also on published reports.

  16. Avoiding medication mixups. Identifiable imprint codes.

    PubMed Central

    Vasudevan, P; Del Gianni, T; Robertson, W O

    1996-01-01

    This study was done to determine if current imprinting of solid medication forms permits health care professionals to identify the manufacturers involved so as to be able to activate the hierarchic identification system mandated by the Food and Drug Administration. We tested 15 representatives of 6 groups of health professionals for their ability to identify the manufacturer after having examined 30 solid-dosage forms drawn from a pseudo-random sample of stock hospital formulary products. The correct identification of the manufacturer was the sole criterion. Of the 2,700 opportunities, the manufacturer was able to be identified for only 43%. Nurses and medical students had a 35% success rate, pharmacists and poison center specialists a 55% success rate, and residents and attending physicians a 40% rate. None approached 95% accuracy. Currently employed imprints fail in their objective to permit health care professionals--or the general public--to rapidly identify prescription drugs. The manufacturers' logotypes need to be modified if this identification system is to be implemented. We propose a simple voluntary collaborative effort by the pharmaceutical industry to solve the problem. PMID:9000855

  17. Identifying Benefit Segments among College Students.

    ERIC Educational Resources Information Center

    Brown, Joseph D.

    1991-01-01

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

  18. Identifying Teaching Methods that Engage Entrepreneurship Students

    ERIC Educational Resources Information Center

    Balan, Peter; Metcalfe, Mike

    2012-01-01

    Purpose: Entrepreneurship education particularly requires student engagement because of the complexity of the entrepreneurship process. The purpose of this paper is to describe how an established measure of engagement can be used to identify relevant teaching methods that could be used to engage any group of entrepreneurship students.…

  19. A screening cascade to identify ERβ ligands

    PubMed Central

    Filgueira, Carly S.; Benod, Cindy; Lou, Xiaohua; Gunamalai, Prem S.; Villagomez, Rosa A.; Strom, Anders; Gustafsson, Jan-Åke; Berkenstam, Anders L.; Webb, Paul

    2014-01-01

    The establishment of effective high throughput screening cascades to identify nuclear receptor (NR) ligands that will trigger defined, therapeutically useful sets of NR activities is of considerable importance. Repositioning of existing approved drugs with known side effect profiles can provide advantages because de novo drug design suffers from high developmental failure rates and undesirable side effects which have dramatically increased costs. Ligands that target estrogen receptor β (ERβ) could be useful in a variety of diseases ranging from cancer to neurological to cardiovascular disorders. In this context, it is important to minimize cross-reactivity with ERα, which has been shown to trigger increased rates of several types of cancer. Because of high sequence similarities between the ligand binding domains of ERα and ERβ, preferentially targeting one subtype can prove challenging. Here, we describe a sequential ligand screening approach comprised of complementary in-house assays to identify small molecules that are selective for ERβ. Methods include differential scanning fluorimetry, fluorescence polarization and a GAL4 transactivation assay. We used this strategy to screen several commercially-available chemical libraries, identifying thirty ERβ binders that were examined for their selectivity for ERβ versus ERα, and tested the effects of selected ligands in a prostate cancer cell proliferation assay. We suggest that this approach could be used to rapidly identify candidates for drug repurposing. PMID:25422593

  20. 34 CFR 300.32 - Personally identifiable.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

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

  1. Identifying Specific Comprehension Deficits in Children

    ERIC Educational Resources Information Center

    Gifford, Diane Baty

    2013-01-01

    Research has shown that educators may be missing an under-identified population of approximately 10 percent of typically developing children, who have fluent, age-appropriate decoding and word recognition skills, yet have specific difficulties with other higher-level text processing factors. These children are said to have specific comprehension…

  2. Diagnostics Tools Identify Faults Prior to Failure

    NASA Technical Reports Server (NTRS)

    2013-01-01

    Through the SBIR program, Rochester, New York-based Impact Technologies LLC collaborated with Ames Research Center to commercialize the Center s Hybrid Diagnostic Engine, or HyDE, software. The fault detecting program is now incorporated into a software suite that identifies potential faults early in the design phase of systems ranging from printers to vehicles and robots, saving time and money.

  3. Interchange. Program Improvement Products Identified through Networking.

    ERIC Educational Resources Information Center

    Ohio State Univ., Columbus. National Center for Research in Vocational Education.

    This catalog lists exemplary field-based program improvement products identified by the Dissemination and Utilization Products and Services Program (D&U) at the National Center for Research in Vocational Education. It is designed to increase awareness of these products among vocational educators and to provide information about them that…

  4. Diffraction gratings used as identifying markers

    DOEpatents

    Deason, Vance A.; Ward, Michael B.

    1991-01-01

    A finely detailed defraction grating is applied to an object as an identifier or tag which is unambiguous, difficult to duplicate, or remove and transfer to another item, and can be read and compared with prior readings with relative ease. The exact pattern of the defraction grating is mapped by diffraction moire techniques and recorded for comparison with future readings of the same grating.

  5. Identifying personal microbiomes using metagenomic codes.

    PubMed

    Franzosa, Eric A; Huang, Katherine; Meadow, James F; Gevers, Dirk; Lemon, Katherine P; Bohannan, Brendan J M; Huttenhower, Curtis

    2015-06-02

    Community composition within the human microbiome varies across individuals, but it remains unknown if this variation is sufficient to uniquely identify individuals within large populations or stable enough to identify them over time. We investigated this by developing a hitting set-based coding algorithm and applying it to the Human Microbiome Project population. Our approach defined body site-specific metagenomic codes: sets of microbial taxa or genes prioritized to uniquely and stably identify individuals. Codes capturing strain variation in clade-specific marker genes were able to distinguish among 100s of individuals at an initial sampling time point. In comparisons with follow-up samples collected 30-300 d later, ∼30% of individuals could still be uniquely pinpointed using metagenomic codes from a typical body site; coincidental (false positive) matches were rare. Codes based on the gut microbiome were exceptionally stable and pinpointed >80% of individuals. The failure of a code to match its owner at a later time point was largely explained by the loss of specific microbial strains (at current limits of detection) and was only weakly associated with the length of the sampling interval. In addition to highlighting patterns of temporal variation in the ecology of the human microbiome, this work demonstrates the feasibility of microbiome-based identifiability-a result with important ethical implications for microbiome study design. The datasets and code used in this work are available for download from huttenhower.sph.harvard.edu/idability.

  6. 34 CFR 300.32 - Personally identifiable.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 34 Education 2 2013-07-01 2013-07-01 false Personally identifiable. 300.32 Section 300.32 Education Regulations of the Offices of the Department of Education (Continued) OFFICE OF SPECIAL EDUCATION AND REHABILITATIVE SERVICES, DEPARTMENT OF EDUCATION ASSISTANCE TO STATES FOR THE EDUCATION...

  7. 34 CFR 300.32 - Personally identifiable.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 34 Education 2 2014-07-01 2013-07-01 true Personally identifiable. 300.32 Section 300.32 Education Regulations of the Offices of the Department of Education (Continued) OFFICE OF SPECIAL EDUCATION AND REHABILITATIVE SERVICES, DEPARTMENT OF EDUCATION ASSISTANCE TO STATES FOR THE EDUCATION OF CHILDREN...

  8. Identifying and Prioritizing Critical Hardwood Resources

    Treesearch

    Sam C. Doak; Sharon Johnson; Marlyce Myers

    1991-01-01

    A logical framework is required to provide a focus for the implementation of a variety of landowner incentive techniques in accordance with existing goals to protect and enhance hardwood resources. A system is presented for identifying and prioritizing critical hardwood resources for site specific conservation purposes. Flexibility is built into this system so that...

  9. Methods for Identifying Versioned and Plagiarized Documents.

    ERIC Educational Resources Information Center

    Hoad, Timothy C.; Zobel, Justin

    2003-01-01

    Describes research that was conducted to develop and evaluate techniques for identifying plagiarism, revisions, and different versions of online documents. Highlights include ranking; parsing; similarity measures; identity measures; fingerprinting documents; measuring effectiveness via recall and precision; and experiments on two document…

  10. Identifying Protein-Calorie Malnutrition Workshop.

    ERIC Educational Resources Information Center

    Walker, Susan S.; Barker, Ellen M.

    Instructional materials are provided for a workshop to enable participants to assist in identifying patients at risk with protein-calorie malnutrition and in corrrecting this nutritional deficiency. Representative topics are nutrients; protein, mineral, and vitamin sources, functions, and deficiency symptoms; malnutrition; nutritional deficiency…

  11. Identifying Benefit Segments among College Students.

    ERIC Educational Resources Information Center

    Brown, Joseph D.

    1991-01-01

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

  12. Identify Your Brand, Before You Market.

    ERIC Educational Resources Information Center

    Claggett, Laura

    2002-01-01

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

  13. Neoplasms identified in free-flying birds

    USGS Publications Warehouse

    Siegfried, L.M.

    1983-01-01

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

  14. How to Identify High-Growth Schools

    ERIC Educational Resources Information Center

    Pfeiffer, Linda E.

    2015-01-01

    When researching school options, parents may want to look for schools with high-growth scores which, according to research, may be indicators of other characteristics such as programming, leadership, culture, and size. This quick guide offers parents tips on how to identify high-growth schools and what to ask when evaluating school options. An…

  15. Identifying Teaching Methods that Engage Entrepreneurship Students

    ERIC Educational Resources Information Center

    Balan, Peter; Metcalfe, Mike

    2012-01-01

    Purpose: Entrepreneurship education particularly requires student engagement because of the complexity of the entrepreneurship process. The purpose of this paper is to describe how an established measure of engagement can be used to identify relevant teaching methods that could be used to engage any group of entrepreneurship students.…

  16. Identifying Mentors for Student Employees on Campus

    ERIC Educational Resources Information Center

    Frock, David

    2015-01-01

    Purpose: This exploratory research project aims to seek an effective process for identifying supervisors of part-time student employees who also serve in a mentoring capacity. Design/methodology/approach: This paper is based on a review of literature and an evaluation process focused on established traits and functions of mentoring as applied to…

  17. Problems identified with home infusion pumps.

    PubMed

    Koeppen, M A; Caspers, S M

    1994-01-01

    A variety of infusion pumps and devices are available on the market today. In this article, the authors examine these products based on questionnaires sent out to typical consumers, including hospitals and caregivers. Using the results of this questionnaire, the authors identify whether or not users of home infusion pumps and devices find them difficult to operate.

  18. Serial Item Contribution Identifier: New SISAC Code.

    ERIC Educational Resources Information Center

    Computers in Libraries, 1993

    1993-01-01

    Discusses the benefits of the Serial Item Contribution Identifier (SICI) standard for serials handling. Developed by the Serials Industry Systems Advisory Committee (SISAC), SICI applications through the use of a SISAC barcode are expected to benefit shipping, ordering, serials processing and claiming, document delivery, and information exchange.…

  19. Do Colleges Identify or Develop Intelligence?

    ERIC Educational Resources Information Center

    Moore, Randy

    2004-01-01

    Most colleges and universities emphasize identifying smartness much more than developing smartness. This value is made explicit in the many influential rankings of colleges and universities, in which elitist schools who recruit students with high SAT scores, grade point averages, and class rankings are declared "better" than other…

  20. Zebrafish phenotypic screen identifies novel Notch antagonists.

    PubMed

    Velaithan, Vithya; Okuda, Kazuhide Shaun; Ng, Mei Fong; Samat, Norazwana; Leong, Sze Wei; Faudzi, Siti Munirah Mohd; Abas, Faridah; Shaari, Khozirah; Cheong, Sok Ching; Tan, Pei Jean; Patel, Vyomesh

    2017-04-01

    Zebrafish represents a powerful in vivo model for phenotype-based drug discovery to identify clinically relevant small molecules. By utilizing this model, we evaluated natural product derived compounds that could potentially modulate Notch signaling that is important in both zebrafish embryogenesis and pathogenic in human cancers. A total of 234 compounds were screened using zebrafish embryos and 3 were identified to be conferring phenotypic alterations similar to embryos treated with known Notch inhibitors. Subsequent secondary screens using HEK293T cells overexpressing truncated Notch1 (HEK293TΔE) identified 2 compounds, EDD3 and 3H4MB, to be potential Notch antagonists. Both compounds reduced protein expression of NOTCH1, Notch intracellular domain (NICD) and hairy and enhancer of split-1 (HES1) in HEK293TΔE and downregulated Notch target genes. Importantly, EDD3 treatment of human oral cancer cell lines demonstrated reduction of Notch target proteins and genes. EDD3 also inhibited proliferation and induced G0/G1 cell cycle arrest of ORL-150 cells through inducing p27(KIP1). Our data demonstrates the utility of the zebrafish phenotypic screen and identifying EDD3 as a promising Notch antagonist for further development as a novel therapeutic agent.

  1. Identifying Depression in Students with Mental Retardation.

    ERIC Educational Resources Information Center

    Stough, Laura M.; Baker, Lynn

    1999-01-01

    Offers guidelines to teachers for identifying depression in students with mental retardation. Discusses prevalence and symptoms of depression, causes of depression, difficulty of diagnosis in students with mental retardation, detecting symptoms in the classroom, treatment of depression, and psychological services. Inserts list ideas for helping…

  2. Identifying Effectiveness Criteria for Internet Payment Systems.

    ERIC Educational Resources Information Center

    Shon, Tae-Hwan; Swatman, Paula M. C.

    1998-01-01

    Examines Internet payment systems (IPS): third-party, card, secure Web server, electronic token, financial electronic data interchange (EDI), and micropayment based. Reports the results of a Delphi survey of experts identifying and classifying IPS effectiveness criteria and classifying types of IPS providers. Includes the survey invitation letter…

  3. Identifying the Cognitive Decrements Caused By HIV

    DTIC Science & Technology

    1994-06-10

    regions with specific tests. Thus, probable sites of lesions or other forms of damage can be identified. Information processing tests generally cannot be...Relationship to severity of disease and brain atrophy. Acta Neurologica Scandinavica, 87, 88-94o Ratcliff, R. (1993). Methods for dealing with reaction time

  4. An Empirical Approach to Identifying Effective Schools.

    ERIC Educational Resources Information Center

    Webster, William J.; Olson, George H.

    One approach to identifying effective schools defines effectiveness in terms of student achievement in reading, mathematics, and language usage. Exceptional school achievement is indicated by performance above or below the level expected if students were merely to maintain their previous rate of growth. Regression analysis is used to compute…

  5. Identifying Protein-Calorie Malnutrition Workshop.

    ERIC Educational Resources Information Center

    Walker, Susan S.; Barker, Ellen M.

    Instructional materials are provided for a workshop to enable participants to assist in identifying patients at risk with protein-calorie malnutrition and in corrrecting this nutritional deficiency. Representative topics are nutrients; protein, mineral, and vitamin sources, functions, and deficiency symptoms; malnutrition; nutritional deficiency…

  6. A test to identify persistent picky eaters.

    PubMed

    Toyama, Hannah; Agras, W Stewart

    2016-12-01

    Picky eating is common and usually relatively brief as new foods are accepted. Persistent picky eating, however, is often associated with comorbid psychopathology. The aim of this study was to use parent-reported child feeding behaviors to identify which picky eaters persist. Participants were a subsample from the Stanford Infant Growth Study a prospective study of child development. Out of the 216 infants, 86 were identified as picky eaters. Picky eaters were separated into two groups using a median split: short-term (n=40) and persistent picky eaters (n=46). Recursive Partitioning detected three significant parent-reported feeding questions that may identify persistent picky eaters at an early age: Is your child a picky eater? (yes), does s/he have strong likes with regard to food (yes), does your child accept new foods readily? (no). These results provide a first step allowing providers to identify persistent picky eaters and possibly enable intervention at an early age. Further studies are needed to replicate and extend these findings in another sample of picky eaters. Copyright © 2016 Elsevier Ltd. All rights reserved.

  7. Identifying the Knowledge Base for School Improvement

    ERIC Educational Resources Information Center

    Beach, Robert H.; Lindahl, Ron

    2004-01-01

    In 1983, a landmark event occurred in public education in the US: the National Commission on Excellence in Education published its now famous report, A Nation at Risk. The report was generally regarded as the catalyst for decades of public and political pressure for large-scale school improvement or reform. Here, Beach and Lindahl identify a…

  8. Embedded sensor having an identifiable orientation

    DOEpatents

    Bennett, Thomas E.; Nelson, Drew V.

    2002-01-01

    An apparatus and method is described wherein a sensor, such as a mechanical strain sensor, embedded in a fiber core, is "flagged" to identify a preferred orientation of the sensor. The identifying "flag" is a composite material, comprising a plurality of non-woven filaments distributed in a resin matrix, forming a small planar tab. The fiber is first subjected to a stimulus to identify the orientation providing the desired signal response, and then sandwiched between first and second layers of the composite material. The fiber, and therefore, the sensor orientation is thereby captured and fixed in place. The process for achieving the oriented fiber includes, after identifying the fiber orientation, carefully laying the oriented fiber onto the first layer of composite, moderately heating the assembled layer for a short period in order to bring the composite resin to a "tacky" state, heating the second composite layer as the first, and assembling the two layers together such that they merge to form a single consolidated block. The consolidated block achieving a roughly uniform distribution of composite filaments near the embedded fiber such that excess resin is prevented from "pooling" around the periphery of the fiber.

  9. Identifying Barriers to Study Abroad Program Participation

    ERIC Educational Resources Information Center

    McKinley, Karen E.

    2014-01-01

    University administrators, industry professionals, and government leaders encourage college students to participate in study abroad programs. Despite an increase in the number of students going abroad, the percentage of students participating in global programs remain low. This study identified barriers to study abroad program participation at a…

  10. Identifying marker typing incompatibilities in linkage analysis

    SciTech Connect

    Stringham, H.M.; Boehnke, M.

    1996-10-01

    A common problem encountered in linkage analyses is that execution of the computer program is halted because of genotypes in the data that are inconsistent with Mendelian inheritance. Such inconsistencies may arise because of pedigree errors or errors in typing. In some cases, the source of the inconsistencies is easily identified by examining the pedigree. In others, the error is not obvious, and substantial time and effort are required to identify the responsible genotypes. We have developed two methods for automatically identifying those individuals whose genotypes are most likely the cause of the inconsistencies. First, we calculate the posterior probability of genotyping error for each member of the pedigree, given the marker data on all pedigree members and allowing anyone in the pedigree to have an error. Second, we identify those individuals whose genotypes could be solely responsible for the inconsistency in the pedigree. We illustrate these methods with two examples: one a pedigree error, the second a genotyping error. These methods have been implemented as a module of the pedigree analysis program package MENDEL. 9 refs., 2 figs., 2 tabs.

  11. Professional Development: Identifying Effective Instructional Coaching Activities

    ERIC Educational Resources Information Center

    Mannino, Gina

    2014-01-01

    The purpose of this study was to identify the instructional coaching activities most used by instructional coaches in southeast Texas school districts and to test if there was a relationship between the use of instructional coaching and perceived improvement in the instructional practices of teachers and student achievement. The participants for…

  12. Data Identifiers and Citations Enable Reproducible Science

    NASA Astrophysics Data System (ADS)

    Tilmes, C.

    2011-12-01

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

  13. Identifying data sharing in biomedical literature.

    PubMed

    Piwowar, Heather A; Chapman, Wendy W; Chapman, Wendy

    2008-11-06

    Many policies and projects now encourage investigators to share their raw research data with other scientists. Unfortunately, it is difficult to measure the effectiveness of these initiatives because data can be shared in such a variety of mechanisms and locations. We propose a novel approach to finding shared datasets: using NLP techniques to identify declarations of dataset sharing within the full text of primary research articles. Using regular expression patterns and machine learning algorithms on open access biomedical literature, our system was able to identify 61% of articles with shared datasets with 80% precision. A simpler version of our classifier achieved higher recall (86%), though lower precision (49%). We believe our results demonstrate the feasibility of this approach and hope to inspire further study of dataset retrieval techniques and policy evaluation.

  14. Trustworthy persistent identifier systems of the future

    NASA Astrophysics Data System (ADS)

    Golodoniuc, Pavel; Klump, Jens; Car, Nicholas

    2016-04-01

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

  15. Identifying essential genes in Arabidopsis thaliana.

    PubMed

    Meinke, David; Muralla, Rosanna; Sweeney, Colleen; Dickerman, Allan

    2008-09-01

    Eight years after publication of the Arabidopsis genome sequence and two years before completing the first phase of an international effort to characterize the function of every Arabidopsis gene, plant biologists remain unable to provide a definitive answer to the following basic question: what is the minimal gene set required for normal growth and development? The purpose of this review is to summarize different strategies employed to identify essential genes in Arabidopsis, an important component of the minimal gene set in plants, to present an overview of the datasets and specific genes identified to date, and to discuss the prospects for future saturation of this important class of genes. The long-term goal of this collaborative effort is to facilitate basic research in plant biology and complement ongoing research with other model organisms.

  16. Framework for Identifying Cybersecurity Risks in Manufacturing

    DOE PAGES

    Hutchins, Margot J.; Bhinge, Raunak; Micali, Maxwell K.; ...

    2015-10-21

    Increasing connectivity, use of digital computation, and off-site data storage provide potential for dramatic improvements in manufacturing productivity, quality, and cost. However, there are also risks associated with the increased volume and pervasiveness of data that are generated and potentially accessible to competitors or adversaries. Enterprises have experienced cyber attacks that exfiltrate confidential and/or proprietary data, alter information to cause an unexpected or unwanted effect, and destroy capital assets. Manufacturers need tools to incorporate these risks into their existing risk management processes. This article establishes a framework that considers the data flows within a manufacturing enterprise and throughout its supplymore » chain. The framework provides several mechanisms for identifying generic and manufacturing-specific vulnerabilities and is illustrated with details pertinent to an automotive manufacturer. Finally, in addition to providing manufacturers with insights into their potential data risks, this framework addresses an outcome identified by the NIST Cybersecurity Framework.« less

  17. Guidelines for identifying suspect/counterfeit material

    SciTech Connect

    1995-09-01

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

  18. Framework for Identifying Cybersecurity Risks in Manufacturing

    SciTech Connect

    Hutchins, Margot J.; Bhinge, Raunak; Micali, Maxwell K.; Robinson, Stefanie L.; Sutherland, John W.; Dornfeld, David

    2015-10-21

    Increasing connectivity, use of digital computation, and off-site data storage provide potential for dramatic improvements in manufacturing productivity, quality, and cost. However, there are also risks associated with the increased volume and pervasiveness of data that are generated and potentially accessible to competitors or adversaries. Enterprises have experienced cyber attacks that exfiltrate confidential and/or proprietary data, alter information to cause an unexpected or unwanted effect, and destroy capital assets. Manufacturers need tools to incorporate these risks into their existing risk management processes. This article establishes a framework that considers the data flows within a manufacturing enterprise and throughout its supply chain. The framework provides several mechanisms for identifying generic and manufacturing-specific vulnerabilities and is illustrated with details pertinent to an automotive manufacturer. Finally, in addition to providing manufacturers with insights into their potential data risks, this framework addresses an outcome identified by the NIST Cybersecurity Framework.

  19. Persistent Identifiers for Dutch cultural heritage institutions

    NASA Astrophysics Data System (ADS)

    Ras, Marcel; Kruithof, Gijsbert

    2016-04-01

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

  20. Wham: Identifying Structural Variants of Biological Consequence

    PubMed Central

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

    2015-01-01

    Existing methods for identifying structural variants (SVs) from short read datasets are inaccurate. This complicates disease-gene identification and efforts to understand the consequences of genetic variation. In response, we have created Wham (Whole-genome Alignment Metrics) to provide a single, integrated framework for both structural variant calling and association testing, thereby bypassing many of the difficulties that currently frustrate attempts to employ SVs in association testing. Here we describe Wham, benchmark it against three other widely used SV identification tools–Lumpy, Delly and SoftSearch–and demonstrate Wham’s ability to identify and associate SVs with phenotypes using data from humans, domestic pigeons, and vaccinia virus. Wham and all associated software are covered under the MIT License and can be freely downloaded from github (https://github.com/zeeev/wham), with documentation on a wiki (http://zeeev.github.io/wham/). For community support please post questions to https://www.biostars.org/. PMID:26625158

  1. Identifying Groundwater Recharge in Arid Regions

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  2. Wham: Identifying Structural Variants of Biological Consequence.

    PubMed

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

    2015-12-01

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

  3. Identifying Potential Noise Sources within Acoustic Signals

    NASA Astrophysics Data System (ADS)

    Holcomb, Victoria; Lewalle, Jacques

    2013-11-01

    We test a new algorithm for its ability to detect sources of noise within random background. The goal of these tests is to better understand how to identify sources within acoustic signals while simultaneously determining the strengths and weaknesses of the algorithm in question. Unlike previously published algorithms, the antenna method does not pinpoint events by looking for the most energetic portions of a signal. The algorithm searches for the ideal lag combinations between three signals by taking excerpts of possible events. The excerpt with the lowest calculated minimum distance between possible events is how the algorithm identifies sources. At the minimum distance, the events are close in time and frequency. This method can be compared to the cross correlation and denoising methods to better understand its effectiveness. This work is supported in part by Spectral Energies LLC, under an SBIR grant from AFRL, as well as the Syracuse University MAE department.

  4. Identifying sex and age of akiapolaau

    USGS Publications Warehouse

    Pratt, T.K.; Fancy, S.G.; Harada, C.K.; Lindsey, G.D.; Jacobi, J.D.

    1994-01-01

    Methods for identifying the sex and age of the Akiapolaau (Hemignathus munroi), an endangered honeycreeper found only on the island of Hawaii, were developed by examination and measurement of 73 museum specimens and 24 live birds captured in mist nests. Akiapolaau probably undergo a single annual molt, with most birds molting between February and July. The mottled juvenal plumage is replaced by a first basic plumage characterized by yellowish-gray or yellowish-green underparts and often by retained wingbars. Male Akiapolaau may not attain adult plumage until their third molt. In adult females, only the throat and upper breast become yellow, whereas in adult males the superciliaries, cheeks, and entire underparts are yellow. Adult males have greater exposed culmen, gonys, wing chord, tail, and tarsus lengths than do females. Akiapolaau in first prebasic molt or older can be identified as to sex by culmen length, that of males being >23.4 mm.

  5. Chemical Proteomic Platform To Identify Citrullinated Proteins

    PubMed Central

    2015-01-01

    Anti-citrullinated protein antibodies (ACPAs) are a hallmark of rheumatoid arthritis (RA) and are routinely used for disease diagnosis. Protein citrullination is also increased in cancer and other autoimmune disorders, suggesting that citrullinated proteins may serve as biomarkers for diseases beyond RA. To identify these citrullinated proteins, we developed biotin-conjugated phenylglyoxal (biotin-PG). Using this probe and our platform technology, we identified >50 intracellular citrullinated proteins. More than 20 of these are involved in RNA splicing, suggesting, for the first time, that citrullination modulates RNA biology. Overall, this chemical proteomic platform will play a key role in furthering our understanding of protein citrullination in rheumatoid arthritis and potentially a wider spectrum of inflammatory diseases. PMID:26360112

  6. Using filtering effects to identify objects

    NASA Astrophysics Data System (ADS)

    Carroll, T. L.; Rachford, Frederic J.

    2012-06-01

    Reflecting signals off of targets is a method widely used to locate objects, but the reflected signal also contains information that can be used to identify the object. In radar or sonar, the signal amplitudes used are small enough that only linear effects are present, so we can consider the effect of the target on the signal as a linear filter. Using the known effects of linear filters on chaotic signals, we can create a reference that allows us to match a particular target to a particular reflected signal. Furthermore, if some parts of this "filter" vary only slowly as the aspect angle of the object changes, we can produce a reference that averages out the parts that are highly angle dependent so that one reference can be used to identify the target over a range of angles.

  7. Identifying Cellular and Molecular Mechanisms for Magnetosensation

    PubMed Central

    Clites, Benjamin L.; Pierce, Jonathan T.

    2017-01-01

    Diverse animals ranging from worms and insects to birds and turtles perf orm impressive journeys using the magnetic field of the earth as a cue. Although major cellular and molecular mechanisms for sensing mechanical and chemical cues have been elucidated over the past three decades, the mechanisms that animals use to sense magnetic fields remain largely mysterious. Here we survey progress on the search for magnetosensory neurons and magnetosensitive molecules important for animal behaviors. Emphasis is placed on magnetosensation in insects and birds, as well as on the magnetosensitive neuron pair AFD in the nematode Caenorhabditis elegans. We also review conventional criteria used to define animal magnetoreceptors and suggest how approaches used to identify receptors for other sensory modalities may be adapted for magnetoreceptors. Finally, we discuss prospects for under-utilized and novel approaches to identify the elusive magnetoreceptors in animals. PMID:28772099

  8. Identifying bilingual semantic neural representations across languages

    PubMed Central

    Buchweitz, Augusto; Shinkareva, Svetlana V.; Mason, Robert A.; Mitchell, Tom M.; Just, Marcel Adam

    2015-01-01

    The goal of the study was to identify the neural representation of a noun's meaning in one language based on the neural representation of that same noun in another language. Machine learning methods were used to train classifiers to identify which individual noun bilingual participants were thinking about in one language based solely on their brain activation in the other language. The study shows reliable (p < .05) pattern-based classification accuracies for the classification of brain activity for nouns across languages. It also shows that the stable voxels used to classify the brain activation were located in areas associated with encoding information about semantic dimensions of the words in the study. The identification of the semantic trace of individual nouns from the pattern of cortical activity demonstrates the existence of a multi-voxel pattern of activation across the cortex for a single noun common to both languages in bilinguals. PMID:21978845

  9. Identifying a novel locus for psoriatic arthritis

    PubMed Central

    Budu-Aggrey, Ashley; Bowes, John

    2016-01-01

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

  10. Identifiability of linear systems in physical coordinates

    NASA Technical Reports Server (NTRS)

    Su, Tzu-Jeng; Juang, Jer-Nan

    1992-01-01

    Identifiability of linear, time-invariant systems in physical coordinates is discussed. It is shown that identification of the system matrix in physical coordinates can be accomplished by determining a transformation matrix that relates the physical locations of actuators and sensors to the test-data-derived input and output matrices. For systems with symmetric matrices, the solution of a constrained optimization problem is used to characterize all the possible solutions of the transformation matrix. Conditions for the existence of a unique transformation matrix are established easily from the explicit form of the solutions. For systems with limited inputs and outputs, the question about which part of the system can be uniquely identified is also answered. A simple mass-spring system is used to verify the conclusions of this study.

  11. Identifying Proper Names in Parallel Medical Terminologies

    PubMed Central

    Bodenreider, Olivier; Zweigenbaum, Pierre

    2006-01-01

    We propose several criteria to identify proper names in biomedical terminologies. Traditional, pattern-based methods that rely on the immediate context of a proper name are not applicable. However, the availability of translations of some terminologies supports methods based on invariant words instead. A combination of five criteria achieved 86% precision and 88% recall on the 16,401 word forms of the International Classification of Diseases. PMID:11187591

  12. Which functional unit to identify sustainable foods?

    PubMed

    Masset, Gabriel; Vieux, Florent; Darmon, Nicole

    2015-09-01

    In life-cycle assessment, the functional unit defines the unit for calculation of environmental indicators. The objective of the present study was to assess the influence of two functional units, 100 g and 100 kcal (420 kJ), on the associations between three dimensions for identifying sustainable foods, namely environmental impact (via greenhouse gas emissions (GHGE)), nutritional quality (using two distinct nutrient profiling systems) and price. GHGE and price data were collected for individual foods, and were each expressed per 100 g and per 100 kcal. Two nutrient profiling models, SAIN,LIM and UK Ofcom, were used to assess foods' nutritional quality. Spearman correlations were used to assess associations between variables. Sustainable foods were identified as those having more favourable values for all three dimensions. The French Individual and National Dietary Survey (INCA2), 2006-2007. Three hundred and seventy-three foods highly consumed in INCA2, covering 65 % of total energy intake of adult participants. When GHGE and price were expressed per 100 g, low-GHGE foods had a lower price and higher SAIN,LIM and Ofcom scores (r=0·59, -0·34 and -0·43, respectively), suggesting a compatibility between the three dimensions; 101 and 100 sustainable foods were identified with SAIN,LIM and Ofcom, respectively. When GHGE and price were expressed per 100 kcal, low-GHGE foods had a lower price but also lower SAIN,LIM and Ofcom scores (r=0·67, 0·51 and 0·47, respectively), suggesting that more environment-friendly foods were less expensive but also less healthy; thirty-four sustainable foods were identified with both SAIN,LIM and Ofcom. The choice of functional unit strongly influenced the compatibility between the sustainability dimensions and the identification of sustainable foods.

  13. Identifying Topics in Microblogs Using Wikipedia

    PubMed Central

    Yıldırım, Ahmet; Üsküdarlı, Suzan; Özgür, Arzucan

    2016-01-01

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

  14. Data Identifiers, Versioning, and Micro-citation

    NASA Astrophysics Data System (ADS)

    Parsons, M. A.; Duerr, R. E.

    2012-12-01

    Data citation, especially using Digital Object Identifiers (DOIs), is an increasingly accepted scientific practice. For example, the AGU Council asserts that data "publications" should "be credited and cited like the products of any other scientific activity," and Thomson Reuters has recently announced a data citation index built from DOIs assigned to data sets. Correspondingly, formal guidelines for how to cite a data set (using DOIs or similar identifiers/locators) have recently emerged, notably those from the international DataCite consortium, the UK Digital Curation Centre, and the US Federation of Earth Science Information Partners. These different data citation guidelines are largely congruent. They agree on the basic practice and elements of data citation, especially for relatively static, whole data collections. There is less agreement on some of the more subtle nuances of data citation. They define different methods for handling different data set versions, especially for the very dynamic, growing data sets that are common in Earth Sciences. They also differ in how people should cite specific, arbitrarily large elements, "passages," or subsets of a larger data collection, i.e., the precise data records actually used in a study. This detailed "micro-citation", and careful reference to exact versions of data are essential to ensure scientific reproducibility. Identifiers such as DOIs are necessary but not sufficient for the precise, detailed, references necessary. Careful practice must be coupled with the use of curated identifiers. In this paper we review the pros and cons of different approaches to versioning and micro-citation. We suggest a workable solution for most existing Earth science data and suggest a more rigorous path forward for the future.

  15. Diffraction gratings used as identifying markers

    DOEpatents

    Deason, V.A.; Ward, M.B.

    1991-03-26

    A finely detailed diffraction grating is applied to an object as an identifier or tag which is unambiguous, difficult to duplicate, or remove and transfer to another item, and can be read and compared with prior readings with relative ease. The exact pattern of the diffraction grating is mapped by diffraction moire techniques and recorded for comparison with future readings of the same grating. 7 figures.

  16. Diffraction gratings used as identifying markers

    SciTech Connect

    Deason, V.A.; Ward, M.B.

    1989-08-03

    A finely detailed defraction grating is applied to an object as an identifier or tag which is unambiguous, difficult to duplicate, or remove and transfer to another item, and can be read and compared with prior readings with relative ease. The exact pattern of the defraction grating is mapped by diffraction moire techniques and recorded for comparison with future readings of the same grating. 7 figs.

  17. Identifying spatial priorities for protecting ecosystem services

    PubMed Central

    Luck, Gary W

    2012-01-01

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

  18. Laser Weather Identifier: Present and Future.

    NASA Astrophysics Data System (ADS)

    Wang, Ting-I.; Lataitis, R.; Lawrence, R. S.; Ochs, G. R.

    1982-11-01

    Prototype Laser Weather Identifier (LWI) systems designed to detect fog, rain and snow were tested for several months at Stapleton International Airport in Denver, and at the AFGL Weather Test Facility at Otis Air Force Base, Massachusetts. We present a detailed analysis of the performance of these systems, compared with human weather observations and tipping-bucket raingages, and suggest modifications for future operational instruments.

  19. Identifying Topics in Microblogs Using Wikipedia.

    PubMed

    Yıldırım, Ahmet; Üsküdarlı, Suzan; Özgür, Arzucan

    2016-01-01

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

  20. Identify needs of women living with HIV.

    PubMed

    Jelliman, Pauline

    This article reports on the development of the Between the Sheets project for women living with HIV. It began with an event that provided a forum to address their unmet needs concerning sexual activity and related issues. Development was informed by a focus group of women with HIV, some of whom also presented their personal stories. Attendees' evaluations have identified further unmet needs and ways HIV services might adapt to better meet the needs of these individuals.

  1. Identifying Fossil Bacteria in Martian Materials

    NASA Technical Reports Server (NTRS)

    Westall, F.; McKay, D. S.; Gibson, E. K., Jr.

    1999-01-01

    Within the next decade, robotic missions are going to Mars with the search for evidence for extant and extinct life as at least one of the mission objectives. Moreover, the first Martian samples will be returned to Earth in 2008. It is therefore imperative that we can be certain that we can identify life in Martian rocks. In this paper we will not be discussing extant life but will concentrate on fossil life.

  2. Identifying Fossil Bacteria in Martian Materials

    NASA Technical Reports Server (NTRS)

    Westall, F.; McKay, D. S.; Gibson, E. K., Jr.

    1999-01-01

    Within the next decade, robotic missions are going to Mars with the search for evidence for extant and extinct life as at least one of the mission objectives. Moreover, the first Martian samples will be returned to Earth in 2008. It is therefore imperative that we can be certain that we can identify life in Martian rocks. In this paper we will not be discussing extant life but will concentrate on fossil life.

  3. Interrogator system for identifying electrical circuits

    DOEpatents

    Jatko, William B.; McNeilly, David R.

    1988-01-01

    A system for interrogating electrical leads to correctly ascertain the identity of equipment attached to remote ends of the leads. The system includes a source of a carrier signal generated in a controller/receiver to be sent over the leads and an identifier unit at the equipment. The identifier is activated by command of the carrier and uses a portion of the carrier to produce a supply voltage. Each identifier is uniquely programmed for a specific piece of equipment, and causes the impedance of the circuit to be modified whereby the carrier signal is modulated according to that program. The modulation can be amplitude, frequency or phase modulation. A demodulator in the controller/receiver analyzes the modulated carrier signal, and if a verified signal is recognized displays and/or records the information. This information can be utilized in a computer system to prepare a wiring diagram of the electrical equipment attached to specific leads. Specific circuit values are given for amplitude modulation, and the system is particularly described for use with thermocouples.

  4. Identifying duplicate content using statistically improbable phrases

    PubMed Central

    Errami, Mounir; Sun, Zhaohui; George, Angela C.; Long, Tara C.; Skinner, Michael A.; Wren, Jonathan D.; Garner, Harold R.

    2010-01-01

    Motivation: Document similarity metrics such as PubMed's ‘Find related articles’ feature, which have been primarily used to identify studies with similar topics, can now also be used to detect duplicated or potentially plagiarized papers within literature reference databases. However, the CPU-intensive nature of document comparison has limited MEDLINE text similarity studies to the comparison of abstracts, which constitute only a small fraction of a publication's total text. Extending searches to include text archived by online search engines would drastically increase comparison ability. For large-scale studies, submitting short phrases encased in direct quotes to search engines for exact matches would be optimal for both individual queries and programmatic interfaces. We have derived a method of analyzing statistically improbable phrases (SIPs) for assistance in identifying duplicate content. Results: When applied to MEDLINE citations, this method substantially improves upon previous algorithms in the detection of duplication citations, yielding a precision and recall of 78.9% (versus 50.3% for eTBLAST) and 99.6% (versus 99.8% for eTBLAST), respectively. Availability: Similar citations identified by this work are freely accessible in the Déjà vu database, under the SIP discovery method category at http://dejavu.vbi.vt.edu/dejavu/ Contact: merrami@collin.edu PMID:20472545

  5. Identifying chemicals that are planetary boundary threats.

    PubMed

    MacLeod, Matthew; Breitholtz, Magnus; Cousins, Ian T; de Wit, Cynthia A; Persson, Linn M; Rudén, Christina; McLachlan, Michael S

    2014-10-07

    Rockström et al. proposed a set of planetary boundaries that delimit a "safe operating space for humanity". Many of the planetary boundaries that have so far been identified are determined by chemical agents. Other chemical pollution-related planetary boundaries likely exist, but are currently unknown. A chemical poses an unknown planetary boundary threat if it simultaneously fulfills three conditions: (1) it has an unknown disruptive effect on a vital Earth system process; (2) the disruptive effect is not discovered until it is a problem at the global scale, and (3) the effect is not readily reversible. In this paper, we outline scenarios in which chemicals could fulfill each of the three conditions, then use the scenarios as the basis to define chemical profiles that fit each scenario. The chemical profiles are defined in terms of the nature of the effect of the chemical and the nature of exposure of the environment to the chemical. Prioritization of chemicals in commerce against some of the profiles appears feasible, but there are considerable uncertainties and scientific challenges that must be addressed. Most challenging is prioritizing chemicals for their potential to have a currently unknown effect on a vital Earth system process. We conclude that the most effective strategy currently available to identify chemicals that are planetary boundary threats is prioritization against profiles defined in terms of environmental exposure combined with monitoring and study of the biogeochemical processes that underlie vital Earth system processes to identify currently unknown disruptive effects.

  6. Anesthesiology leadership rounding: identifying opportunities for improvement.

    PubMed

    Gravenstein, Dietrich; Ford, Susan; Enneking, F Kayser

    2012-01-01

    Rounding that includes participation of individuals with authority to implement changes has been advocated as important to the transformation of an institution into a high-quality and safe organization. We describe a Department of Anesthesiology's experience with leadership rounding. The Department Chair or other senior faculty designate, a quality coordinator, up to four residents, the ward charge nurse, and patient nurses participated in rounds at bedsides. During a 23-month period, 14 significant opportunities to improve care were identified. Nurses identified 5 of these opportunities, primary team physicians 2, the rounding team 4, and patients or their family members another 3. The anesthesiology service had sole or shared responsibility for 10 improvements. A variety of organizations track specific measures across all phases of the patient experience to gauge quality of care. Chart auditing tools for detecting threats to safety are often used. These measures and tools missed opportunities for improvement that were discovered only through rounding. We conclude that the introduction of leadership rounding by an anesthesiology service can identify opportunities for improving quality that are not captured by conventional efforts.

  7. Dynamic Method for Identifying Collected Sample Mass

    NASA Technical Reports Server (NTRS)

    Carson, John

    2008-01-01

    G-Sample is designed for sample collection missions to identify the presence and quantity of sample material gathered by spacecraft equipped with end effectors. The software method uses a maximum-likelihood estimator to identify the collected sample's mass based on onboard force-sensor measurements, thruster firings, and a dynamics model of the spacecraft. This makes sample mass identification a computation rather than a process requiring additional hardware. Simulation examples of G-Sample are provided for spacecraft model configurations with a sample collection device mounted on the end of an extended boom. In the absence of thrust knowledge errors, the results indicate that G-Sample can identify the amount of collected sample mass to within 10 grams (with 95-percent confidence) by using a force sensor with a noise and quantization floor of 50 micrometers. These results hold even in the presence of realistic parametric uncertainty in actual spacecraft inertia, center-of-mass offset, and first flexibility modes. Thrust profile knowledge is shown to be a dominant sensitivity for G-Sample, entering in a nearly one-to-one relationship with the final mass estimation error. This means thrust profiles should be well characterized with onboard accelerometers prior to sample collection. An overall sample-mass estimation error budget has been developed to approximate the effect of model uncertainty, sensor noise, data rate, and thrust profile error on the expected estimate of collected sample mass.

  8. Identifying differentially regulated subnetworks from phosphoproteomic data

    PubMed Central

    2010-01-01

    Background Various high throughput methods are available for detecting regulations at the level of transcription, translation or posttranslation (e.g. phosphorylation). Integrating these data with protein networks should make it possible to identify subnetworks that are significantly regulated. Furthermore, such integration can support identification of regulated entities from often noisy high throughput data. In particular, processing mass spectrometry-based phosphoproteomic data in this manner may expose signal transduction pathways and, in the case of experiments with drug-treated cells, reveal the drug's mode of action. Results Here, we introduce SubExtractor, an algorithm that combines phosphoproteomic data with protein network information from STRING to identify differentially regulated subnetworks and individual proteins. The method is based on a Bayesian probabilistic model combined with a genetic algorithm and rigorous significance testing. The Bayesian model accounts for information about both differential regulation and network topology. The method was tested with artificial data and subsequently applied to a comprehensive phosphoproteomics study investigating the mode of action of sorafenib, a small molecule kinase inhibitor. Conclusions SubExtractor reliably identifies differentially regulated subnetworks from phosphoproteomic data by integrating protein networks. The method can also be applied to gene or protein expression data. PMID:20584295

  9. DBSI: DNA-binding site identifier

    PubMed Central

    Zhu, Xiaolei; Ericksen, Spencer S.; Mitchell, Julie C.

    2013-01-01

    In this study, we present the DNA-Binding Site Identifier (DBSI), a new structure-based method for predicting protein interaction sites for DNA binding. DBSI was trained and validated on a data set of 263 proteins (TRAIN-263), tested on an independent set of protein-DNA complexes (TEST-206) and data sets of 29 unbound (APO-29) and 30 bound (HOLO-30) protein structures distinct from the training data. We computed 480 candidate features for identifying protein residues that bind DNA, including new features that capture the electrostatic microenvironment within shells near the protein surface. Our iterative feature selection process identified features important in other models, as well as features unique to the DBSI model, such as a banded electrostatic feature with spatial separation comparable with the canonical width of the DNA minor groove. Validations and comparisons with established methods using a range of performance metrics clearly demonstrate the predictive advantage of DBSI, and its comparable performance on unbound (APO-29) and bound (HOLO-30) conformations demonstrates robustness to binding-induced protein conformational changes. Finally, we offer our feature data table to others for integration into their own models or for testing improved feature selection and model training strategies based on DBSI. PMID:23873960

  10. DBSI: DNA-binding site identifier.

    PubMed

    Zhu, Xiaolei; Ericksen, Spencer S; Mitchell, Julie C

    2013-09-01

    In this study, we present the DNA-Binding Site Identifier (DBSI), a new structure-based method for predicting protein interaction sites for DNA binding. DBSI was trained and validated on a data set of 263 proteins (TRAIN-263), tested on an independent set of protein-DNA complexes (TEST-206) and data sets of 29 unbound (APO-29) and 30 bound (HOLO-30) protein structures distinct from the training data. We computed 480 candidate features for identifying protein residues that bind DNA, including new features that capture the electrostatic microenvironment within shells near the protein surface. Our iterative feature selection process identified features important in other models, as well as features unique to the DBSI model, such as a banded electrostatic feature with spatial separation comparable with the canonical width of the DNA minor groove. Validations and comparisons with established methods using a range of performance metrics clearly demonstrate the predictive advantage of DBSI, and its comparable performance on unbound (APO-29) and bound (HOLO-30) conformations demonstrates robustness to binding-induced protein conformational changes. Finally, we offer our feature data table to others for integration into their own models or for testing improved feature selection and model training strategies based on DBSI.

  11. DEVELOPMENT OF A MOLECULAR METHOD TO IDENTIFY ...

    EPA Pesticide Factsheets

    Hepatitis E virus (HEV) is an emerging pathogen that causes significant illness in the developing world. Like the hepatitis A virus, it is transmitted via the fecal-oral route and can cause short-term, acute hepatitis. In addition, hepatitis E has been found to cause a significant rate of mortality in pregnant women. Thus far, a hepatitis E outbreak has not been reported in the U. S. although a swine variant of the virus is common in Midwestern hogs. Since it will be important to identify the presence of this virus in the water supply, we have developed and are testing a reverse transcription-polymerase chain reaction (RT-PCR) method that should be able to identify all of the known HEV strains. Develop sensitive techniques to detect and identify emerging human waterborne pathogenic viruses and viruses on the CCL.Determine effectiveness of viral indicators to measure microbial quality in water matrices.Support activities: (a) culture and distribution of mammalian cells for Agency and scientific community research needs, (b) provide operator expertise for research requiring confocal and electron microscopy, (c) glassware cleaning, sterilization and biological waste disposal for the Cincinnati EPA facility, (d) operation of infectious pathogenic suite, (e) maintenance of walk-in constant temperature rooms and (f) provide Giardia cysts.

  12. Identifying duplicate content using statistically improbable phrases.

    PubMed

    Errami, Mounir; Sun, Zhaohui; George, Angela C; Long, Tara C; Skinner, Michael A; Wren, Jonathan D; Garner, Harold R

    2010-06-01

    Document similarity metrics such as PubMed's 'Find related articles' feature, which have been primarily used to identify studies with similar topics, can now also be used to detect duplicated or potentially plagiarized papers within literature reference databases. However, the CPU-intensive nature of document comparison has limited MEDLINE text similarity studies to the comparison of abstracts, which constitute only a small fraction of a publication's total text. Extending searches to include text archived by online search engines would drastically increase comparison ability. For large-scale studies, submitting short phrases encased in direct quotes to search engines for exact matches would be optimal for both individual queries and programmatic interfaces. We have derived a method of analyzing statistically improbable phrases (SIPs) for assistance in identifying duplicate content. When applied to MEDLINE citations, this method substantially improves upon previous algorithms in the detection of duplication citations, yielding a precision and recall of 78.9% (versus 50.3% for eTBLAST) and 99.6% (versus 99.8% for eTBLAST), respectively. Similar citations identified by this work are freely accessible in the Déjà vu database, under the SIP discovery method category at http://dejavu.vbi.vt.edu/dejavu/.

  13. DEVELOPMENT OF A MOLECULAR METHOD TO IDENTIFY ...

    EPA Pesticide Factsheets

    Hepatitis E virus (HEV) is an emerging pathogen that causes significant illness in the developing world. Like the hepatitis A virus, it is transmitted via the fecal-oral route and can cause short-term, acute hepatitis. In addition, hepatitis E has been found to cause a significant rate of mortality in pregnant women. Thus far, a hepatitis E outbreak has not been reported in the U. S. although a swine variant of the virus is common in Midwestern hogs. Since it will be important to identify the presence of this virus in the water supply, we have developed and are testing a reverse transcription-polymerase chain reaction (RT-PCR) method that should be able to identify all of the known HEV strains. Develop sensitive techniques to detect and identify emerging human waterborne pathogenic viruses and viruses on the CCL.Determine effectiveness of viral indicators to measure microbial quality in water matrices.Support activities: (a) culture and distribution of mammalian cells for Agency and scientific community research needs, (b) provide operator expertise for research requiring confocal and electron microscopy, (c) glassware cleaning, sterilization and biological waste disposal for the Cincinnati EPA facility, (d) operation of infectious pathogenic suite, (e) maintenance of walk-in constant temperature rooms and (f) provide Giardia cysts.

  14. Identifying Broadband Rotational Spectra with Neural Networks

    NASA Astrophysics Data System (ADS)

    Zaleski, Daniel P.; Prozument, Kirill

    2017-06-01

    A typical broadband rotational spectrum may contain several thousand observable transitions, spanning many species. Identifying the individual spectra, particularly when the dynamic range reaches 1,000:1 or even 10,000:1, can be challenging. One approach is to apply automated fitting routines. In this approach, combinations of 3 transitions can be created to form a "triple", which allows fitting of the A, B, and C rotational constants in a Watson-type Hamiltonian. On a standard desktop computer, with a target molecule of interest, a typical AUTOFIT routine takes 2-12 hours depending on the spectral density. A new approach is to utilize machine learning to train a computer to recognize the patterns (frequency spacing and relative intensities) inherit in rotational spectra and to identify the individual spectra in a raw broadband rotational spectrum. Here, recurrent neural networks have been trained to identify different types of rotational spectra and classify them accordingly. Furthermore, early results in applying convolutional neural networks for spectral object recognition in broadband rotational spectra appear promising. Perez et al. "Broadband Fourier transform rotational spectroscopy for structure determination: The water heptamer." Chem. Phys. Lett., 2013, 571, 1-15. Seifert et al. "AUTOFIT, an Automated Fitting Tool for Broadband Rotational Spectra, and Applications to 1-Hexanal." J. Mol. Spectrosc., 2015, 312, 13-21. Bishop. "Neural networks for pattern recognition." Oxford university press, 1995.

  15. Identifying familiar strangers in human encounter networks

    NASA Astrophysics Data System (ADS)

    Liang, Di; Li, Xiang; Zhang, Yi-Qing

    2016-10-01

    Familiar strangers, pairs of individuals who encounter repeatedly but never know each other, have been discovered for four decades yet lack an effective method to identify. Here we propose a novel method called familiar stranger classifier (FSC) to identify familiar strangers from three empirical datasets, and classify human relationships into four types, i.e., familiar stranger (FS), in-role (IR), friend (F) and stranger (S). The analyses of the human encounter networks show that the average number of FS one may encounter is finite but larger than the Dunbar Number, and their encounters are structurally more stable and denser than those of S, indicating the encounters of FS are not limited by the social capacity, and more robust than the random scenario. Moreover, the temporal statistics of encounters between FS over the whole time span show strong periodicity, which are diverse from the bursts of encounters within one day, suggesting the significance of longitudinal patterns of human encounters. The proposed method to identify FS in this paper provides a valid framework to understand human encounter patterns and analyse complex human social behaviors.

  16. Identifying web usage behavior of bank customers

    NASA Astrophysics Data System (ADS)

    Araya, Sandro; Silva, Mariano; Weber, Richard

    2002-03-01

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

  17. Interrogator system for identifying electrical circuits

    DOEpatents

    Jatko, W.B.; McNeilly, D.R.

    1988-04-12

    A system for interrogating electrical leads to correctly ascertain the identity of equipment attached to remote ends of the leads is disclosed. The system includes a source of a carrier signal generated in a controller/receiver to be sent over the leads and an identifier unit at the equipment. The identifier is activated by command of the carrier and uses a portion of the carrier to produce a supply voltage. Each identifier is uniquely programmed for a specific piece of equipment, and causes the impedance of the circuit to be modified whereby the carrier signal is modulated according to that program. The modulation can be amplitude, frequency or phase modulation. A demodulator in the controller/receiver analyzes the modulated carrier signal, and if a verified signal is recognized displays and/or records the information. This information can be utilized in a computer system to prepare a wiring diagram of the electrical equipment attached to specific leads. Specific circuit values are given for amplitude modulation, and the system is particularly described for use with thermocouples. 6 figs.

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

    NASA Astrophysics Data System (ADS)

    Murphy, Fiona; Lehnert, Kerstin; Hanson, Brooks

    2016-04-01

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

  19. Identifying suitable sites for Florida panther reintroduction

    USGS Publications Warehouse

    Thatcher, Cindy; van Manen, Frank T.; Clark, Joseph D.

    2006-01-01

    A major objective of the 1995 Florida Panther (Puma concolor cory) Recovery Plan is the establishment of 2 additional panther populations within the historic range. Our goal was to identify prospective sites for Florida panther reintroduction within the historic range based on quantitative landscape assessments. First, we delineated 86 panther home ranges using telemetry data collected from 1981 to 2001 in south Florida to develop a Mahalanobis distance (D2) habitat model, using 4 anthropogenic variables and 3 landscape variables mapped at a 500-m resolution. From that analysis, we identified 9 potential reintroduction sites of sufficient size to support a panther population. We then developed a similar D2 model at a higher spatial resolution to quantify the area of favorable panther habitat at each site. To address potential for the population to expand, we calculated the amount of favorable habitat adjacent to each prospective reintroduction site within a range of dispersal distances of female panthers. We then added those totals to the contiguous patches to estimate the total amount of effective panther habitat at each site. Finally, we developed an expert-assisted model to rank and incorporate potentially important habitat variables that were not appropriate for our empirical analysis (e.g., area of public lands, livestock density). Anthropogenic factors heavily influenced both the landscape and the expert-assisted models. Of the 9 areas we identified, the Okefenokee National Wildlife Refuge, Ozark National Forest, and Felsenthal National Wildlife Refuge regions had the highest combination of effective habitat area and expert opinion scores. Sensitivity analyses indicated that variability among key model parameters did not affect the high ranking of those sites. Those sites should be considered as starting points for the field evaluation of potential reintroduction sites.

  20. Identifying Airborne Pathogens in Time to Respond

    SciTech Connect

    Hazi, A

    2006-01-25

    Among the possible terrorist activities that might threaten national security is the release of an airborne pathogen such as anthrax. Because the potential damage to human health could be severe, experts consider 1 minute to be an operationally useful time limit for identifying the pathogen and taking action. Many commercial systems can identify airborne pathogenic microbes, but they take days or, at best, hours to produce results. The Department of Homeland Security (DHS) and other U.S. government agencies are interested in finding a faster approach. To answer this national need, a Livermore team, led by scientist Eric Gard, has developed the bioaerosol mass spectrometry (BAMS) system--the only instrument that can detect and identify spores at low concentrations in less than 1 minute. BAMS can successfully distinguish between two related but different spore species. It can also sort out a single spore from thousands of other particles--biological and nonbiological--with no false positives. The BAMS team won a 2005 R&D 100 Award for developing the system. Livermore's Laboratory Directed Research and Development (LDRD) Program funded the biomedical aspects of the BAMS project, and the Department of Defense's Technical Support Working Group and Defense Advanced Research Project Agency funded the biodefense efforts. Developing a detection system that can analyze small samples so quickly has been challenging. Livermore engineer Vincent Riot, who worked on the BAMS project, explains, ''A typical spore weighs approximately one-trillionth of a gram and is dispersed in the atmosphere, which contains naturally occurring particles that could be present at concentrations thousands of times higher. Previous systems also had difficulty separating benign organisms from those that are pathogenic but very similar, which has resulted in false alarms''.

  1. [Identifying children at risk for cardiorespiratory arrest].

    PubMed

    Carrillo Alvarez, A; Martínez Gutiérrez, A; Salvat Germán, F

    2004-08-01

    Cardiorespiratory arrest in children with severe disease does not usually present suddenly or unexpectedly but is often the result of a progressive deterioration of respiratory and/or circulatory function. Before failure of these functions occurs, there is a series of clinical signs that serve as a warning. Health professionals should not only evaluate clinical signs of respiratory and/or circulatory insufficiency but should also be able to identify these warning signs as early as possible, preferably in the compensation phase, given that the possibility that this process can be reversed by therapeutic measures decreases as the process progresses.

  2. Identifying related journals through log analysis

    PubMed Central

    Lu, Zhiyong; Xie, Natalie; Wilbur, W. John

    2009-01-01

    Motivation: With the explosion of biomedical literature and the evolution of online and open access, scientists are reading more articles from a wider variety of journals. Thus, the list of core journals relevant to their research may be less obvious and may often change over time. To help researchers quickly identify appropriate journals to read and publish in, we developed a web application for finding related journals based on the analysis of PubMed log data. Availability: http://www.ncbi.nlm.nih.gov/IRET/Journals Contact: luzh@ncbi.nlm.nih.gov Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19734155

  3. IDENTIFYING PERFORMANCE ASSURANCE CHALLENGES FOR SMART MANUFACTURING.

    PubMed

    Helu, Moneer; Morris, Katherine; Jung, Kiwook; Lyons, Kevin; Leong, Swee

    2015-10-01

    Smart manufacturing has the potential to address many of the challenges faced by industry. However, the manufacturing community often needs assistance to leverage available technologies to improve their systems. To assure the performance of these technologies, this paper proposes a shared knowledge base that collects problem areas, solutions, and best practices for manufacturing technology. An Implementation Risk Assessment Framework (IRAF) is also described to identify the primary weaknesses of technologies in specific manufacturing contexts. Such approaches have the potential to stimulate new ideas and drive standardization activities critical to scale up and deploy smart manufacturing technologies successfully and quickly.

  4. IDENTIFYING PERFORMANCE ASSURANCE CHALLENGES FOR SMART MANUFACTURING

    PubMed Central

    Helu, Moneer; Morris, Katherine; Jung, Kiwook; Lyons, Kevin; Leong, Swee

    2015-01-01

    Smart manufacturing has the potential to address many of the challenges faced by industry. However, the manufacturing community often needs assistance to leverage available technologies to improve their systems. To assure the performance of these technologies, this paper proposes a shared knowledge base that collects problem areas, solutions, and best practices for manufacturing technology. An Implementation Risk Assessment Framework (IRAF) is also described to identify the primary weaknesses of technologies in specific manufacturing contexts. Such approaches have the potential to stimulate new ideas and drive standardization activities critical to scale up and deploy smart manufacturing technologies successfully and quickly. PMID:26783512

  5. Nocturnal Sleep Dynamics Identify Narcolepsy Type 1

    PubMed Central

    Pizza, Fabio; Vandi, Stefano; Iloti, Martina; Franceschini, Christian; Liguori, Rocco; Mignot, Emmanuel; Plazzi, Giuseppe

    2015-01-01

    Study Objectives: To evaluate the reliability of nocturnal sleep dynamics in the differential diagnosis of central disorders of hypersomnolence. Design: Cross-sectional. Setting: Sleep laboratory. Patients: One hundred seventy-five patients with hypocretin-deficient narcolepsy type 1 (NT1, n = 79), narcolepsy type 2 (NT2, n = 22), idiopathic hypersomnia (IH, n = 22), and “subjective” hypersomnolence (sHS, n = 52). Interventions: None. Methods: Polysomnographic (PSG) work-up included 48 h of continuous PSG recording. From nocturnal PSG conventional sleep macrostructure, occurrence of sleep onset rapid eye movement period (SOREMP), sleep stages distribution, and sleep stage transitions were calculated. Patient groups were compared, and receiver operating characteristic (ROC) curve analysis was used to test the diagnostic utility of nocturnal PSG data to identify NT1. Results: Sleep macrostructure was substantially stable in the 2 nights of each diagnostic group. NT1 and NT2 patients had lower latency to rapid eye movement (REM) sleep, and NT1 patients showed the highest number of awakenings, sleep stage transitions, and more time spent in N1 sleep, as well as most SOREMPs at daytime PSG and at multiple sleep latency test (MSLT) than all other groups. ROC curve analysis showed that nocturnal SOREMP (area under the curve of 0.724 ± 0.041, P < 0.0001), percent of total sleep time spent in N1 (0.896 ± 0.023, P < 0.0001), and the wakefulness-sleep transition index (0.796 ± 0.034, P < 0.0001) had a good sensitivity and specificity profile to identify NT1 sleep, especially when used in combination (0.903 ± 0.023, P < 0.0001), similarly to SOREMP number at continuous daytime PSG (0.899 ± 0.026, P < 0.0001) and at MSLT (0.956 ± 0.015, P < 0.0001). Conclusions: Sleep macrostructure (i.e. SOREMP, N1 timing) including stage transitions reliably identifies hypocretin-deficient narcolepsy type 1 among central disorders of hypersomnolence. Citation: Pizza F, Vandi S

  6. Identifying inference attacks against healthcare data repositories

    PubMed Central

    Vaidya, Jaideep; Shafiq, Basit; Jiang, Xiaoqian; Ohno-Machado, Lucila

    Health care data repositories play an important role in driving progress in medical research. Finding new pathways to discovery requires having adequate data and relevant analysis. However, it is critical to ensure the privacy and security of the stored data. In this paper, we identify a dangerous inference attack against naive suppression based approaches that are used to protect sensitive information. We base our attack on the querying system provided by the Healthcare Cost and Utilization Project, though it applies in general to any medical database providing a query capability. We also discuss potential solutions to this problem. PMID:24303279

  7. Identifying bacterial predictors of honey bee health.

    PubMed

    Budge, Giles E; Adams, Ian; Thwaites, Richard; Pietravalle, Stéphane; Drew, Georgia C; Hurst, Gregory D D; Tomkies, Victoria; Boonham, Neil; Brown, Mike

    2016-11-01

    Non-targeted approaches are useful tools to identify new or emerging issues in bee health. Here, we utilise next generation sequencing to highlight bacteria associated with healthy and unhealthy honey bee colonies, and then use targeted methods to screen a wider pool of colonies with known health status. Our results provide the first evidence that bacteria from the genus Arsenophonus are associated with poor health in honey bee colonies. We also discovered Lactobacillus and Leuconostoc spp. were associated with healthier honey bee colonies. Our results highlight the importance of understanding how the wider microbial population relates to honey bee colony health.

  8. Method of identifying defective particle coatings

    DOEpatents

    Cohen, Mark E.; Whiting, Carlton D.

    1986-01-01

    A method for identifying coated particles having defective coatings desig to retain therewithin a build-up of gaseous materials including: (a) Pulling a vacuum on the particles; (b) Backfilling the particles at atmospheric pressure with a liquid capable of wetting the exterior surface of the coated particles, said liquid being a compound which includes an element having an atomic number higher than the highest atomic number of any element in the composition which forms the exterior surface of the particle coating; (c) Drying the particles; and (d) Radiographing the particles. By television monitoring, examination of the radiographs is substantially enhanced.

  9. Identifying tandem Ankyrin repeats in protein structures.

    PubMed

    Chakrabarty, Broto; Parekh, Nita

    2014-12-30

    Tandem repetition of structural motifs in proteins is frequently observed across all forms of life. Topology of repeating unit and its frequency of occurrence are associated to a wide range of structural and functional roles in diverse proteins, and defects in repeat proteins have been associated with a number of diseases. It is thus desirable to accurately identify specific repeat type and its copy number. Weak evolutionary constraints on repeat units and insertions/deletions between them make their identification difficult at the sequence level and structure based approaches are desired. The proposed graph spectral approach is based on protein structure represented as a graph for detecting one of the most frequently observed structural repeats, Ankyrin repeat. It has been shown in a large number of studies that 3-dimensional topology of a protein structure is well captured by a graph, making it possible to analyze a complex protein structure as a mathematical entity. In this study we show that eigen spectra profile of a protein structure graph exhibits a unique repetitive profile for contiguous repeating units enabling the detection of the repeat region and the repeat type. The proposed approach uses a non-redundant set of 58 Ankyrin proteins to define rules for the detection of Ankyrin repeat motifs. It is evaluated on a set of 370 proteins comprising 125 known Ankyrin proteins and remaining non-solenoid proteins and the prediction compared with UniProt annotation, sequence-based approach, RADAR, and structure-based approach, ConSole. To show the efficacy of the approach, we analyzed the complete PDB structural database and identified 641 previously unrecognized Ankyrin repeat proteins. We observe a unique eigen spectra profile for different repeat types and show that the method can be easily extended to detect other repeat types. It is implemented as a web server, AnkPred. It is freely available at 'bioinf.iiit.ac.in/AnkPred'. AnkPred provides an elegant and

  10. EVA: Visual Analytics to Identify Fraudulent Events.

    PubMed

    Leite, Roger A; Gschwandtner, Theresia; Miksch, Silvia; Kriglstein, Simone; Pohl, Margit; Gstrein, Erich; Kuntner, Johannes

    2017-08-31

    Financial institutions are interested in ensuring security and quality for their customers. Banks, for instance, need to identify and stop harmful transactions in a timely manner. In order to detect fraudulent operations, data mining techniques and customer profile analysis are commonly used. However, these approaches are not supported by Visual Analytics techniques yet. Visual Analytics techniques have potential to considerably enhance the knowledge discovery process and increase the detection and prediction accuracy of financial fraud detection systems. Thus, we propose EVA, a Visual Analytics approach for supporting fraud investigation, fine-tuning fraud detection algorithms, and thus, reducing false positive alarms.

  11. Subject Matter Expert Workshop to Identify Cybersecurity ...

    EPA Pesticide Factsheets

    Report In recognition of the growing need to better address cyber risk and cyber management, the U.S. Environmental Protection Agency’s (EPA) National Homeland Security Research Center (NHSRC) held a Subject Matter Expert Workshop to Identify Cybersecurity Research Gaps and Needs of the Nation’s Water and Wastewater Systems Sector on March 30th and 31st, 2016, at the Ronald Reagan Building in Washington, D.C. The workshop was designed to create a forum for subject matter experts (SMEs) to exchange ideas and address important cybersecurity challenges facing the water sector.

  12. Identifying discourse connectives in biomedical text.

    PubMed

    Ramesh, Balaji Polepalli; Yu, Hong

    2010-11-13

    Discourse connectives are words or phrases that connect or relate two coherent sentences or phrases and indicate the presence of discourse relations. Automatic recognition of discourse connectives may benefit many natural language processing applications. In this pilot study, we report the development of the supervised machine-learning classifiers with conditional random fields (CRFs) for automatically identifying discourse connectives in full-text biomedical articles. Our first classifier was trained on the open-domain 1 million token Penn Discourse Tree Bank (PDTB). We performed cross validation on biomedical articles (approximately 100K word tokens) that we annotated. The results show that the classifier trained on PDTB data attained a 0.55 F1-score for identifying discourse connectives in biomedical text, while the cross-validation results in the biomedical text attained a 0.69 F1-score, a much better performance despite a much smaller training size. Our preliminary analysis suggests the existence of domain-specific features, and we speculate that domain-adaption approaches may further improve performance.

  13. White dwarfs identified in LAMOST DR 2

    NASA Astrophysics Data System (ADS)

    Guo, Jincheng; Zhao, Jingkun; Tziamtzis, Anestis; Liu, Jifeng; Li, Lifang; Zhang, Yong; Hou, Yonghui; Wang, Yuefei

    2015-12-01

    Here we present a catalogue of 1056 spectroscopically identified hydrogen-dominated white dwarfs (DAWDs), 34 helium-dominated white dwarfs (DBWDs) and 276 white dwarf main sequence (WDMS) binaries from the Large sky Area Multi-Object Fiber Spectroscopic Telescope (LAMOST) survey data release 2 (DR2). 383 DAWDs, 4 DBWDs and 138 WDMSs are new identifications after cross-match with literature. There are ˜4100 k spectra in total from DR 2. The low ratio of white dwarfs found in LAMOST is attributed to biased selection of LAMOST input catalogue and much brighter targets relative to stars observed in Sloan Digital Sky Survey. In this paper, a new DAWD selection method is adopted as a new attempt and supplement to the traditional methods. The effective temperature, surface gravity, mass, cooling age and distance of high signal-to-noise DAWDs are estimated. The peak of the mass distribution is found to be ˜0.6 M⊙, which is consistent with previous work. The parameters of WDMS binaries are also provided in this paper. As the foundation of our future work, which is to identify more WDs with debris disc, WDs found in LAMOST showed a lot of potential. Interesting infrared-excess WDs will be reported in our forthcoming paper.

  14. Using Dissimilarity Metrics to Identify Interesting Designs

    NASA Technical Reports Server (NTRS)

    Feather, Martin; Kiper, James

    2006-01-01

    A computer program helps to blend the power of automated-search software, which is able to generate large numbers of design solutions, with the insight of expert designers, who are able to identify preferred designs but do not have time to examine all the solutions. From among the many automated solutions to a given design problem, the program selects a smaller number of solutions that are worthy of scrutiny by the experts in the sense that they are sufficiently dissimilar from each other. The program makes the selection in an interactive process that involves a sequence of data-mining steps interspersed with visual displays of results of these steps to the experts. At crucial points between steps, the experts provide directives to guide the process. The program uses heuristic search techniques to identify nearly optimal design solutions and uses dissimilarity metrics defined by the experts to characterize the degree to which solutions are interestingly different. The search, data-mining, and visualization features of the program were derived from previously developed risk-management software used to support a risk-centric design methodology

  15. Identifying Bitcoin users by transaction behavior

    NASA Astrophysics Data System (ADS)

    Monaco, John V.

    2015-05-01

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

  16. Strategies to identify natural antisense transcripts.

    PubMed

    Sun, Yulong; Li, Dijie; Zhang, Ru; Peng, Shang; Zhang, Ge; Yang, Tuanmin; Qian, Airong

    2017-01-01

    Natural antisense transcripts, originally considered as transcriptional noises arising from so-called "junk DNA″, are recently recognized as important modulators for gene regulation. They are prevalent in nearly all realms of life and have been found to modulate gene expression positively or negatively. By affecting almost all stages of gene expression range from pre-transcriptional, transcriptional and post-transcriptional to translation, NATs are fundamentally involved in various biological processes. However, compared to increasing huge data from transcriptional analysis especially high-throughput sequencing technologies (such as RNA-seq), limited functional NATs (around 70) are so far reported, which hinder our advanced comprehensive understanding for this field. Hence, efficient strategies for identifying NATs are urgently desired. In this review, we discussed the current strategies for identifying NATs, with a focus on the advantages, disadvantages, and applications of methods isolating functional NATs. Moreover, publicly available databases for NATs were also discussed. Copyright © 2016 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

  17. Identifying nonlinear biomechanical models by multicriteria analysis

    NASA Astrophysics Data System (ADS)

    Srdjevic, Zorica; Cveticanin, Livija

    2012-02-01

    In this study, the methodology developed by Srdjevic and Cveticanin (International Journal of Industrial Ergonomics 34 (2004) 307-318) for the nonbiased (objective) parameter identification of the linear biomechanical model exposed to vertical vibrations is extended to the identification of n-degree of freedom (DOF) nonlinear biomechanical models. The dynamic performance of the n-DOF nonlinear model is described in terms of response functions in the frequency domain, such as the driving-point mechanical impedance and seat-to-head transmissibility function. For randomly generated parameters of the model, nonlinear equations of motion are solved using the Runge-Kutta method. The appropriate data transformation from the time-to-frequency domain is performed by a discrete Fourier transformation. Squared deviations of the response functions from the target values are used as the model performance evaluation criteria, thus shifting the problem into the multicriteria framework. The objective weights of criteria are obtained by applying the Shannon entropy concept. The suggested methodology is programmed in Pascal and tested on a 4-DOF nonlinear lumped parameter biomechanical model. The identification process over the 2000 generated sets of parameters lasts less than 20 s. The model response obtained with the imbedded identified parameters correlates well with the target values, therefore, justifying the use of the underlying concept and the mathematical instruments and numerical tools applied. It should be noted that the identified nonlinear model has an improved accuracy of the biomechanical response compared to the accuracy of a linear model.

  18. Identifying Novel Transcriptional Regulators with Circadian Expression

    PubMed Central

    Schick, Sandra; Thakurela, Sudhir; Fournier, David; Hampel, Mareike Hildegard

    2015-01-01

    Organisms adapt their physiology and behavior to the 24-h day-night cycle to which they are exposed. On a cellular level, this is regulated by intrinsic transcriptional-translational feedback loops that are important for maintaining the circadian rhythm. These loops are organized by members of the core clock network, which further regulate transcription of downstream genes, resulting in their circadian expression. Despite progress in understanding circadian gene expression, only a few players involved in circadian transcriptional regulation, including transcription factors, epigenetic regulators, and long noncoding RNAs, are known. Aiming to discover such genes, we performed a high-coverage transcriptome analysis of a circadian time course in murine fibroblast cells. In combination with a newly developed algorithm, we identified many transcription factors, epigenetic regulators, and long intergenic noncoding RNAs that are cyclically expressed. In addition, a number of these genes also showed circadian expression in mouse tissues. Furthermore, the knockdown of one such factor, Zfp28, influenced the core clock network. Mathematical modeling was able to predict putative regulator-effector interactions between the identified circadian genes and may help for investigations into the gene regulatory networks underlying circadian rhythms. PMID:26644408

  19. ABCB5 identifies immunoregulatory dermal cells

    PubMed Central

    Schatton, Tobias; Yang, Jun; Kleffel, Sonja; Uehara, Mayuko; Barthel, Steven R.; Schlapbach, Christoph; Zhan, Qian; Dudeney, Stephen; Mueller, Hansgeorg; Lee, Nayoung; de Vries, Juliane C.; Meier, Barbara; Vander Beken, Seppe; Kluth, Mark A.; Ganss, Christoph; Sharpe, Arlene H.; Waaga-Gasser, Ana Maria; Sayegh, Mohamed H.; Abdi, Reza; Scharffetter-Kochanek, Karin; Murphy, George F.; Kupper, Thomas S.; Frank, Natasha Y.; Frank, Markus H.

    2015-01-01

    Summary Cell-based strategies represent a new frontier in the treatment of immune-mediated disorders. However, the paucity of markers for isolation of molecularly-defined immunomodulatory cell populations poses a barrier to this field. Here we show that ATP-binding cassette member B5 (ABCB5) identifies dermal immunoregulatory cells (DIRCs) capable of exerting therapeutic immunoregulatory functions through engagement of programmed cell death 1 (PD-1). Purified Abcb5+ DIRCs suppressed T-cell proliferation, evaded immune rejection, homed to recipient immune tissues and induced Tregs in vivo. In fully MHC-mismatched cardiac allotransplantation models, allogeneic DIRCs significantly prolonged allograft survival. Blockade of DIRC-expressed PD-1 reversed the inhibitory effects of DIRCs on T-cell activation, inhibited DIRC-dependent Treg induction, and attenuated DIRC-induced prolongation of cardiac allograft survival, indicating that DIRC immunoregulatory function is mediated, at least in part, through PD-1. Our results identify ABCB5+ DIRCs as a distinct immunoregulatory cell population and suggest promising roles of this expandable cell subset in cellular immunotherapy. PMID:26321644

  20. Identifying turbulent flow in carbonate aquifers

    NASA Astrophysics Data System (ADS)

    Worthington, Stephen R. H.; Soley, Robert W. N.

    2017-09-01

    Turbulent flow has a different hydraulic response compared to laminar flow and so it is important to be able to identify its occurrence in an aquifer, and to predict where it is likely to be found. Turbulent flow is associated with large apertures and rapid velocities, and these occur most frequently in carbonate aquifers. Methods for identifying turbulent flow include correlating spring discharge with head variation, calculating Reynolds numbers from spring discharge and tracer velocity, and plotting the spatial variation of head differences between high flow and low flow. The probability of turbulent flow increases as a function of permeability and of spring discharge, and the probability increases in a downgradient direction in an aquifer. Spring discharge is a key parameter for evaluating the presence of turbulent flow, which is likely to occur where a spring with a discharge > 1 L/s is fed by a single channel. Turbulent flow appears to be a major contributing factor to the occurrence of groundwater flooding in carbonate aquifers.

  1. DNA Barcoding Identifies Illegal Parrot Trade.

    PubMed

    Gonçalves, Priscila F M; Oliveira-Marques, Adriana R; Matsumoto, Tania E; Miyaki, Cristina Y

    2015-01-01

    Illegal trade threatens the survival of many wild species, and molecular forensics can shed light on various questions raised during the investigation of cases of illegal trade. Among these questions is the identity of the species involved. Here we report a case of a man who was caught in a Brazilian airport trying to travel with 58 avian eggs. He claimed they were quail eggs, but authorities suspected they were from parrots. The embryos never hatched and it was not possible to identify them based on morphology. As 29% of parrot species are endangered, the identity of the species involved was important to establish a stronger criminal case. Thus, we identified the embryos' species based on the analyses of mitochondrial DNA sequences (cytochrome c oxidase subunit I gene [COI] and 16S ribosomal DNA). Embryonic COI sequences were compared with those deposited in BOLD (The Barcode of Life Data System) while their 16S sequences were compared with GenBank sequences. Clustering analysis based on neighbor-joining was also performed using parrot COI and 16S sequences deposited in BOLD and GenBank. The results, based on both genes, indicated that 57 embryos were parrots (Alipiopsitta xanthops, Ara ararauna, and the [Amazona aestiva/A. ochrocephala] complex), and 1 was an owl. This kind of data can help criminal investigations and to design species-specific anti-poaching strategies, and demonstrate how DNA sequence analysis in the identification of bird species is a powerful conservation tool.

  2. Identifying barriers to Muslim integration in France.

    PubMed

    Adida, Claire L; Laitin, David D; Valfort, Marie-Anne

    2010-12-28

    Is there a Muslim disadvantage in economic integration for second-generation immigrants to Europe? Previous research has failed to isolate the effect that religion may have on an immigrant family's labor market opportunities because other factors, such as country of origin or race, confound the result. This paper uses a correspondence test in the French labor market to identify and measure this religious effect. The results confirm that in the French labor market, anti-Muslim discrimination exists: a Muslim candidate is 2.5 times less likely to receive a job interview callback than is his or her Christian counterpart. A high-n survey reveals, consistent with expectations from the correspondence test, that second-generation Muslim households in France have lower income compared with matched Christian households. The paper thereby contributes to both substantive debates on the Muslim experience in Europe and methodological debates on how to measure discrimination. Following the National Academy of Sciences' 2001 recommendations on combining a variety of methodologies and applying them to real-world situations, this research identifies, measures, and infers consequences of discrimination based on religious affiliation, controlling for potentially confounding factors, such as race and country of origin.

  3. Identifying Synonymous Regulatory Elements in Vertebrate Genomes

    SciTech Connect

    Ovcharenko, I; Nobrega, M A

    2005-02-07

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

  4. Identifying barriers to Muslim integration in France

    PubMed Central

    Adida, Claire L.; Laitin, David D.; Valfort, Marie-Anne

    2010-01-01

    Is there a Muslim disadvantage in economic integration for second-generation immigrants to Europe? Previous research has failed to isolate the effect that religion may have on an immigrant family's labor market opportunities because other factors, such as country of origin or race, confound the result. This paper uses a correspondence test in the French labor market to identify and measure this religious effect. The results confirm that in the French labor market, anti-Muslim discrimination exists: a Muslim candidate is 2.5 times less likely to receive a job interview callback than is his or her Christian counterpart. A high-n survey reveals, consistent with expectations from the correspondence test, that second-generation Muslim households in France have lower income compared with matched Christian households. The paper thereby contributes to both substantive debates on the Muslim experience in Europe and methodological debates on how to measure discrimination. Following the National Academy of Sciences’ 2001 recommendations on combining a variety of methodologies and applying them to real-world situations, this research identifies, measures, and infers consequences of discrimination based on religious affiliation, controlling for potentially confounding factors, such as race and country of origin. PMID:21098283

  5. Identifying hearing loss by means of iridology.

    PubMed

    Stearn, Natalie; Swanepoel, De Wet

    2006-11-13

    Isolated reports of hearing loss presenting as markings on the iris exist, but to date the effectiveness of iridology to identify hearing loss has not been investigated. This study therefore aimed to determine the efficacy of iridological analysis in the identification of moderate to profound sensorineural hearing loss in adolescents. A controlled trial was conducted with an iridologist, blind to the actual hearing status of participants, analyzing the irises of participants with and without hearing loss. Fifty hearing impaired and fifty normal hearing subjects, between the ages of 15 and 19 years, controlled for gender, participated in the study. An experienced iridologist analyzed the randomised set of participants' irises. A 70% correct identification of hearing status was obtained by iridological analyses with a false negative rate of 41% compared to a 19% false positive rate. The respective sensitivity and specificity rates therefore came to 59% and 81%. Iridological analysis of hearing status indicated a statistically significant relationship to actual hearing status (P < 0.05). Although statistically significant sensitivity and specificity rates for identifying hearing loss by iridology were not comparable to those of traditional audiological screening procedures.

  6. Identifiability, reducibility, and adaptability in allosteric macromolecules.

    PubMed

    Bohner, Gergő; Venkataraman, Gaurav

    2017-05-01

    The ability of macromolecules to transduce stimulus information at one site into conformational changes at a distant site, termed "allostery," is vital for cellular signaling. Here, we propose a link between the sensitivity of allosteric macromolecules to their underlying biophysical parameters, the interrelationships between these parameters, and macromolecular adaptability. We demonstrate that the parameters of a canonical model of the mSlo large-conductance Ca(2+)-activated K(+) (BK) ion channel are non-identifiable with respect to the equilibrium open probability-voltage relationship, a common functional assay. We construct a reduced model with emergent parameters that are identifiable and expressed as combinations of the original mechanistic parameters. These emergent parameters indicate which coordinated changes in mechanistic parameters can leave assay output unchanged. We predict that these coordinated changes are used by allosteric macromolecules to adapt, and we demonstrate how this prediction can be tested experimentally. We show that these predicted parameter compensations are used in the first reported allosteric phenomena: the Bohr effect, by which hemoglobin adapts to varying pH. © 2017 Bohner and Venkataraman.

  7. Intraoperative molecular imaging to identify lung adenocarcinomas

    PubMed Central

    Newton, Andrew D.; Kennedy, Gregory T.; Predina, Jarrod D.; Low, Philip S.

    2016-01-01

    Intraoperative molecular imaging is a promising new technology with numerous applications in lung cancer surgery. Accurate identification of small nodules and assessment of tumor margins are two challenges in pulmonary resections for cancer, particularly with increasing use of video-assisted thoracoscopic surgery (VATS). One potential solution to these problems is intraoperative use of a fluorescent contrast agent to improve detection of cancer cells. This technology requires both a targeted fluorescent dye that will selectively accumulate in cancer cells and a specialized imaging system to detect the cells. In several studies, we have shown that intraoperative imaging with indocyanine green (ICG) can be used to accurately identify indeterminate pulmonary nodules. The use of a folate-tagged fluorescent molecule targeted to the folate receptor-α (FRα) further improves the sensitivity and specificity of detecting lung adenocarcinomas. We have demonstrated this technology can be used as an “optical biopsy” to differentiate adenocarcinoma versus other histological subtypes of pulmonary nodules. This strategy has potential applications in assessing bronchial stump margins, identifying synchronous or metachronous lesions, and rapidly assessing lymph nodes for lung adenocarcinoma. PMID:28066672

  8. Identifying MMORPG Bots: A Traffic Analysis Approach

    NASA Astrophysics Data System (ADS)

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

    2008-12-01

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

  9. Identifying emotional intelligence in professional nursing practice.

    PubMed

    Kooker, Barbara Molina; Shoultz, Jan; Codier, Estelle E

    2007-01-01

    The National Center for Health Workforce Analysis projects that the shortage of registered nurses in the United States will double by 2010 and will nearly quadruple to 20% by 2015 (Bureau of Health Professionals Health Resources and Services Administration. [2002]. Projected supply, demand, and shortages of registered nurses, 2000-2020 [On-line]. Available: http:bhpr.hrsa.gov/healthworkforce/reports/rnprojects/report.htm). The purpose of this study was to use the conceptual framework of emotional intelligence to analyze nurses' stories about their practice to identify factors that could be related to improved nurse retention and patient/client outcomes. The stories reflected evidence of the competencies and domains of emotional intelligence and were related to nurse retention and improved outcomes. Nurses recognized their own strengths and limitations, displayed empathy and recognized client needs, nurtured relationships, used personal influence, and acted as change agents. Nurses were frustrated when organizational barriers conflicted with their knowledge/intuition about nursing practice, their communications were disregarded, or their attempts to create a shared vision and teamwork were ignored. Elements of professional nursing practice, such as autonomy, nurse satisfaction, respect, and the professional practice environment, were identified in the excerpts of the stories. The shortage of practicing nurses continues to be a national issue. The use of emotional intelligence concepts may provide fresh insights into ways to keep nurses engaged in practice and to improve nurse retention and patient/client outcomes.

  10. Military unique curriculum: identifying and prioritizing content.

    PubMed

    Cloonan, Clifford; Fauver, Howard E; Holloway, Harry C; Hospenthal, Duane R; Hutton, John; Lewis, Evelyn; Madrigal, Vinicio E; Maliner, Beverly; Nelson, Michael; Reynolds, Paul C; Staunton, Michael; Wayne, Barry A; Roy, Michael J

    2003-09-01

    We have identified and prioritized a series of objectives that warrant inclusion in the continuum of military medical education. Although participants in the 16th Conference on Military Medicine also discussed whether each objective should be taught at the medical student, resident, or staff physician level, to a large extent this distinction is not helpful, since many, if not most, of these topic areas would likely require incorporation at each of these three levels to achieve the desired level of competence in staff physicians. Incorporation of new curricular elements poses a significant challenge, since it is already difficult to fit the existing curriculum into the available time. It is not reasonable to consider increasing the number of lecture hours. Therefore, it is probable that some elements of the existing curriculum will need to be pared down or eliminated to incorporate new material. In the past, when new material has been added to the existing curriculum, such as when the pathogenesis of human immunodeficiency virus was added, it has generally been done at the individual teacher or at most departmental level. Although this approach has the advantage of having a subject matter expert decide how best to insert new material within the fabric of the existing curriculum, there are a couple of problems with widespread use of this approach. First, some of these new objectives may not fit clearly within an existing course curriculum or department's educational mission. Second, such an approach may not provide the degree of coordination that is necessary to ensure that a new curricular item is adequately covered in all respects, and it may result in unnecessary overlap in instruction when different professors incorporate similar elements. Therefore, the prioritization of newer curricular items, as has been done during this conference, may serve as a useful guide in this process. However, a corresponding effort is needed to identify and prioritize existing

  11. Regional Seismic Methods of Identifying Explosions

    NASA Astrophysics Data System (ADS)

    Walter, W. R.; Ford, S. R.; Pasyanos, M.; Pyle, M. L.; Hauk, T. F.

    2013-12-01

    A lesson from the 2006, 2009 and 2013 DPRK declared nuclear explosion Ms:mb observations is that our historic collection of data may not be representative of future nuclear test signatures (e.g. Selby et al., 2012). To have confidence in identifying future explosions amongst the background of other seismic signals, we need to put our empirical methods on a firmer physical footing. Here we review the two of the main identification methods: 1) P/S ratios and 2) Moment Tensor techniques, which can be applied at the regional distance (200-1600 km) to very small events, improving nuclear explosion monitoring and confidence in verifying compliance with the Comprehensive Nuclear-Test-Ban Treaty (CTBT). Amplitude ratios of seismic P-to-S waves at sufficiently high frequencies (~>2 Hz) can identify explosions among a background of natural earthquakes (e.g. Walter et al., 1995). However the physical basis for the generation of explosion S-waves, and therefore the predictability of this P/S technique as a function of event properties such as size, depth, geology and path, remains incompletely understood. Calculated intermediate period (10-100s) waveforms from regional 1-D models can match data and provide moment tensor results that separate explosions from earthquakes and cavity collapses (e.g. Ford et al. 2009). However it has long been observed that some nuclear tests produce large Love waves and reversed Rayleigh waves that complicate moment tensor modeling. Again the physical basis for the generation of these effects from explosions remains incompletely understood. We are re-examining regional seismic data from a variety of nuclear test sites including the DPRK and the former Nevada Test Site (now the Nevada National Security Site (NNSS)). Newer relative amplitude techniques can be employed to better quantify differences between explosions and used to understand those differences in term of depth, media and other properties. We are also making use of the Source Physics

  12. Nocturnal Sleep Dynamics Identify Narcolepsy Type 1.

    PubMed

    Pizza, Fabio; Vandi, Stefano; Iloti, Martina; Franceschini, Christian; Liguori, Rocco; Mignot, Emmanuel; Plazzi, Giuseppe

    2015-08-01

    To evaluate the reliability of nocturnal sleep dynamics in the differential diagnosis of central disorders of hypersomnolence. Cross-sectional. Sleep laboratory. One hundred seventy-five patients with hypocretin-deficient narcolepsy type 1 (NT1, n = 79), narcolepsy type 2 (NT2, n = 22), idiopathic hypersomnia (IH, n = 22), and "subjective" hypersomnolence (sHS, n = 52). None. Polysomnographic (PSG) work-up included 48 h of continuous PSG recording. From nocturnal PSG conventional sleep macrostructure, occurrence of sleep onset rapid eye movement period (SOREMP), sleep stages distribution, and sleep stage transitions were calculated. Patient groups were compared, and receiver operating characteristic (ROC) curve analysis was used to test the diagnostic utility of nocturnal PSG data to identify NT1. Sleep macrostructure was substantially stable in the 2 nights of each diagnostic group. NT1 and NT2 patients had lower latency to rapid eye movement (REM) sleep, and NT1 patients showed the highest number of awakenings, sleep stage transitions, and more time spent in N1 sleep, as well as most SOREMPs at daytime PSG and at multiple sleep latency test (MSLT) than all other groups. ROC curve analysis showed that nocturnal SOREMP (area under the curve of 0.724 ± 0.041, P < 0.0001), percent of total sleep time spent in N1 (0.896 ± 0.023, P < 0.0001), and the wakefulness-sleep transition index (0.796 ± 0.034, P < 0.0001) had a good sensitivity and specificity profile to identify NT1 sleep, especially when used in combination (0.903 ± 0.023, P < 0.0001), similarly to SOREMP number at continuous daytime PSG (0.899 ± 0.026, P < 0.0001) and at MSLT (0.956 ± 0.015, P < 0.0001). Sleep macrostructure (i.e. SOREMP, N1 timing) including stage transitions reliably identifies hypocretin-deficient narcolepsy type 1 among central disorders of hypersomnolence. © 2015 Associated Professional Sleep Societies, LLC.

  13. Process Architecture for Managing Digital Object Identifiers

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  14. Identifying seasonal stars in Kaurna astronomical traditions

    NASA Astrophysics Data System (ADS)

    Hamacher, Duane W.

    2015-03-01

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

  15. Identifying DNA methylation in a nanochannel

    PubMed Central

    Sun, Xiaoyin; Yasui, Takao; Yanagida, Takeshi; Kaji, Noritada; Rahong, Sakon; Kanai, Masaki; Nagashima, Kazuki; Kawai, Tomoji; Baba, Yoshinobu

    2016-01-01

    Abstract DNA methylation is a stable epigenetic modification, which is well known to be involved in gene expression regulation. In general, however, analyzing DNA methylation requires rather time consuming processes (24–96 h) via DNA replication and protein modification. Here we demonstrate a methodology to analyze DNA methylation at a single DNA molecule level without any protein modifications by measuring the contracted length and relaxation time of DNA within a nanochannel. Our methodology is based on the fact that methylation makes DNA molecules stiffer, resulting in a longer contracted length and a longer relaxation time (a slower contraction rate). The present methodology offers a promising way to identify DNA methylation without any protein modification at a single DNA molecule level within 2 h. PMID:27877910

  16. Identifying biochemical phenotypic differences between cryptic species

    PubMed Central

    Liebeke, Manuel; Bruford, Michael W.; Donnelly, Robert K.; Ebbels, Timothy M. D.; Hao, Jie; Kille, Peter; Lahive, Elma; Madison, Rachael M.; Morgan, A. John; Pinto-Juma, Gabriela A.; Spurgeon, David J.; Svendsen, Claus; Bundy, Jacob G.

    2014-01-01

    Molecular genetic methods can distinguish divergent evolutionary lineages in what previously appeared to be single species, but it is not always clear what functional differences exist between such cryptic species. We used a metabolomic approach to profile biochemical phenotype (metabotype) differences between two putative cryptic species of the earthworm Lumbricus rubellus. There were no straightforward metabolite biomarkers of lineage, i.e. no metabolites that were always at higher concentration in one lineage. Multivariate methods, however, identified a small number of metabolites that together helped distinguish the lineages, including uncommon metabolites such as Nε-trimethyllysine, which is not usually found at high concentrations. This approach could be useful for characterizing functional trait differences, especially as it is applicable to essentially any species group, irrespective of its genome sequencing status. PMID:25252836

  17. Identifying biochemical phenotypic differences between cryptic species.

    PubMed

    Liebeke, Manuel; Bruford, Michael W; Donnelly, Robert K; Ebbels, Timothy M D; Hao, Jie; Kille, Peter; Lahive, Elma; Madison, Rachael M; Morgan, A John; Pinto-Juma, Gabriela A; Spurgeon, David J; Svendsen, Claus; Bundy, Jacob G

    2014-09-01

    Molecular genetic methods can distinguish divergent evolutionary lineages in what previously appeared to be single species, but it is not always clear what functional differences exist between such cryptic species. We used a metabolomic approach to profile biochemical phenotype (metabotype) differences between two putative cryptic species of the earthworm Lumbricus rubellus. There were no straightforward metabolite biomarkers of lineage, i.e. no metabolites that were always at higher concentration in one lineage. Multivariate methods, however, identified a small number of metabolites that together helped distinguish the lineages, including uncommon metabolites such as Nε-trimethyllysine, which is not usually found at high concentrations. This approach could be useful for characterizing functional trait differences, especially as it is applicable to essentially any species group, irrespective of its genome sequencing status. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  18. Dynamic compensation, parameter identifiability, and equivariances

    PubMed Central

    2017-01-01

    A recent paper by Karin et al. introduced a mathematical notion called dynamical compensation (DC) of biological circuits. DC was shown to play an important role in glucose homeostasis as well as other key physiological regulatory mechanisms. Karin et al. went on to provide a sufficient condition to test whether a given system has the DC property. Here, we show how DC can be formulated in terms of a well-known concept in systems biology, statistics, and control theory—that of parameter structural non-identifiability. Viewing DC as a parameter identification problem enables one to take advantage of powerful theoretical and computational tools to test a system for DC. We obtain as a special case the sufficient criterion discussed by Karin et al. We also draw connections to system equivalence and to the fold-change detection property. PMID:28384175

  19. Identifying States of a Financial Market

    NASA Astrophysics Data System (ADS)

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

    2012-09-01

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

  20. Advances in Identifying Beryllium Sensitization and Disease

    PubMed Central

    Middleton, Dan; Kowalski, Peter

    2010-01-01

    Beryllium is a lightweight metal with unique qualities related to stiffness, corrosion resistance, and conductivity. While there are many useful applications, researchers in the 1930s and l940s linked beryllium exposure to a progressive occupational lung disease. Acute beryllium disease is a pulmonary irritant response to high exposure levels, whereas chronic beryllium disease (CBD) typically results from a hypersensitivity response to lower exposure levels. A blood test, the beryllium lymphocyte proliferation test (BeLPT), was an important advance in identifying individuals who are sensitized to beryllium (BeS) and thus at risk for developing CBD. While there is no true “gold standard” for BeS, basic epidemiologic concepts have been used to advance our understanding of the different screening algorithms. PMID:20195436

  1. Advances in identifying beryllium sensitization and disease.

    PubMed

    Middleton, Dan; Kowalski, Peter

    2010-01-01

    Beryllium is a lightweight metal with unique qualities related to stiffness, corrosion resistance, and conductivity. While there are many useful applications, researchers in the 1930s and 1940s linked beryllium exposure to a progressive occupational lung disease. Acute beryllium disease is a pulmonary irritant response to high exposure levels, whereas chronic beryllium disease (CBD) typically results from a hypersensitivity response to lower exposure levels. A blood test, the beryllium lymphocyte proliferation test (BeLPT), was an important advance in identifying individuals who are sensitized to beryllium (BeS) and thus at risk for developing CBD. While there is no true "gold standard" for BeS, basic epidemiologic concepts have been used to advance our understanding of the different screening algorithms.

  2. Identifying states of a financial market.

    PubMed

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

    2012-01-01

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

  3. Identifying Health-Related Topics on Twitter

    NASA Astrophysics Data System (ADS)

    Prier, Kyle W.; Smith, Matthew S.; Giraud-Carrier, Christophe; Hanson, Carl L.

    Public health-related topics are difficult to identify in large conversational datasets like Twitter. This study examines how to model and discover public health topics and themes in tweets. Tobacco use is chosen as a test case to demonstrate the effectiveness of topic modeling via LDA across a large, representational dataset from the United States, as well as across a smaller subset that was seeded by tobacco-related queries. Topic modeling across the large dataset uncovers several public health-related topics, although tobacco is not detected by this method. However, topic modeling across the tobacco subset provides valuable insight about tobacco use in the United States. The methods used in this paper provide a possible toolset for public health researchers and practitioners to better understand public health problems through large datasets of conversational data.

  4. Method of identifying features in indexed data

    DOEpatents

    Jarman, Kristin H [Richland, WA; Daly, Don Simone [Richland, WA; Anderson, Kevin K [Richland, WA; Wahl, Karen L [Richland, WA

    2001-06-26

    The present invention is a method of identifying features in indexed data, especially useful for distinguishing signal from noise in data provided as a plurality of ordered pairs. Each of the plurality of ordered pairs has an index and a response. The method has the steps of: (a) providing an index window having a first window end located on a first index and extending across a plurality of indices to a second window end; (b) selecting responses corresponding to the plurality of indices within the index window and computing a measure of dispersion of the responses; and (c) comparing the measure of dispersion to a dispersion critical value. Advantages of the present invention include minimizing signal to noise ratio, signal drift, varying baseline signal and combinations thereof.

  5. QTLminer: identifying genes regulating quantitative traits.

    PubMed

    Alberts, Rudi; Schughart, Klaus

    2010-10-15

    Quantitative trait locus (QTL) mapping identifies genomic regions that likely contain genes regulating a quantitative trait. However, QTL regions may encompass tens to hundreds of genes. To find the most promising candidate genes that regulate the trait, the biologist typically collects information from multiple resources about the genes in the QTL interval. This process is very laborious and time consuming. QTLminer is a bioinformatics tool that automatically performs QTL region analysis. It is available in GeneNetwork and it integrates information such as gene annotation, gene expression and sequence polymorphisms for all the genes within a given genomic interval. QTLminer substantially speeds up discovery of the most promising candidate genes within a QTL region.

  6. Identifying Multiquark Hadrons from Heavy Ion Collisions

    SciTech Connect

    Cho, Sungtae; Furumoto, Takenori; Yazaki, Koichi; Hyodo, Tetsuo; Jido, Daisuke; Ohnishi, Akira; Ko, Che Ming; Lee, Su Houng; Nielsen, Marina; Sekihara, Takayasu; Yasui, Shigehiro

    2011-05-27

    Identifying hadronic molecular states and/or hadrons with multiquark components either with or without exotic quantum numbers is a long-standing challenge in hadronic physics. We suggest that studying the production of these hadrons in relativistic heavy ion collisions offers a promising resolution to this problem as yields of exotic hadrons are expected to be strongly affected by their structures. Using the coalescence model for hadron production, we find that, compared to the case of a nonexotic hadron with normal quark numbers, the yield of an exotic hadron is typically an order of magnitude smaller when it is a compact multiquark state and a factor of 2 or more larger when it is a loosely bound hadronic molecule. We further find that some of the newly proposed heavy exotic states could be produced and realistically measured in these experiments.

  7. Identifying and Analyzing Web Server Attacks

    SciTech Connect

    Seifert, Christian; Endicott-Popovsky, Barbara E.; Frincke, Deborah A.; Komisarczuk, Peter; Muschevici, Radu; Welch, Ian D.

    2008-08-29

    Abstract: Client honeypots can be used to identify malicious web servers that attack web browsers and push malware to client machines. Merely recording network traffic is insufficient to perform comprehensive forensic analyses of such attacks. Custom tools are required to access and analyze network protocol data. Moreover, specialized methods are required to perform a behavioral analysis of an attack, which helps determine exactly what transpired on the attacked system. This paper proposes a record/replay mechanism that enables forensic investigators to extract application data from recorded network streams and allows applications to interact with this data in order to conduct behavioral analyses. Implementations for the HTTP and DNS protocols are presented and their utility in network forensic investigations is demonstrated.

  8. Identifying the immunomodulatory components of helminths.

    PubMed

    Shepherd, C; Navarro, S; Wangchuk, P; Wilson, D; Daly, N L; Loukas, A

    2015-06-01

    Immunomodulatory components of helminths offer great promise as an entirely new class of biologics for the treatment of inflammatory diseases. Here, we discuss the emerging themes in helminth-driven immunomodulation in the context of therapeutic drug discovery. We broadly define the approaches that are currently applied by researchers to identify these helminth molecules, highlighting key areas of potential exploitation that have been mostly neglected thus far, notably small molecules. Finally, we propose that the investigation of immunomodulatory compounds will enable the translation of current and future research efforts into potential treatments for autoimmune and allergic diseases, while at the same time yielding new insights into the molecular interface of host-parasite biology.

  9. Deep Neural Networks for Identifying Cough Sounds.

    PubMed

    Amoh, Justice; Odame, Kofi

    2016-10-01

    In this paper, we consider two different approaches of using deep neural networks for cough detection. The cough detection task is cast as a visual recognition problem and as a sequence-to-sequence labeling problem. A convolutional neural network and a recurrent neural network are implemented to address these problems, respectively. We evaluate the performance of the two networks and compare them to other conventional approaches for identifying cough sounds. In addition, we also explore the effect of the network size parameters and the impact of long-term signal dependencies in cough classifier performance. Experimental results show both network architectures outperform traditional methods. Between the two, our convolutional network yields a higher specificity 92.7% whereas the recurrent attains a higher sensitivity of 87.7%.

  10. Identifying miRNAs, targets and functions

    PubMed Central

    Liu, Bing; Li, Jiuyong

    2014-01-01

    microRNAs (miRNAs) are small endogenous non-coding RNAs that function as the universal specificity factors in post-transcriptional gene silencing. Discovering miRNAs, identifying their targets and further inferring miRNA functions have been a critical strategy for understanding normal biological processes of miRNAs and their roles in the development of disease. In this review, we focus on computational methods of inferring miRNA functions, including miRNA functional annotation and inferring miRNA regulatory modules, by integrating heterogeneous data sources. We also briefly introduce the research in miRNA discovery and miRNA-target identification with an emphasis on the challenges to computational biology. PMID:23175680

  11. Identifying the significance of nonlinear normal modes

    PubMed Central

    Cammarano, A.; Neild, S. A.; Barton, D. A. W.

    2017-01-01

    Nonlinear normal modes (NNMs) are widely used as a tool for understanding the forced responses of nonlinear systems. However, the contemporary definition of an NNM also encompasses a large number of dynamic behaviours which are not observed when a system is forced and damped. As such, only a few NNMs are required to understand the forced dynamics. This paper firstly demonstrates the complexity that may arise from the NNMs of a simple nonlinear system—highlighting the need for a method for identifying the significance of NNMs. An analytical investigation is used, alongside energy arguments, to develop an understanding of the mechanisms that relate the NNMs to the forced responses. This provides insight into which NNMs are pertinent to understanding the forced dynamics, and which may be disregarded. The NNMs are compared with simulated forced responses to verify these findings. PMID:28413342

  12. Identifying States of a Financial Market

    PubMed Central

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

    2012-01-01

    The understanding of complex systems has become a central issue because such systems exist in a wide range of scientific disciplines. We here focus on financial markets as an example of a complex system. In particular we analyze financial data from the S&P 500 stocks in the 19-year period 1992–2010. We propose a definition of state for a financial market and use it to identify points of drastic change in the correlation structure. These points are mapped to occurrences of financial crises. We find that a wide variety of characteristic correlation structure patterns exist in the observation time window, and that these characteristic correlation structure patterns can be classified into several typical “market states”. Using this classification we recognize transitions between different market states. A similarity measure we develop thus affords means of understanding changes in states and of recognizing developments not previously seen. PMID:22966419

  13. Identifying financial crises in real time

    NASA Astrophysics Data System (ADS)

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

    2013-03-01

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

  14. Automatic Prosodic Analysis to Identify Mild Dementia

    PubMed Central

    Gonzalez-Moreira, Eduardo; Torres-Boza, Diana; Kairuz, Héctor Arturo; Ferrer, Carlos; Garcia-Zamora, Marlene; Espinoza-Cuadros, Fernando; Hernandez-Gómez, Luis Alfonso

    2015-01-01

    This paper describes an exploratory technique to identify mild dementia by assessing the degree of speech deficits. A total of twenty participants were used for this experiment, ten patients with a diagnosis of mild dementia and ten participants like healthy control. The audio session for each subject was recorded following a methodology developed for the present study. Prosodic features in patients with mild dementia and healthy elderly controls were measured using automatic prosodic analysis on a reading task. A novel method was carried out to gather twelve prosodic features over speech samples. The best classification rate achieved was of 85% accuracy using four prosodic features. The results attained show that the proposed computational speech analysis offers a viable alternative for automatic identification of dementia features in elderly adults. PMID:26558287

  15. Identifying decohering paths in closed quantum systems

    NASA Technical Reports Server (NTRS)

    Albrecht, Andreas

    1990-01-01

    A specific proposal is discussed for how to identify decohering paths in a wavefunction of the universe. The emphasis is on determining the correlations among subsystems and then considering how these correlations evolve. The proposal is similar to earlier ideas of Schroedinger and of Zeh, but in other ways it is closer to the decoherence functional of Griffiths, Omnes, and Gell-Mann and Hartle. There are interesting differences with each of these which are discussed. Once a given coarse-graining is chosen, the candidate paths are fixed in this scheme, and a single well defined number measures the degree of decoherence for each path. The normal probability sum rules are exactly obeyed (instantaneously) by these paths regardless of the level of decoherence. Also briefly discussed is how one might quantify some other aspects of classicality. The important role that concrete calculations play in testing this and other proposals is stressed.

  16. Newly Identified Pathogens Associated with Periodontitis

    PubMed Central

    Pérez-Chaparro, P.J.; Gonçalves, C.; Figueiredo, L.C.; Faveri, M.; Lobão, E.; Tamashiro, N.; Duarte, P.; Feres, M.

    2014-01-01

    There is substantial evidence supporting the role of certain oral bacteria species in the onset and progression of periodontitis. Nevertheless, results of independent-culture diagnostic methods introduced about a decade ago have pointed to the existence of new periodontal pathogens. However, the data of these studies have not been evaluated together, which may generate some misunderstanding on the actual role of these microorganisms in the etiology of periodontitis. The aim of this systematic review was to determine the current weight of evidence for newly identified periodontal pathogens based on the results of “association” studies. This review was conducted and reported in accordance with the PRISMA statement. The MEDLINE, EMBASE, and Cochrane databases were searched up to September 2013 for studies (1) comparing microbial data of subgingival plaque samples collected from subjects with periodontitis and periodontal health and (2) evaluating at least 1 microorganism other than the already-known periodontal pathogens. From 1,450 papers identified, 41 studies were eligible. The data were extracted and registered in predefined piloted forms. The results suggested that there is moderate evidence in the literature to support the association of 17 species or phylotypes from the phyla Bacteroidetes, Candidatus Saccharibacteria, Firmicutes, Proteobacteria, Spirochaetes, and Synergistetes. The phylum Candidatus Saccharibacteria and the Archaea domain also seem to have an association with disease. These data point out the importance of previously unidentified species in the etiology of periodontitis and might guide future investigations on the actual role of these suspected new pathogens in the onset and progression of this infection. PMID:25074492

  17. Vulnerability of critical infrastructures : identifying critical nodes.

    SciTech Connect

    Cox, Roger Gary; Robinson, David Gerald

    2004-06-01

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

  18. Melanoma Biomolecules: Independently Identified but Functionally Intertwined

    PubMed Central

    Dye, Danielle E.; Medic, Sandra; Ziman, Mel; Coombe, Deirdre R.

    2013-01-01

    The majority of patients diagnosed with melanoma present with thin lesions and generally these patients have a good prognosis. However, 5% of patients with early melanoma (<1 mm thick) will have recurrence and die within 10 years, despite no evidence of local or metastatic spread at the time of diagnosis. Thus, there is a need for additional prognostic markers to help identify those patients that may be at risk of recurrent disease. Many studies and several meta-analyses have compared gene and protein expression in melanocytes, naevi, primary, and metastatic melanoma in an attempt to find informative prognostic markers for these patients. However, although a large number of putative biomarkers have been described, few of these molecules are informative when used in isolation. The best approach is likely to involve a combination of molecules. We believe one approach could be to analyze the expression of a group of interacting proteins that regulate different aspects of the metastatic pathway. This is because a primary lesion expressing proteins involved in multiple stages of metastasis may be more likely to lead to secondary disease than one that does not. This review focuses on five putative biomarkers – melanoma cell adhesion molecule (MCAM), galectin-3 (gal-3), matrix metalloproteinase 2 (MMP-2), chondroitin sulfate proteoglycan 4 (CSPG4), and paired box 3 (PAX3). The goal is to provide context around what is known about the contribution of these biomarkers to melanoma biology and metastasis. Although each of these molecules have been independently identified as likely biomarkers, it is clear from our analyses that each are closely linked with each other, with intertwined roles in melanoma biology. PMID:24069584

  19. Identifying hidden voice and video streams

    NASA Astrophysics Data System (ADS)

    Fan, Jieyan; Wu, Dapeng; Nucci, Antonio; Keralapura, Ram; Gao, Lixin

    2009-04-01

    Given the rising popularity of voice and video services over the Internet, accurately identifying voice and video traffic that traverse their networks has become a critical task for Internet service providers (ISPs). As the number of proprietary applications that deliver voice and video services to end users increases over time, the search for the one methodology that can accurately detect such services while being application independent still remains open. This problem becomes even more complicated when voice and video service providers like Skype, Microsoft, and Google bundle their voice and video services with other services like file transfer and chat. For example, a bundled Skype session can contain both voice stream and file transfer stream in the same layer-3/layer-4 flow. In this context, traditional techniques to identify voice and video streams do not work. In this paper, we propose a novel self-learning classifier, called VVS-I , that detects the presence of voice and video streams in flows with minimum manual intervention. Our classifier works in two phases: training phase and detection phase. In the training phase, VVS-I first extracts the relevant features, and subsequently constructs a fingerprint of a flow using the power spectral density (PSD) analysis. In the detection phase, it compares the fingerprint of a flow to the existing fingerprints learned during the training phase, and subsequently classifies the flow. Our classifier is not only capable of detecting voice and video streams that are hidden in different flows, but is also capable of detecting different applications (like Skype, MSN, etc.) that generate these voice/video streams. We show that our classifier can achieve close to 100% detection rate while keeping the false positive rate to less that 1%.

  20. Identifying Crucial Parameter Correlations Maintaining Bursting Activity

    PubMed Central

    Doloc-Mihu, Anca; Calabrese, Ronald L.

    2014-01-01

    Recent experimental and computational studies suggest that linearly correlated sets of parameters (intrinsic and synaptic properties of neurons) allow central pattern-generating networks to produce and maintain their rhythmic activity regardless of changing internal and external conditions. To determine the role of correlated conductances in the robust maintenance of functional bursting activity, we used our existing database of half-center oscillator (HCO) model instances of the leech heartbeat CPG. From the database, we identified functional activity groups of burster (isolated neuron) and half-center oscillator model instances and realistic subgroups of each that showed burst characteristics (principally period and spike frequency) similar to the animal. To find linear correlations among the conductance parameters maintaining functional leech bursting activity, we applied Principal Component Analysis (PCA) to each of these four groups. PCA identified a set of three maximal conductances (leak current, Leak; a persistent K current, K2; and of a persistent Na+ current, P) that correlate linearly for the two groups of burster instances but not for the HCO groups. Visualizations of HCO instances in a reduced space suggested that there might be non-linear relationships between these parameters for these instances. Experimental studies have shown that period is a key attribute influenced by modulatory inputs and temperature variations in heart interneurons. Thus, we explored the sensitivity of period to changes in maximal conductances of Leak, K2, and P, and we found that for our realistic bursters the effect of these parameters on period could not be assessed because when varied individually bursting activity was not maintained. PMID:24945358

  1. Melanoma biomolecules: independently identified but functionally intertwined.

    PubMed

    Dye, Danielle E; Medic, Sandra; Ziman, Mel; Coombe, Deirdre R

    2013-09-24

    The majority of patients diagnosed with melanoma present with thin lesions and generally these patients have a good prognosis. However, 5% of patients with early melanoma (<1 mm thick) will have recurrence and die within 10 years, despite no evidence of local or metastatic spread at the time of diagnosis. Thus, there is a need for additional prognostic markers to help identify those patients that may be at risk of recurrent disease. Many studies and several meta-analyses have compared gene and protein expression in melanocytes, naevi, primary, and metastatic melanoma in an attempt to find informative prognostic markers for these patients. However, although a large number of putative biomarkers have been described, few of these molecules are informative when used in isolation. The best approach is likely to involve a combination of molecules. We believe one approach could be to analyze the expression of a group of interacting proteins that regulate different aspects of the metastatic pathway. This is because a primary lesion expressing proteins involved in multiple stages of metastasis may be more likely to lead to secondary disease than one that does not. This review focuses on five putative biomarkers - melanoma cell adhesion molecule (MCAM), galectin-3 (gal-3), matrix metalloproteinase 2 (MMP-2), chondroitin sulfate proteoglycan 4 (CSPG4), and paired box 3 (PAX3). The goal is to provide context around what is known about the contribution of these biomarkers to melanoma biology and metastasis. Although each of these molecules have been independently identified as likely biomarkers, it is clear from our analyses that each are closely linked with each other, with intertwined roles in melanoma biology.

  2. Identifying cryptic diversity with predictive phylogeography.

    PubMed

    Espíndola, Anahí; Ruffley, Megan; Smith, Megan L; Carstens, Bryan C; Tank, David C; Sullivan, Jack

    2016-10-26

    Identifying units of biological diversity is a major goal of organismal biology. An increasing literature has focused on the importance of cryptic diversity, defined as the presence of deeply diverged lineages within a single species. While most discoveries of cryptic lineages proceed on a taxon-by-taxon basis, rapid assessments of biodiversity are needed to inform conservation policy and decision-making. Here, we introduce a predictive framework for phylogeography that allows rapidly identifying cryptic diversity. Our approach proceeds by collecting environmental, taxonomic and genetic data from codistributed taxa with known phylogeographic histories. We define these taxa as a reference set, and categorize them as either harbouring or lacking cryptic diversity. We then build a random forest classifier that allows us to predict which other taxa endemic to the same biome are likely to contain cryptic diversity. We apply this framework to data from two sets of disjunct ecosystems known to harbour taxa with cryptic diversity: the mesic temperate forests of the Pacific Northwest of North America and the arid lands of Southwestern North America. The predictive approach presented here is accurate, with prediction accuracies placed between 65% and 98.79% depending of the ecosystem. This seems to indicate that our method can be successfully used to address ecosystem-level questions about cryptic diversity. Further, our application for the prediction of the cryptic/non-cryptic nature of unknown species is easily applicable and provides results that agree with recent discoveries from those systems. Our results demonstrate that the transition of phylogeography from a descriptive to a predictive discipline is possible and effective. © 2016 The Author(s).

  3. IDENTIFYING PREDICTORS OF A DIFFICULT THYROIDECTOMY

    PubMed Central

    Mok, Valerie M.; Oltmann, Sarah C.; Chen, Herbert; Sippel, Rebecca S.; Schneider, David F.

    2014-01-01

    Introduction A Thyroidectomy Difficulty Scale (TDS) was previously developed that identified more difficult operations, which correlated with longer operative times and higher complication rates. The purpose of this study was to identify pre-operative variables predictive of a more difficult thyroidectomy using the TDS. Methods A four item, 20-point TDS, was used to score the difficulty of thyroid operations. Patient and disease factors were recorded for each patient. Difficult thyroidectomy (DT) and non-difficult thyroidectomy (NDT) patients were compared. A final multivariate logistic regression model was constructed with significant (p<0.05) variables from a univariate analysis. Results 189 patients were scored using TDS. 69 (36.5%) suffered from hyperthyroidism, 42 (22.2%) from Hashimoto’s, 34 (18.0%) from thyroid cancer and 36 (19.0%) from multinodular goiter. Among hyperthyroid patients, the DT group had a greater number preoperatively treated with Lugol’s potassium iodide (81.6% DT vs. 58.1% NDT, p=0.032), presence of ophthalmopathy (31.6% DT vs. 9.7% NDT, p=0.028) and presence of (>4 IU/mL) anti-thyroglobulin antibodies (34.2% DT vs. 12.9% NDT, p=0.05). Using multivariate analysis, hyperthyroidism (OR 4.35, 95% CI 1.23–15.36, p=0.02), presence of anti-thyroglobulin antibody (OR 3.51, 95% CI 1.28–9.66, p=0.015), and high (>150 ng/mL) thyroglobulin (OR 2.61, 95% CI 1.06–6.42, p=0.037) were independently associated with DT. Conclusion Using TDS, we demonstrated that a diagnosis of hyperthyroidism, pre-operative elevation of serum thyroglobulin and anti-thyroglobulin antibodies are associated with DT. This tool can assist surgeons in counseling patients regarding personalized operative risk and improve OR scheduling. PMID:24750986

  4. Identifying environmental correlates of intraspecific genetic variation.

    PubMed

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

    2016-09-01

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

  5. Ultrasonic Detectors Safely Identify Dangerous, Costly Leaks

    NASA Technical Reports Server (NTRS)

    2013-01-01

    In 1990, NASA grounded its space shuttle fleet. The reason: leaks detected in the hydrogen fuel systems of the Space Shuttles Atlantis and Columbia. Unless the sources of the leaks could be identified and fixed, the shuttles would not be safe to fly. To help locate the existing leaks and check for others, Kennedy Space Center engineers used portable ultrasonic detectors to scan the fuel systems. As a gas or liquid escapes from a leak, the resulting turbulence creates ultrasonic noise, explains Gary Mohr, president of Elmsford, New York-based UE Systems Inc., a long-time leader in ultrasonic detector technologies. "In lay terms, the leak is like a dog whistle, and the detector is like the dog ear." Because the ultrasound emissions from a leak are highly localized, they can be used not only to identify the presence of a leak but also to help pinpoint a leak s location. The NASA engineers employed UE s detectors to examine the shuttle fuel tanks and solid rocket boosters, but encountered difficulty with the devices limited range-certain areas of the shuttle proved difficult or unsafe to scan up close. To remedy the problem, the engineers created a long-range attachment for the detectors, similar to "a zoom lens on a camera," Mohr says. "If you are on the ground, and the leak is 50 feet away, the detector would now give you the same impression as if you were only 25 feet away." The enhancement also had the effect of reducing background noise, allowing for a clearer, more precise detection of a leak s location.

  6. TargetIdentifier: a webserver for identifying full-length cDNAs from EST sequences

    PubMed Central

    Min, Xiang Jia; Butler, Gregory; Storms, Reginald; Tsang, Adrian

    2005-01-01

    TargetIdentifier is a webserver that identifies full-length cDNA sequences from the expressed sequence tag (EST)-derived contig and singleton data. To accomplish this TargetIdentifier uses BLASTX alignments as a guide to locate protein coding regions and potential start and stop codons. This information is then used to determine whether the EST-derived sequences include their translation start codons. The algorithm also uses the BLASTX output to assign putative functions to the query sequences. The server is available at . PMID:15980559

  7. Identifying sites for elk restoration in Arkansas

    USGS Publications Warehouse

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

    2007-01-01

    We used spatial data to identify potential areas for elk (Cervus elaphus) restoration in Arkansas. To assess habitat, we used locations of 239 elk groups collected from helicopter surveys in the Buffalo National River area of northwestern Arkansas, USA, from 1992 to 2002. We calculated the Mahalanobis distance (D2) statistic based on the relationship between those elk-group locations and a suite of 9 landscape variables to evaluate winter habitat in Arkansas. We tested model performance in the Buffalo National River area by comparing the D2 values of pixels representing areas with and without elk pellets along 19 fixed-width transects surveyed in March 2002. Pixels with elk scat had lower D2 values than pixels in which we found no pellets (logistic regression: Wald χ2 = 24.37, P < 0.001), indicating that habitat characteristics were similar to those selected by the aerially surveyed elk. Our D2 model indicated that the best elk habitat primarily occurred in northern and western Arkansas and was associated with areas of high landscape heterogeneity, heavy forest cover, gently sloping ridge tops and valleys, low human population density, and low road densities. To assess the potential for elk–human conflicts in Arkansas, we used the analytical hierarchy process to rank the importance of 8 criteria based on expert opinion from biologists involved in elk management. The biologists ranked availability of forage on public lands as having the strongest influence on the potential for elk–human conflict (33%), followed by human population growth rate (22%) and the amount of private land in row crops (18%). We then applied those rankings in a weighted linear summation to map the relative potential for elk–human conflict. Finally, we used white-tailed deer (Odocoileus virginianus) densities to identify areas where success of elk restoration may be hampered due to meningeal worm (Parelaphostrongylus tenuis) transmission. By combining results of the 3 spatial data layers

  8. Using Hyperspectral Imagery to Identify Turfgrass Stresses

    NASA Technical Reports Server (NTRS)

    Hutto, Kendall; Shaw, David

    2008-01-01

    The use of a form of remote sensing to aid in the management of large turfgrass fields (e.g. golf courses) has been proposed. A turfgrass field of interest would be surveyed in sunlight by use of an airborne hyperspectral imaging system, then the raw observational data would be preprocessed into hyperspectral reflectance image data. These data would be further processed to identify turfgrass stresses, to determine the spatial distributions of those stresses, and to generate maps showing the spatial distributions. Until now, chemicals and water have often been applied, variously, (1) indiscriminately to an entire turfgrass field without regard to localization of specific stresses or (2) to visible and possibly localized signs of stress for example, browning, damage from traffic, or conspicuous growth of weeds. Indiscriminate application is uneconomical and environmentally unsound; the amounts of water and chemicals consumed could be insufficient in some areas and excessive in most areas, and excess chemicals can leak into the environment. In cases in which developing stresses do not show visible signs at first, it could be more economical and effective to take corrective action before visible signs appear. By enabling early identification of specific stresses and their locations, the proposed method would provide guidance for planning more effective, more economical, and more environmentally sound turfgrass-management practices, including application of chemicals and water, aeration, and mowing. The underlying concept of using hyperspectral imagery to generate stress maps as guides to efficient management of vegetation in large fields is not new; it has been applied in the growth of crops to be harvested. What is new here is the effort to develop an algorithm that processes hyperspectral reflectance data into spectral indices specific to stresses in turfgrass. The development effort has included a study in which small turfgrass plots that were, variously, healthy or

  9. Use of lice to identify cowbird hosts

    USGS Publications Warehouse

    Hahn, D.C.; Price, R.D.; Osenton, P.C.

    2000-01-01

    The host specificity of avian lice (Phthiraptera) may be utilized by biologists to investigate the brood parasitism patterns of Brown-headed Cowbirds (Molothrus ater). As nestlings, brood parasites have a unique opportunity to encounter lice that are typically host specific. Lice are permanent hemimetabolic ectoparasites, a group found strictly on the body of the host, and they are transferred almost exclusively by bodily contact between hosts during care of young and at copulation. We investigated whether cowbird nestlings become infested with avian lice from their host parents and carry these lice away when they fledge, in effect bearing ectoparasite indicators of the species that raised them. The technique of examining the lice on cowbird fledglings to identify their foster parents would be much less costly than hiring a team of experts to determine parasitism patterns in the conventional way by finding hundreds of songbird nests. We examined 244 cowbird fledglings and found that they carried a rich fauna of lice representing 11 species and six genera, almost the entire spectrum of louse genera known to occur on passerines. We also examined 320 songbirds from 30 species, all known hosts of the Brown-headed Cowbird. As a group the host birds bore a diversity of louse species comparable to that on the fledgling cowbirds: 13 species of lice from seven genera. In contrast, most individual passerine host species yielded only 1 or 2 louse species, significantly fewer than the cowbird fledglings (p < 0.0001). Of 44 fledgling cowbirds carrying lice, 11 were linked to their probable avian foster parents via louse indicators, and these are the Wood Thrush and Red-winged Blackbird. Eighteen additional fledglings were linked to one of two possible foster parents. We concluded that cowbird fledglings do carry away host lice and this survey technique provides a partial assessment of local community parasitism patterns. The incomplete state of passerine louse taxonomy requires

  10. Pseudonymization of patient identifiers for translational research.

    PubMed

    Aamot, Harald; Kohl, Christian Dominik; Richter, Daniela; Knaup-Gregori, Petra

    2013-07-24

    The usage of patient data for research poses risks concerning the patients' privacy and informational self-determination. Next-generation-sequencing technologies and various other methods gain data from biospecimen, both for translational research and personalized medicine. If these biospecimen are anonymized, individual research results from genomic research, which should be offered to patients in a clinically relevant timeframe, cannot be associated back to the individual. This raises an ethical concern and challenges the legitimacy of anonymized patient samples. In this paper we present a new approach which supports both data privacy and the possibility to give feedback to patients about their individual research results. We examined previously published privacy concepts regarding a streamlined de-pseudonymization process and a patient-based pseudonym as applicable to research with genomic data and warehousing approaches. All concepts identified in the literature review were compared to each other and analyzed for their applicability to translational research projects. We evaluated how these concepts cope with challenges implicated by personalized medicine. Therefore, both person-centricity issues and a separation of pseudonymization and de-pseudonymization stood out as a central theme in our examination. This motivated us to enhance an existing pseudonymization method regarding a separation of duties. The existing concepts rely on external trusted third parties, making de-pseudonymization a multistage process involving additional interpersonal communication, which might cause critical delays in patient care. Therefore we propose an enhanced method with an asymmetric encryption scheme separating the duties of pseudonymization and de-pseudonymization. The pseudonymization service provider is unable to conclude the patient identifier from the pseudonym, but assigns this ability to an authorized third party (ombudsman) instead. To solve person-centricity issues, a

  11. Use of lice to identify cowbird hosts

    USGS Publications Warehouse

    Hahn, D.C.; Price, R.D.; Osenton, P.C.

    2000-01-01

    The host specificity of avian lice (Phthiraptera) may be utilized by biologists to investigate the brood parasitism patterns of Brown-headed Cowbirds (Molothrus ater). As nestlings, brood parasites have a unique opportunity to encounter lice that are typically host specific. Lice are permanent hemimetabolic ectoparasites, a group found strictly on the body of the host, and they are transferred almost exclusively by bodily contact between hosts during care of young and at copulation. We investigated whether cowbird nestlings become infested with avian lice from their host parents and carry these lice away when they fledge, in effect bearing ectoparasite indicators of the species that raised them. The technique of examining the lice on cowbird fledglings to identify their foster parents would be much less costly than hiring a team of experts to determine parasitism patterns in the conventional way by finding hundreds of songbird nests. We examined 244 cowbird fledglings and found that they carried a rich fauna of lice representing 11 species and six genera, almost the entire spectrum of louse genera known to occur on passerines. We also examined 320 songbirds from 30 species, all known hosts of the Brown-headed Cowbird. As a group the host birds bore a diversity of louse species comparable to that on the fledgling cowbirds: 13 species of lice from seven genera. In contrast, most individual passerine host species yielded only 1 or 2 louse species, significantly fewer than the cowbird fledglings (p < 0.0001). Of 44 fledgling cowbirds carrying lice, 11 were linked to their probable avian foster parents via louse indicators, and these are the Wood Thrush and Red-winged Blackbird. Eighteen additional fledglings were linked to one of two possible foster parents. We concluded that cowbird fledglings do carry away host lice and this survey technique provides a partial assessment of local community parasitism patterns. The incomplete state of passerine louse taxonomy requires

  12. Identifying protein complexes based on brainstorming strategy.

    PubMed

    Shen, Xianjun; Zhou, Jin; Yi, Li; Hu, Xiaohua; He, Tingting; Yang, Jincai

    2016-11-01

    Protein complexes comprising of interacting proteins in protein-protein interaction network (PPI network) play a central role in driving biological processes within cells. Recently, more and more swarm intelligence based algorithms to detect protein complexes have been emerging, which have become the research hotspot in proteomics field. In this paper, we propose a novel algorithm for identifying protein complexes based on brainstorming strategy (IPC-BSS), which is integrated into the main idea of swarm intelligence optimization and the improved K-means algorithm. Distance between the nodes in PPI network is defined by combining the network topology and gene ontology (GO) information. Inspired by human brainstorming process, IPC-BSS algorithm firstly selects the clustering center nodes, and then they are separately consolidated with the other nodes with short distance to form initial clusters. Finally, we put forward two ways of updating the initial clusters to search optimal results. Experimental results show that our IPC-BSS algorithm outperforms the other classic algorithms on yeast and human PPI networks, and it obtains many predicted protein complexes with biological significance. Copyright © 2016 Elsevier Inc. All rights reserved.

  13. Identifying Wind and Solar Ramping Events: Preprint

    SciTech Connect

    Florita, A.; Hodge, B. M.; Orwig, K.

    2013-01-01

    Wind and solar power are playing an increasing role in the electrical grid, but their inherent power variability can augment uncertainties in power system operations. One solution to help mitigate the impacts and provide more flexibility is enhanced wind and solar power forecasting; however, its relative utility is also uncertain. Within the variability of solar and wind power, repercussions from large ramping events are of primary concern. At the same time, there is no clear definition of what constitutes a ramping event, with various criteria used in different operational areas. Here the Swinging Door Algorithm, originally used for data compression in trend logging, is applied to identify variable generation ramping events from historic operational data. The identification of ramps in a simple and automated fashion is a critical task that feeds into a larger work of 1) defining novel metrics for wind and solar power forecasting that attempt to capture the true impact of forecast errors on system operations and economics, and 2) informing various power system models in a data-driven manner for superior exploratory simulation research. Both allow inference on sensitivities and meaningful correlations, as well as the ability to quantify the value of probabilistic approaches for future use in practice.

  14. Can we identify source lithology of basalt?

    PubMed

    Yang, Zong-Feng; Zhou, Jun-Hong

    2013-01-01

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

  15. IDENTIFYING ANOMALIES IN GRAVITATIONAL LENS TIME DELAYS

    SciTech Connect

    Congdon, Arthur B.; Keeton, Charles R.; Nordgren, C. Erik E-mail: keeton@physics.rutgers.ed

    2010-02-01

    We examine the ability of gravitational lens time delays to reveal complex structure in lens potentials. In a previous paper, we predicted how the time delay between the bright pair of images in a 'fold' lens scales with the image separation, for smooth lens potentials. Here we show that the proportionality constant increases with the quadrupole moment of the lens potential, and depends only weakly on the position of the source along the caustic. We use Monte Carlo simulations to determine the range of time delays that can be produced by realistic smooth lens models consisting of isothermal ellipsoid galaxies with tidal shear. We can then identify outliers as 'time delay anomalies'. We find evidence for anomalies in close image pairs in the cusp lenses RX J1131 - 1231 and B1422+231. The anomalies in RX J1131 - 1231 provide strong evidence for substructure in the lens potential, while at this point the apparent anomalies in B1422+231 mainly indicate that the time delay measurements need to be improved. We also find evidence for time delay anomalies in larger-separation image pairs in the fold lenses, B1608+656 and WFI 2033 - 4723, and the cusp lens RX J0911+0551. We suggest that these anomalies are caused by some combination of substructure and a complex lens environment. Finally, to assist future monitoring campaigns we use our smooth models with shear to predict the time delays for all known four-image lenses.

  16. Identifying lubricant options for compressor bearing designs

    NASA Astrophysics Data System (ADS)

    Karnaz, J.; Seeton, C.; Dixon, L.

    2017-08-01

    Today’s refrigeration and air conditioning market is not only driven by the environmental aspects of the refrigerants, but also by the energy efficiency and reliability of system operation. Numerous types of compressor designs are used in refrigeration and air conditioning applications which means that different bearings are used; and in some cases, multiple bearing types within a single compressor. Since only one lubricant is used, it is important to try to optimize the lubricant to meet the various demands and requirements for operation. This optimization entails investigating different types of lubricant chemistries, viscosities, and various formulation options. What makes evaluating these options more challenging is the refrigerant which changes the properties of the lubricant delivered to the bearing. Once the lubricant and refrigerant interaction are understood, through various test methods, then work can start on collaborating with compressor engineers on identifying the lubricant chemistry and formulation options. These interaction properties are important to the design engineer to make decisions on the adequacy of the lubricant before compressor tests are started. This paper will discuss the process to evaluate lubricants for various types of compressors and bearing design with focus on what’s needed for current refrigerant trends. In addition, the paper will show how the lubricant chemistry choice can be manipulated through understanding of the bearing design and knowledge of interaction with the refrigerant to maximize performance. Emphasis will be placed on evaluation of synthetic lubricants for both natural and synthetic low GWP refrigerants.

  17. Identifying dark matter interactions in monojet searches

    DOE PAGES

    Agrawal, Prateek; Rentala, Vikram

    2014-05-22

    We study the discrimination of quark-initiated jets from gluon-initiated jets in monojet searches for dark matter using the technique of averaged jet energy profiles. We demonstrate our results in the context of effective field theories of dark matter interactions with quarks and gluons, but our methods apply more generally to a wide class of models. Different effective theories of dark matter and the standard model backgrounds each have a characteristic quark/gluon fraction for the leading jet. When used in conjunction with the traditional cut-and-count monojet search, the jet energy profile can be used to set stronger bounds on contact interactionsmore » of dark matter. In the event of a discovery of a monojet excess at the 14 TeV LHC, contact interactions between dark matter with quarks or with gluons can be differentiated at the 95% confidence level. For a given rate at the LHC, signal predictions at direct detection experiments for different dark matter interactions can span five orders of magnitude. Lastly, the ability to identify these interactions allows us to make a tighter connection between LHC searches and direct detection experiments.« less

  18. Identifying murder victims with endodontic radiographs

    PubMed Central

    Silva, Rhonan Ferreira; Franco, Ademir; Mendes, Solon Diego Santos Carvalho; Picoli, Fernando Fortes; Nunes, Fernando Gomes; Estrela, Carlos

    2016-01-01

    Endodontics is a special branch of dentistry constantly guided by imaging examinations. From a forensic scope, endodontics plays a valuable role providing solid antemortem (AM) radiographic evidence for comparison with postmortem findings in human identifications. This study illustrates the interface between endodontics and forensic odontology describing three cases of human identification based on radiographic endodontic records. From 2009 to 2012, three unknown male victims of murder were examined in a local Brazilian medico-legal institute to retrieve identity and potential cause of death. Specifically, when asked for AM data, a relative of the three victims provided periapical radiographs of endodontic treatments. Based on that, forensic dentists reproduced the same imaging acquisition techniques obtaining similar periapical radiographs, enabling a comparative dental identification. All the victims were positively identified based on patterns of dental morphology and treatment intervention. This study draws the attention of general and forensic dentists highlight the importance of properly recording dental treatments and searching for evidence in AM endodontic data, respectively. PMID:28123272

  19. Identifying Lagrangian fronts with favourable fishery conditions

    NASA Astrophysics Data System (ADS)

    Prants, S. V.; Budyansky, M. V.; Uleysky, M. Yu.

    2014-08-01

    Lagrangian fronts (LFs) in the ocean are defined as boundaries between surface waters with strongly different Lagrangian properties. They can be accurately detected in a given velocity field by computing synoptic maps for displacements of synthetic tracers and other Lagrangian indicators. We use Pacific saury catch and location data for a number of commercial fishery seasons in the region of the northwest Pacific with one of the richest fishery in the world. It is shown statistically that the saury fishing grounds with maximal catches are not randomly distributed over the region but located mainly along the sharp LFs where productive cold waters of the Oyashio Current, warmer waters of the southern branch of the Soya Current, and waters of warm-core Kuroshio rings converge. Computation of those fronts in altimetric geostrophic velocity fields both in the years with the First and Second Oyashio Intrusions shows that in spite of different oceanographic conditions LF locations may serve as good indicators of potential fishing grounds. Possible biophysical reasons for saury aggregation near sharp LFs are discussed. We propose a mechanism for effective export of nutrient rich waters based on stretching of material lines in the vicinity of hyperbolic objects in the ocean. The developed method, based on identifying LFs in any velocity fields, is quite general and may be applied to find potential fishing grounds for the other pelagic fish.

  20. Pharmaceutical identifier confirmation via DART-TOF.

    PubMed

    Easter, Jacob L; Steiner, Robert R

    2014-07-01

    Pharmaceutical analysis comprises a large amount of the casework in forensic controlled substances laboratories. In order to reduce the time of analysis for pharmaceuticals, a Direct Analysis in Real Time ion source coupled with an accurate mass time-of-flight (DART-TOF) mass spectrometer was used to confirm identity. DART-TOF spectral data for pharmaceutical samples were analyzed and evaluated by comparison to standard spectra. Identical mass pharmaceuticals were differentiated using collision induced dissociation fragmentation, present/absent ions, and abundance comparison box plots; principal component analysis (PCA) and linear discriminant analysis (LDA) were used for differentiation of identical mass mixed drug spectra. Mass assignment reproducibility and robustness tests were performed on the DART-TOF spectra. Impacts on the forensic science community include a decrease in analysis time over the traditional gas chromatograph/mass spectrometry (GC/MS) confirmations, better laboratory efficiency, and simpler sample preparation. Using physical identifiers and the DART-TOF to confirm pharmaceutical identity will eliminate the use of GC/MS and effectively reduce analysis time while still complying with accepted analysis protocols. This will prove helpful in laboratories with large backlogs and will simplify the confirmation process. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  1. Identifying murder victims with endodontic radiographs.

    PubMed

    Silva, Rhonan Ferreira; Franco, Ademir; Mendes, Solon Diego Santos Carvalho; Picoli, Fernando Fortes; Nunes, Fernando Gomes; Estrela, Carlos

    2016-01-01

    Endodontics is a special branch of dentistry constantly guided by imaging examinations. From a forensic scope, endodontics plays a valuable role providing solid antemortem (AM) radiographic evidence for comparison with postmortem findings in human identifications. This study illustrates the interface between endodontics and forensic odontology describing three cases of human identification based on radiographic endodontic records. From 2009 to 2012, three unknown male victims of murder were examined in a local Brazilian medico-legal institute to retrieve identity and potential cause of death. Specifically, when asked for AM data, a relative of the three victims provided periapical radiographs of endodontic treatments. Based on that, forensic dentists reproduced the same imaging acquisition techniques obtaining similar periapical radiographs, enabling a comparative dental identification. All the victims were positively identified based on patterns of dental morphology and treatment intervention. This study draws the attention of general and forensic dentists highlight the importance of properly recording dental treatments and searching for evidence in AM endodontic data, respectively.

  2. Defining and identifying Sleeping Beauties in science.

    PubMed

    Ke, Qing; Ferrara, Emilio; Radicchi, Filippo; Flammini, Alessandro

    2015-06-16

    A Sleeping Beauty (SB) in science refers to a paper whose importance is not recognized for several years after publication. Its citation history exhibits a long hibernation period followed by a sudden spike of popularity. Previous studies suggest a relative scarcity of SBs. The reliability of this conclusion is, however, heavily dependent on identification methods based on arbitrary threshold parameters for sleeping time and number of citations, applied to small or monodisciplinary bibliographic datasets. Here we present a systematic, large-scale, and multidisciplinary analysis of the SB phenomenon in science. We introduce a parameter-free measure that quantifies the extent to which a specific paper can be considered an SB. We apply our method to 22 million scientific papers published in all disciplines of natural and social sciences over a time span longer than a century. Our results reveal that the SB phenomenon is not exceptional. There is a continuous spectrum of delayed recognition where both the hibernation period and the awakening intensity are taken into account. Although many cases of SBs can be identified by looking at monodisciplinary bibliographic data, the SB phenomenon becomes much more apparent with the analysis of multidisciplinary datasets, where we can observe many examples of papers achieving delayed yet exceptional importance in disciplines different from those where they were originally published. Our analysis emphasizes a complex feature of citation dynamics that so far has received little attention, and also provides empirical evidence against the use of short-term citation metrics in the quantification of scientific impact.

  3. Identifying Metabolically Active Chemicals Using a Consensus ...

    EPA Pesticide Factsheets

    Endocrine disrupting chemicals (EDCs) are abundant throughout the environment and can alter neurodevelopment, behavior, and reproductive success of humans and other species by perturbing signaling pathways related to the estrogen receptor (ER). A recent study compared results across 18 ER-related assays in the ToxCast™ in vitro screening program to predict the likelihood of a chemical exhibiting in vivo estrogenic activity, with the purpose of eliminating chemicals that may produce a false signal by interfering with the technological attributes of an individual assay. However, flaws in in vitro assay design can also prevent induction of signal activity by EDCs. Another reason for not observing activity for some EDCs in in vitro assays is that metabolic activation is required to perturb ER-related pathways. In the current study, 1,024 chemicals were identified as lacking ER activity after establishing a consensus across each of the 18 ER-related in vitro assays, and nearly 2,000 primary and 3,700 secondary unique metabolites were predicted for these chemicals. The ER binding activity for each metabolite was then predicted using an existing ER activity quantitative structure activity relationship (QSAR) consensus model. Binding activity was predicted for 2-3% of the metabolites within each generation. Of the inactive parent compounds generating at least one metabolite predicted to have ER-binding activity, nearly 30% were found to have metabolites from both gene

  4. Can we identify source lithology of basalt?

    PubMed Central

    Yang, Zong-Feng; Zhou, Jun-Hong

    2013-01-01

    The nature of source rocks of basaltic magmas plays a fundamental role in understanding the composition, structure and evolution of the solid earth. However, identification of source lithology of basalts remains uncertainty. Using a parameterization of multi-decadal melting experiments on a variety of peridotite and pyroxenite, we show here that a parameter called FC3MS value (FeO/CaO-3*MgO/SiO2, all in wt%) can identify most pyroxenite-derived basalts. The continental oceanic island basalt-like volcanic rocks (MgO>7.5%) (C-OIB) in eastern China and Mongolia are too high in the FC3MS value to be derived from peridotite source. The majority of the C-OIB in phase diagrams are equilibrium with garnet and clinopyroxene, indicating that garnet pyroxenite is the dominant source lithology. Our results demonstrate that many reputed evolved low magnesian C-OIBs in fact represent primary pyroxenite melts, suggesting that many previous geological and petrological interpretations of basalts based on the single peridotite model need to be reconsidered. PMID:23676779

  5. Monoclonal Antibodies Identify Novel Neural Antigens

    NASA Astrophysics Data System (ADS)

    Hawkes, Richard; Niday, Evelyn; Matus, Andrew

    1982-04-01

    Monoclonal antibodies (Mabs) were raised against synaptic plasma membranes from rat cerebellum. The hybridomas were screened with a solid-phase immunoassay, the positive lines were characterized by their immunoperoxidase staining pattern on cerebellum, and the specific polypeptide antigens were identified on protein blots. Among the Mabs described are some that stain only neurons or only glia and others that react with specific parts of cells, such as axons, dendrites, and synapses. Many Mabs reveal novel relationships between antigens and the cells in which they occur. For example, a Mab designated 7D5 reacts with a family of > 30 proteins but stains only glial cells. Several Mabs stain punctate sites of synaptic size and distribution in the cerebellar cortex but each reacts with a different subset of polypeptides. One of the most restricted cytological staining patterns is given by 12D5, which stains punctate sites in the granular layer of the cerebellar cortex and reacts with a single polypeptide band of apparent Mr 270,000. These results illustrate the feasibility of raising Mabs that can be used to follow the expression of specific gene products during brain development.

  6. Identifying a new particle with jet substructures

    NASA Astrophysics Data System (ADS)

    Han, Chengcheng; Kim, Doojin; Kim, Minho; Kong, Kyoungchul; Lim, Sung Hak; Park, Myeonghun

    2017-01-01

    We investigate a potential of determining properties of a new heavy resonance of mass O(1) TeV which decays to collimated jets via heavy Standard Model intermediary states, exploiting jet substructure techniques. Employing the Z gauge boson as a concrete example for the intermediary state, we utilize a "merged jet" defined by a large jet size to capture the two quarks from its decay. The use of the merged jet benefits the identification of a Z-induced jet as a single, reconstructed object without any combinatorial ambiguity. We find that jet substructure procedures may enhance features in some kinematic observables formed with subjet four-momenta extracted from a merged jet. This observation motivates us to feed subjet momenta into the matrix elements associated with plausible hypotheses on the nature of the heavy resonance, which are further processed to construct a matrix element method (MEM)-based observable. For both moderately and highly boosted Z bosons, we demonstrate that the MEM in combination with jet substructure techniques can be a very powerful tool for identifying its physical properties. We also discuss effects from choosing different jet sizes for merged jets and jet-grooming parameters upon the MEM analyses.

  7. RECOGNIZING AND IDENTIFYING PEOPLE: A neuropsychological review

    PubMed Central

    Barton, Jason J S; Corrow, Sherryse L

    2016-01-01

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

  8. Unique Transcriptional Programs Identify Subtypes of AKI.

    PubMed

    Xu, Katherine; Rosenstiel, Paul; Paragas, Neal; Hinze, Christian; Gao, Xiaobo; Huai Shen, Tian; Werth, Max; Forster, Catherine; Deng, Rong; Bruck, Efrat; Boles, Roger W; Tornato, Alexandra; Gopal, Tejashree; Jones, Madison; Konig, Justin; Stauber, Jacob; D'Agati, Vivette; Erdjument-Bromage, Hediye; Saggi, Subodh; Wagener, Gebhard; Schmidt-Ott, Kai M; Tatonetti, Nicholas; Tempst, Paul; Oliver, Juan A; Guarnieri, Paolo; Barasch, Jonathan

    2017-06-01

    Two metrics, a rise in serum creatinine concentration and a decrease in urine output, are considered tantamount to the injury of the kidney tubule and the epithelial cells thereof (AKI). Yet neither criterion emphasizes the etiology or the pathogenetic heterogeneity of acute decreases in kidney excretory function. In fact, whether decreased excretory function due to contraction of the extracellular fluid volume (vAKI) or due to intrinsic kidney injury (iAKI) actually share pathogenesis and should be aggregated in the same diagnostic group remains an open question. To examine this possibility, we created mouse models of iAKI and vAKI that induced a similar increase in serum creatinine concentration. Using laser microdissection to isolate specific domains of the kidney, followed by RNA sequencing, we found that thousands of genes responded specifically to iAKI or to vAKI, but very few responded to both stimuli. In fact, the activated gene sets comprised different, functionally unrelated signal transduction pathways and were expressed in different regions of the kidney. Moreover, we identified distinctive gene expression patterns in human urine as potential biomarkers of either iAKI or vAKI, but not both. Hence, iAKI and vAKI are biologically unrelated, suggesting that molecular analysis should clarify our current definitions of acute changes in kidney excretory function. Copyright © 2017 by the American Society of Nephrology.

  9. Indexing molecules with chemical graph identifiers.

    PubMed

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

    2011-09-01

    Fast and robust algorithms for indexing molecules have been historically considered strategic tools for the management and storage of large chemical libraries. This work introduces a modified and further extended version of the molecular equivalence number naming adaptation of the Morgan algorithm (J Chem Inf Comput Sci 2001, 41, 181-185) for the generation of a chemical graph identifier (CGI). This new version corrects for the collisions recognized in the original adaptation and includes the ability to deal with graph canonicalization, ensembles (salts), and isomerism (tautomerism, regioisomerism, optical isomerism, and geometrical isomerism) in a flexible manner. Validation of the current CGI implementation was performed on the open NCI database and the drug-like subset of the ZINC database containing 260,071 and 5,348,089 structures, respectively. The results were compared with those obtained with some of the most widely used indexing codes, such as the CACTVS hash code and the new InChIKey. The analyses emphasize the fact that compound management activities, like duplicate analysis of chemical libraries, are sensitive to the exact definition of compound uniqueness and thus still depend, to a minor extent, on the type and flexibility of the molecular index being used. Copyright © 2011 Wiley Periodicals, Inc.

  10. Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes

    PubMed Central

    Edmunds, Richard C.; Su, Baofeng; Balhoff, James P.; Eames, B. Frank; Dahdul, Wasila M.; Lapp, Hilmar; Lundberg, John G.; Vision, Todd J.; Dunham, Rex A.; Mabee, Paula M.; Westerfield, Monte

    2016-01-01

    Phenotypes resulting from mutations in genetic model organisms can help reveal candidate genes for evolutionarily important phenotypic changes in related taxa. Although testing candidate gene hypotheses experimentally in nonmodel organisms is typically difficult, ontology-driven information systems can help generate testable hypotheses about developmental processes in experimentally tractable organisms. Here, we tested candidate gene hypotheses suggested by expert use of the Phenoscape Knowledgebase, specifically looking for genes that are candidates responsible for evolutionarily interesting phenotypes in the ostariophysan fishes that bear resemblance to mutant phenotypes in zebrafish. For this, we searched ZFIN for genetic perturbations that result in either loss of basihyal element or loss of scales phenotypes, because these are the ancestral phenotypes observed in catfishes (Siluriformes). We tested the identified candidate genes by examining their endogenous expression patterns in the channel catfish, Ictalurus punctatus. The experimental results were consistent with the hypotheses that these features evolved through disruption in developmental pathways at, or upstream of, brpf1 and eda/edar for the ancestral losses of basihyal element and scales, respectively. These results demonstrate that ontological annotations of the phenotypic effects of genetic alterations in model organisms, when aggregated within a knowledgebase, can be used effectively to generate testable, and useful, hypotheses about evolutionary changes in morphology. PMID:26500251

  11. Identifying a new particle with jet substructures

    DOE PAGES

    Han, Chengcheng; Kim, Doojin; Kim, Minho; ...

    2017-01-09

    Here, we investigate a potential of determining properties of a new heavy resonance of mass O(1)TeV which decays to collimated jets via heavy Standard Model intermediary states, exploiting jet substructure techniques. Employing the Z gauge boson as a concrete example for the intermediary state, we utilize a "merged jet" defined by a large jet size to capture the two quarks from its decay. The use of the merged jet bene ts the identification of a Z-induced jet as a single, reconstructed object without any combinatorial ambiguity. We also find that jet substructure procedures may enhance features in some kinematic observablesmore » formed with subjet four-momenta extracted from a merged jet. This observation motivates us to feed subjet momenta into the matrix elements associated with plausible hypotheses on the nature of the heavy resonance, which are further processed to construct a matrix element method (MEM)-based observable. For both moderately and highly boosted Z bosons, we demonstrate that the MEM in combination with jet substructure techniques can be a very powerful tool for identifying its physical properties. Finally, we discuss effects from choosing different jet sizes for merged jets and jet-grooming parameters upon the MEM analyses.« less

  12. Identifying transudates misclassified by Light's criteria.

    PubMed

    Porcel, José M

    2013-07-01

    Light's criteria combine three dichotomous tests into a decision rule that is considered positive if any one of the tests is positive. This strategy clearly maximizes sensitivity, although at the expense of specificity. Although Light's criteria identify 98% of pleural exudates, they misclassify about 25% of transudates as exudates. The way to overcome this limitation is discussed in this review. Traditionally, measurement of the protein gradient between the serum and pleural fluid has been recommended to decrease the misclassification rate of Light's criteria. A recent study demonstrated that a gradient between the albumin levels in the serum and the pleural fluid more than 1.2 g/dl performs significantly better than a protein gradient more than 3.1 g/dl to correctly categorize mislabeled cardiac effusions (83 vs. 55%). On the other hand, the accuracy of a pleural fluid to serum albumin ratio less than 0.6 excelled when compared with albumin and protein gradients in patients with miscategorized hepatic hydrothoraces (77 vs. 62 vs. 61%). The simplest strategy to reveal the true transudative nature of heart failure-related effusions, labeled as exudates by Light's criteria, is to calculate the serum to pleural fluid albumin gradient. Conversely, for misclassified hepatic hydrothoraces, measurement of the pleural to serum albumin ratio is recommended. The serum to pleural fluid protein gradient should no longer be considered the preferred test for this purpose.

  13. Identifying Bully Victims: Definitional versus Behavioral Approaches

    PubMed Central

    Green, Jennifer Greif; Felix, Erika D.; Sharkey, Jill D.; Furlong, Michael J.; Kras, Jennifer E.

    2013-01-01

    Schools frequently assess bullying and the Olweus Bully/Victimization Questionnaire (BVQ; Olweus, 1996) is the most widely adopted tool for this purpose. The BVQ is a self-report survey that uses a definitional measurement method — describing “bullying” as involving repeated, intentional aggression in a relationship where there is an imbalance of power, and then asking respondents to indicate how frequently they experienced this type of victimization. Few studies have examined BVQ validity and whether this definitional method truly identifies the repetition and power differential that distinguish bullying from other forms of peer victimization. This study examined concurrent validity of the BVQ definitional question among 435 students reporting peer victimization. BVQ definitional responses were compared with responses to a behavioral measure that did not use the term “bullying,” but instead included items that asked about its defining characteristics (repetition, intentionality, power imbalance). Concordance between the two approaches was moderate, with an area under the receiver-operating curve of .72. BVQ responses were more strongly associated with students indicating repeated victimization and multiple forms of victimization, than with power imbalance in their relationship with the bully. Findings indicate that the BVQ is a valid measure of repeated victimization and a broad range of victimization experiences, but may not detect the more subtle and complex power imbalances that distinguish bullying from other forms of peer victimization. PMID:23244644

  14. Identifying and quantifying urban recharge: a review

    NASA Astrophysics Data System (ADS)

    Lerner, David N.

    2002-02-01

    The sources of and pathways for groundwater recharge in urban areas are more numerous and complex than in rural environments. Buildings, roads, and other surface infrastructure combine with man-made drainage networks to change the pathways for precipitation. Some direct recharge is lost, but additional recharge can occur from storm drainage systems. Large amounts of water are imported into most cities for supply, distributed through underground pipes, and collected again in sewers or septic tanks. The leaks from these pipe networks often provide substantial recharge. Sources of recharge in urban areas are identified through piezometry, chemical signatures, and water balances. All three approaches have problems. Recharge is quantified either by individual components (direct recharge, water-mains leakage, septic tanks, etc.) or holistically. Working with individual components requires large amounts of data, much of which is uncertain and is likely to lead to large uncertainties in the final result. Recommended holistic approaches include the use of groundwater modelling and solute balances, where various types of data are integrated. Urban recharge remains an under-researched topic, with few high-quality case studies reported in the literature.

  15. Canopy hot-spot as crop identifier

    SciTech Connect

    Gerstl, S.A.W.; Simmer, C.; Powers, B.J.

    1986-05-01

    Illuminating any reflective rough or structured surface by a directional light source results in an angular reflectance distribution that shows a narrow peak in the direction of retro-reflection. This is called the Heiligenschein or hot-spot of vegetation canopies and is caused by mutual shading of leaves. The angular intensity distribution of the hot-spot, its brightness and slope, are therefore indicators of the plant's geometry. We propose the use of hot-spot characteristics as crop identifiers in satellite remote sensing because the canopy hot-spot carries information about plant stand architecture that is more distinctive for different plant species than, for instance, their spectral reflectance characteristics. A simple three-dimensional Monte Carlo/ray tracing model and an analytic two-dimensional model are developed to estimate the angular distribution of the hot-spot as a function of the size of the plant leaves. The results show that the brightness-distribution and slope of the hot-spot change distinctively for different leaf sizes indicating a much more peaked maximum for the smaller leaves.

  16. Astrobiology: Identifying Bacteria from Extreme Environments

    NASA Astrophysics Data System (ADS)

    Quan, Tiffany K.; Dorighi, Kristel M.; Cooksey, Kathy L.

    2010-12-01

    COSMOS is a four-week summer residential academic and enrichment program for high school students interested in science and mathematics, sponsored by the University of California. Since 2001, participants in the Center for Adaptive Optics (CfAO) Professional Development Program (PDP) have developed and instructed a general astronomy and biology COSMOS course cluster. This cluster provides an optimal venue for piloting newly designed activities, as well as an opportunity for PDP participants to obtain practical teaching experience. In 2007, we designed an astrobiology-based project for five of the 17 students in our cluster. This project aimed to bridge the gap between the astronomy and biology sides of Cluster 7: Stars and Cells. We facilitated the process whereby the students designed and implemented their own experimental plan to identify unknown extremophilic bacteria. Their findings allowed them to extrapolate and discuss what it means to be alive and how these factors would impact life on other planets. Here we provide details of the entire project design and reflect on its success.

  17. Identifying dark matter interactions in monojet searches

    SciTech Connect

    Agrawal, Prateek; Rentala, Vikram

    2014-05-22

    We study the discrimination of quark-initiated jets from gluon-initiated jets in monojet searches for dark matter using the technique of averaged jet energy profiles. We demonstrate our results in the context of effective field theories of dark matter interactions with quarks and gluons, but our methods apply more generally to a wide class of models. Different effective theories of dark matter and the standard model backgrounds each have a characteristic quark/gluon fraction for the leading jet. When used in conjunction with the traditional cut-and-count monojet search, the jet energy profile can be used to set stronger bounds on contact interactions of dark matter. In the event of a discovery of a monojet excess at the 14 TeV LHC, contact interactions between dark matter with quarks or with gluons can be differentiated at the 95% confidence level. For a given rate at the LHC, signal predictions at direct detection experiments for different dark matter interactions can span five orders of magnitude. Lastly, the ability to identify these interactions allows us to make a tighter connection between LHC searches and direct detection experiments.

  18. Identifying orthoimages in Web Map Services

    NASA Astrophysics Data System (ADS)

    Florczyk, A. J.; Nogueras-Iso, J.; Zarazaga-Soria, F. J.; Béjar, R.

    2012-10-01

    Orthoimages are essential in many Web applications to facilitate the background context that helps to understand other georeferenced information. Catalogues and service registries of Spatial Data Infrastructures do not necessarily register all the services providing access to imagery data on the Web, and it is not easy to automatically identify whether the data offered by a Web service are directly imagery data or not. This work presents a method for an automatic detection of the orthoimage layers offered by Web Map Services. The method combines two types of heuristics. The first one consists in analysing the text in the capabilities document. The second type is content-based heuristics, which analyse the content offered by the Web Map Service layers. These heuristics gather and analyse the colour features of a sample collection of image fragments that represent the offered content. An experiment has been performed over a set of Web Map Service layers, which have been fetched from a repository of capabilities documents gathered from the Web. This has proven the efficiency of the method (precision of 87% and recall of 60%). This functionality has been offered as a Web Processing Service, and it has been integrated within the Virtual Spain project to provide a catalogue of orthoimages and build realistic 3D views.

  19. Identifying recycled ash in basaltic eruptions.

    PubMed

    D'Oriano, Claudia; Bertagnini, Antonella; Cioni, Raffaello; Pompilio, Massimo

    2014-07-28

    Deposits of mid-intensity basaltic explosive eruptions are characterized by the coexistence of different types of juvenile clasts, which show a large variability of external properties and texture, reflecting alternatively the effects of primary processes related to magma storage or ascent, or of syn-eruptive modifications occurred during or immediately after their ejection. If fragments fall back within the crater area before being re-ejected during the ensuing activity, they are subject to thermally- and chemically-induced alterations. These 'recycled' clasts can be considered as cognate lithic for the eruption/explosion they derive. Their exact identification has consequences for a correct interpretation of eruption dynamics, with important implications for hazard assessment. On ash erupted during selected basaltic eruptions (at Stromboli, Etna, Vesuvius, Gaua-Vanuatu), we have identified a set of characteristics that can be associated with the occurrence of intra-crater recycling processes, based also on the comparison with results of reheating experiments performed on primary juvenile material, at variable temperature and under different redox conditions.

  20. Identifying core competencies for public health epidemiologists.

    PubMed

    Bondy, Susan J; Johnson, Ian; Cole, Donald C; Bercovitz, Kim

    2008-01-01

    Public health authorities have prioritized the identification of competencies, yet little empirical data exist to support decisions on competency selection among particular disciplines. We sought perspectives on important competencies among epidemiologists familiar with or practicing in public health settings (local to national). Using a sequential, qualitative-quantitative mixed method design, we conducted key informant interviews with 12 public health practitioners familiar with front-line epidemiologists' practice, followed by a web-based survey of members of a provincial association of public health epidemiologists (90 respondents of 155 eligible) and a consensus workshop. Competency statements were drawn from existing core competency lists and those identified by key informants, and ranked by extent of agreement in importance for entry-level practitioners. Competencies in quantitative methods and analysis, critical appraisal of scientific evidence and knowledge transfer of scientific data to other members of the public health team were all regarded as very important for public health epidemiologists. Epidemiologist competencies focused on the provision, interpretation and 'translation' of evidence to inform decision-making by other public health professionals. Considerable tension existed around some potential competency items, particularly in the areas of more advanced database and data-analytic skills. Empirical data can inform discussions of discipline-specific competencies as one input to decisions about competencies appropriate for epidemiologists in the public health workforce.

  1. A Novel Method for Identifying Exoplanetary Rings

    NASA Astrophysics Data System (ADS)

    Zuluaga, Jorge I.; Kipping, David M.; Sucerquia, Mario; Alvarado, Jaime A.

    2015-04-01

    The discovery of rings around extrasolar planets (“exorings”) is one of the next breakthroughs in exoplanetary research. Previous studies have explored the feasibility of detecting exorings with present and future photometric sensitivities by seeking anomalous deviations in the residuals of a standard transit light curve fit, at the level of ≃ 100 ppm for Kronian rings. In this work, we explore two much larger observational consequences of exorings: (1) the significant increase in transit depth that may lead to the misclassification of ringed planetary candidates as false-positives and/or the underestimation of planetary density; and (2) the so-called “photo-ring” effect, a new asterodensity profiling effect, revealed by a comparison of the light curve derived stellar density to that measured with independent methods (e.g., asteroseismology). While these methods do not provide an unambiguous detection of exorings, we show that the large amplitude of these effects, combined with their relatively simple analytic description, makes them highly suited to large-scale surveys to identify candidate ringed planets worthy of more detailed investigation. Moreover, these methods lend themselves to ensemble analyses seeking to uncover evidence of a population of ringed planets. We describe the method in detail, develop the basic underlying formalism, and test it in the parameter space of rings and transit configuration. We discuss the prospects of using this method for the first systematic search of exoplanetary rings in the Kepler database and provide a basic computational code for implementing it.

  2. Identifying the extent of a Superfund site

    SciTech Connect

    Gowland, P.A.; Chantry, W.; Wisniewski, R.

    1995-12-31

    There has been considerable misunderstanding regarding the extent of private and Federal facility sites listed under the Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) or Superfund program. This problem, which occurs primarily at the time of proposal or finalization of a site to the National Priorities List (NPL), seems to be due both to semantics and errors in perception. The term ``site`` has been used differently in performing CERCLA removal and remediation activities, in the installation restoration programs of various Federal agencies, and by the public when preparing comments on proposed NPL sites. It has been confused with the terms source, solid waste management unit, and facility. The most common interpretation by the public of the term ``site`` and its extent is that the site encompasses the property owned by the facility named in the NPL designation or at which a removal has occurred. However, based on the related definitions in CERCLA, a site is best defined as the location of a release (or releases) of hazardous substances and wherever the hazardous substances have come to be located. The extent of a site neither is limited by property boundaries, nor does it include clean areas within a facility`s boundaries. This paper will identify the basis for the Environmental Protection Agency`s (EPA`s) definition of site for Superfund purposes, including aggregated sites, relevant court decisions and statements of EPA policy, and provide case histories of how this definition has been applied at both private and Federal facilities.

  3. Identifying image preferences based on demographic attributes

    NASA Astrophysics Data System (ADS)

    Fedorovskaya, Elena A.; Lawrence, Daniel R.

    2014-02-01

    The intent of this study is to determine what sorts of images are considered more interesting by which demographic groups. Specifically, we attempt to identify images whose interestingness ratings are influenced by the demographic attribute of the viewer's gender. To that end, we use the data from an experiment where 18 participants (9 women and 9 men) rated several hundred images based on "visual interest" or preferences in viewing images. The images were selected to represent the consumer "photo-space" - typical categories of subject matter found in consumer photo collections. They were annotated using perceptual and semantic descriptors. In analyzing the image interestingness ratings, we apply a multivariate procedure known as forced classification, a feature of dual scaling, a discrete analogue of principal components analysis (similar to correspondence analysis). This particular analysis of ratings (i.e., ordered-choice or Likert) data enables the investigator to emphasize the effect of a specific item or collection of items. We focus on the influence of the demographic item of gender on the analysis, so that the solutions are essentially confined to subspaces spanned by the emphasized item. Using this technique, we can know definitively which images' ratings have been influenced by the demographic item of choice. Subsequently, images can be evaluated and linked, on one hand, to their perceptual and semantic descriptors, and, on the other hand, to the preferences associated with viewers' demographic attributes.

  4. The Ku-band polarization identifier

    NASA Astrophysics Data System (ADS)

    Gundersen, J. O.; Kupid Collaboration

    2003-12-01

    The Ku-band polarization identifier (KUPID) will integrate a very low noise 12-18 GHz, correlation polarimeter onto the Crawford Hill seven meter, millimeter-wave antenna. The primary components of the polarimeter will be built at the University of Miami and other key components, including the microwave horn and data acquisition system will be built at the University of Chicago and Princeton University. This project will measure the Q and U Stokes parameters in regions near the north celestial pole, in regions of low galactic contamination, and in regions near the galactic plane. The KUPID survey experiment makes use of many of the techniques employed in the Princeton IQU experiment (PIQUE) that was developed by the members of this collaboration to detect CMB polarization at shorter wavelengths. The KUPID experiment will be constructed in parallel and on the same timescale as the CAPMAP experiment (see Barkats, this volume) which is the follow-on experiment to PIQUE. KUPID will observe on the Crawford Hill antenna from late spring until early autumn, while CAPMAP will observe during the lower water vapor months of late autumn until early spring.

  5. Identifying recycled ash in basaltic eruptions

    NASA Astrophysics Data System (ADS)

    D'Oriano, Claudia; Bertagnini, Antonella; Cioni, Raffaello; Pompilio, Massimo

    2014-07-01

    Deposits of mid-intensity basaltic explosive eruptions are characterized by the coexistence of different types of juvenile clasts, which show a large variability of external properties and texture, reflecting alternatively the effects of primary processes related to magma storage or ascent, or of syn-eruptive modifications occurred during or immediately after their ejection. If fragments fall back within the crater area before being re-ejected during the ensuing activity, they are subject to thermally- and chemically-induced alterations. These `recycled' clasts can be considered as cognate lithic for the eruption/explosion they derive. Their exact identification has consequences for a correct interpretation of eruption dynamics, with important implications for hazard assessment. On ash erupted during selected basaltic eruptions (at Stromboli, Etna, Vesuvius, Gaua-Vanuatu), we have identified a set of characteristics that can be associated with the occurrence of intra-crater recycling processes, based also on the comparison with results of reheating experiments performed on primary juvenile material, at variable temperature and under different redox conditions.

  6. Using computers to identify complications after surgery.

    PubMed Central

    Roos, L L; Cageorge, S M; Austen, E; Lohr, K N

    1985-01-01

    We used the Health Services Commission data from Manitoba, Canada to identify complications resulting from hysterectomy, cholecystectomy, and prostatectomy which led to hospital readmissions. For each procedure, two specialists independently judged whether the readmissions were for surgery-related complications on the basis of liberally interpreted literature guidelines. Then, each pair of physicians met to resolve differences; only complications agreed upon by physicians were retained in our computer-based analysis. The analysis was done in three steps: algorithms were developed using guidelines from the literature, physician input, and 1974 hospital claims; these were then modified using 1975 data; finally, the algorithms were tested with 1976 data. The computerized algorithms developed were compared with the clinical decisions of physician panels. The results showed high specificity, sensitivity, and predictive value. Given the increasing availability of routinely collected data bases, the possibilities for inexpensively monitoring the outcomes of different providers and institutions are appealing. More extensive validation and application of the methodology to a greater number of procedures are necessary to implement such a program. PMID:4051065

  7. Strategies for identifying new prions in yeast.

    PubMed

    MacLea, Kyle S; Ross, Eric D

    2011-01-01

    The unexpected discovery of two prions, [URE3] and [PSI+], in Saccharomyces cerevisiae led to questions about how many other proteins could undergo similar prion-based structural conversions. However, [URE3] and [PSI+] were discovered by serendipity in genetic screens. Cataloging the full range of prions in yeast or in other organisms will therefore require more systematic search methods. Taking advantage of some of the unique features of prions, various researchers have developed bioinformatic and experimental methods for identifying novel prion proteins. These methods have generated long lists of prion candidates. The systematic testing of some of these prion candidates has led to notable successes; however, even in yeast, where rapid growth rate and ease of genetic manipulation aid in testing for prion activity, such candidate testing is laborious. Development of better methods to winnow the field of prion candidates will greatly aid in the discovery of new prions, both in yeast and in other organisms, and help us to better understand the role of prions in biology.

  8. Identifying recycled ash in basaltic eruptions

    PubMed Central

    D'Oriano, Claudia; Bertagnini, Antonella; Cioni, Raffaello; Pompilio, Massimo

    2014-01-01

    Deposits of mid-intensity basaltic explosive eruptions are characterized by the coexistence of different types of juvenile clasts, which show a large variability of external properties and texture, reflecting alternatively the effects of primary processes related to magma storage or ascent, or of syn-eruptive modifications occurred during or immediately after their ejection. If fragments fall back within the crater area before being re-ejected during the ensuing activity, they are subject to thermally- and chemically-induced alterations. These ‘recycled' clasts can be considered as cognate lithic for the eruption/explosion they derive. Their exact identification has consequences for a correct interpretation of eruption dynamics, with important implications for hazard assessment. On ash erupted during selected basaltic eruptions (at Stromboli, Etna, Vesuvius, Gaua-Vanuatu), we have identified a set of characteristics that can be associated with the occurrence of intra-crater recycling processes, based also on the comparison with results of reheating experiments performed on primary juvenile material, at variable temperature and under different redox conditions. PMID:25069064

  9. Utilizing Surface Sensors to Identify Wake Regimes

    NASA Astrophysics Data System (ADS)

    Wang, Mengying; Hemati, Maziar S.

    2016-11-01

    Marine swimmers often exploit external flow structures to reduce locomotive effort. To achieve this advantage, these swimmers utilize mechanosensory organs on the surface of their bodies to detect hydrodynamic signals from the surrounding fluid, which can then be used to inform the control task. Recently, there has been a growing interest in developing similar flow sensing systems to achieve enhanced propulsive efficiency and maneuverability in human-engineered underwater vehicles. In particular, much attention has been given to the problem of wake sensing; however, these investigations have concentrated on a restricted class of wakes-i.e., Kármán-type vortex streets-whereas more complicated wake structures can arise in practice. In this talk, we will explore the possibility of identifying wake regimes through the use of surface sensors. Potential flow theory is adopted to simulate the interactions of various wakes with a fish-like body. Wakes in different dynamical regimes impart distinct hydrodynamic signatures on the body, which permits these regimes to be distinguished from one another in an automated fashion. Our results can provide guidance for improving flow sensing capabilities in human-engineered systems and hint at how marine swimmers may sense their hydrodynamic surroundings.

  10. Identifying distinct thermal components of a creek

    NASA Astrophysics Data System (ADS)

    Boughton, David A.; Hatch, Christine; Mora, Ethan

    2012-09-01

    Statistical and heat budget methods for analyzing temperature dynamics of creeks are limited by the ability to resolve thermal processes and fine-grained thermal structures, respectively. Here we describe a hybrid method that identifies distinct thermal components in a stream's heat budget using only temperature data and an algorithm that employs mutual information to "unmix" signals in the temperature data. Spatial resolution is limited only by the number of temperature-logging sensors, which can be quite high for distributed-temperature sensors. Process resolution is at the level of thermal components, defined as distinct collections of heat flux elements sharing coordinated (nonindependent) dynamics. Inference can be used to relate thermal components to meteorological forcing and structural heterogeneity in the fluvial system and to suggest novel hypotheses for further testing with targeted heat budget studies. Applying the method to a small, arid-land creek produced two novel hypotheses: (1) lateral conduction of heat from adjacent dry land (bed, terraces) appeared to cause a substantial heating of the stream, augmented by off-channel flow paths, and (2) riparian vegetation was associated with a subtraction of heat from the stream at a rate proportionate to solar insolation, exceeding the maximum decoupling effect of shade by at least 2°C at midday, and suggesting upwelling heat flux from water to tree canopy proportional to sunlight. The method appears useful for generating new hypotheses, for selecting informative sites for detailed heat budgets, for determining the dimensionality of heat budgets in natural streams, and more broadly for associating thermal components to fluvial structure and processes.

  11. Identifying Predictive Markers for Personalized Treatment Selection

    PubMed Central

    Shen, Yuanyuan

    2017-01-01

    Summary It is now well recognized that the effectiveness and potential risk of a treatment often vary by patient subgroups. Although trial-and-error and one-size-fits-all approaches to treatment selection remains a common practice, much recent focus has been placed on individualized treatment selection based on patient information (La Thangue and Kerr, 2011; Ong et al., 2012). Genetic and molecular markers are becoming increasingly available to guide treatment selection for various diseases including HIV and breast cancer (Mallal et al., 2008; Zujewski and Kamin, 2008). In recent years, many statistical procedures for developing individualized treatment rules (ITRs) have been proposed. However, less focus has been given to efficient selection of predictive biomarkers for treatment selection. The standard Wald test for interactions between treatment and the set of markers of interest may not work well when the marker effects are non-linear. Furthermore, interaction based test is scale dependent and may fail to capture markers useful for predicting individualized treatment differences. In this paper, we propose to overcome these difficulties by developing a kernel machine (KM) score test that can efficiently identify markers predictive of treatment difference. Simulation studies show that our proposed KM based score test is more powerful than the Wald test when there is non-linear effect among the predictors and when the outcome is binary with non-linear link functions. Furthermore, when there is high-correlation among predictors and when the number of predictors is not small, our method also over-performs Wald test. The proposed method is illustrated with two randomized clinical trials. PMID:26999054

  12. Identifying Fishes through DNA Barcodes and Microarrays

    PubMed Central

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

    2010-01-01

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

  13. Electroencephalographic identifiers of motor adaptation learning.

    PubMed

    Özdenizci, Ozan; Yalçın, Mustafa; Erdoğan, Ahmetcan; Patoğlu, Volkan; Grosse-Wentrup, Moritz; Çetin, Müjdat

    2017-04-03

    Recent brain-computer interface (BCI) assisted stroke rehabilitation protocols tend to focus on sensorimotor activity of the brain. Relying on evidence claiming that a variety of brain rhythms beyond sensorimotor areas are related to the extent of motor deficits, we propose to identify neural correlates of motor learning beyond sensorimotor areas spatially and spectrally for further use in novel BCI-assisted neurorehabilitation settings. Electroencephalographic (EEG) data were recorded from healthy subjects participating in a physical force-field adaptation task involving reaching movements through a robotic handle. EEG activity recorded during rest prior to the experiment and during pre-trial movement preparation was used as features to predict motor adaptation learning performance across subjects. Subjects learned to perform straight movements under the force-field at different adaptation rates. Both resting-state and pre-trial EEG features were predictive of individual adaptation rates with relevance of a broad network of beta activity. Beyond sensorimotor regions, a parieto-occipital cortical component observed across subjects was involved strongly in predictions and a fronto-parietal cortical component showed significant decrease in pre-trial beta-powers for users with higher adaptation rates and increase in pre-trial beta-powers for users with lower adaptation rates. Including sensorimotor areas, a large-scale network of beta activity is presented as predictive of motor learning. Strength of resting-state parieto-occipital beta activity or pre-trial fronto-parietal beta activity can be considered in BCI-assisted stroke rehabilitation protocols with neurofeedback training or volitional control of neural activity for brain-robot interfaces to induce plasticity.

  14. Identifying potential PARIS homologs in D. melanogaster.

    PubMed

    Merzetti, E M; Staveley, B E

    2016-11-03

    Mitochondrial destruction leads to the formation of reactive oxygen species, increases cellular stress, causes apoptotic cell death, and involves a cascade of proteins including PARKIN, PINK1, and Mitofusin2. Mitochondrial biogenesis pathways depend upon the activity of the protein PGC-1α. These two processes are coordinated by the activity of a transcriptional repressor, Parkin interacting substrate (PARIS). The PARIS protein is degraded through the activity of the PARKIN protein, which in turn eliminates the transcriptional repression that PARIS imposes upon a downstream target, PGC-1α. Genes in this pathway have been implicated in Parkinson's disease, and there is a strong relationship between mitochondrial dysfunction and pre-mature neuron death. The identification of a PARIS homolog in Drosophila melanogaster would increase our understanding of the roles that PARIS and interacting genes play in higher organisms. We identified three potential PARIS homologs in D. melanogaster, one of which encodes a protein with similar domains to the Homo sapiens PARIS protein, CG15436. The Drosophila eye is formed from neuronal precursors, making it an ideal system to assay the effects of altered gene expression on neuronal tissue formation. The eye-specific expression of RNAi constructs for these genes revealed that both CG15269 and Crol caused neurodegenerative phenotypes, whereas CG15436 produced a phenotype similar to srl-EY. Crol-RNAi expression reduced mean lifespan when expressed in dopaminergic neurons, whereas CG15436-RNAi significantly increased lifespan. CG15436 was PARIS-like in both structure and function, and we characterized the effects of decreased gene expression in both the neuron-rich D. melanogaster eye and in dopaminergic neurons.

  15. Quality gaps identified through mortality review

    PubMed Central

    Kobewka, Daniel M; van Walraven, Carl; Turnbull, Jeffrey; Worthington, James; Calder, Lisa; Forster, Alan

    2017-01-01

    Background Hospital mortality rate is a common measure of healthcare quality. Morbidity and mortality meetings are common but there are few reports of hospital-wide mortality-review processes to provide understanding of quality-of-care problems associated with patient deaths. Objective To describe the implementation and results from an institution-wide mortality-review process. Design A nurse and a physician independently reviewed every death that occurred at our multisite teaching institution over a 3-month period. Deaths judged by either reviewer to be unanticipated or to have any opportunity for improvement were reviewed by a multidisciplinary committee. We report characteristics of patients with unanticipated death or opportunity for improved care and summarise the opportunities for improved care. Results Over a 3-month period, we reviewed all 427 deaths in our hospital in detail; 33 deaths (7.7%) were deemed unanticipated and 100 (23.4%) were deemed to be associated with an opportunity for improvement. We identified 97 opportunities to improve care. The most common gap in care was: ‘goals of care not discussed or the discussion was inadequate’ (n=25 (25.8%)) and ‘delay or failure to achieve a timely diagnosis’ (n=8 (8.3%)). Patients who had opportunities for improvement had longer length of stay and a lower baseline predicted risk of death in hospital. Nurse and physician reviewers spent approximately 142 h reviewing cases outside of committee meetings. Conclusions Our institution-wide mortality review found many quality gaps among decedents, in particular inadequate discussion of goals of care. PMID:26856617

  16. Identifying the Subtle Presentation of Decompression Sickness.

    PubMed

    Alea, Kenneth

    2015-12-01

    Decompression sickness is an inherent occupational hazard that has the possibility to leave its victims with significant long-lasting effects that can potentially impact an aircrew's flight status. The relative infrequency of this hazard within the military flying community along with the potentially subtle presentation of decompression sickness (DCS) has the potential to result in delayed diagnosis and treatment, leading to residual deficits that can impact a patient's daily life or even lead to death. The patient presented in this work was diagnosed with a Type II DCS 21 h after a cabin decompression at 35,000 ft (10,668 m). The patient had been asymptomatic with a completely normal physical/neurological exam following his flight. The following day, he presented with excessive fatigue and on re-evaluation was recommended for hyperbaric therapy, during which his symptoms completely resolved. He was re-evaluated 14 d later and cleared to resume flight duties without further incident. The manifestation of this patient's decompression sickness was subtle and followed an evaluation that failed to identify any focal findings. A high index of suspicion with strict follow-up contributed to the identification of DCS in this case, resulting in definitive treatment and resolution of the patient's symptoms. Determination of the need for hyperbaric therapy following oxygen supplementation and a thorough history and physical is imperative. If the diagnosis is in question, consider preemptive hyperbaric therapy as the benefits of treatment in DCS outweigh the risks of treatment. Finally, this work introduces the future potential of neuropsychological testing for both the diagnosis of DCS as well as assessing the effectiveness of hyperbaric therapy in Type II DCS.

  17. Defining and identifying Sleeping Beauties in science

    PubMed Central

    Ke, Qing; Ferrara, Emilio; Radicchi, Filippo; Flammini, Alessandro

    2015-01-01

    A Sleeping Beauty (SB) in science refers to a paper whose importance is not recognized for several years after publication. Its citation history exhibits a long hibernation period followed by a sudden spike of popularity. Previous studies suggest a relative scarcity of SBs. The reliability of this conclusion is, however, heavily dependent on identification methods based on arbitrary threshold parameters for sleeping time and number of citations, applied to small or monodisciplinary bibliographic datasets. Here we present a systematic, large-scale, and multidisciplinary analysis of the SB phenomenon in science. We introduce a parameter-free measure that quantifies the extent to which a specific paper can be considered an SB. We apply our method to 22 million scientific papers published in all disciplines of natural and social sciences over a time span longer than a century. Our results reveal that the SB phenomenon is not exceptional. There is a continuous spectrum of delayed recognition where both the hibernation period and the awakening intensity are taken into account. Although many cases of SBs can be identified by looking at monodisciplinary bibliographic data, the SB phenomenon becomes much more apparent with the analysis of multidisciplinary datasets, where we can observe many examples of papers achieving delayed yet exceptional importance in disciplines different from those where they were originally published. Our analysis emphasizes a complex feature of citation dynamics that so far has received little attention, and also provides empirical evidence against the use of short-term citation metrics in the quantification of scientific impact. PMID:26015563

  18. Identifying natural flow regimes using fish communities

    NASA Astrophysics Data System (ADS)

    Chang, Fi-John; Tsai, Wen-Ping; Wu, Tzu-Ching; Chen, Hung-kwai; Herricks, Edwin E.

    2011-10-01

    SummaryModern water resources management has adopted natural flow regimes as reasonable targets for river restoration and conservation. The characterization of a natural flow regime begins with the development of hydrologic statistics from flow records. However, little guidance exists for defining the period of record needed for regime determination. In Taiwan, the Taiwan Eco-hydrological Indicator System (TEIS), a group of hydrologic statistics selected for fisheries relevance, is being used to evaluate ecological flows. The TEIS consists of a group of hydrologic statistics selected to characterize the relationships between flow and the life history of indigenous species. Using the TEIS and biosurvey data for Taiwan, this paper identifies the length of hydrologic record sufficient for natural flow regime characterization. To define the ecological hydrology of fish communities, this study connected hydrologic statistics to fish communities by using methods to define antecedent conditions that influence existing community composition. A moving average method was applied to TEIS statistics to reflect the effects of antecedent flow condition and a point-biserial correlation method was used to relate fisheries collections with TEIS statistics. The resulting fish species-TEIS (FISH-TEIS) hydrologic statistics matrix takes full advantage of historical flows and fisheries data. The analysis indicates that, in the watersheds analyzed, averaging TEIS statistics for the present year and 3 years prior to the sampling date, termed MA(4), is sufficient to develop a natural flow regime. This result suggests that flow regimes based on hydrologic statistics for the period of record can be replaced by regimes developed for sampled fish communities.

  19. STK11 Mutation Identified in Thyroid Carcinoma.

    PubMed

    Wei, Shuanzeng; LiVolsi, Virginia A; Brose, Marcia S; Montone, Kathleen T; Morrissette, Jennifer J D; Baloch, Zubair W

    2016-03-01

    Peutz-Jeghers syndrome (PJS) is an autosomal-dominant disorder, in which germline mutation of serine threonine-protein kinase 11 (STK11) is identified in up to 90 % of the patients who meet clinical criteria for PJS. Hematoxylin and eosin (H&E) slides of the tumor were reviewed to confirm areas with at least 25 % of tumor cellularity. Then, the designated area was extracted for genomic DNA. Targeted next-generation sequencing analysis was performed using a 47-gene panel. Case 1 is a 71-year-old man with high grade follicular thyroid carcinoma with clear cell and oncocytic features. The carcinoma showed a missense mutation in TP53 (p.R342G, c.1024C > G) and a 16-nucleotide intronic deletion started next to the 3' of exon 6 (involving the canonical +1 and +2 bases of the splice donor site) in STK11 (p.?, c.862 + 1_862 + 16delGTGGGAGCCTCATCCC). Case 2 is a 76-year-old woman with tall cell variant papillary thyroid carcinoma. The carcinoma demonstrated a missense mutation in BRAF (p.V600E, c.1799T > A) and a missense mutation in STK11 (p.F354L, c.1062C > G). In summary, we present two elderly patients with thyroid carcinoma harboring STK11 mutation without clinical manifestation of PJS. The findings suggest that STK11 may play a role in thyroid carcinoma development.

  20. An algorithm for identifying mothball composition().

    PubMed

    Moss, Michael J; Maskell, Kevin F; Hieger, Michelle A; Wills, Brandon K; Cumpston, Kirk L

    2017-09-01

    Unintentional mothball ingestions may cause serious toxicity in small children. Camphor, naphthalene, and paradichlorobenzene mothballs are difficult to distinguish without packaging. Symptoms and management differ based on the ingested compound. Previous studies have used a variety of antiquated, impractical and potentially dangerous techniques to identify the mothballs. The goal of this study is to discover a simplified identification technique using materials readily available in an emergency department. Mothballs made of naphthalene and paradichlorobenzene along with camphor tablets were tested. Each material was tested both intact and after being fragmented to simulate a partially ingested mothball. Each of these six sample types were then immersed in 40 ml each of 11 fluids: water, 0.45% NaCl, 0.9% NaCl, lactated Ringer's, 5% dextrose in water, 5% dextrose in 0.9% NaCl, 50% dextrose in water, 8.4% NaHCO3, 3% H2O2, 70% isopropanol, and 91% isopropanol. All tests were conducted in standard urinalysis sample cups to replicate available materials. Three toxicologists blinded to the identities of samples and solutions visually evaluated each sample. Observations included assessing response to immersion: sink, float, or dissolve. All evaluators agreed in their description of 62/66 (94%) of the samples, with all four disagreements being on sinking and dissolving versus sinking only. A two-fluid algorithm utilizing 50% dextrose and water was sufficient to distinguish the sample types. Camphor will float in water while both paradichlorobenzene and naphthalene will sink. In 50% dextrose, both naphthalene and camphor will float while paradichlorobenzene will sink. Mothball materials can be distinguished by immersion in water and 50% dextrose. Limitations of this study include using camphor tablets as a substitute for mothballs given lack of availability.