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Sample records for ictaluri identifies virulence-related

  1. An automated high-throughput cell-based multiplexed flow cytometry assay to identify novel compounds to target Candida albicans virulence-related proteins.

    PubMed

    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

  2. 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

  3. 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

  4. 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

  5. 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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  7. Comparative catfish macrophage function in families expressing high and low survivor phenotype following experimental challenge with Edwardsiella ictaluri

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Two channel catfish families were identified as displaying a high (>90%) or low (<10%) survival phenotype in repeated experimental challenge with Edwardsiella ictaluri. In order to gain understanding of the biological basis of these phenotypes, primary macrophages were prepared from head kidney tiss...

  8. 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.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  12. Molecular Characterization of a LacZ-Type Beta-Galactosidase Activity from Edwardsiella ictaluri

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Enteric septicemia of catfish, caused by Edwardsiella ictaluri, is among the most common disease of channel catfish (Ictalurus punctatus) and is responsible for $50 - 60 million economic losses to catfish producers annually in the Southeastern U.S. After immunoscreening an E. ictaluri genomic libra...

  13. IncA/C Plasmid-Mediated Florfenicol Resistance in the Catfish Pathogen Edwardsiella ictaluri

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Florfenicol has recently been approved for the treatment of enteric septicemia of catfish caused by Edwardsiella ictaluri. Here we report the identification of florfenicol resistance in a clinical isolate of E. ictaluri. Resistance in this isolate is associated with a mobile IncA/C plasmid conferrin...

  14. 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.

  15. Identification and expression profile of multiple genes in the anterior kidney of channel catfish induced by modified live Edwardsiella ictaluri vaccination.

    PubMed

    Pridgeon, Julia W; Shoemaker, Craig A; Klesius, Phillip H

    2010-04-15

    Using PCR-select subtractive cDNA hybridization technique, 57 expressed sequence tags (ESTs) were isolated from 240 clones of a modified live Edwardsiella ictaluri vaccinated vs. sham-vaccinated channel catfish anterior kidney subtractive library. The transcription levels of the 57 ESTs in response to E. ictaluri vaccination were then evaluated by quantitative PCR (QPCR). Of the 57 ESTs, 43 were induced at least 2-fold higher in all three vaccinated fish compared to unvaccinated control fish. Of the 43 upregulated genes, five were consistently upregulated greater than 10-fold, including two highly upregulated (>20-fold) glycosyltransferase and Toll-like receptor 5. The transcriptional levels of GTPase 1, coatomer protein complex zeta 1, and type II arginine deiminase were consistently induced greater than 10-fold. MHC class I alpha chain and transposase were upregulated greater than 10-fold in two of the three vaccinated fish. The 43 upregulated genes also included 19 moderately upregulated (3-10-fold) and 17 slightly upregulated (2-3-fold). Our results suggest that subtractive cDNA hybridization and QPCR are powerful cost-effective techniques to identify differentially expressed genes in response to modified live E. ictaluri vaccination.

  16. [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. PMID:26281603

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  18. Clinical significance of virulence-related assay of Yersinia species.

    PubMed

    Noble, M A; Barteluk, R L; Freeman, H J; Subramaniam, R; Hudson, J B

    1987-05-01

    During the 42-month period from June 1982 through December 1985, 215 fecal specimens from 171 patients were found to be positive for yersiniae by using a combination of CIN agar and cold enrichment. Isolates were tested for markers of virulence including carriage of a plasmid 42 megadaltons in size, calcium dependence, autoagglutination, Congo red uptake, pyrazinamidase activity, fermentation of salicin, and hydrolysis of esculin. The results were correlated to symptoms in patients. A total of 80 Yersinia enterocolitica and 52 Y. enterocolitica-like strains (42 Y. frederiksenii, 8 Y. intermedia, and 2 Y. kristensenii) were examined. Positive virulence-related tests were as follows (for Y. enterocolitica, Y. frederiksenii, Y. intermedia, and Y. kristensenii, respectively): pyrazinamidase negativity, 12.5, 0, 0, and 50%; Congo red positivity, 5, 7.1, 87.5 and 0%; calcium dependence, 3.8, 0, 0, and 0%; autoagglutination positivity, 8.8, 0, 0, and 0%; carriage of the 42-megadalton plasmid, 28.6, 73.2, 5.7, and 0; salicin and esculin negativity, 12.5, 0, 0, and 50%. The isolates recovered from symptomatic patients were characterized in relation to the presenting symptoms. Isolates from 12 of 32 (37.5%) patients with acute-onset diarrhea and 9 of 30 (30.0%) patients with chronic symptoms expressed at least one virulence feature. No individual test or group of tests was consistently associated with onset or either type of symptoms. Routine testing of plasmid carriage, uptake of Congo red, calcium dependence, autoagglutination, and pyrazinamidase activity did not appear to provide information that would link the presence of symptoms with the virulence potential of fecal isolates of yersiniae.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  20. 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

  1. 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.

  2. 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.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  8. Transferable green fluorescence-tagged pEI2 in Edwardsiella ictaluri

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The pEI2 plasmid of Edwardsiella ictaluri isolate, I49, was tagged using a Tn10-GFP-kan cassette to create the green fluorescence-expressing derivative I49-gfp. The Tn10-GFP-kan insertion site was mapped by plasmid sequencing to 663 bp upstream of orf2 and appeared to be at a neutral site in the pla...

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

    PubMed

    Pridgeon, J W; Mu, X; Klesius, P H

    2012-03-01

    Using quantitative polymerase chain reaction (QPCR), 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, cathepsin D, hepcidin and liver-expressed AMP 2) in response to Edwardsiella ictaluri infection were determined. None of the AMP genes tested was significantly upregulated at 2 h post-infection. Hepcidin was the only one that was significantly (P<0.05) upregulated at 4, 6 and 12 h post-infection. At 24 and 48 h post-infection, four AMPs (hepcidin, NK-lysin type 1, NK-lysin type 3 and cathepsin D) were significantly (P<0.05) upregulated. Among all the AMPs that were significantly upregulated at different time points, hepcidin at 4, 6 and 12 h post-infection was upregulated the most. When catfish were injected with different doses of E. ictaluri, all lethal doses were able to induce significant (P <0.05) upregulation of hepcidin in the posterior kidney, whereas sublethal doses failed to induce any significant upregulation of hepcidin. In vitro growth studies revealed that the presence of synthetic hepcidin peptide at a concentration of 16 μm or higher significantly inhibited the cell proliferation of E. ictaluri. Taken together, our results suggest that hepcidin might play an important role in the channel catfish defence against E. ictaluri infection.

  10. Global transcription analysis of vaccinated channel catfish following challenge with virulent Edwardsiella ictaluri.

    PubMed

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

    2012-03-15

    To determine the identities of genes involved in either innate or adaptive immunity, microarray analysis of 65,182 UniGene transcripts were performed to compare gene expression in vaccinated channel catfish after challenge with a virulent Edwardsiella ictaluri compared to that in sham-vaccinated fish without challenge. With a filter of false-discovery rate less than 0.05 and fold change greater than 2, a total of 167 functionally known unique transcripts were found to be up-regulated, whereas 40 were down-regulated. The 167 up-regulated transcripts represent genes with putative functions in the following eight major categories: (1) immunity (30%); (2) metabolism and energy production (22%); (3) transcription or translation (12%); (4) protein degradation (11%); (5) signal transduction (6%); (6) traffic and transport (6%); (7) cell structure or cell cycle (8%); and (8) others (5%). The 40 down-regulated transcripts represent genes with putative functions in the following six major categories: (1) metabolism (27.5%); (2) immunity (17.5%); (3) cell structure (17.5%); (4) cell motility (10%); (5) signal transduction (15%); and (6) others (12.5%). Microarray analysis revealed that lysozyme c was up-regulated the most (70-fold) in vaccinated fish at 48 h post challenge of virulent E. ictaluri whereas myotubularin related protein 1a and cytochrome P450 2J27 were down-regulated the most (8.1 fold). Differential regulation of eight randomly selected transcripts in vaccinated fish after challenge with virulent E. ictaluri was also validated by quantitative PCR. Our results suggest that these differentially regulated genes might play important roles in channel catfish immunity against E. ictaluri.

  11. 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.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  17. Development of a novobiocin-resistant Edwardsiella ictaluri as a novel vaccine in channel catfish (Ictalurus punctatus).

    PubMed

    Pridgeon, Julia W; Klesius, Phillip H

    2011-08-01

    The efficacy of a novel attenuated Edwardsiella ictaluri vaccine (B-50348) was determined in channel catfish (Ictalurus punctatus) by bath immersion and intraperitoneal (IP) injection. The vaccine was developed from a virulent strain of E. ictaluri (AL93-58) through selection for novobiocin resistance. When channel catfish (average weight 10 g) were IP injected with 4.2 × 10⁶ colony-forming units (CFU) of the attenuated vaccine B-50348, no fish died. However, when the same age and size matched group of the catfish were IP injected with a lesser amount (2.4 × 10⁶ CFU/fish) of modified live RE-33 vaccine or the AL93-58 virulent strain (2.5 × 10⁶ CFU/fish) of E. ictaluri, 65% and 95% fish died, respectively. When channel catfish were challenged with AL93-58, relative percent survival values of vaccinated fish were all greater than 90% at 22, 32, and 63 days post B-50348 vaccination through intraperitoneal injection. By bath immersion, at 37 and 57 days post vaccination of B-50348, relative percent survival values were both 100% when fish were challenged by virulent E. ictaluri AL93-58. Our results suggest that B-50348 could be used as a novel safe and efficacious vaccine against ESC in channel catfish.

  18. 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

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

    PubMed

    Pridgeon, Julia W; Yeh, Hung-Yueh; Shoemaker, Craig A; Mu, Xingjiang; Klesius, Phillip H

    2012-04-01

    To understand the global gene expression in channel catfish after immersion vaccination with an attenuated Edwardsiella ictaluri (AquaVac-ESC™), microarray analysis of 65,182 UniGene transcripts was performed. With a filter of false-discovery rate less than 0.05 and fold change greater than 2, a total of 52 unique transcripts were found to be upregulated in vaccinated fish at 48 h post vaccination, whereas a total of 129 were downregulated. The 52 upregulated transcripts represent genes with putative functions in the following seven major categories: (1) hypothetical (25%); (2) novel (23%); (3) immune response (17%); (4) signal transduction (15%); (5) cell structure (8%); (6) metabolism (4%); and (7) others (8%). The 129 downregulated transcripts represent genes with putative functions in the following ten major categories: (1) novel (25%); (2) immune response (23%); (3) hypothetical (12%); (4) metabolism (10%); (5) signal transduction (7%); (6) protein synthesis (6.2%); (7) cell structure (5%); (8) apoptosis (3%); (9) transcription/translation (2%); and (10) others (6%). Microarray analysis revealed that apolipoprotein A-I was upregulated the most (8.5 fold, P = 0.011) at 48 h post vaccination whereas a novel protein (accession no. CV995854) was downregulated the most (342 fold, P = 0.001). Differential regulation of several randomly selected transcripts in vaccinated fish was also validated by quantitative PCR. Our results suggest that these differentially regulated genes elicited by the vaccination might play important roles in the protection of channel catfish against E. ictaluri.

  20. Pleiotropic effects of acyltransferases on various virulence-related phenotypes of Pseudomonas aeruginosa.

    PubMed

    Yeom, Doo Hwan; Kim, Soo-Kyoung; Lee, Mi-Nan; Lee, Joon-Hee

    2013-08-01

    Pseudomonas aeruginosa, an opportunistic pathogen causing various infections, expresses various virulence factors under the control of quorum sensing (QS), a cell density-sensing mechanism. Because the major signal molecules of QS are acyl homoserine lactones (acyl-HSLs), acyltransferases, the enzymes that act upon acyl group transfer could affect the QS signaling and QS-related virulence phenotypes. In this study, we overexpressed acyltransferases of P. aeruginosa and screened them for the activity influencing the QS and QS-related virulence phenotypes. Among seven acyltransferases tested in this study, two acyltransferases, PA3984 (apolipoprotein N-acyltransferase) and PA2537 (putative acyltransferase), significantly affected both growth of P. aeruginosa and the activity of LasR, a major QS regulator, when overexpressed. These acyltransferases also reduced virulence and swarming motility of P. aeruginosa. The other acyltransferase, PA3646 (UDP-3-O-[3-hydroxylauroyl] glucosamine N-acyltransferase), reduced the LasR activity, swarming motility, protease production and virulence without any influence on growth. These effects by PA3646 over-expression were caused by less production of QS signal. PA3644 (UDP-N-acetylglucosamine acyltransferase) enhanced biofilm formation and swarming motility with no effect on the growth and QS activity. These results suggest that acyltransferases may be an important factor regulating the cellular activity about virulence-related phenotypes. PMID:23848169

  1. Synergies between vaccination and dietary arginine and glutamine supplementation improve the immune response of channel catfish against Edwardsiella ictaluri.

    PubMed

    Pohlenz, Camilo; Buentello, Alejandro; Criscitiello, Michael F; Mwangi, Waithaka; Smith, Roger; Gatlin, Delbert M

    2012-09-01

    Channel catfish was used to investigate the enhancement of vaccine efficacy following dietary supplementation with arginine (ARG, 4% of diet), glutamine (GLN, 2% of diet), or a combination of both. After vaccination against Edwardsiella ictaluri, humoral and cellular immune responses, along with lymphoid organ responses were evaluated. E. ictaluri-specific antibody titers in plasma were higher (P < 0.05) in fish fed the supplemented diets compared to those fed the basal diet as early as 7 d post-vaccination (dpv). B-cell proportion in head-kidney was higher (P < 0.05) at 14 dpv in vaccinated fish fed the GLN diet. The responsiveness of spleen and head-kidney lymphocytes against E. ictaluri was enhanced (P < 0.05) by dietary supplementation of ARG or GLN at 14 dpv. Additionally, at 7 dpv, vaccinated fish fed the GLN diet had higher (P < 0.05) head kidney weights relative to the other dietary treatments, and vaccinated fish fed ARG-supplemented diets had higher (P < 0.05) protein content in this tissue. Results from this study suggest that dietary supplementation of ARG and GLN may improve specific cellular and humoral mechanisms, enhancing the acquired immunity in vaccinated channel catfish.

  2. 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. PMID:26439415

  3. 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.

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

    PubMed Central

    Sakai, Fuminori; Talekar, Sharmila J.; 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 ≥104 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. PMID:23825636

  5. 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). PMID:26306332

  6. Mutation of a novel virulence-related gene mltD in Vibrio anguillarum enhances lethality in zebra fish.

    PubMed

    Xu, Zinan; Wang, Ying; Han, Yin; Chen, Jixiang; Zhang, Xiao-Hua

    2011-01-01

    Vibrio anguillarum, a halophilic Gram-negative bacterium, is the causative agent of vibriosis, which is a major problem for the aquaculture industry worldwide. Previously, a virulence-related gene fragment of V. anguillarum was obtained from a suppression subtractive hybridization (SSH) library. In this study, the complete gene sequence was obtained by long and accurate PCR (LA-PCR). After sequence analysis and homologous comparison, this new virulence-related gene was revealed to encode a putative membrane-bound lytic murein transglycosylase D (MltD), which consisted of 547 amino acids, and showed 34% identity to the MltD in Escherichia coli. An mltD mutant of pathogenic V. anguillarum CW-1 was constructed by homologous recombination. Production of extracellular gelatinase and protease of the mltD mutant decreased markedly compared with those of the wild-type strain, and the hemolytic activity was totally lost. Sodium chloride challenge and antibiotic sensitivity assay showed that the resistance of the mltD mutant to high concentrations of sodium chloride, and rocephin, fortun, cefobid, gentamicin, kanamycin and carbenicillin was enhanced. Most importantly, virulence of the mltD mutant was enhanced compared with that of the wild type when it was inoculated intraperitoneally into zebra fish; the LD₅₀ of the wild type and the mutant was 3.92 × 10³ CFU and 1.01 × 10² CFU fish⁻¹, respectively. The mltD was cloned and overexpressed in E. coli, and the recombinant MltD protein showed hemolytic, phospholipase, gelatinase and diastase activities. This is the first report that MltD possibly has a virulence-related function. PMID:21070855

  7. Population structure and distribution of virulence-related genes of Bacteroides fragilis isolates from Korea and Japan.

    PubMed

    Ko, Kwan Soo; Kuwahara, Tomomi; Lee, Kyungwon; Kook, Yoon-Hoh

    2009-07-01

    Sequences for rpoB, gyrB, pdiA, and ompA were determined from 63 Bacteroides fragilis isolates, which were from Korea and Japan and include 4 reference strains. All 4 gene sequences supported clear separation of the cfi(+) group from the cfi(-) group. Combined sequences of the 60 division I isolates (cfi(-)) produced 45 different clones. Apparent discordance of gene trees, index of association, maximum likelihood test, and homoplasy ratio all supported a high frequency of recombination. There was no association between the presence of virulence-related genes and phylogenetic clustering in any gene tree.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 ...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  10. 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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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. 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.

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

    PubMed

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

    2016-01-01

    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

  14. 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

  15. Expression profiles of toll-like receptors in anterior kidney of channel catfish, Ictalurus punctatus (Rafinesque), acutely infected by Edwardsiella ictaluri.

    PubMed

    Pridgeon, J W; Russo, R; Shoemaker, C A; Klesius, P H

    2010-06-01

    Using quantitative PCR (QPCR), the relative transcriptional levels of five toll-like receptors (TLR2, TLR3, TLR5, TLR20a and TLR21) were studied in the channel catfish, Ictalurus punctatus (Rafinesque), under uninfected and acutely infected conditions [1-, 2-, 4-, 6-, 12-, 24-, 36- and 48-h post-injection (hpi)]. Under uninfected conditions, the transcriptional levels of the five TLRs were significantly lower than that of 18S rRNA (P < 0.001). QPCR results also revealed that the transcriptional levels of TLR20a and TLR5 were higher than those of TLR2, TLR3 or TLR21. The transcriptional level of TLR3 was significantly lower than that of the other four TLRs (P < 0.001). However, when channel catfish were acutely infected by Edwardsiella ictaluri through intraperitoneal injection, the transcriptional levels of TLRs increased significantly (P < 0.005) at 6 hpi. Among the five TLRs studied, the transcriptional levels of TLR3, TLR5 and TLR21 were never significantly lower than under uninfected conditions (P = 0.16, 0.27 and 0.19, respectively), suggesting these three TLRs might play important roles in host defence against infection by E. ictaluri. The amount of E. ictaluri in the anterior kidney increased at 12 and 24 hpi but decreased at 36 and 48 hpi. Our results suggest that TLRs are important components in the immune system in the channel catfish, and their rapid transcriptional upregulation (within 6 hpi) in response to acute E. ictaluri infection might be important for survival from enteric septicaemia of catfish.

  16. 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

  17. 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

  18. 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

  19. 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

  20. Expression of Virulence-Related Genes in Listeria monocytogenes Grown on Danish Hard Cheese as Affected by NaCl Content.

    PubMed

    Larsen, Nadja; Jespersen, Lene

    2015-06-01

    Expression of virulence-related genes in Listeria monocytogenes incubated on cheese was assessed by real-time quantitative polymerase chain reaction. The objective of the study was to investigate the impact of sodium chloride concentration in cheese on transcription of virulence genes and, thereby, virulence potential of L. monocytogenes. The expression studies were performed with L. monocytogenes strains characterized by different tolerance to salt stress. Strains ATCC(®) 51779 and DSMZ 15675 were incubated on the Danish hard-cheese type Samsoe, with low (<0.15% [wt/wt]) and high (3.6% [wt/wt]) content of NaCl. Genes differentially expressed (p<0.05) through the 48-h incubation were transcriptional regulators prfA and agrA, genes of the main virulence cluster inlA, hly, actA, involved in invasion of the epithelial cells, and genes bsh, opuC, gadC, clpP, and ami, associated with osmotic stress responses in L. monocytogenes. The more sensitive strain ATCC(®) 51779 was most responsive, showing significant upregulation of prfA, actA, hly, and bsh both at low and high NaCl. Strain DSMZ 15675 was less responsive to NaCl stress, showing reduced or consistent gene transcription at all conditions. Decreased transcription of agrA, ami, gadC, and opuC in both strains was promoted by low NaCl content. The study indicated that virulence gene expression of L. monocytogenes grown in cheese was affected by NaCl content and that effect was more significant in strains sensitive to both hypo- and hyperosmotic stresses.

  1. Expression of Virulence-Related Genes in Listeria monocytogenes Grown on Danish Hard Cheese as Affected by NaCl Content.

    PubMed

    Larsen, Nadja; Jespersen, Lene

    2015-06-01

    Expression of virulence-related genes in Listeria monocytogenes incubated on cheese was assessed by real-time quantitative polymerase chain reaction. The objective of the study was to investigate the impact of sodium chloride concentration in cheese on transcription of virulence genes and, thereby, virulence potential of L. monocytogenes. The expression studies were performed with L. monocytogenes strains characterized by different tolerance to salt stress. Strains ATCC(®) 51779 and DSMZ 15675 were incubated on the Danish hard-cheese type Samsoe, with low (<0.15% [wt/wt]) and high (3.6% [wt/wt]) content of NaCl. Genes differentially expressed (p<0.05) through the 48-h incubation were transcriptional regulators prfA and agrA, genes of the main virulence cluster inlA, hly, actA, involved in invasion of the epithelial cells, and genes bsh, opuC, gadC, clpP, and ami, associated with osmotic stress responses in L. monocytogenes. The more sensitive strain ATCC(®) 51779 was most responsive, showing significant upregulation of prfA, actA, hly, and bsh both at low and high NaCl. Strain DSMZ 15675 was less responsive to NaCl stress, showing reduced or consistent gene transcription at all conditions. Decreased transcription of agrA, ami, gadC, and opuC in both strains was promoted by low NaCl content. The study indicated that virulence gene expression of L. monocytogenes grown in cheese was affected by NaCl content and that effect was more significant in strains sensitive to both hypo- and hyperosmotic stresses. PMID:26067229

  2. The Pathogen of the Great Barrier Reef Sponge Rhopaloeides odorabile Is a New Strain of Pseudoalteromonas agarivorans Containing Abundant and Diverse Virulence-Related Genes.

    PubMed

    Choudhury, Jayanta D; Pramanik, Arnab; Webster, Nicole S; Llewellyn, Lyndon E; Gachhui, Ratan; Mukherjee, Joydeep

    2015-08-01

    Sponge diseases have increased dramatically, yet the causative agents of disease outbreaks have eluded identification. We undertook a polyphasic taxonomic analysis of the only confirmed sponge pathogen and identified it as a novel strain of Pseudoalteromonas agarivorans. 16S ribosomal RNA (rRNA) and gyraseB (gyrB) gene sequences along with phenotypic characteristics demonstrated that strain NW4327 was most closely related to P. agarivorans. DNA-DNA hybridization and in silico genome comparisons established NW4327 as a novel strain of P. agarivorans. Genes associated with type IV pili, mannose-sensitive hemagglutinin pili, and curli formation were identified in NW4327. One gene cluster encoding ATP-binding cassette (ABC) transporter, HlyD and TolC, and two clusters related to the general secretion pathway indicated the presence of type I secretion system (T1SS) and type II secretion system (T2SS), respectively. A contiguous gene cluster of at least 19 genes related to type VI secretion system (T6SS) which included all 13 core genes was found. The absence of T1SS and T6SS in nonpathogenic P. agarivorans S816 established NW4327 as the virulent strain. Serine proteases and metalloproteases of the classes S8, S9, M4, M6, M48, and U32 were identified in NW4327, many of which can degrade collagen. Collagenase activity in NW4327 and its absence in the nonpathogenic P. agarivorans KMM 255(T) reinforced the invasiveness of NW4327. This is the first report unambiguously identifying a sponge pathogen and providing the first insights into the virulence genes present in any pathogenic Pseudoalteromonas genome. The investigation supports a theoretical study predicting high abundance of terrestrial virulence gene homologues in marine bacteria.

  3. 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

  4. 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.

  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. Detection of Edwardsiella ictaluri in frozen catfish: Epidemiological application

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  7. 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.

  8. Caenorhabditis elegans-based screen identifies Salmonella virulence factors required for conserved host-pathogen interactions.

    PubMed

    Tenor, Jennifer L; McCormick, Beth A; Ausubel, Frederick M; Aballay, Alejandro

    2004-06-01

    A Caenorhabditis elegans-Salmonella enterica host-pathogen model was used to identify both novel and previously known S. enterica virulence factors (HilA, HilD, InvH, SptP, RhuM, Spi4-F, PipA, VsdA, RepC, Sb25, RfaL, GmhA, LeuO, CstA, and RecC), including several related to the type III secretion system (TTSS) encoded in Salmonella pathogenicity island 1 (SPI-1). Mutants corresponding to presumptive novel virulence-related genes exhibited diminished ability to invade epithelial cells and/or to induce polymorphonuclear leukocyte migration in a tissue culture model of mammalian enteropathogenesis. When expressed in C. elegans intestinal cells, the S. enterica TTSS-exported effector protein SptP inhibited a conserved p38 MAPK signaling pathway and suppressed the diminished pathogenicity phenotype of an S. enterica sptP mutant. These results show that C. elegans is an attractive model to study the interaction between Salmonella effector proteins and components of the innate immune response, in part because there is a remarkable overlap between Salmonella virulence factors required for human and nematode pathogenesis.

  9. Identifying and Managing Risk.

    ERIC Educational Resources Information Center

    Abraham, Janice M.

    1999-01-01

    The role of the college or university chief financial officer in institutional risk management is (1) to identify risk (physical, casualty, fiscal, business, reputational, workplace safety, legal liability, employment practices, general liability), (2) to develop a campus plan to reduce and control risk, (3) to transfer risk, and (4) to track and…

  10. 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).

  11. 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.

  12. Identifying conical singularities

    SciTech Connect

    Oliveira-Neto, G. |

    1996-09-01

    A method based upon the concept of holonomy of a metric space{endash}time ({ital M},{ital g}), in order to identify the presence of conical singularities in {ital M} is proposed. The validity and usefulness of this so-called holonomy method is proven by applying it to a set of four-dimensional space{endash}times and one three-dimensional space{endash}time. The holonomy method predictions are confirmed by the comparison with the predictions obtained after coordinate transformations which take the metrics {ital g}, to a new basis where the global properties of conical singularities are explicitly seen. {copyright} {ital 1996 American Institute of Physics.}

  13. 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.”

  14. 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

  15. 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

  16. 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.

  17. Near Identifiability of Dynamical Systems

    NASA Technical Reports Server (NTRS)

    Hadaegh, F. Y.; Bekey, G. A.

    1987-01-01

    Concepts regarding approximate mathematical models treated rigorously. Paper presents new results in analysis of structural identifiability, equivalence, and near equivalence between mathematical models and physical processes they represent. Helps establish rigorous mathematical basis for concepts related to structural identifiability and equivalence revealing fundamental requirements, tacit assumptions, and sources of error. "Structural identifiability," as used by workers in this field, loosely translates as meaning ability to specify unique mathematical model and set of model parameters that accurately predict behavior of corresponding physical system.

  18. Diverse protist grazers select for virulence-related traits in Legionella.

    PubMed

    Amaro, Francisco; Wang, Wen; Gilbert, Jack A; Anderson, O Roger; Shuman, Howard A

    2015-07-01

    It is generally accepted that selection for resistance to grazing by protists has contributed to the evolution of Legionella pneumophila as a pathogen. Grazing resistance is becoming more generally recognized as having an important role in the ecology and evolution of bacterial pathogenesis. However, selection for grazing resistance presupposes the existence of protist grazers that provide the selective pressure. To determine whether there are protists that graze on pathogenic Legionella species, we investigated the existence of such organisms in a variety of environmental samples. We isolated and characterized diverse protists that graze on L. pneumophila and determined the effects of adding L. pneumophila on the protist community structures in microcosms made from these environmental samples. Several unrelated organisms were able to graze efficiently on L. pneumophila. The community structures of all samples were markedly altered by the addition of L. pneumophila. Surprisingly, some of the Legionella grazers were closely related to species that are known hosts for L. pneumophila, indicating the presence of unknown specificity determinants for this interaction. These results provide the first direct support for the hypothesis that protist grazers exert selective pressure on Legionella to acquire and retain adaptations that contribute to survival, and that these properties are relevant to the ability of the bacteria to cause disease in people. We also report a novel mechanism of killing of amoebae by one Legionella species that requires an intact Type IV secretion system but does not involve intracellular replication. We refer to this phenomenon as 'food poisoning'.

  19. Diverse protist grazers select for virulence-related traits in Legionella.

    PubMed

    Amaro, Francisco; Wang, Wen; Gilbert, Jack A; Anderson, O Roger; Shuman, Howard A

    2015-07-01

    It is generally accepted that selection for resistance to grazing by protists has contributed to the evolution of Legionella pneumophila as a pathogen. Grazing resistance is becoming more generally recognized as having an important role in the ecology and evolution of bacterial pathogenesis. However, selection for grazing resistance presupposes the existence of protist grazers that provide the selective pressure. To determine whether there are protists that graze on pathogenic Legionella species, we investigated the existence of such organisms in a variety of environmental samples. We isolated and characterized diverse protists that graze on L. pneumophila and determined the effects of adding L. pneumophila on the protist community structures in microcosms made from these environmental samples. Several unrelated organisms were able to graze efficiently on L. pneumophila. The community structures of all samples were markedly altered by the addition of L. pneumophila. Surprisingly, some of the Legionella grazers were closely related to species that are known hosts for L. pneumophila, indicating the presence of unknown specificity determinants for this interaction. These results provide the first direct support for the hypothesis that protist grazers exert selective pressure on Legionella to acquire and retain adaptations that contribute to survival, and that these properties are relevant to the ability of the bacteria to cause disease in people. We also report a novel mechanism of killing of amoebae by one Legionella species that requires an intact Type IV secretion system but does not involve intracellular replication. We refer to this phenomenon as 'food poisoning'. PMID:25575308

  20. Diverse protist grazers select for virulence-related traits in Legionella

    PubMed Central

    Amaro, Francisco; Wang, Wen; Gilbert, Jack A; Roger Anderson, O; Shuman, Howard A

    2015-01-01

    It is generally accepted that selection for resistance to grazing by protists has contributed to the evolution of Legionella pneumophila as a pathogen. Grazing resistance is becoming more generally recognized as having an important role in the ecology and evolution of bacterial pathogenesis. However, selection for grazing resistance presupposes the existence of protist grazers that provide the selective pressure. To determine whether there are protists that graze on pathogenic Legionella species, we investigated the existence of such organisms in a variety of environmental samples. We isolated and characterized diverse protists that graze on L. pneumophila and determined the effects of adding L. pneumophila on the protist community structures in microcosms made from these environmental samples. Several unrelated organisms were able to graze efficiently on L. pneumophila. The community structures of all samples were markedly altered by the addition of L. pneumophila. Surprisingly, some of the Legionella grazers were closely related to species that are known hosts for L. pneumophila, indicating the presence of unknown specificity determinants for this interaction. These results provide the first direct support for the hypothesis that protist grazers exert selective pressure on Legionella to acquire and retain adaptations that contribute to survival, and that these properties are relevant to the ability of the bacteria to cause disease in people. We also report a novel mechanism of killing of amoebae by one Legionella species that requires an intact Type IV secretion system but does not involve intracellular replication. We refer to this phenomenon as ‘food poisoning'. PMID:25575308

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

    PubMed

    Priest, Shelby J; Lorenz, Michael C

    2015-09-01

    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

  2. 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.

  3. 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)

  4. 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)

  5. 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

    2016-04-01

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

  6. 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. PMID:23615061

  7. 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.

  8. 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

  9. "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…

  10. 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

  11. Identifying Intellectually Superior Black Children.

    ERIC Educational Resources Information Center

    Ryan, Judith S.

    1983-01-01

    The effectiveness of several methods used to identify intellectually superior black children was evaluated. Findings suggest that less commonly used identification methods, such as parents' opinion and the Leiter International Performance Scale, may point out these children more accurately than do traditional measures. (Author/PP)

  12. 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…

  13. 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…

  14. [Identifying victims of a disaster].

    PubMed

    de Boer, Hans H; Kloosterman, Ate D; de Bruijn, Arie G; Maat, George J R

    2014-01-01

    Identifying the victims of a disaster is important for the next of kin, to issue a death certificate and, if necessary, for forensic investigations. In the Netherlands victims are identified by the Dutch disaster victim identification team, which is part of the national forensic investigation team ('Landelijk Team Forensische Opsporing'). Ante-mortem data are collected during the identification process; these include the victim's specific medical characteristics and the DNA profile of the victim and their family members. The victim's own doctor can play an important role in the ante-mortem investigation because of his or her knowledge of their personal medical details, and of the possible availability of samples for establishing a DNA profile. The ante-mortem data are then compared with post-mortem data. For a definitive identification at least 1 primary identification characteristic has to be established from the physical remains - dermatoglyphics, the DNA profile or the dental status.

  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 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

  17. 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.

  18. 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. PMID:20628167

  19. "Geriatricizing" hospitalists: identifying educational opportunities.

    PubMed

    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 caring for hospitalized older adults, targeting areas previously defined as central to taking care of older hospitalized patients. Overall, geriatricians had more confidence and more knowledge in caring for older hospitalized adults. The areas in which hospitalists expressed the least confidence were in caring for patients with dementia, self-care issues, and care planning. Geriatricians reported more routine medication reviews, functional and cognitive assessments, and fall evaluations. Geriatricians and hospitalists differ in their approach to older adults. Where these differences reflect lack of knowledge or experience, they set the stage for developing curricula to help narrow these gaps. PMID:23971409

  20. Important caves to be identified

    NASA Astrophysics Data System (ADS)

    Criteria to identify significant caves on federal land are being developed by the Interior Department's Bureau of Land Management and the Agriculture Department's Forest Service under requirements of the Federal Cave Resources Protection Act of 1988. The departments gave advance notice of proposed rulemaking March 3 and invited suggestions and comments from the public for 30 days.The law requires protection, to the extent practical, of significant caves on lands administered by the Secretaries of Agriculture and Interior and includes authority to issue and revoke permits for collection and removal of cave resources and special provisions for regulation of cave resources on Indian lands. Final regulations must be published by August 18, 1989.

  1. Identifying vulnerable surface water utilities

    SciTech Connect

    Clark, R.M.; Grayman, W.M.; Males, R.M.; Kilgore, R.

    1989-01-01

    Although industrial discharges from point sources are regulated by the Federal Water Pollution Control Acts, National Pollutant Discharge Elimination System (NPDES), some toxic pollutants continue to be discharged into surface waters. Frequently these same surface waters are major sources of drinking water. The Safe Drinking Water Act Amendments have specified a large number of new contaminant levels, (MCLs) at the microgram per liter level. It is possible that many water utilities finding that these new MCLs are violated will seek to identify upstream dischargers and request that regulatory agencies force them to install discharge controls rather than pay for expensive water treatment processes. The study reported in the paper documents the development of a data base management system and a water quality modeling approach that allows drinking water utilities to assess the impact of these upstream discharges on raw water quality. The report makes recommendations to USEPA for modifying its NPDES procedures.

  2. 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

  3. 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.

  4. 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.

  5. Identifying representative trees from ensembles.

    PubMed

    Banerjee, Mousumi; Ding, Ying; Noone, Anne-Michelle

    2012-07-10

    Tree-based methods have become popular for analyzing complex data structures where the primary goal is risk stratification of patients. Ensemble techniques improve the accuracy in prediction and address the instability in a single tree by growing an ensemble of trees and aggregating. However, in the process, individual trees get lost. In this paper, we propose a methodology for identifying the most representative trees in an ensemble on the basis of several tree distance metrics. Although our focus is on binary outcomes, the methods are applicable to censored data as well. For any two trees, the distance metrics are chosen to (1) measure similarity of the covariates used to split the trees; (2) reflect similar clustering of patients in the terminal nodes of the trees; and (3) measure similarity in predictions from the two trees. Whereas the latter focuses on prediction, the first two metrics focus on the architectural similarity between two trees. The most representative trees in the ensemble are chosen on the basis of the average distance between a tree and all other trees in the ensemble. Out-of-bag estimate of error rate is obtained using neighborhoods of representative trees. Simulations and data examples show gains in predictive accuracy when averaging over such neighborhoods. We illustrate our methods using a dataset of kidney cancer treatment receipt (binary outcome) and a second dataset of breast cancer survival (censored outcome).

  6. 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

  7. Can tests identify creative people?

    NASA Astrophysics Data System (ADS)

    Bell, Peter M.

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

  8. Identifying barriers to billing compliance.

    PubMed

    Lorence, Daniel P; Ibrahim, Ibrahim Awad

    2003-01-01

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

  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. DNA Microarrays for Identifying Fishes

    PubMed Central

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

    2008-01-01

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

  11. 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

    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. 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

  12. 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.

  13. NIH Researchers Identify OCD Risk Gene

    MedlinePlus

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

  14. 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...

  15. 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...

  16. 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.

  17. 47 CFR 2.926 - FCC identifier.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

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

  18. 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.

  19. 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…

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 ...

  1. Proteomic analysis of head kidney tissue from resistant and susceptible families following challenge with Edwarsiella ictaluri

    Technology Transfer Automated Retrieval System (TEKTRAN)

    One of the goals of the Catfish Genetics Research Unit is the identification of genetic markers for resistance to viral and bacterial diseases in channel catfish for use in selective breeding. A pilot study was performed to compare proteomic profiles of resistant and susceptible families of channel ...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  3. A Priori Identifiability Analysis of Cardiovascular Models

    PubMed Central

    Kirk, Jonathan A.; Saccomani, Maria P.; Shroff, Sanjeev G.

    2013-01-01

    Model parameters, estimated from experimentally measured data, can provide insight into biological processes that are not experimentally measurable. Whether this optimized parameter set is a physiologically relevant complement to the experimentally measured data, however, depends on the optimized parameter set being unique, a model property known as a priori global identifiability. However, a priori identifiability analysis is not common practice in the biological world, due to the lack of easy-to-use tools. Here we present a program, Differential Algebra for Identifiability of Systems (DAISY), that facilitates identifiability analysis. We applied DAISY to several cardiovascular models: systemic arterial circulation (Windkessel, T-Tube) and cardiac muscle contraction (complex stiffness, crossbridge cycling-based). All models were globally identifiable except the T-Tube model. In this instance, DAISY was able to provide insight into making the model identifiable. We applied numerical parameter optimization techniques to estimate unknown parameters in a model DAISY found globally identifiable. While all the parameters could be accurately estimated, a sensitivity analysis was first necessary to identify the required experimental data. Global identifiability is a prerequisite for numerical parameter optimization, and in a variety of cardiovascular models, DAISY provided a reliable, fast, and simple platform to provide this identifiability analysis. PMID:26726299

  4. 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 ...

  5. 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.

  6. 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

  7. 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.

  8. 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…

  9. 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…

  10. 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.

  11. 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. PMID:20552931

  12. 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…

  13. 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.

  14. 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

  15. 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

  16. Discrimination of SM-identified individuals.

    PubMed

    Wright, Susan

    2006-01-01

    The belief that sadomasochism (SM) is violence or abusive behavior has resulted in harassment, physical attacks, and discrimination against SM-identified individuals. Historically, they were often opposed by self-identified feminists. One reason the women who practiced SM were targeted was the official opposition to sadomasochistic practices promulgated by the National Organization for Women (NOW). Current statistics of incidents of discrimination, harassment and physical attacks against SM-identified individuals and SM groups are compiled by the National Coalition for Sexual Freedom (NCSF). PMID:16803765

  17. Researchers Identify Genes Linked to Hot Flashes

    MedlinePlus

    ... fullstory_161579.html Researchers Identify Genes Linked to Hot Flashes Mutations found in women of all races, ... Some women may be genetically predisposed to suffer hot flashes before or during menopause, a new study ...

  18. Identifying Pornographic Materials with Judgment Analysis

    ERIC Educational Resources Information Center

    Houston, Judith A.; Houston, Samuel R.

    1974-01-01

    The primary purpose of this study was to determine if a policy-capturing methodology (JAN) which has been successfully utilized in military and educational research could be adapted for use as a procedure in identifying pornographic material. (Author)

  19. Study Identifies Genetic Subtypes of Crohn's Disease

    MedlinePlus

    ... medlineplus.gov/news/fullstory_161499.html Study Identifies Genetic Subtypes of Crohn's Disease Findings may help explain ... disease appears to have at least two distinct genetic subtypes, which could explain why the condition is ...

  20. 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.

  1. 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. PMID:26853673

  2. Asteroid Redirect Mission: Identify, Redirect, Explore

    NASA Video Gallery

    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...

  3. 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.

  4. 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.

  5. 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. PMID:27054531

  6. Connecting Research and Researchers: ORCID Identifiers (Invited)

    NASA Astrophysics Data System (ADS)

    Haak, L.; Bryant, R.

    2013-12-01

    Lack of standards for identification of researchers is a major challenge for the research community. It is difficult not only to unambiguously associate researchers with their own work, but also to track use and re-use of those works. The goal of ORCID (orcid.org) is to connect research with researchers, ultimately saving researchers time in entering data, improving discoverability, and facilitating the flow of research information and data re-use. ORCID is a community-driven non-profit organization that provides an open registry of unique persistent identifiers for researchers. We work collaboratively with the research community to embed these identifiers in research workflows, including manuscript submission, grant application, and data set deposit. In this presentation, we will provide an overview of ORCID, an in particular how it is being used as a switchboard to connect existing but fragmented researcher identifiers. ORCID also provides researchers search and link tools to link their ORCID identifier to their existing datasets, grants, other research works, and an automated method to link new works to their identifier. ORCID is fundamental to solving the name ambiguity problem for researchers and scholars. Together with unique and persistent identifiers for publications, data sets, and research samples, ORCID is an essential underpinning needed to support interoperability between research systems.

  7. 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.

  8. Identifying glass compositions in fly ash

    NASA Astrophysics Data System (ADS)

    Aughenbaugh, Katherine; Stutzman, Paul; Juenger, Maria

    2016-01-01

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

  9. 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.

  10. Identifying Adverse Drug Events by Relational Learning.

    PubMed

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

    2012-07-01

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

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. Identifying, analysing and solving problems in practice.

    PubMed

    Hewitt-Taylor, Jaqui

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

  17. Inverted File Compression through Document Identifier Reassignment.

    ERIC Educational Resources Information Center

    Shieh, Wann-Yun; Chen, Tien-Fu; Shann, Jean Jyh-Jiun; Chung, Chung-Ping

    2003-01-01

    Discusses the use of inverted files in information retrieval systems and proposes a document identifier reassignment method to reduce the average gap values in an inverted file. Highlights include the d-gap technique; document similarity; heuristic algorithms; file compression; and performance evaluation from a simulation environment. (LRW)

  18. 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...

  19. 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…

  20. 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…

  1. 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

  2. Identifying the Culturally Different Gifted Student.

    ERIC Educational Resources Information Center

    Chambers, Jack A.; Barron, Frank

    The study was designed to provide a relatively simple method of identifying gifted Mexican-American elementary school children, using as Ss approximately 298 Mexican-Americans (in grades 3-6) from both urban and rural schools. Ss were rated by present and former teachers on traits found to be characteristic of highly creative and talented…

  3. 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…

  4. 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…

  5. 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.

  6. 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…

  7. 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…

  8. 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…

  9. DOI: A New Identifier for Digital Content.

    ERIC Educational Resources Information Center

    Berinstein, Paula

    1998-01-01

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

  10. The SAT Gender Gap: Identifying the Causes.

    ERIC Educational Resources Information Center

    Rosser, Phyllis

    Questions on the Scholastic Aptitude Test (SAT) with the largest score differences between women and men of all racial and ethnic groups were identified. Patterns of difficulty that would explain the SAT's continuing underprediction of female first-year college performance were studied. An item analysis of one form of the June 1986 SAT for 1,112…

  11. 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…

  12. Can Effective Teacher Behavior Be Identified?

    ERIC Educational Resources Information Center

    Bonesronning, Hans

    2004-01-01

    The present paper departs from the hypothesis that successful teachers are characterized by being able to manipulate student effort. Grading is identified as a potential teachers' tool, and its quantitative importance is investigated by estimation of an education production function. The main econometric problems are omitted variables biases due…

  13. 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)

  14. 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.

  15. 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…

  16. Identifying Determinants of Commitment and Turnover Behavior.

    ERIC Educational Resources Information Center

    Grady, Thomas L.

    A study tested the precursors to vocational teachers' commitment to teaching as suggested by the commitment model proposed by Pierce and Dunham. Important consequences of commitment were examined by identifying relationships between commitment, behavioral intentions, and resulting turnover. The study examined the entire population of teachers…

  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 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…

  19. 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.…

  20. 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.

  1. 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…

  2. 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…

  3. 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.

  4. 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…

  5. Techniques for identifying predators of goose nests

    USGS Publications Warehouse

    Anthony, R.M.; 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).

  6. Odor recognition: familiarity, identifiability, and encoding consistency.

    PubMed

    Rabin, M D; Cain, W S

    1984-04-01

    The investigation examined the association between the perceived identity of odorous stimuli and the ability to recognize the previous occurrence of them. The stimuli comprised 20 relatively familiar odorous objects such as chocolate, leather, popcorn, and soy sauce. Participants rated the familiarity of the odors and sought to identify them. At various intervals up to 7 days after initial inspection, the participants sought to recognize the odors among sets of distractor odors that included such items as soap, cloves, pipe tobacco, and so on. The recognition response entailed a confidence rating as to whether or not an item had appeared in the original set. At the time of testing, the participants also sought to identify the stimuli again. The results upheld previous findings of excellent initial recognition memory for environmentally relevant odors and slow forgetting. The results also uncovered, for the first time, a strong association between recognition memory and identifiability, rated familiarity, and the ability to use an odor label consistently at inspection and subsequent testing. Encodability seems to enhance rather than to permit recognizability. Even items identified incorrectly or inconsistently were recognized at levels above chance.

  7. 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…

  8. 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.

  9. Automated igneous rock identifiers for Mars Exploration

    NASA Astrophysics Data System (ADS)

    Gulick, V. C.; Morris, R. L.; Gazis, P.; Bishop, J. L.; Alena, R.; Hart, S. D.; Horton, A.

    2003-04-01

    A key task for human or robotic explorers on the surface of Mars is choosing which particular rock or mineral samples should be selected for more intensive study. The usual challenges of such a task are compounded by the lack of sensory input available to a suited astronaut or the limited downlink bandwidth available to a rover. Additional challenges facing a human mission include limited surface time and the similarities in appearance of important minerals (e.g. carbonates, silicates, salts). Yet the choice of which sample to collect is critical. To address this challenge we are developing science analysis algorithms to interface with a Geologist's Field Assistant (GFA) device that will allow robotic or human remote explorers to better sense and explore their surroundings during limited surface excursions [1]. We aim for our algorithms to interpret spectral and imaging data obtained by various sensors. Our algorithms, for example, will identify key minerals, rocks, and sediments from mid-IR, Raman, and visible/near-IR spectra as well as from high-resolution and microscopic images to help interpret data and to provide high-level advice to the remote explorer. A top-level system will consider multiple inputs from raw sensor data output by imagers and spectrometers (visible/near-IR, mid-IR, and Raman) as well as human opinion to identify rock and mineral samples. Our prototype image analysis system identifies some igneous rocks from texture and color information. Spectral analysis algorithms have also been developed that successfully identify quartz, silica polymorphs, calcite, pyroxene, and jarosite from both visible/near-IR and mid-IR spectra. We have also developed spectral recognizers that identify high-iron pyroxenes and iron-bearing minerals using visible/near-IR spectra only. We are building a combined image and spectral database of rocks and minerals with which to continue development of our algorithms. Future plans include developing algorithms to identify

  10. 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.

  11. 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

  12. 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/.

  13. 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.

  14. 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.

  15. Identifying, analysing and solving problems in practice.

    PubMed

    Hewitt-Taylor, Jaqui

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

  16. 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

  17. 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

  18. 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

  19. Using filtering effects to identify objects.

    PubMed

    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.

  20. Identifying bilingual semantic neural representations across languages.

    PubMed

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

    2012-03-01

    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.

  1. 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.

  2. 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

  3. 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

  4. Identifying the learning needs of senior nurses.

    PubMed

    Cerinus, Marie

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

  5. 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. PMID:26991442

  6. 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.

  7. 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

  8. 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.

  9. Identifying the Universal Part of TMDs

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

  10. Identifying spatial priorities for protecting ecosystem services.

    PubMed

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

    2012-01-01

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

  11. 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.

  12. 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

  13. 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

  14. Identifying personal microbiomes using metagenomic codes

    PubMed Central

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

    2015-01-01

    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. PMID:25964341

  15. 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.

  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. 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.

  19. Identifiability of large phylogenetic mixture models.

    PubMed

    Rhodes, John A; Sullivant, Seth

    2012-01-01

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

  20. 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

    2014-10-01

    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.

  1. 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

  2. Identifying predictive factors in melanoma progression.

    PubMed

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

    1998-01-01

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

  3. 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.

  4. 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''.

  5. Identifying Data in the Earth Sciences (Invited)

    NASA Astrophysics Data System (ADS)

    Duerr, R. E.

    2010-12-01

    The problem of identity has vexed humanity throughout all of recorded history. A wide variety of methods; from assigned identifiers to taxonomic techniques and beyond; have historically been used to resolve the issue of whether this thing, whatever or whomever it may be, is what it purports to be. Yet none have ultimately proved to be flawless. Not surprisingly then, the issue of identity is just as much an issue in this digital era as it has ever been. Given the mutability of digital objects it would be surprising indeed if it were not more of an issue. This presents a quandary for science given its foundations in the concept of repeatability. How can one repeat what cannot be identified? In the Earth sciences the problem is even more acute. Unlike other fields of research, the majority of observations in the Earth sciences are not repeatable, they occur at a distinct place and time and are therefore unique and irreplaceable. One would think that this uniqueness would make identification easier; yet the realities of current scientific practice and technology means that it just isn't so. Not surprisingly then, a number of identification schemes have been implemented by various communities - academic, commercial, and non-profit. Many of these schemes purport to be the answer to the question of identification, at least for that community. But is this so for the Earth Sciences? That is the question that was posed to the data lifecycle focus group of the Earth Science Data Systems Technology Infusion Working Group (ESDSWG TIWG) and the Preservation Cluster of the Federation of Earth Science Information Partners (ESIP). In this talk, an assessment of the applicability of these technologies and identification schemes to the Earth Sciences is summarized, and ongoing identifier test-bed activities within the ESIP Federation are described.

  6. [MRSA clones identified in outpatient dermatology clinics].

    PubMed

    Hosoya, Shino; Ito, Teruyo; Misawa, Shigeki; Yoshiike, Takashi; Oguri, Toyoko; Hiramatsu, Keiichi

    2014-11-01

    To know the characteristics of methicillin-resistant Staphylococcus aureus (MRSA) strains disseminating through the Japanese community, we have determined types of Staphylococcal cassette chromosome mec (SCCmec) elements, Multi-Locus Sequence Typing (MLST), and carriages of four exotoxin genes (toxic-shock syndrome toxin, Panton-Valentine Leukocidine, and exfoliative toxins a and b) using 54 MRSA strains isolated from outpatients attending dermatology clinics at the four university hospitals of Juntendo University. Ten clonal complexes and 12 SCCmec types have been identified. As a result, more than 15 MRSA clones that were defined by the combination of genotype and SCCmec type, were identified. Among them, Clonal Complex (CC) 5-type IIa SCCmec strains were the most major (16 strains). In contrast to the fact that CC5- type IIa SCCmec strains known as a hospital-associated MRSA clone in Japan carried toxic-shock syndrome toxin gene (tst), only 2 of 16 strains have been shown to carry tst. Thirty-eight (70.4%) of isolates belonged to the clones distinct from the CC5-type IIa SCCmec strains. Among them, CC8 strains were major (12 strains), which contained 9 tst-positive CC8-type IVl SCCmec clones and a CC8-type IVa SCCmec strain carrying the Panton Valentine Leukocidin gene (lukS, F-PV). Clones related to impetigo were also identified: 7 exfoliative toxin b (etb) -positive clones, CC89-type IIa SCCmec and CC89-type V SCCmec strains; and 2 exfoliative toxin a (eta) -positive CC121-type V SCCmec strains. Other clones were as follows: CC1-type IVa SCCmec, CC8-type I SCCmec, CC81-type IVg SCCmec, CC97-type IVc SCCmec, CC91-type IVa SCCmec, CC59-type IVg SCCmec, CC45-type IIn SCCmec, CC89-SCCmec nontypeable, and CC8-type IVm, novel subtype of type IV SCCmec were identified in this study. Our data showed that many novel MRSA clones have emerged in the community. PMID:25764806

  7. Identifying and managing malnutrition in the community.

    PubMed

    McEvilly, Aimee

    2016-01-01

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

  8. 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

  9. Identifying PHM market and network opportunities.

    PubMed

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

    2015-11-01

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

  10. 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

  11. Identifying insanity acquittals: is it any easier?

    PubMed

    Cirincione, C; Jacobs, C

    1999-08-01

    Following the highly publicized insanity acquittal of John Hinckley in 1982, legislators throughout the country attempted to reform the insanity defense. At the time, policy makers had virtually no empirical evidence with which to guide their reforms. The focus of this research is to determine if more informed policy-making would be possible today? Results show that more states are able to identify cases involving an insanity acquittal than during the 1980's and provide annual data on the number of rate of insanity acquittals. The data collected by many of the states have significant limitation.

  12. Anti-Rga: identifying serologic characteristics.

    PubMed

    Strohm, P L; Molthan, L

    1982-12-01

    Anti-Rga is a rare alloantibody that is difficult to recognize and identify. Although posing no apparent transfusion risk itself, it can mask the presence of underlying alloantibodies which could be transfusion risks. The five patients reported here demonstrate the serologic findings characteristic of anti-Rga. Known Rg(a-) test cells and multiple "target cells" in neutralization studies are needed to demonstrate partial neutralization findings and to detect underlying alloantibody. Other observations were that clotted samples of red cells retained Rga reactivity for 49 days, whereas EDTA-anticoagulated red cell samples lost such reactivity after 13 days. Frozen red cells tested within hours of deglycerolization showed excellent Rga reactivity.

  13. Defining the criteria for identifying constitutional epimutations.

    PubMed

    Sloane, Mathew A; Ward, Robyn L; Hesson, Luke B

    2016-01-01

    In the January 2016 issue of Clinical Epigenetics, Quiñonez-Silva et al. (Clin Epigenetics 8:1, 2016) described a possible constitutional epimutation of the RB1 gene as a cause of hereditary predisposition to retinoblastoma. The term constitutional epimutation describes an epigenetic aberration in normal tissues that predisposes to disease. The data presented by Quiñonez-Silva et al. are interesting, but further analysis is required to demonstrate a constitutional epimutation in this family. Here, we define the criteria and describe the experimental approach necessary to identify an epigenetic aberration as a constitutional epimutation. PMID:27096027

  14. 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

  15. 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.

  16. 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.

  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 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. PMID:17292131

  19. 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.

  20. 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

  1. 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

  2. Identifying separate components of surround suppression.

    PubMed

    Schallmo, Michael-Paul; Murray, Scott O

    2016-01-01

    Surround suppression is a well-known phenomenon in which the response to a visual stimulus is diminished by the presence of neighboring stimuli. This effect is observed in neural responses in areas such as primary visual cortex, and also manifests in visual contrast perception. Studies in animal models have identified at least two separate mechanisms that may contribute to surround suppression: one that is monocular and resistant to contrast adaptation, and another that is binocular and strongly diminished by adaptation. The current study was designed to investigate whether these two mechanisms exist in humans and if they can be identified psychophysically using eye-of-origin and contrast adaptation manipulations. In addition, we examined the prediction that the monocular suppression component is broadly tuned for orientation, while suppression between eyes is narrowly tuned. Our results confirmed that when center and surrounding stimuli were presented dichoptically (in opposite eyes), suppression was orientation-tuned. Following adaptation in the surrounding region, no dichoptic suppression was observed, and monoptic suppression no longer showed orientation selectivity. These results are consistent with a model of surround suppression that depends on both low-level and higher level components. This work provides a method to assess the separate contributions of these components during spatial context processing in human vision.

  3. 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.

  4. 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.

  5. 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. PMID:26245790

  6. A novel method for identifying shahtoosh.

    PubMed

    Fei, Jing; Yang, Juan; Zhou, Hui; Tang, Minfeng; Lu, Weiming; Yan, An; Hou, Yin; Zhang, Shuyu

    2014-05-01

    Shahtoosh, the down hair of the Tibetan antelope (Pantholops hodgsonii), is the noblest and most expensive wool in the world. The population of the animal has declined dramatically due to commercial poaching for the fiber. Traditional inspection for detection of shahtoosh has been performed by microscopic analysis. We developed a TaqMan real-time PCR-based DNA analysis method for identifying shahtoosh fibers. A set of probe and primers for the mitochondrial 12S ribosomal RNA gene that binds specifically to Tibetan antelope DNA was designed. A signal was detected with sensitivity to the 1:10,000 dilution of shahtoosh DNA. A fiber mixture of 1% of shahtoosh mixed with cashmere and even a single fiber can be detected with this method. The method is faster, more cost-effective and more sensitive than other traditional sequencing methods and can be directly applied to identify shahtoosh and its processed products, which will be of value in illegal trade investigations. PMID:24502476

  7. 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.

  8. 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

  9. 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

  10. Identifying the seasonal origins of human campylobacteriosis.

    PubMed

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

    2013-06-01

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

  11. 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.

  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 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.

  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. Automatic Prosodic Analysis to Identify Mild Dementia.

    PubMed

    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

  16. Identifying the seasonal origins of human campylobacteriosis

    PubMed Central

    STRACHAN, N. J. C.; ROTARIU, O.; SMITH-PALMER, A.; COWDEN, J.; SHEPPARD, S. K.; O’BRIEN, S. J.; MAIDEN, M. C. J.; MACRAE, M.; BESSELL, P. R.; MATTHEWS, L.; REID, S. W. J.; INNOCENT, G. T.; OGDEN, I. D.; FORBES, K. J.

    2014-01-01

    SUMMARY Human campylobacteriosis exhibits a distinctive seasonality in temperate regions. This paper aims to identify the origins of this seasonality. Clinical isolates [typed by multi-locus sequence typing (MLST)] and epidemiological data were collected from Scotland. Young rural children were found to have an increased burden of disease in the late spring due to strains of non-chicken origin (e.g. ruminant and wild bird strains from environmental sources). In contrast the adult population had an extended summer peak associated with chicken strains. Travel abroad and UK mainland travel were associated with up to 17% and 18% of cases, respectively. International strains were associated with chicken, had a higher diversity than indigenous strains and a different spectrum of MLST types representative of these countries. Integrating empirical epidemiology and molecular subtyping can successfully elucidate the seasonal components of human campylobacteriosis. The findings will enable public health officials to focus strategies to reduce the disease burden. PMID:22989449

  17. Identifying Dyads and their conservation in Drosphila.

    NASA Astrophysics Data System (ADS)

    Dan, Debasis

    2007-03-01

    Core promoter regions in Drosophila are enriched with binding sites like TATA, Inr, DPE, MTE, etc. They have very strict spacing between each other in promoters where they occur together. For example, in Drosophila melanogaster TATA-Inr has a spacing of 25-30 bp. Our aim in this work is to identify all such pair of motifs having strict positional constraint in the core promoters of all Drosophila species. We discover how these motifs and the spacing between them evolve within Drosophila species. For this we analyze 700 bp upstream and 300 bp downstream of TSS in D. melanogaster and the corresponding orthologous region in other Drosophila species. For each species, this 1000 bp region is searched for statistically over-represented compound words of the form W1NLW2, where L is the spacing between words W1 and W2. These compound words are systematically clustered for further analysis.

  18. 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.

  19. 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

  20. 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.

  1. 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

  2. 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.

  3. 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

  4. 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. PMID:22966419

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. Photomaximization test for identifying photoallergic contact sensitizers.

    PubMed

    Kaidbey, K H; Kligman, A M

    1980-04-01

    The photomaximization procedure was designed to identify topical photocontact sensitizers following the format of the maximization test for contact sensitizers. The test agent is applied for 24 hours followed by exposure to three Minimal Erythema Doses (MED) of solar simulated radiation twice weekly for 3 weeks (six exposures) in a panel of 25 white Caucasoids. The subjects are challenged 2 weeks later with 4.0 J/cm2 of long-wave ultraviolet radiation (UV-A). Photocontact sensitization was induced to 3,3'4',5-tetrachlorosalicylanilide (TCSA); dibromosalicylanilide (DBS) but not to tribomosalicylanilide unless the latter was contaminated with DBS. Jadit and bithionol were weak photoallergens. The highest rate of sensitization was given by 6-methylcoumarin, a widely used synthetic fragrance. Hexachlorophene and trichlorocarbanilide were negative. PMID:7389322

  10. Photomaximization test for identifying photoallergic contact sensitizers.

    PubMed

    Kaidbey, K H; Kligman, A M

    1980-04-01

    The photomaximization procedure was designed to identify topical photocontact sensitizers following the format of the maximization test for contact sensitizers. The test agent is applied for 24 hours followed by exposure to three Minimal Erythema Doses (MED) of solar simulated radiation twice weekly for 3 weeks (six exposures) in a panel of 25 white Caucasoids. The subjects are challenged 2 weeks later with 4.0 J/cm2 of long-wave ultraviolet radiation (UV-A). Photocontact sensitization was induced to 3,3'4',5-tetrachlorosalicylanilide (TCSA); dibromosalicylanilide (DBS) but not to tribomosalicylanilide unless the latter was contaminated with DBS. Jadit and bithionol were weak photoallergens. The highest rate of sensitization was given by 6-methylcoumarin, a widely used synthetic fragrance. Hexachlorophene and trichlorocarbanilide were negative.

  11. Device for identifying a circumferential position

    DOEpatents

    Mikesell, Charles R.

    1985-01-01

    A device is described which accurately and reproducibly identifies points on the circumference of a non-vertical pipe for use as reference marks for pipe inspections. The device comprises a light-permeable disk-shaped chamber having a plurality of pockets spaced about its circumference, a light source transmitting a beam of light through the chamber, and a light-activated switch positioned to detect the light beam. The chamber contains a freely moving ball sized to be retained by the pockets. The device is mounted to revolve about the axis of the pipe. As it revolves the ball moves from one pocket of the chamber to another, interrupting the beam of light and triggering the light-activated switch, thereby indicating that the device has passed to a pre-selected circumferential position on the non-vertical pipe.

  12. Device for identifying a circumferential position

    DOEpatents

    Mikesell, C.R.

    1982-06-29

    A device is described which accurately and reproducibly identifies points on the circumference of a non-vertical pipe for use as reference marks for pipe inspections. The device comprises a light-permeable disk-shaped chamber having a plurality of pockets spaced about its circumference, a light source transmitting a beam of light through the chamber, and a light-activated switch positioned to detect the light beam. The chamber contains a freely moving ball sized to be retained by the pockets. The device is mounted to revolve about the axis of the pipe. As it revolves the ball moves from one pocket of the chamber to another, interrupting the beam of light and triggering the light-activated switch, thereby indicating that the device has passed to a pre-selected circumferential position on the non-vertical pipe.

  13. 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). PMID:27273322

  14. 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.

  15. 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.

  16. 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%.

  17. 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).

  18. 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

  19. 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

  20. 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

  1. 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

  2. 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

  3. Pseudonymization of patient identifiers for translational research

    PubMed Central

    2013-01-01

    Background 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. Methods 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. Results 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

  4. 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.

  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. Asteroid Secular Dynamics: Ceres’ Fingerprint Identified

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

    Here we report on the significant role of a so far overlooked dynamical aspect, namely, a secular resonance between the dwarf planet Ceres and other asteroids. We demonstrate that this type of secular resonance can be the dominant dynamical factor in certain regions of the main asteroid belt. Specifically, we performed a dynamical analysis of the asteroids belonging to the (1726) Hoffmeister family. To identify which dynamical mechanisms are actually at work in this part of the main asteroid belt, i.e., to isolate the main perturber(s), we study the evolution of this family in time. The study is accomplished using numerical integrations of test particles performed within different dynamical models. The obtained results reveal that the post-impact evolution of the Hoffmeister asteroid family is a direct consequence of the nodal secular resonance with Ceres. This leads us to the conclusion that similar effects must exist in other parts of the asteroid belt. In this respect, the obtained results shed light on an important and entirely new aspect of the long-term dynamics of small bodies. Ceres’ fingerprint in asteroid dynamics, expressed through the discovered secular resonance effect, completely changes our understanding of the way in which perturbations by Ceres-like objects affect the orbits of nearby bodies.

  7. Identifying the sea level signal: Surf's up

    NASA Astrophysics Data System (ADS)

    Maggs, William Ward

    Of all the dire consequences of the greenhouse effect, global sea level rise is potentially the most destructive to human life and property. But the processes that increase the volume of the oceans are so poorly understood that theoreticians are taking their lead from scientists trying to actually measure current changes in sea level that might be caused by the greenhouse effect. As with surface temperature, precipitation, and other measures of climate change, identifying the greenhouse signal is a daunting problem.Climate models that predict mean temperature increases around the world of up to several degrees C in the next 50-100 years in response to human-induced global warming have given rise to a scientific consensus that mountain glaciers and ice sheets will begin to melt and the water in oceans will slightly expand, raising sea level. Such increases would inundate some of the most densely populated and highly cultivated areas on the planet, displacing and endangering many millions of people at a devastating economic and social cost.

  8. 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.

  9. 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.

  10. 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.

  11. Ebola virus infection modeling and identifiability problems

    PubMed Central

    Nguyen, Van Kinh; Binder, Sebastian C.; Boianelli, Alessandro; Meyer-Hermann, Michael; Hernandez-Vargas, Esteban A.

    2015-01-01

    The recent outbreaks of Ebola virus (EBOV) infections have underlined the impact of the virus as a major threat for human health. Due to the high biosafety classification of EBOV (level 4), basic research is very limited. Therefore, the development of new avenues of thinking to advance quantitative comprehension of the virus and its interaction with the host cells is urgently needed to tackle this lethal disease. Mathematical modeling of the EBOV dynamics can be instrumental to interpret Ebola infection kinetics on quantitative grounds. To the best of our knowledge, a mathematical modeling approach to unravel the interaction between EBOV and the host cells is still missing. In this paper, a mathematical model based on differential equations is used to represent the basic interactions between EBOV and wild-type Vero cells in vitro. Parameter sets that represent infectivity of pathogens are estimated for EBOV infection and compared with influenza virus infection kinetics. The average infecting time of wild-type Vero cells by EBOV is slower than in influenza infection. Simulation results suggest that the slow infecting time of EBOV could be compensated by its efficient replication. This study reveals several identifiability problems and what kind of experiments are necessary to advance the quantification of EBOV infection. A first mathematical approach of EBOV dynamics and the estimation of standard parameters in viral infections kinetics is the key contribution of this work, paving the way for future modeling works on EBOV infection. PMID:25914675

  12. 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.

  13. Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes.

    PubMed

    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

  14. GT-Scan: identifying unique genomic targets

    PubMed Central

    O’Brien, Aidan; Bailey, Timothy L.

    2014-01-01

    Summary: A number of technologies, including CRISPR/Cas, transcription activator-like effector nucleases and zinc-finger nucleases, allow the user to target a chosen locus for genome editing or regulatory interference. Specificity, however, is a major problem, and the targeted locus must be chosen with care to avoid inadvertently affecting other loci (‘off-targets’) in the genome. To address this we have created ‘Genome Target Scan’ (GT-Scan), a flexible web-based tool that ranks all potential targets in a user-selected region of a genome in terms of how many off-targets they have. GT-Scan gives the user flexibility to define the desired characteristics of targets and off-targets via a simple ‘target rule’, and its interactive output allows detailed inspection of each of the most promising candidate targets. GT-Scan can be used to identify optimal targets for CRISPR/Cas systems, but its flexibility gives it potential to be adapted to other genome-targeting technologies as well. Availability and implementation: GT-Scan can be run via the web at: http://gt-scan.braembl.org.au. Contact: t.bailey@uq.edu.au PMID:24860161

  15. Identifying materials limits of chemically amplified photoresists

    NASA Astrophysics Data System (ADS)

    Wu, Wen-li; Prabhu, Vivek M.; Lin, Eric K.

    2007-03-01

    Chemically amplified photoresists are likely to remain the primary imaging materials for the semiconductor industry. As feature sizes decrease to dimensions comparable to the characteristic size of the molecules in the photoresist, a significant challenge lies in identifying the ultimate resolution limit of these materials. To address this challenge, we investigated model photoresist materials with high resolution measurements to examine the effect of individual factors among interdependent process steps on line-edge roughness (LER). Using a bilayer film sample geometry, we measured the internal deprotection interface with nanometer resolution as a function of photoacid size, initial resist copolymer composition, and amine base quencher by neutron reflectivity and infrared spectroscopy. After development, we found that the resist chemistry and additives can play an important role in LER through its influence on acid diffusion. However, these model experiments suggest that there is a limit in LER even with an idealized exposure image contrast and decreases in the width of the reaction-diffusion front. However, there may be opportunities to further decrease LER during development by tuning the response of the photoresist to the developer solution.

  16. Experimental approaches for identifying schizophrenia risk genes.

    PubMed

    Mantripragada, Kiran K; Carroll, Liam S; Williams, Nigel M

    2010-01-01

    Schizophrenia is a severe, debilitating and common psychiatric disorder, which directly affects approximately 1% of the population worldwide. Although previous studies have unequivocally shown that schizophrenia has a strong genetic component, our understanding of its pathophysiology remains limited. The precise genetic architecture of schizophrenia remains elusive and is likely to be complex. It is believed that multiple genetic variants, with each contributing a modest effect on disease risk, interact with environmental factors resulting in the phenotype. In this chapter, we summarise the main molecular genetic approaches that have been utilised in identifying susceptibility genes for schizophrenia and discuss the advantages and disadvantages of each approach. First, we detail the findings of linkage mapping in pedigrees (affected families), which analyse the co-segregation of polymorphic genetic markers with disease phenotype. Second, the contribution of targeted and genome-wide association studies, which compare differential allelic frequencies in schizophrenia cases and matched controls, is presented. Third, we discuss about the identification of susceptibility genes through analysis of chromosomal structural variation (gains and losses of genetic material). Lastly, we introduce the concept of re-sequencing, where the entire genome/exome is sequenced both in affected and unaffected individuals. This approach has the potential to provide a clarified picture of the majority of the genetic variation underlying disease pathogenesis. PMID:21312414

  17. Identifying Cognitive States Using Regularity Partitions

    PubMed Central

    2015-01-01

    Functional Magnetic Resonance (fMRI) data can be used to depict functional connectivity of the brain. Standard techniques have been developed to construct brain networks from this data; typically nodes are considered as voxels or sets of voxels with weighted edges between them representing measures of correlation. Identifying cognitive states based on fMRI data is connected with recording voxel activity over a certain time interval. Using this information, network and machine learning techniques can be applied to discriminate the cognitive states of the subjects by exploring different features of data. In this work we wish to describe and understand the organization of brain connectivity networks under cognitive tasks. In particular, we use a regularity partitioning algorithm that finds clusters of vertices such that they all behave with each other almost like random bipartite graphs. Based on the random approximation of the graph, we calculate a lower bound on the number of triangles as well as the expectation of the distribution of the edges in each subject and state. We investigate the results by comparing them to the state of the art algorithms for exploring connectivity and we argue that during epochs that the subject is exposed to stimulus, the inspected part of the brain is organized in an efficient way that enables enhanced functionality. PMID:26317983

  18. 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.

  19. 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.

  20. [Techniques for identifying the epidural space].

    PubMed

    Figueredo, E

    2005-01-01

    A large part of the success of epidural anesthesia rests on correct identification of the epidural space. The last hundred years have seen the description of numerous techniques for locating the space in the most straightforward, effective, safe, and reliable manner. To evaluate the advantages and disadvantages of these approaches and the complications associated with each, we carried out a MEDLINE search using the following key words: "epidural analgesia," "epidural anesthesia," "epidural space," "identification," and "loss of resistance" (LOR). Traditional, complementary, and instrument-guided techniques used to identify the epidural space were analyzed. The results of clinical trials comparing different LOR techniques were evaluated. LOR with air, with isotonic saline, or a combination of both were the techniques shown to be simplest and safest. With respect to safety, LOR with air led to the greatest number of complications (pneumocephalus, air embolism, insufficient analgesia, higher incidence of dural puncture, nerve root compression, subcutaneous emphysema). When a small air bubble is created inside the syringe, LOR with saline solution is reliable and teachable, as well as safe and effective.

  1. 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.

  2. Identifying dark matter interactions in monojet searches

    DOE PAGESBeta

    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

  3. 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

  4. 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. PMID:21647928

  5. Identifying and helping battered pregnant women.

    PubMed

    Parker, B; McFarlane, J

    1991-01-01

    This article highlights strategies in identifying and helping battered pregnant women. Studies report that 40-60% of battered women were abused during pregnancy inflicted in the form of blows to the abdomen, injuries to the breasts and genitals, and sexual assault. Because battering during pregnancy has been a prevalent occurrence, assessment during prenatal visits is most critical. This paper outlines several assessment approaches in dealing with battered pregnant women in specific circumstances, giving important consideration to her safety due to the potential risk of homicide. A Danger Assessment tool is utilized in assessing for potential homicide. Intervening with victims of abuse is difficult. The role of the nurse is to assist in the development of problem-solving and decision-making skills while the woman is still in extreme confusion or feeling of conflicting loyalties. Routine assessment for physical and sexual abuse during the prenatal period is recommended in order to prevent further abuse thus promoting maternal-child well being. PMID:2056861

  6. Functional genomics identifies drivers of medulloblastoma dissemination.

    PubMed

    Mumert, Michael; Dubuc, Adrian; Wu, Xiaochong; Northcott, Paul A; Chin, Steven S; Pedone, Carolyn A; Taylor, Michael D; Fults, Daniel W

    2012-10-01

    Medulloblastomas are malignant brain tumors that arise in the cerebellum in children and disseminate via the cerebrospinal fluid to the leptomeningeal spaces of the brain and spinal cord. Challenged by the poor prognosis for patients with metastatic dissemination, pediatric oncologists have developed aggressive treatment protocols, combining surgery, craniospinal radiation, and high-dose chemotherapy, that often cause disabling neurotoxic effects in long-term survivors. Insights into the genetic control of medulloblastoma dissemination have come from transposon insertion mutagenesis studies. Mobilizing the Sleeping Beauty transposon in cerebellar neural progenitor cells caused widespread dissemination of typically nonmetastatic medulloblastomas in Patched(+/-) mice, in which Shh signaling is hyperactive. Candidate metastasis genes were identified by sequencing the insertion sites and then mapping these sequences back to the mouse genome. To determine whether genes located at transposon insertion sites directly caused medulloblastomas to disseminate, we overexpressed candidate genes in Nestin(+) neural progenitors in the cerebella of mice by retroviral transfer in combination with Shh. We show here that ectopic expression of Eras, Lhx1, Ccrk, and Akt shifted the in vivo growth characteristics of Shh-induced medulloblastomas from a localized pattern to a disseminated pattern in which tumor cells seeded the leptomeningeal spaces of the brain and spinal cord. PMID:22875024

  7. 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.

  8. 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.

  9. 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

  10. Identifying the causes of contact dermatitis.

    PubMed

    Jones, Ruth; Horn, Helen M

    2014-06-01

    Contact dermatitis results from skin contact with an exogenous substance. It can be caused by direct contact, airborne particles, vapours or light. Individuals of any age can be affected. The two most common variants are irritant contact dermatitis (ICD) and allergic contact dermatitis (ACD). ICD is more common and has a worse prognosis. Other less common forms of contact dermatitis include photocontact allergy and, in food handlers, protein contact dermatitis. ICD is a form of eczema and is induced by direct inflammatory pathways without prior sensitisation. Classical ACD is mediated by type 4 cell-mediated immunity. Sensitisation occurs within 5 to 16 days of skin contact with a potential allergen but at this first exposure there is no inflammation. Frequent exposure and high concentrations of potential allergens increase the risk of sensitisation. If eczema is recurrent/persistent, or occurs in an individual with no previous history of eczema, contact dermatitis should be considered. Dorsal aspects of the hands are most often affected by ICD, usually with involvement of the finger webs. Cumulative effects of water, soaps and detergents are the most common cause of ICD which affects the hands more often than any other site. Nickel, fragrances, rubber accelerators and biocides are the most common sensitisers in ACD. Patients with leg ulcers and stasis eczema are at especially high risk of developing allergies to ingredients of their topical treatments, dressings and bandages. If ACD is suspected the patient should be referred to secondary care for patch testing. Age should not be a deterrent to patch testing. Accurate diagnosis, avoidance of identified allergens and protection from irritants are the key to successful treatment.

  11. A newly-identified lineage of Schistosoma.

    PubMed

    Morgan, Jess A T; DeJong, Randall J; Kazibwe, Francis; Mkoji, Gerald M; Loker, Eric S

    2003-08-01

    Because of their role in causing schistosomiasis, flukes of the genus Schistosoma are the best known of all digeneans. The genus has traditionally been divided into four familiar species groups. Here we report on three poorly known species of Schistosoma, one of which, Schistosoma hippopotami, is known from the hippopotamus, one of which is provisionally identified as Schistosoma edwardiense, another hippo parasite, and a third that has not previously been described. All were collected from freshwater snails obtained from Lake Edward, western Uganda, the type locality for both known hippo schistosomes. The three different kinds of schistosome cercariae differ from one another in size, and all are readily differentiated by their long tail stems from the cercariae of human-infecting species. Furthermore, each was recovered from a different genus of snail host, Biomphalaria sudanica, Bulinus truncatus or Ceratophallus natalensis. Molecular analysis, based on 8350 bases of combined nuclear and mitochondrial DNA, groups these three long tail-stem cercariae into a well supported clade that does not associate with any of the recognised species groups. The placement of this clade, basal to all African species plus several Asian species, suggests that there has been an ancient association between Schistosoma and hippos. This new African Schistosoma clade advocates the need for further modification of the traditional species group-based classification. Two of the four species groups are paraphyletic. It also suggests that Schistosoma has been remarkably plastic with respect to adapting to snail hosts-three distantly related genera of planorbid snails have been exploited by worms within a single clade. Finally, it adds a new layer of complexity to deciphering the origins of Schistosoma, often considered to be African but recently challenged as being Asian. In the late Cenozoic the distribution of hippo species straddled both Africa and Asia and they may have provided a means

  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. Identifying Groundwater Droughts using standardized Water Levels

    NASA Astrophysics Data System (ADS)

    Haas, J. C.; Birk, S.

    2015-12-01

    Drought indices are frequently used to compare the occurrence and characteristics of droughts at different sites as well as to characterize different hydrometeorological aspects of drought. The existing indices have been mostly focused on precipitation, soil moisture, and surface waters though. To enable a comparison of groundwater drought with other hydrometeorological aspects of drought, the Standardized Groundwater level Index SGI was proposed by Bloomfield and Marchant (2013). So far, the SGI has been applied only to consolidated aquifers in the UK. The purpose of this work is to assess the applicability and performance of the SGI in unconsolidated, porous aquifers situated in valleys, which represent the main sources of drinking water in many regions. For this purpose, long-term time series of groundwater levels both in wet and dry regions of Austria are analyzed and compared with time series of precipitation, evapotranspiration and river stages. It is shown that large drought events, such as 2003 with only 79% of the long-term average precipitation, but also less severe events are reflected by negative SGI anomalies. To identify and classify time periods with a groundwater deficit, such benchmark years are used to propose a threshold value of the SGI defining the onset of a drought. Time periods where a clear drop in SGI does not correspond to a significant anomaly in precipitation are also visible in the data. More detailed investigations into small valley fill aquifers in the south-east of Austria reveal that the SGI may closely correlate with river stage fluctuations. Also, effects of the geographic setting (mountainous area vs. lowland) and the impacts of human activities (hydropower, drinking water extraction) are shown. Bloomfield, J. P., Marchant, B. P., Analysis of groundwater drought building on the standardised precipitation index approach, Hydrology and Earth System Sciences, 17, 4769-4787, 2013.

  14. Identifying Hendra virus diversity in pteropid bats.

    PubMed

    Smith, Ina; Broos, Alice; de Jong, Carol; Zeddeman, Anne; Smith, Craig; Smith, Greg; Moore, Fred; Barr, Jennifer; Crameri, Gary; Marsh, Glenn; Tachedjian, Mary; Yu, Meng; Kung, Yu Hsin; Wang, Lin-Fa; Field, Hume

    2011-01-01

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

  15. Identifying Periods of Drowsy Driving Using EEG

    PubMed Central

    Brown, Timothy; Johnson, Robin; Milavetz, Gary

    2013-01-01

    Drowsy driving is a significant contributor to death and injury crashes on our nation’s highways. Predictive neurophysiologic/physiologic solutions to reduce these incidences have been proposed and developed. EEG based metrics were found to be promising in initial studies, but remain controversial in their efficacy, primarily due to failures to develop replication studies within the simulation settings used for development, and real-world validation. This analysis sought to address these short comings by assessing the utility of the B-Alert algorithms, in a replication study of driving and drowsiness. Data were collected on the National Advanced Driving Simulator from 72 volunteer drivers exposed to three types of roadways at three times of day representing different levels of drowsiness. EEG metrics, collected using the B-Alert X10 Wireless Headset were evaluated to determine their utility in future predictive studies. The replication of the B-Alert algorithms was a secondary focus for this analysis, resulting in highly variable start times within each time of day segment, leading to EEG data being confounded by the diurnal variations that occur in the basal EEG signal. Regardless of this limitation, the analysis revealed promising outcomes. The EEG based algorithms for sleep onset, drowsiness, as well as fatigue related power spectral bandwidths (i.e. lateral central, and parietal alpha) varied with time of day of the drives. Interestingly, EEG metrics of cognitive workload were also sensative to the terrain of the drives. The replicaiton of the B-Alert algorithms were a secondary focuse in the study design, Taken together, these data indicate great potential of carefully designed studies to utilize neurophysiologic metrics to identify time of day and task and road conditions that may be at greatest risk during fatigued/drowsy periods. PMID:24406950

  16. 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.

  17. Identifying periods of drowsy driving using EEG.

    PubMed

    Brown, Timothy; Johnson, Robin; Milavetz, Gary

    2013-01-01

    Drowsy driving is a significant contributor to death and injury crashes on our nation's highways. Predictive neurophysiologic/physiologic solutions to reduce these incidences have been proposed and developed. EEG based metrics were found to be promising in initial studies, but remain controversial in their efficacy, primarily due to failures to develop replication studies within the simulation settings used for development, and real-world validation. This analysis sought to address these short comings by assessing the utility of the B-Alert algorithms, in a replication study of driving and drowsiness. Data were collected on the National Advanced Driving Simulator from 72 volunteer drivers exposed to three types of roadways at three times of day representing different levels of drowsiness. EEG metrics, collected using the B-Alert X10 Wireless Headset were evaluated to determine their utility in future predictive studies. The replication of the B-Alert algorithms was a secondary focus for this analysis, resulting in highly variable start times within each time of day segment, leading to EEG data being confounded by the diurnal variations that occur in the basal EEG signal. Regardless of this limitation, the analysis revealed promising outcomes. The EEG based algorithms for sleep onset, drowsiness, as well as fatigue related power spectral bandwidths (i.e. lateral central, and parietal alpha) varied with time of day of the drives. Interestingly, EEG metrics of cognitive workload were also sensative to the terrain of the drives. The replicaiton of the B-Alert algorithms were a secondary focuse in the study design, Taken together, these data indicate great potential of carefully designed studies to utilize neurophysiologic metrics to identify time of day and task and road conditions that may be at greatest risk during fatigued/drowsy periods.

  18. Identifying Hendra virus diversity in pteropid bats.

    PubMed

    Smith, Ina; Broos, Alice; de Jong, Carol; Zeddeman, Anne; Smith, Craig; Smith, Greg; Moore, Fred; Barr, Jennifer; Crameri, Gary; Marsh, Glenn; Tachedjian, Mary; Yu, Meng; Kung, Yu Hsin; Wang, Lin-Fa; Field, Hume

    2011-01-01

    Hendra virus (HeV) causes a zoonotic disease with high mortality that is transmitted to humans from bats of the genus Pteropus (flying foxes) via an intermediary equine host. Factors promoting spillover from bats to horses are uncertain at this time, but plausibly encompass host and/or agent and/or environmental factors. There is a lack of HeV sequence information derived from the natural bat host, as previously sequences have only been obtained from horses or humans following spillover events. In order to obtain an insight into possible variants of HeV circulating in flying foxes, collection of urine was undertaken in multiple flying fox roosts in Queensland, Australia. HeV was found to be geographically widespread in flying foxes with a number of HeV variants circulating at the one time at multiple locations, while at times the same variant was found circulating at disparate locations. Sequence diversity within variants allowed differentiation on the basis of nucleotide changes, and hypervariable regions in the genome were identified that could be used to differentiate circulating variants. Further, during the study, HeV was isolated from the urine of flying foxes on four occasions from three different locations. The data indicates that spillover events do not correlate with particular HeV isolates, suggesting that host and/or environmental factors are the primary determinants of bat-horse spillover. Thus future spillover events are likely to occur, and there is an on-going need for effective risk management strategies for both human and animal health. PMID:21980413

  19. Understanding and identifying amino acid repeats.

    PubMed

    Luo, Hong; Nijveen, Harm

    2014-07-01

    Amino acid repeats (AARs) are abundant in protein sequences. They have particular roles in protein function and evolution. Simple repeat patterns generated by DNA slippage tend to introduce length variations and point mutations in repeat regions. Loss of normal and gain of abnormal function owing to their variable length are potential risks leading to diseases. Repeats with complex patterns mostly refer to the functional domain repeats, such as the well-known leucine-rich repeat and WD repeat, which are frequently involved in protein–protein interaction. They are mainly derived from internal gene duplication events and stabilized by ‘gate-keeper’ residues, which play crucial roles in preventing inter-domain aggregation. AARs are widely distributed in different proteomes across a variety of taxonomic ranges, and especially abundant in eukaryotic proteins. However, their specific evolutionary and functional scenarios are still poorly understood. Identifying AARs in protein sequences is the first step for the further investigation of their biological function and evolutionary mechanism. In principle, this is an NP-hard problem, as most of the repeat fragments are shaped by a series of sophisticated evolutionary events and become latent periodical patterns. It is not possible to define a uniform criterion for detecting and verifying various repeat patterns. Instead, different algorithms based on different strategies have been developed to cope with different repeat patterns. In this review, we attempt to describe the amino acid repeat-detection algorithms currently available and compare their strategies based on an in-depth analysis of the biological significance of protein repeats. PMID:23418055

  20. Quantitative proteomics for identifying biomarkers for Rabies

    PubMed Central

    2013-01-01

    Introduction Rabies is a fatal acute viral disease of the central nervous system, which is a serious public health problem in Asian and African countries. Based on the clinical presentation, rabies can be classified into encephalitic (furious) or paralytic (numb) rabies. Early diagnosis of this disease is particularly important as rabies is invariably fatal if adequate post exposure prophylaxis is not administered immediately following the bite. Methods In this study, we carried out a quantitative proteomic analysis of the human brain tissue from cases of encephalitic and paralytic rabies along with normal human brain tissues using an 8-plex isobaric tags for relative and absolute quantification (iTRAQ) strategy. Results and conclusion We identified 402 proteins, of which a number of proteins were differentially expressed between encephalitic and paralytic rabies, including several novel proteins. The differentially expressed molecules included karyopherin alpha 4 (KPNA4), which was overexpressed only in paralytic rabies, calcium calmodulin dependent kinase 2 alpha (CAMK2A), which was upregulated in paralytic rabies group and glutamate ammonia ligase (GLUL), which was overexpressed in paralytic as well as encephalitic rabies. We validated two of the upregulated molecules, GLUL and CAMK2A, by dot blot assays and further validated CAMK2A by immunohistochemistry. These molecules need to be further investigated in body fluids such as cerebrospinal fluid in a larger cohort of rabies cases to determine their potential use as antemortem diagnostic biomarkers in rabies. This is the first study to systematically profile clinical subtypes of human rabies using an iTRAQ quantitative proteomics approach. PMID:23521751

  1. 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

  2. Identifying human influences on atmospheric temperature.

    PubMed

    Santer, Benjamin D; Painter, Jeffrey F; Mears, Carl A; Doutriaux, Charles; Caldwell, Peter; Arblaster, Julie M; Cameron-Smith, Philip J; Gillett, Nathan P; Gleckler, Peter J; Lanzante, John; Perlwitz, Judith; Solomon, Susan; Stott, Peter A; Taylor, Karl E; Terray, Laurent; Thorne, Peter W; Wehner, Michael F; Wentz, Frank J; Wigley, Tom M L; Wilcox, Laura J; Zou, Cheng-Zhi

    2013-01-01

    We perform a multimodel detection and attribution study with climate model simulation output and satellite-based measurements of tropospheric and stratospheric temperature change. We use simulation output from 20 climate models participating in phase 5 of the Coupled Model Intercomparison Project. This multimodel archive provides estimates of the signal pattern in response to combined anthropogenic and natural external forcing (the fingerprint) and the noise of internally generated variability. Using these estimates, we calculate signal-to-noise (S/N) ratios to quantify the strength of the fingerprint in the observations relative to fingerprint strength in natural climate noise. For changes in lower stratospheric temperature between 1979 and 2011, S/N ratios vary from 26 to 36, depending on the choice of observational dataset. In the lower troposphere, the fingerprint strength in observations is smaller, but S/N ratios are still significant at the 1% level or better, and range from three to eight. We find no evidence that these ratios are spuriously inflated by model variability errors. After removing all global mean signals, model fingerprints remain identifiable in 70% of the tests involving tropospheric temperature changes. Despite such agreement in the large-scale features of model and observed geographical patterns of atmospheric temperature change, most models do not replicate the size of the observed changes. On average, the models analyzed underestimate the observed cooling of the lower stratosphere and overestimate the warming of the troposphere. Although the precise causes of such differences are unclear, model biases in lower stratospheric temperature trends are likely to be reduced by more realistic treatment of stratospheric ozone depletion and volcanic aerosol forcing.

  3. Identifying human influences on atmospheric temperature

    PubMed Central

    Santer, Benjamin D.; Painter, Jeffrey F.; Mears, Carl A.; Doutriaux, Charles; Caldwell, Peter; Arblaster, Julie M.; Cameron-Smith, Philip J.; Gillett, Nathan P.; Gleckler, Peter J.; Lanzante, John; Perlwitz, Judith; Solomon, Susan; Stott, Peter A.; Taylor, Karl E.; Terray, Laurent; Thorne, Peter W.; Wehner, Michael F.; Wentz, Frank J.; Wigley, Tom M. L.; Wilcox, Laura J.; Zou, Cheng-Zhi

    2013-01-01

    We perform a multimodel detection and attribution study with climate model simulation output and satellite-based measurements of tropospheric and stratospheric temperature change. We use simulation output from 20 climate models participating in phase 5 of the Coupled Model Intercomparison Project. This multimodel archive provides estimates of the signal pattern in response to combined anthropogenic and natural external forcing (the fingerprint) and the noise of internally generated variability. Using these estimates, we calculate signal-to-noise (S/N) ratios to quantify the strength of the fingerprint in the observations relative to fingerprint strength in natural climate noise. For changes in lower stratospheric temperature between 1979 and 2011, S/N ratios vary from 26 to 36, depending on the choice of observational dataset. In the lower troposphere, the fingerprint strength in observations is smaller, but S/N ratios are still significant at the 1% level or better, and range from three to eight. We find no evidence that these ratios are spuriously inflated by model variability errors. After removing all global mean signals, model fingerprints remain identifiable in 70% of the tests involving tropospheric temperature changes. Despite such agreement in the large-scale features of model and observed geographical patterns of atmospheric temperature change, most models do not replicate the size of the observed changes. On average, the models analyzed underestimate the observed cooling of the lower stratosphere and overestimate the warming of the troposphere. Although the precise causes of such differences are unclear, model biases in lower stratospheric temperature trends are likely to be reduced by more realistic treatment of stratospheric ozone depletion and volcanic aerosol forcing. PMID:23197824

  4. Identifying hidden sexual bridging communities in Chicago.

    PubMed

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

    2009-07-01

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

  5. Identifying Canadian Freshwater Fishes through DNA Barcodes

    PubMed Central

    Hubert, Nicolas; Hanner, Robert; Holm, Erling; Mandrak, Nicholas E.; Taylor, Eric; Burridge, Mary; Watkinson, Douglas; Dumont, Pierre; Curry, Allen; Bentzen, Paul; Zhang, Junbin; April, Julien; Bernatchez, Louis

    2008-01-01

    efficiently identified through the use of DNA barcoding, especially the species complex of small-sized species, and that the present COI library can be used for subsequent applications in ecology and systematics. PMID:22423312

  6. Identifying Thoracic Malignancies Through Pleural Fluid Biomarkers

    PubMed Central

    Porcel, José M.; Esquerda, Aureli; Martínez-Alonso, Montserrat; Bielsa, Silvia; Salud, Antonieta

    2016-01-01

    Abstract The diagnosis of malignant pleural effusions may be challenging when cytological examination of aspirated pleural fluid is equivocal or noncontributory. The purpose of this study was to identify protein candidate biomarkers differentially expressed in the pleural fluid of patients with mesothelioma, lung adenocarcinoma, lymphoma, and tuberculosis (TB). A multiplex protein biochip comprising 120 biomarkers was used to determine the pleural fluid protein profile of 29 mesotheliomas, 29 lung adenocarcinomas, 12 lymphomas, and 35 tuberculosis. The relative abundance of these predetermined biomarkers among groups served to establish the differential diagnosis of: malignant versus benign (TB) effusions, lung adenocarcinoma versus mesothelioma, and lymphoma versus TB. The selected putative markers were validated using widely available commercial techniques in an independent sample of 102 patients. Significant differences were found in the protein expressions of metalloproteinase-9 (MMP-9), cathepsin-B, C-reactive protein, and chondroitin sulfate between malignant and TB effusions. When integrated into a scoring model, these proteins yielded 85% sensitivity, 100% specificity, and an area under the curve (AUC) of 0.98 for labeling malignancy in the verification sample. For lung adenocarcinoma–mesothelioma discrimination, combining CA19-9, CA15-3, and kallikrein-12 had maximal discriminatory capacity (65% sensitivity, 100% specificity, AUC 0.94); figures which also refer to the validation set. Last, cathepsin-B in isolation was only moderately useful (sensitivity 89%, specificity 62%, AUC 0.75) in separating lymphomatous and TB effusions. However, this last differentiation improved significantly when cathepsin-B was used with respect to the patient's age (sensitivity 72%, specificity 100%, AUC 0.94). In conclusion, panels of 4 (i.e., MMP-9, cathepsin-B, C-reactive protein, chondroitin sulfate), or 3 (i.e., CA19-9, CA15-3, kallikrein-12) different protein

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  8. 7 CFR 56.41 - Check grading officially identified product.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... (CONTINUED) VOLUNTARY GRADING OF SHELL EGGS Grading of Shell Eggs Prerequisites to Packaging Shell Eggs Identified with Grademarks § 56.41 Check grading officially identified product. Officially identified...

  9. CFHT and VLT Identify Extremely Remote Galaxy

    NASA Astrophysics Data System (ADS)

    2003-05-01

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

  10. 28 CFR 22.25 - Final disposition of identifiable materials.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... RESEARCH AND STATISTICAL INFORMATION § 22.25 Final disposition of identifiable materials. Upon completion of a research or statistical project the security of identifiable research or statistical...

  11. 28 CFR 22.25 - Final disposition of identifiable materials.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... RESEARCH AND STATISTICAL INFORMATION § 22.25 Final disposition of identifiable materials. Upon completion of a research or statistical project the security of identifiable research or statistical...

  12. 28 CFR 22.25 - Final disposition of identifiable materials.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... RESEARCH AND STATISTICAL INFORMATION § 22.25 Final disposition of identifiable materials. Upon completion of a research or statistical project the security of identifiable research or statistical...

  13. 28 CFR 22.25 - Final disposition of identifiable materials.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... RESEARCH AND STATISTICAL INFORMATION § 22.25 Final disposition of identifiable materials. Upon completion of a research or statistical project the security of identifiable research or statistical...

  14. 28 CFR 22.25 - Final disposition of identifiable materials.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... RESEARCH AND STATISTICAL INFORMATION § 22.25 Final disposition of identifiable materials. Upon completion of a research or statistical project the security of identifiable research or statistical...

  15. Effect of supplemental taurine on juvenile channel catfish Ictalurus punctatus growth and survival after challenge with Edwardsiella ictaluri

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Juvenile channel catfish, Ictalurus punctatus, were fed a basal diet that contained major protein (soybean meal, cottonseed meal) and energy (ground corn grain) ingredients that were derived from plant sources. Plant-source ingredients are considered to be low (< 5 ppm) for taurine content. In add...

  16. Effects of vitamin C on percent neurulation, hatch, growth, and survival of hybrid catfish challenged with virulent Edwardsiella ictaluri

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Vitamin C (ascorbic acid) is an essential micronutrient involved in several physiological processes such as growth, reproduction, and immune response. Requirements of vitamin C during gamete formation and early life stages of catfish are not known. Ascorbic acid (1 mg/mL/kg BW) was administered in...

  17. 3 Drugs Identified to Potentially Fight Zika Virus

    MedlinePlus

    ... 160680.html 3 Drugs Identified to Potentially Fight Zika Virus But only one is already approved in ... developing fetuses protection against the damaging effects of Zika virus, a new multicenter study reports. Researchers identified ...

  18. Identifying Novice Student Programming Misconceptions and Errors from Summative Assessments

    ERIC Educational Resources Information Center

    Veerasamy, Ashok Kumar; D'Souza, Daryl; Laakso, Mikko-Jussi

    2016-01-01

    This article presents a study aimed at examining the novice student answers in an introductory programming final e-exam to identify misconceptions and types of errors. Our study used the Delphi concept inventory to identify student misconceptions and skill, rule, and knowledge-based errors approach to identify the types of errors made by novices…

  19. 28 CFR 22.21 - Use of identifiable data.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... STATISTICAL INFORMATION § 22.21 Use of identifiable data. Research or statistical information identifiable to a private person may be used only for research or statistical purposes. ... 28 Judicial Administration 1 2010-07-01 2010-07-01 false Use of identifiable data. 22.21...

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

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-26

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

  1. 26 CFR 41.6109-1 - Identifying numbers.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 26 Internal Revenue 16 2010-04-01 2010-04-01 true Identifying numbers. 41.6109-1 Section 41.6109-1... Application to Tax On Use of Certain Highway Motor Vehicles § 41.6109-1 Identifying numbers. Every person required under § 41.6011(a)-1 to make a return must provide the identifying number required by...

  2. 26 CFR 41.6109-1 - Identifying numbers.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 26 Internal Revenue 16 2011-04-01 2011-04-01 false Identifying numbers. 41.6109-1 Section 41.6109... Application to Tax On Use of Certain Highway Motor Vehicles § 41.6109-1 Identifying numbers. Every person required under § 41.6011(a)-1 to make a return must provide the identifying number required by...

  3. 12 CFR 210.27 - Reliance on identifying number.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 12 Banks and Banking 2 2011-01-01 2011-01-01 false Reliance on identifying number. 210.27 Section... J) Funds Transfers Through Fedwire § 210.27 Reliance on identifying number. (a) Reliance by a Federal Reserve Bank on number to identify an intermediary bank or beneficiary's bank. A Federal...

  4. 25 CFR 23.82 - Assistance in identifying language interpreters.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 25 Indians 1 2011-04-01 2011-04-01 false Assistance in identifying language interpreters. 23.82... WELFARE ACT Assistance to State Courts § 23.82 Assistance in identifying language interpreters. Upon the... shall assist in identifying language interpreters. Such requests for assistance should be sent to...

  5. 25 CFR 23.82 - Assistance in identifying language interpreters.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 25 Indians 1 2010-04-01 2010-04-01 false Assistance in identifying language interpreters. 23.82... WELFARE ACT Assistance to State Courts § 23.82 Assistance in identifying language interpreters. Upon the... shall assist in identifying language interpreters. Such requests for assistance should be sent to...

  6. Which are the best identifiers for record linkage?

    PubMed

    Quantin, Catherine; Binquet, Christine; Bourquard, Karima; Pattisina, Ronny; Gouyon-Cornet, Béatrice; Ferdynus, Cyril; Gouyon, Jean-Bernard; François-André, Allaert

    2004-01-01

    As a linkage using less informative identifiers could lead to linkage errors, it is essential to quantify the information associated to each identifier. The aim of this study was to estimate the discriminating power of different identifiers susceptible to be used in a record linkage process. This work showed the interest of three identifiers when linking data concerning a same patient using an automatic procedure based on the method proposed by Jaro; the date of birth, the first and the last names seemed to be the more appropriate identifiers. Including a poorly discriminating identifier like gender did not improve the results. Moreover, adding a second christian name, often missing, increased linkage errors. On the contrary, it seemed that using a phonetic treatment adapted to the French language could improve the results of linkage in comparison to the Soundex. However, whatever, the method used it seems necessary to improve the quality of identifier collection as it could greatly influence linkage results.

  7. 40 CFR 174.529 - Bacillus thuringiensis modified Cry1Ab protein as identified under OECD Unique Identifier SYN...

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... protein as identified under OECD Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement... Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement of a tolerance. Residues of... exempt from the requirement of a tolerance when used as a plant-incorporated protectant in cotton;...

  8. 40 CFR 174.529 - Bacillus thuringiensis modified Cry1Ab protein as identified under OECD Unique Identifier SYN...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... protein as identified under OECD Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement... Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement of a tolerance. Residues of... exempt from the requirement of a tolerance when used as a plant-incorporated protectant in cotton;...

  9. 40 CFR 174.529 - Bacillus thuringiensis modified Cry1Ab protein as identified under OECD Unique Identifier SYN...

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... protein as identified under OECD Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement... Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement of a tolerance. Residues of... exempt from the requirement of a tolerance when used as a plant-incorporated protectant in cotton;...

  10. 40 CFR 174.529 - Bacillus thuringiensis modified Cry1Ab protein as identified under OECD Unique Identifier SYN...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... protein as identified under OECD Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement... Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement of a tolerance. Residues of... exempt from the requirement of a tolerance when used as a plant-incorporated protectant in cotton;...

  11. 40 CFR 174.529 - Bacillus thuringiensis modified Cry1Ab protein as identified under OECD Unique Identifier SYN...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... protein as identified under OECD Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement... Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement of a tolerance. Residues of... exempt from the requirement of a tolerance when used as a plant-incorporated protectant in cotton;...

  12. The icmF3 locus is involved in multiple adaptation- and virulence-related characteristics in Pseudomonas aeruginosa PAO1

    PubMed Central

    Lin, Jinshui; Cheng, Juanli; Chen, Keqi; Guo, Chenghao; Zhang, Weipeng; Yang, Xu; Ding, Wei; Ma, Li; Wang, Yao; Shen, Xihui

    2015-01-01

    The type VI secretion system (T6SS) is widely distributed in Gram-negative bacteria. Three separate T6SSs called H1-, H2-, and H3-T6SS have been discovered in Pseudomonas aeruginosa PAO1. Recent studies suggest that, in contrast to the H1-T6SS that targets prokaryotic cells, H2- and H3-T6SS are involved in interactions with both prokaryotic and eukaryotic cells. However, the detailed functions of T6SS components are still uncharacterized. The intracellular multiplication factor (IcmF) protein is conserved in type VI secretion systems (T6SS) of all different bacterial pathogens. Bioinformatic analysis revealed that IcmF3 in P. aeruginosa PAO1 is different from other IcmF homologs and may represent a new branch of these proteins with distinct functions. Herein, we have investigated the function of IcmF3 in this strain. We have shown that deletion of the icmF3 gene in P. aeruginosa PAO1 is associated with pleiotropic phenotypes. The icmF3 mutant has variant colony morphology and an hypergrowth phenotype in iron-limiting medium. Surprisingly, this mutant is also defective for the production of pyoverdine, as well as defects in swimming motility and virulence in a C. elegans worm model. The icmF3 mutant exhibits higher conjugation frequency than the wild type and increased biofilm formation on abiotic surfaces. Additionally, expression of two phenazine biosynthetic loci is increased in the icmF3 mutant, leading to the overproduction of pyocyanin. Finally, the mutant exhibits decreased susceptibility to aminoglycosides such as tobramycin and gentamicin. And the detected phenotypes can be restored completely or partially by trans complementation of wild type icmF3 gene. The pleiotropic effects observed upon icmF3 deletion demonstrate that icmF3 plays critical roles in both pathogenesis and environmental adaptation in P. aeruginosa PAO1. PMID:26484316

  13. The icmF3 locus is involved in multiple adaptation- and virulence-related characteristics in Pseudomonas aeruginosa PAO1.

    PubMed

    Lin, Jinshui; Cheng, Juanli; Chen, Keqi; Guo, Chenghao; Zhang, Weipeng; Yang, Xu; Ding, Wei; Ma, Li; Wang, Yao; Shen, Xihui

    2015-01-01

    The type VI secretion system (T6SS) is widely distributed in Gram-negative bacteria. Three separate T6SSs called H1-, H2-, and H3-T6SS have been discovered in Pseudomonas aeruginosa PAO1. Recent studies suggest that, in contrast to the H1-T6SS that targets prokaryotic cells, H2- and H3-T6SS are involved in interactions with both prokaryotic and eukaryotic cells. However, the detailed functions of T6SS components are still uncharacterized. The intracellular multiplication factor (IcmF) protein is conserved in type VI secretion systems (T6SS) of all different bacterial pathogens. Bioinformatic analysis revealed that IcmF3 in P. aeruginosa PAO1 is different from other IcmF homologs and may represent a new branch of these proteins with distinct functions. Herein, we have investigated the function of IcmF3 in this strain. We have shown that deletion of the icmF3 gene in P. aeruginosa PAO1 is associated with pleiotropic phenotypes. The icmF3 mutant has variant colony morphology and an hypergrowth phenotype in iron-limiting medium. Surprisingly, this mutant is also defective for the production of pyoverdine, as well as defects in swimming motility and virulence in a C. elegans worm model. The icmF3 mutant exhibits higher conjugation frequency than the wild type and increased biofilm formation on abiotic surfaces. Additionally, expression of two phenazine biosynthetic loci is increased in the icmF3 mutant, leading to the overproduction of pyocyanin. Finally, the mutant exhibits decreased susceptibility to aminoglycosides such as tobramycin and gentamicin. And the detected phenotypes can be restored completely or partially by trans complementation of wild type icmF3 gene. The pleiotropic effects observed upon icmF3 deletion demonstrate that icmF3 plays critical roles in both pathogenesis and environmental adaptation in P. aeruginosa PAO1. PMID:26484316

  14. Two Different Virulence-Related Regulatory Pathways in Borrelia burgdorferi Are Directly Affected by Osmotic Fluxes in the Blood Meal of Feeding Ixodes Ticks

    PubMed Central

    Bontemps-Gallo, Sébastien; Lawrence, Kevin; Gherardini, Frank C.

    2016-01-01

    Lyme disease, caused by Borrelia burgdorferi, is a vector-borne illness that requires the bacteria to adapt to distinctly different environments in its tick vector and various mammalian hosts. Effective colonization (acquisition phase) of a tick requires the bacteria to adapt to tick midgut physiology. Successful transmission (transmission phase) to a mammal requires the bacteria to sense and respond to the midgut environmental cues and up-regulate key virulence factors before transmission to a new host. Data presented here suggest that one environmental signal that appears to affect both phases of the infective cycle is osmolarity. While constant in the blood, interstitial fluid and tissue of a mammalian host (300 mOsm), osmolarity fluctuates in the midgut of feeding Ixodes scapularis. Measured osmolarity of the blood meal isolated from the midgut of a feeding tick fluctuates from an initial osmolarity of 600 mOsm to blood-like osmolarity of 300 mOsm. After feeding, the midgut osmolarity rebounded to 600 mOsm. Remarkably, these changes affect the two independent regulatory networks that promote acquisition (Hk1-Rrp1) and transmission (Rrp2-RpoN-RpoS) of B. burgdorferi. Increased osmolarity affected morphology and motility of wild-type strains, and lysed Hk1 and Rrp1 mutant strains. At low osmolarity, Borrelia cells express increased levels of RpoN-RpoS-dependent virulence factors (OspC, DbpA) required for the mammalian infection. Our results strongly suggest that osmolarity is an important part of the recognized signals that allow the bacteria to adjust gene expression during the acquisition and transmission phases of the infective cycle of B. burgdorferi. PMID:27525653

  15. Two Different Virulence-Related Regulatory Pathways in Borrelia burgdorferi Are Directly Affected by Osmotic Fluxes in the Blood Meal of Feeding Ixodes Ticks.

    PubMed

    Bontemps-Gallo, Sébastien; Lawrence, Kevin; Gherardini, Frank C

    2016-08-01

    Lyme disease, caused by Borrelia burgdorferi, is a vector-borne illness that requires the bacteria to adapt to distinctly different environments in its tick vector and various mammalian hosts. Effective colonization (acquisition phase) of a tick requires the bacteria to adapt to tick midgut physiology. Successful transmission (transmission phase) to a mammal requires the bacteria to sense and respond to the midgut environmental cues and up-regulate key virulence factors before transmission to a new host. Data presented here suggest that one environmental signal that appears to affect both phases of the infective cycle is osmolarity. While constant in the blood, interstitial fluid and tissue of a mammalian host (300 mOsm), osmolarity fluctuates in the midgut of feeding Ixodes scapularis. Measured osmolarity of the blood meal isolated from the midgut of a feeding tick fluctuates from an initial osmolarity of 600 mOsm to blood-like osmolarity of 300 mOsm. After feeding, the midgut osmolarity rebounded to 600 mOsm. Remarkably, these changes affect the two independent regulatory networks that promote acquisition (Hk1-Rrp1) and transmission (Rrp2-RpoN-RpoS) of B. burgdorferi. Increased osmolarity affected morphology and motility of wild-type strains, and lysed Hk1 and Rrp1 mutant strains. At low osmolarity, Borrelia cells express increased levels of RpoN-RpoS-dependent virulence factors (OspC, DbpA) required for the mammalian infection. Our results strongly suggest that osmolarity is an important part of the recognized signals that allow the bacteria to adjust gene expression during the acquisition and transmission phases of the infective cycle of B. burgdorferi. PMID:27525653

  16. Identifying and integrating helpful and harmful religious beliefs into psychotherapy.

    PubMed

    Rosenfield, George W

    2010-12-01

    The 2 main roles of the psychotherapist involve identifying and understanding the client's problems/strengths and treating problems. Suggestions are offered to guide addressing or avoiding religious beliefs in both roles. Types of religious beliefs that contribute to distress, particularly for youth, are identified and treatment options are offered.

  17. 37 CFR 211.5 - Deposit of identifying material.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... material. 211.5 Section 211.5 Patents, Trademarks, and Copyrights COPYRIGHT OFFICE, LIBRARY OF CONGRESS COPYRIGHT OFFICE AND PROCEDURES MASK WORK PROTECTION § 211.5 Deposit of identifying material. (a) General. This section prescribes rules pertaining to the deposit of identifying material for registration of...

  18. 37 CFR 211.5 - Deposit of identifying material.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... material. 211.5 Section 211.5 Patents, Trademarks, and Copyrights COPYRIGHT OFFICE, LIBRARY OF CONGRESS COPYRIGHT OFFICE AND PROCEDURES MASK WORK PROTECTION § 211.5 Deposit of identifying material. (a) General. This section prescribes rules pertaining to the deposit of identifying material for registration of...

  19. 42 CFR 433.138 - Identifying liable third parties.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 42 Public Health 4 2011-10-01 2011-10-01 false Identifying liable third parties. 433.138 Section... SERVICES (CONTINUED) MEDICAL ASSISTANCE PROGRAMS STATE FISCAL ADMINISTRATION Third Party Liability § 433.138 Identifying liable third parties. (a) Basic provisions. The agency must take reasonable...

  20. National variety trials identify clones with high potential

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  1. 45 CFR 162.506 - Standard unique health plan identifier.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 45 Public Welfare 1 2013-10-01 2013-10-01 false Standard unique health plan identifier. 162.506 Section 162.506 Public Welfare DEPARTMENT OF HEALTH AND HUMAN SERVICES ADMINISTRATIVE DATA STANDARDS AND RELATED REQUIREMENTS ADMINISTRATIVE REQUIREMENTS Standard Unique Health Identifier for Health Plans §...

  2. Gasoline identifier based on SH0 plate acoustic waves.

    PubMed

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

    2016-08-01

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

  3. 48 CFR 2009.570-7 - Conflicts identified after award.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 48 Federal Acquisition Regulations System 6 2011-10-01 2011-10-01 false Conflicts identified after... COMMISSION COMPETITION AND ACQUISITION PLANNING CONTRACTOR QUALIFICATIONS Organizational Conflicts of Interest 2009.570-7 Conflicts identified after award. If potential organizational conflicts of interest...

  4. 48 CFR 2009.570-7 - Conflicts identified after award.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 6 2010-10-01 2010-10-01 true Conflicts identified after... COMMISSION COMPETITION AND ACQUISITION PLANNING CONTRACTOR QUALIFICATIONS Organizational Conflicts of Interest 2009.570-7 Conflicts identified after award. If potential organizational conflicts of interest...

  5. Identifiability Results for Several Classes of Linear Compartment Models.

    PubMed

    Meshkat, Nicolette; Sullivant, Seth; Eisenberg, Marisa

    2015-08-01

    Identifiability concerns finding which unknown parameters of a model can be estimated, uniquely or otherwise, from given input-output data. If some subset of the parameters of a model cannot be determined given input-output data, then we say the model is unidentifiable. In this work, we study linear compartment models, which are a class of biological models commonly used in pharmacokinetics, physiology, and ecology. In past work, we used commutative algebra and graph theory to identify a class of linear compartment models that we call identifiable cycle models, which are unidentifiable but have the simplest possible identifiable functions (so-called monomial cycles). Here we show how to modify identifiable cycle models by adding inputs, adding outputs, or removing leaks, in such a way that we obtain an identifiable model. We also prove a constructive result on how to combine identifiable models, each corresponding to strongly connected graphs, into a larger identifiable model. We apply these theoretical results to several real-world biological models from physiology, cell biology, and ecology. PMID:26337290

  6. Identifying Evidence of Reflective Ability in Preservice Teacher Electronic Portfolios

    ERIC Educational Resources Information Center

    Sulzen, James

    2011-01-01

    Results of this study identified "evidence markers" that characterize reflection in preservice teacher electronic portfolios. Examples of such markers include openness to self-learning, willingness to self-critique, analytical detail of reflections, and taking responsibility for pupil learning challenges. To identify the markers, school of…

  7. Identifying causal effects of climate extremes on societies

    NASA Astrophysics Data System (ADS)

    Hsiang, S. M.

    2015-12-01

    We discuss recent advances in the application of quasi-experimental techniques to identify causal effects of climate extremes on human societies using historical data. Results identifying effects on economic productivity, violence, migration, and global trade will be discussed. We will discuss how these statistical findings can be applied to calibrate modeling exercises and areas for future research.

  8. Method of identifying hairpin DNA probes by partial fold analysis

    DOEpatents

    Miller, Benjamin L.; Strohsahl, Christopher M.

    2009-10-06

    Method of identifying molecular beacons in which a secondary structure prediction algorithm is employed to identify oligonucleotide sequences within a target gene having the requisite hairpin structure. Isolated oligonucleotides, molecular beacons prepared from those oligonucleotides, and their use are also disclosed.

  9. Method of identifying hairpin DNA probes by partial fold analysis

    DOEpatents

    Miller, Benjamin L.; Strohsahl, Christopher M.

    2008-10-28

    Methods of identifying molecular beacons in which a secondary structure prediction algorithm is employed to identify oligonucleotide sequences within a target gene having the requisite hairpin structure. Isolated oligonucleotides, molecular beacons prepared from those oligonucleotides, and their use are also disclosed.

  10. Identifying a K-10 Developmental Framework for Teaching Philosophy

    ERIC Educational Resources Information Center

    Poulton, Janette

    2014-01-01

    The intention of the study was to identify predictable opportunities for teachers to scaffold middle year students' philosophical learning. Such opportunities were identified in terms of students' readiness to learn certain behaviours in the context of a "community of inquiry". Thus it was hoped that the project would provide a…

  11. 25 CFR 23.81 - Assistance in identifying witnesses.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 25 Indians 1 2010-04-01 2010-04-01 false Assistance in identifying witnesses. 23.81 Section 23.81 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR HUMAN SERVICES INDIAN CHILD WELFARE ACT Assistance to State Courts § 23.81 Assistance in identifying witnesses. Upon the request of a party in...

  12. 33 CFR 23.12 - Coast Guard identifying insignia.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Coast Guard identifying insignia. 23.12 Section 23.12 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY GENERAL DISTINCTIVE MARKINGS FOR COAST GUARD VESSELS AND AIRCRAFT § 23.12 Coast Guard identifying...

  13. 33 CFR 23.12 - Coast Guard identifying insignia.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Coast Guard identifying insignia. 23.12 Section 23.12 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY GENERAL DISTINCTIVE MARKINGS FOR COAST GUARD VESSELS AND AIRCRAFT § 23.12 Coast Guard identifying...

  14. 33 CFR 23.12 - Coast Guard identifying insignia.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Coast Guard identifying insignia. 23.12 Section 23.12 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY GENERAL DISTINCTIVE MARKINGS FOR COAST GUARD VESSELS AND AIRCRAFT § 23.12 Coast Guard identifying...

  15. 33 CFR 23.12 - Coast Guard identifying insignia.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Coast Guard identifying insignia. 23.12 Section 23.12 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY GENERAL DISTINCTIVE MARKINGS FOR COAST GUARD VESSELS AND AIRCRAFT § 23.12 Coast Guard identifying...

  16. 33 CFR 23.12 - Coast Guard identifying insignia.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Coast Guard identifying insignia. 23.12 Section 23.12 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY GENERAL DISTINCTIVE MARKINGS FOR COAST GUARD VESSELS AND AIRCRAFT § 23.12 Coast Guard identifying...

  17. 25 CFR 304.5 - Dies to identify tribe.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 25 Indians 2 2013-04-01 2013-04-01 false Dies to identify tribe. 304.5 Section 304.5 Indians INDIAN ARTS AND CRAFTS BOARD, DEPARTMENT OF THE INTERIOR NAVAJO, PUEBLO, AND HOPI SILVER, USE OF GOVERNMENT MARK § 304.5 Dies to identify tribe. Dies are marked with name of tribe. A Navajo stamp will...

  18. 25 CFR 304.5 - Dies to identify tribe.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 25 Indians 2 2011-04-01 2011-04-01 false Dies to identify tribe. 304.5 Section 304.5 Indians INDIAN ARTS AND CRAFTS BOARD, DEPARTMENT OF THE INTERIOR NAVAJO, PUEBLO, AND HOPI SILVER, USE OF GOVERNMENT MARK § 304.5 Dies to identify tribe. Dies are marked with name of tribe. A Navajo stamp will...

  19. 25 CFR 304.5 - Dies to identify tribe.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 25 Indians 2 2010-04-01 2010-04-01 false Dies to identify tribe. 304.5 Section 304.5 Indians INDIAN ARTS AND CRAFTS BOARD, DEPARTMENT OF THE INTERIOR NAVAJO, PUEBLO, AND HOPI SILVER, USE OF GOVERNMENT MARK § 304.5 Dies to identify tribe. Dies are marked with name of tribe. A Navajo stamp will...

  20. 25 CFR 304.5 - Dies to identify tribe.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 25 Indians 2 2014-04-01 2014-04-01 false Dies to identify tribe. 304.5 Section 304.5 Indians INDIAN ARTS AND CRAFTS BOARD, DEPARTMENT OF THE INTERIOR NAVAJO, PUEBLO, AND HOPI SILVER, USE OF GOVERNMENT MARK § 304.5 Dies to identify tribe. Dies are marked with name of tribe. A Navajo stamp will...

  1. 25 CFR 304.5 - Dies to identify tribe.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 25 Indians 2 2012-04-01 2012-04-01 false Dies to identify tribe. 304.5 Section 304.5 Indians INDIAN ARTS AND CRAFTS BOARD, DEPARTMENT OF THE INTERIOR NAVAJO, PUEBLO, AND HOPI SILVER, USE OF GOVERNMENT MARK § 304.5 Dies to identify tribe. Dies are marked with name of tribe. A Navajo stamp will...

  2. 30 CFR 47.21 - Identifying hazardous chemicals.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... standards in 30 CFR chapter I. (3) Occupational Safety and Health Administration (OSHA), 29 CFR part 1910... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Identifying hazardous chemicals. 47.21 Section... TRAINING HAZARD COMMUNICATION (HazCom) Hazard Determination § 47.21 Identifying hazardous chemicals....

  3. 30 CFR 47.21 - Identifying hazardous chemicals.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... standards in 30 CFR chapter I. (3) Occupational Safety and Health Administration (OSHA), 29 CFR part 1910... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Identifying hazardous chemicals. 47.21 Section... TRAINING HAZARD COMMUNICATION (HazCom) Hazard Determination § 47.21 Identifying hazardous chemicals....

  4. 42 CFR 401.118 - Deletion of identifying details.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 42 Public Health 2 2010-10-01 2010-10-01 false Deletion of identifying details. 401.118 Section 401.118 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN... Deletion of identifying details. When CMS publishes or otherwise makes available an opinion or...

  5. 30 CFR 47.21 - Identifying hazardous chemicals.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... standards in 30 CFR chapter I. (3) Occupational Safety and Health Administration (OSHA), 29 CFR part 1910... 30 Mineral Resources 1 2012-07-01 2012-07-01 false Identifying hazardous chemicals. 47.21 Section... TRAINING HAZARD COMMUNICATION (HazCom) Hazard Determination § 47.21 Identifying hazardous chemicals....

  6. 30 CFR 47.21 - Identifying hazardous chemicals.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... standards in 30 CFR chapter I. (3) Occupational Safety and Health Administration (OSHA), 29 CFR part 1910... 30 Mineral Resources 1 2014-07-01 2014-07-01 false Identifying hazardous chemicals. 47.21 Section... TRAINING HAZARD COMMUNICATION (HazCom) Hazard Determination § 47.21 Identifying hazardous chemicals....

  7. 30 CFR 47.21 - Identifying hazardous chemicals.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... standards in 30 CFR chapter I. (3) Occupational Safety and Health Administration (OSHA), 29 CFR part 1910... 30 Mineral Resources 1 2013-07-01 2013-07-01 false Identifying hazardous chemicals. 47.21 Section... TRAINING HAZARD COMMUNICATION (HazCom) Hazard Determination § 47.21 Identifying hazardous chemicals....

  8. Gasoline identifier based on SH0 plate acoustic waves.

    PubMed

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

    2016-08-01

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

  9. Identifying, Measuring and Monitoring Value during Project Development

    ERIC Educational Resources Information Center

    Kliniotou, Maria

    2004-01-01

    This paper describes the findings of the research done by Loughborough University in conjunction with ten construction industry collaborators in an attempt to identify what construction professionals mean by value. The aim of the research is to establish a common approach to identify value in projects and to monitor its development throughout the…

  10. 36 CFR 1223.16 - How are vital records identified?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... ADMINISTRATION RECORDS MANAGEMENT MANAGING VITAL RECORDS § 1223.16 How are vital records identified? Agencies identify vital records in the context of the emergency management function. Vital records are those that are needed to perform the most critical functions of the agency and those needed to protect legal...

  11. 49 CFR 7.6 - Deletion of identifying detail.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 1 2010-10-01 2010-10-01 false Deletion of identifying detail. 7.6 Section 7.6 Transportation Office of the Secretary of Transportation PUBLIC AVAILABILITY OF INFORMATION Information Required To Be Made Public by DOT § 7.6 Deletion of identifying detail. Whenever it is determined to...

  12. 75 FR 60309 - Furnishing Identifying Number of Tax Return Preparer

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-30

    ... Treasury Department and the IRS published in the Federal Register (75 FR 14539) a notice of proposed... Internal Revenue Service 26 CFR Parts 1 and 602 RIN 1545-BI28 Furnishing Identifying Number of Tax Return... how the IRS will define the identifying number of tax return preparers and set forth requirements...

  13. 44 CFR 5.27 - Deletion of identifying details.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

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

  14. Identifying costs for capitation in psychiatric case management.

    PubMed

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

    1998-01-01

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

  15. The Language Adviser's Role: Identifying and Responding to Needs

    ERIC Educational Resources Information Center

    Reinders, Hayo; Hacker, Penny; Lewis, Marilyn

    2004-01-01

    Tertiary institutions increasingly offer language advisory sessions for second language students and staff. Advisers help students to identify language and learning needs, they recommend resources and strategies and they provide feedback and encouragement. Especially in the first few sessions, identifying and prioritising needs are arguably among…

  16. 26 CFR 31.6109-1 - Supplying of identifying numbers.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 15, 1974. See 26 CFR § 31.6109-1 (revised as of April 1, 1973) for provisions with respect to... 26 Internal Revenue 15 2010-04-01 2010-04-01 false Supplying of identifying numbers. 31.6109-1... Subtitle F, Internal Revenue Code of 1954) § 31.6109-1 Supplying of identifying numbers. (a) In...

  17. 26 CFR 1.6109-1 - Identifying numbers.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ..., see 26 CFR § 1.6109-1 (revised as of April 1, 1973). ... 26 Internal Revenue 13 2011-04-01 2011-04-01 false Identifying numbers. 1.6109-1 Section 1.6109-1...) INCOME TAXES (CONTINUED) Miscellaneous Provisions § 1.6109-1 Identifying numbers. (a) Information to...

  18. 26 CFR 1.6109-1 - Identifying numbers.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ..., see 26 CFR § 1.6109-1 (revised as of April 1, 1973). ... 26 Internal Revenue 13 2010-04-01 2010-04-01 false Identifying numbers. 1.6109-1 Section 1.6109-1...) INCOME TAXES Miscellaneous Provisions § 1.6109-1 Identifying numbers. (a) Information to be...

  19. 28 CFR 22.22 - Revelation of identifiable data.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... STATISTICAL INFORMATION § 22.22 Revelation of identifiable data. (a) Except as noted in paragraph (b) of this section, research and statistical information relating to a private person may be revealed in identifiable... Act. (3) Persons or organizations for research or statistical purposes. Information may only...

  20. Identifying and integrating helpful and harmful religious beliefs into psychotherapy.

    PubMed

    Rosenfield, George W

    2010-12-01

    The 2 main roles of the psychotherapist involve identifying and understanding the client's problems/strengths and treating problems. Suggestions are offered to guide addressing or avoiding religious beliefs in both roles. Types of religious beliefs that contribute to distress, particularly for youth, are identified and treatment options are offered. PMID:21198239

  1. 28 CFR 22.22 - Revelation of identifiable data.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... STATISTICAL INFORMATION § 22.22 Revelation of identifiable data. (a) Except as noted in paragraph (b) of this section, research and statistical information relating to a private person may be revealed in identifiable... Act. (3) Persons or organizations for research or statistical purposes. Information may only...

  2. 28 CFR 22.22 - Revelation of identifiable data.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... STATISTICAL INFORMATION § 22.22 Revelation of identifiable data. (a) Except as noted in paragraph (b) of this section, research and statistical information relating to a private person may be revealed in identifiable... Act. (3) Persons or organizations for research or statistical purposes. Information may only...

  3. 28 CFR 22.22 - Revelation of identifiable data.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... STATISTICAL INFORMATION § 22.22 Revelation of identifiable data. (a) Except as noted in paragraph (b) of this section, research and statistical information relating to a private person may be revealed in identifiable... Act. (3) Persons or organizations for research or statistical purposes. Information may only...

  4. 28 CFR 22.22 - Revelation of identifiable data.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... STATISTICAL INFORMATION § 22.22 Revelation of identifiable data. (a) Except as noted in paragraph (b) of this section, research and statistical information relating to a private person may be revealed in identifiable... Act. (3) Persons or organizations for research or statistical purposes. Information may only...

  5. Public participation GIS: a method for identifying ecosystems services

    USGS Publications Warehouse

    Brown, Greg; Montag, Jessica; Lyon, Katie

    2012-01-01

    This study evaluated the use of an Internet-based public participation geographic information system (PPGIS) to identify ecosystem services in Grand County, Colorado. Specific research objectives were to examine the distribution of ecosystem services, identify the characteristics of participants in the study, explore potential relationships between ecosystem services and land use and land cover (LULC) classifications, and assess the methodological strengths and weakness of the PPGIS approach for identifying ecosystem services. Key findings include: (1) Cultural ecosystem service opportunities were easiest to identify while supporting and regulatory services most challenging, (2) participants were highly educated, knowledgeable about nature and science, and have a strong connection to the outdoors, (3) some LULC classifications were logically and spatially associated with ecosystem services, and (4) despite limitations, the PPGIS method demonstrates potential for identifying ecosystem services to augment expert judgment and to inform public or environmental policy decisions regarding land use trade-offs.

  6. [Comparison of different methods in order to identify Proteus spp].

    PubMed

    Castro, S T; Rodríguez, C R; Perazzi, B E; Radice, M; Paz Sticott, M; Muzio, H; Juárez, J; Gutkind, G; Famiglietti, A M R; Santini, P I; Vay, C A

    2006-01-01

    Comparison of different methods in order to identify Proteus spp. The objectives were: (a) to identify Proteus strains to species level, following Farmer's and O'Hara's conventional biochemical reactions; b) to evaluate the sensitivity and specificity of both the API 20E method and a schema of reduced reactions (TSI and MIO agar: motility, indole and ornithine) comparing them with conventional methodology, and c) to evaluate the utility of SDS-PAGE (total proteins) in order to identify Proteus strains to species level. Two hundred and five Proteus spp. clinical isolates, were collected between January 1998 and September 2004, from inpatients and outpatients at Hospital de Clinicas. Strains were identified by means of conventional methodology, the API 20E method, and a schema of reduced reactions. SDS-PAGE (total proteins) was used in 48 out of the 205 strains. The API 20E method identified 79 out of 87 (90.8%) strains of P. mirabilis, 103 out of 103 P. vulgaris complex, and 15 out of 15 P. penneri. Eight strains of P. mirabilis were identified as Proteus spp., the acid production from maltose being necessary to identify them to species level. The schema of reduced reactions identified 205 out of 205 (100%) strains, that is, this schema of reduced reactions identified all the strains to species level without any additional tests, in marked contrast to the API 20E method. The SDS-PAGE (total proteins) identified the three species of the genus, even if the strains of P. mirabilis showed different biochemical reactions. PMID:17152651

  7. Identifiability of PBPK models with applications to dimethylarsinic acid exposure.

    PubMed

    Garcia, Ramon I; Ibrahim, Joseph G; Wambaugh, John F; Kenyon, Elaina M; Setzer, R Woodrow

    2015-12-01

    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 discete 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. PMID:26194069

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

    PubMed

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

    2016-01-01

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

  9. Identifying influential nodes in complex networks based on expansion factor

    NASA Astrophysics Data System (ADS)

    Liu, Dong; Jing, Yun; Chang, Baofang

    2016-03-01

    Identifying the top influential spreaders in a network has practical significance. In this paper, we propose a novel centrality to identify influential spreaders based on expansion factor. Nodes with high expansion factor centrality (EFC) have strong spreading capability. During the course of the work, an improved strategy is proposed to reduce the time complexity of EFC. We discuss the correlations between EFC and the other five classical indicators. Simulation results on the Susceptible-Infected-Removed (SIR) model manifest that EFC can identify influential nodes and find some critical influential nodes neglected by other indicators.

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

    NASA Technical Reports Server (NTRS)

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

    1972-01-01

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

  11. Individual heterogeneity and identifiability in capture-recapture models

    USGS Publications Warehouse

    Link, W.A.

    2004-01-01

    Individual heterogeneity in detection probabilities is a far more serious problem for capture-recapture modeling than has previously been recognized. In this note, I illustrate that population size is not an identifiable parameter under the general closed population mark-recapture model Mh. The problem of identifiability is obvious if the population includes individuals with pi = 0, but persists even when it is assumed that individual detection probabilities are bounded away from zero. Identifiability may be attained within parametric families of distributions for pi, but not among parametric families of distributions. Consequently, in the presence of individual heterogeneity in detection probability, capture-recapture analysis is strongly model dependent.

  12. Method and system for identifying and authenticating an object

    NASA Technical Reports Server (NTRS)

    Schramm, Jr., Harry F. (Inventor)

    2009-01-01

    An object has a taggant placed in a first portion thereof and has a visible symbol placed on a second portion thereof. When the object is to be identified and authenticated, the taggant is made to radiate with a specific energy signature. The energy signature and at least one image of the symbol are recorded along with a relative location that identifies the first portion of the object. The combination of the energy signature, symbol image and relative location are used to repeatedly identify and authenticate the object.

  13. GENE EXPRESSION PROFILING TO IDENTIFY BIOMARKERS OF REPRODUCTIVE TOXICITY

    EPA Science Inventory

    SOT 2005 SESSION ABSTRACT

    GENE EXPRESSION PROFILING TO IDENTIFY BIOMARKERS OF REPRODUCTIVE TOXICITY

    David J. Dix. National Health and Environmental Effects Research Laboratory, Office of Research and Development, US Environmental Protection Agency, Research Triangle...

  14. 19. Engine identified as a single cylinder vacuum assist engine ...

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

    19. Engine identified as a single cylinder vacuum assist engine for the Filer and Stowell 15-inch continuous mill. - Carnegie Steel-Ohio Works, Steam Engines, 912 Salt Springs Road, Youngstown, Mahoning County, OH

  15. 21. Engine identified as a 'single cylinder vacuum assist engine ...

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

    21. Engine identified as a 'single cylinder vacuum assist engine for Tod tandem compound engine' showing compressor. - Carnegie Steel-Ohio Works, Steam Engines, 912 Salt Springs Road, Youngstown, Mahoning County, OH

  16. 20. Engine identified as a 'single cylinder vacuum assist engine ...

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

    20. Engine identified as a 'single cylinder vacuum assist engine for the Tod tandem compound engine' showing crank end. - Carnegie Steel-Ohio Works, Steam Engines, 912 Salt Springs Road, Youngstown, Mahoning County, OH

  17. Urban Extension Programs: Faculty Identify Programming Concerns and Needs.

    ERIC Educational Resources Information Center

    Fehlis, Chester P.

    1992-01-01

    A telephone survey of extension directors in 13 urban areas determined current extension organizational structures and programing methods. Results revealed a variety of programing and approaches and identified common problems and frustrations. (JOW)

  18. Field potential soil variability index to identify precision agriculture opportunity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Precision agriculture (PA) technologies used for identifying and managing within-field variability are not widely used despite decades of advancement. Technological innovations in agronomic tools, such as canopy reflectance or electrical conductivity sensors, have created opportunities to achieve a ...

  19. 2. VIEW TOWARD EAST, WEST FACADE Subsequent views identified by ...

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

    2. VIEW TOWARD EAST, WEST FACADE Subsequent views identified by bay. Four bays numbered sequentially one to four from north. - U.S. Military Academy, Ice House, Mills Road at Howze Place, West Point, Orange County, NY

  20. 36 CFR 1223.16 - How are vital records identified?

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... emergency plans and related records that specify how an agency will respond to an emergency. The... identify vital records in the context of the emergency management function. Vital records are those...

  1. Identifying characteristics of children requiring sedation for urodynamics.

    PubMed

    Sweeney, Heidi; Rzepski, Barbara; Hochman, Howard; Kim, Christina; Lerer, Trudy; Ferrer, Fernando

    2008-08-01

    The aim of this study was to identify characteristics of children requiring sedation for urodynamics. Findings suggest children between the ages of 3 and 7 are more likely to require sedation for urodynamics when compared to other age groups.

  2. 3. VIEW OF WEST HEADWALL AND CARVED STONE UNIT IDENTIFYING ...

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

    3. VIEW OF WEST HEADWALL AND CARVED STONE UNIT IDENTIFYING THE BUILDER AND YEAR OF CONSTRUCTION, FACING NORTHEAST. - Cut Stone Bridge, Southern Pacific Railroad line spanning runoff channel at South Spruce Avenue, South San Francisco, San Mateo County, CA

  3. Can Zebrafish be used to Identify Developmentally Neurotoxic Chemicals

    EPA Science Inventory

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

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

    SciTech Connect

    Schreck, Carl

    1991-09-01

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

  5. 7 CFR 70.55 - Check grading officially identified product.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... (CONTINUED) VOLUNTARY GRADING OF POULTRY PRODUCTS AND RABBIT PRODUCTS Grading of Poultry Products and Rabbit... identified poultry or rabbit products may be subject to final check grading prior to their shipment....

  6. 7 CFR 70.55 - Check grading officially identified product.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... (CONTINUED) VOLUNTARY GRADING OF POULTRY PRODUCTS AND RABBIT PRODUCTS Grading of Poultry Products and Rabbit... identified poultry or rabbit products may be subject to final check grading prior to their shipment....

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

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... (CONTINUED) VOLUNTARY GRADING OF POULTRY PRODUCTS AND RABBIT PRODUCTS Grading of Poultry Products and Rabbit... identified poultry or rabbit products may be subject to final check grading prior to their shipment....

  8. 7 CFR 70.55 - Check grading officially identified product.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... (CONTINUED) VOLUNTARY GRADING OF POULTRY PRODUCTS AND RABBIT PRODUCTS Grading of Poultry Products and Rabbit... identified poultry or rabbit products may be subject to final check grading prior to their shipment....

  9. 7 CFR 70.55 - Check grading officially identified product.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... (CONTINUED) VOLUNTARY GRADING OF POULTRY PRODUCTS AND RABBIT PRODUCTS Grading of Poultry Products and Rabbit... identified poultry or rabbit products may be subject to final check grading prior to their shipment....

  10. Identifying Planar Deformation Features Using EBSD and FIB

    NASA Astrophysics Data System (ADS)

    Pickersgill, A. E.; Lee, M. R.

    2015-09-01

    Planar deformation features in quartz grains from the Gow Lake impact structure have been successfully identified and indexed using electron backscatter diffraction in combination with focused ion beam milling.

  11. Experiences of female partners of masculine identifying trans persons

    PubMed Central

    Theron, Liesl; Collier, Kate L.

    2013-01-01

    This study explores the intimate relationship experiences of cisgender (i.e., not transgender) female partners of masculine identifying transgender persons, with a particular focus on these partners’ self-understanding of their sexual orientation. Limited research about this topic has been conducted to date. Semi-structured interviews were conducted with eight South African women who are or have been cisgender female partners of masculine identifying trans persons. Although the interviews showed that the relationship experiences of female partners of masculine identifying trans persons are diverse, several common themes emerged in the narratives. The way that participants labelled their sexual orientation did not change from before to after their relationship with a transgender partner. The participants reported varied family and community responses to their relationships. Specific emotional and informational support needs for women with transgender partners were identified. PMID:23668602

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

    SciTech Connect

    Schreck, Carl

    1993-10-01

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

  13. Identifying Minerals from Their Infra-red Spectra.

    ERIC Educational Resources Information Center

    Paterson, W. G.

    1986-01-01

    Describes a British secondary school's use of a spectrometer to identify minerals. Discusses the origins of mineral spectra, the preparation of the specimen, the actual spectroscopic scanning, and the interpretation of the spectra. (TW)

  14. Experiences of female partners of masculine-identifying trans persons.

    PubMed

    Theron, Liesl; Collier, Kate L

    2013-01-01

    This paper explores the intimate relationship experiences of the cisgender (i.e., not transgender) female partners of masculine-identifying transgender persons, with a particular focus on these partners' self-understanding of their sexual orientation. Limited research about this topic has been conducted to date. Semi-structured interviews were conducted with eight South African women who are or have been cisgender female partners of masculine-identifying trans persons. Although the interviews showed that the relationship experiences of female partners of masculine-identifying trans persons are diverse, several common themes emerged in the narratives. The way that participants labelled their sexual orientation did not change from before to after their relationship with a transgender partner. The participants reported varied family and community responses to their relationships. Specific emotional and informational support needs for women with transgender partners were identified.

  15. Most lay people can correctly identify indigenous venomous snakes.

    PubMed

    Corbett, Stephen W; Anderson, Brian; Nelson, Brett; Bush, Sean; Hayes, William K; Cardwell, Mike D

    2005-10-01

    We attempted to determine how accurately members of the public can identify venomous snakes. Six different snakes indigenous to southern California were displayed in cages for 265 people to view at a street fair. These included 4 nonvenomous snakes and 2 venomous snakes. People were asked whether the snake was venomous and the name of the snake, if they knew it. Overall, people recognized whether a snake was venomous or nonvenomous 81% of the time. They were most accurate at identifying rattlesnakes as being venomous (95%) but incorrectly identified nonvenomous snakes as being venomous 25% of the time. Men were more accurate than women, and adults were more accurate than children. Subjects were less well able to identify the exact species of snakes. The results suggest that there may be no need to capture, kill, or bring a snake to the hospital for identification, at least in this geographic area.

  16. Phenotypic lentivirus screens to identify functional single domain antibodies.

    PubMed

    Schmidt, Florian I; Hanke, Leo; Morin, Benjamin; Brewer, Rebeccah; Brusic, Vesna; Whelan, Sean P J; Ploegh, Hidde L

    2016-01-01

    Manipulation of proteins is key in assessing their in vivo function. Although genetic ablation is straightforward, reversible and specific perturbation of protein function remains a challenge. Single domain antibody fragments, such as camelid-derived VHHs, can serve as inhibitors or activators of intracellular protein function, but functional testing of identified VHHs is laborious. To address this challenge, we have developed a lentiviral screening approach to identify VHHs that elicit a phenotype when expressed intracellularly. We identified 19 antiviral VHHs that protect human A549 cells from lethal infection with influenza A virus (IAV) or vesicular stomatitis virus (VSV), respectively. Both negative-sense RNA viruses are vulnerable to VHHs uniquely specific for their respective nucleoproteins. Antiviral VHHs prevented nuclear import of viral ribonucleoproteins or mRNA transcription, respectively, and may provide clues for novel antiviral reagents. In principle, the screening approach described here should be applicable to identify inhibitors of any pathogen or biological pathway. PMID:27573105

  17. Identifying mechanistic indicators of childhood asthma from blood gene expression

    EPA Science Inventory

    Asthmatic individuals have been identified as a susceptible subpopulation for air pollutants. However, asthma represents a syndrome with multiple probable etiologies, and the identification of these asthma endotypes is critical to accurately define the most susceptible subpopula...

  18. Identifiability of Additive Actuator and Sensor Faults by State Augmentation

    NASA Technical Reports Server (NTRS)

    Joshi, Suresh; Gonzalez, Oscar R.; Upchurch, Jason M.

    2014-01-01

    A class of fault detection and identification (FDI) methods for bias-type actuator and sensor faults is explored in detail from the point of view of fault identifiability. The methods use state augmentation along with banks of Kalman-Bucy filters for fault detection, fault pattern determination, and fault value estimation. A complete characterization of conditions for identifiability of bias-type actuator faults, sensor faults, and simultaneous actuator and sensor faults is presented. It is shown that FDI of simultaneous actuator and sensor faults is not possible using these methods when all sensors have unknown biases. The fault identifiability conditions are demonstrated via numerical examples. The analytical and numerical results indicate that caution must be exercised to ensure fault identifiability for different fault patterns when using such methods.

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

    PubMed

    Carroll, Roberta

    2016-01-01

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

  20. Identifying high-level components in combinational circuits

    SciTech Connect

    Doom, T.; White, J.; Wojcik, A.; Chisholm, G.

    1998-07-01

    The problem of finding meaningful subcircuits in a logic layout appears in many contexts in computer-aided design. Existing techniques rely upon finding exact matchings of subcircuit structure within the layout. These syntactic techniques fail to identify functionally equivalent subcircuits that are differently implemented, optimized, or otherwise obfuscated. The authors present a mechanism for identifying functionally equivalent subcircuits that can overcome many of these limitations. Such semantic matching is particularly useful in the field of design recovery.

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

    PubMed

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

    2016-08-01

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

  2. Whole exome sequencing to identify genetic causes of short stature

    PubMed Central

    Guo, Michael H.; Shen, Yiping; Walvoord, Emily C.; Miller, Timothy C.; Moon, Jennifer E.; Hirschhorn, Joel N; Dauber, Andrew

    2014-01-01

    Background/Aims Short stature is a common reason for presentation to pediatric endocrinology clinics. However, for most patients, no cause for the short stature can be identified. As genetics plays a strong role in height, we sought to identify known and novel genetic causes of short stature. Methods We recruited 14 children with severe short stature of unknown etiology. We conducted whole exome sequencing of the patients and their family members. We used an analysis pipeline to identify rare nonsynonymous genetic variants that cause the short stature. Results We identified a genetic cause of short stature in 5 of the 14 patients. This included cases of Floating Harbor syndrome, Kenny-Caffey syndrome, the progeroid form of Ehlers-Danlos syndrome, as well as two cases of the 3-M syndrome. For remaining patients, we have generated lists of candidate variants. Conclusions Whole exome sequencing can help identify genetic causes of short stature in the context of defined genetic syndromes, but may be less effective in identifying novel genetic causes of short stature in individual families. Utilized in the clinic, whole exome sequencing can provide clinically relevant diagnoses for these patients. Rare syndromic causes of short stature may be under-recognized and under-diagnosed in pediatric endocrinology clinics. PMID:24970356

  3. Structural constraints identified with covariation analysis in ribosomal RNA.

    PubMed

    Shang, Lei; Xu, Weijia; Ozer, Stuart; Gutell, Robin R

    2012-01-01

    Covariation analysis is used to identify those positions with similar patterns of sequence variation in an alignment of RNA sequences. These constraints on the evolution of two positions are usually associated with a base pair in a helix. While mutual information (MI) has been used to accurately predict an RNA secondary structure and a few of its tertiary interactions, early studies revealed that phylogenetic event counting methods are more sensitive and provide extra confidence in the prediction of base pairs. We developed a novel and powerful phylogenetic events counting method (PEC) for quantifying positional covariation with the Gutell lab's new RNA Comparative Analysis Database (rCAD). The PEC and MI-based methods each identify unique base pairs, and jointly identify many other base pairs. In total, both methods in combination with an N-best and helix-extension strategy identify the maximal number of base pairs. While covariation methods have effectively and accurately predicted RNAs secondary structure, only a few tertiary structure base pairs have been identified. Analysis presented herein and at the Gutell lab's Comparative RNA Web (CRW) Site reveal that the majority of these latter base pairs do not covary with one another. However, covariation analysis does reveal a weaker although significant covariation between sets of nucleotides that are in proximity in the three-dimensional RNA structure. This reveals that covariation analysis identifies other types of structural constraints beyond the two nucleotides that form a base pair.

  4. Comparison of Two Computer Algorithms To Identify Surgical Site Infections

    PubMed Central

    Apte, Mandar; Landers, Timothy; Furuya, Yoko; Hyman, Sandra

    2011-01-01

    Abstract Background Surgical site infections (SSIs), the second most common healthcare-associated infections, increase hospital stay and healthcare costs significantly. Traditional surveillance of SSIs is labor-intensive. Mandatory reporting and new non-payment policies for some SSIs increase the need for efficient and standardized surveillance methods. Computer algorithms using administrative, clinical, and laboratory data collected routinely have shown promise for complementing traditional surveillance. Methods Two computer algorithms were created to identify SSIs in inpatient admissions to an urban, academic tertiary-care hospital in 2007 using the International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) diagnosis codes (Rule A) and laboratory culture data (Rule B). We calculated the number of SSIs identified by each rule and both rules combined and the percent agreement between the rules. In a subset analysis, the results of the rules were compared with those of traditional surveillance in patients who had undergone coronary artery bypass graft surgery (CABG). Results Of the 28,956 index hospital admissions, 5,918 patients (20.4%) had at least one major surgical procedure. Among those and readmissions within 30 days, the ICD-9-CM-only rule identified 235 SSIs, the culture-only rule identified 287 SSIs; combined, the rules identified 426 SSIs, of which 96 were identified by both rules. Positive and negative agreement between the rules was 36.8% and 97.1%, respectively, with a kappa of 0.34 (95% confidence interval [CI] 0.27–0.41). In the subset analysis of patients who underwent CABG, of the 22 SSIs identified by traditional surveillance, Rule A identified 19 (86.4%) and Rule B identified 13 (59.1%) cases. Positive and negative agreement between Rules A and B within these “positive controls” was 81.3% and 50.0% with a kappa of 0.37 (95% CI 0.04–0.70). Conclusion Differences in the rates of SSI identified by computer

  5. Two statistics for evaluating parameter identifiability and error reduction

    USGS Publications Warehouse

    Doherty, John; Hunt, Randall J.

    2009-01-01

    Two statistics are presented that can be used to rank input parameters utilized by a model in terms of their relative identifiability based on a given or possible future calibration dataset. Identifiability is defined here as the capability of model calibration to constrain parameters used by a model. Both statistics require that the sensitivity of each model parameter be calculated for each model output for which there are actual or presumed field measurements. Singular value decomposition (SVD) of the weighted sensitivity matrix is then undertaken to quantify the relation between the parameters and observations that, in turn, allows selection of calibration solution and null spaces spanned by unit orthogonal vectors. The first statistic presented, "parameter identifiability", is quantitatively defined as the direction cosine between a parameter and its projection onto the calibration solution space. This varies between zero and one, with zero indicating complete non-identifiability and one indicating complete identifiability. The second statistic, "relative error reduction", indicates the extent to which the calibration process reduces error in estimation of a parameter from its pre-calibration level where its value must be assigned purely on the basis of prior expert knowledge. This is more sophisticated than identifiability, in that it takes greater account of the noise associated with the calibration dataset. Like identifiability, it has a maximum value of one (which can only be achieved if there is no measurement noise). Conceptually it can fall to zero; and even below zero if a calibration problem is poorly posed. An example, based on a coupled groundwater/surface-water model, is included that demonstrates the utility of the statistics. ?? 2009 Elsevier B.V.

  6. Fungi Identify the Geographic Origin of Dust Samples

    PubMed Central

    Grantham, Neal S.; Reich, Brian J.; Pacifici, Krishna; Laber, Eric B.; Menninger, Holly L.; Henley, Jessica B.; Barberán, Albert; Leff, Jonathan W.; Fierer, Noah; Dunn, Robert R.

    2015-01-01

    There is a long history of archaeologists and forensic scientists using pollen found in a dust sample to identify its geographic origin or history. Such palynological approaches have important limitations as they require time-consuming identification of pollen grains, a priori knowledge of plant species distributions, and a sufficient diversity of pollen types to permit spatial or temporal identification. We demonstrate an alternative approach based on DNA sequencing analyses of the fungal diversity found in dust samples. Using nearly 1,000 dust samples collected from across the continental U.S., our analyses identify up to 40,000 fungal taxa from these samples, many of which exhibit a high degree of geographic endemism. We develop a statistical learning algorithm via discriminant analysis that exploits this geographic endemicity in the fungal diversity to correctly identify samples to within a few hundred kilometers of their geographic origin with high probability. In addition, our statistical approach provides a measure of certainty for each prediction, in contrast with current palynology methods that are almost always based on expert opinion and devoid of statistical inference. Fungal taxa found in dust samples can therefore be used to identify the origin of that dust and, more importantly, we can quantify our degree of certainty that a sample originated in a particular place. This work opens up a new approach to forensic biology that could be used by scientists to identify the origin of dust or soil samples found on objects, clothing, or archaeological artifacts. PMID:25875229

  7. Fungi identify the geographic origin of dust samples.

    PubMed

    Grantham, Neal S; Reich, Brian J; Pacifici, Krishna; Laber, Eric B; Menninger, Holly L; Henley, Jessica B; Barberán, Albert; Leff, Jonathan W; Fierer, Noah; Dunn, Robert R

    2015-01-01

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

  8. Expression profiling identifies genes involved in emphysema severity.

    PubMed

    Francis, Santiyagu M Savarimuthu; Larsen, Jill E; Pavey, Sandra J; Bowman, Rayleen V; Hayward, Nicholas K; Fong, Kwun M; Yang, Ian A

    2009-01-01

    Chronic obstructive pulmonary disease (COPD) is a major public health problem. The aim of this study was to identify genes involved in emphysema severity in COPD patients.Gene expression profiling was performed on total RNA extracted from non-tumor lung tissue from 30 smokers with emphysema. Class comparison analysis based on gas transfer measurement was performed to identify differentially expressed genes. Genes were then selected for technical validation by quantitative reverse transcriptase-PCR (qRT-PCR) if also represented on microarray platforms used in previously published emphysema studies. Genes technically validated advanced to tests of biological replication by qRT-PCR using an independent test set of 62 lung samples.Class comparison identified 98 differentially expressed genes (p < 0.01). Fifty-one of those genes had been previously evaluated in differentiation between normal and severe emphysema lung. qRT-PCR confirmed the direction of change in expression in 29 of the 51 genes and 11 of those validated, remaining significant at p < 0.05. Biological replication in an independent cohort confirmed the altered expression of eight genes, with seven genes differentially expressed by greater than 1.3 fold, identifying these as candidate determinants of emphysema severity.Gene expression profiling of lung from emphysema patients identified seven candidate genes associated with emphysema severity including COL6A3, SERPINF1, ZNHIT6, NEDD4, CDKN2A, NRN1 and GSTM3. PMID:19723343

  9. Expression profiling identifies genes involved in emphysema severity

    PubMed Central

    2009-01-01

    Chronic obstructive pulmonary disease (COPD) is a major public health problem. The aim of this study was to identify genes involved in emphysema severity in COPD patients. Gene expression profiling was performed on total RNA extracted from non-tumor lung tissue from 30 smokers with emphysema. Class comparison analysis based on gas transfer measurement was performed to identify differentially expressed genes. Genes were then selected for technical validation by quantitative reverse transcriptase-PCR (qRT-PCR) if also represented on microarray platforms used in previously published emphysema studies. Genes technically validated advanced to tests of biological replication by qRT-PCR using an independent test set of 62 lung samples. Class comparison identified 98 differentially expressed genes (p < 0.01). Fifty-one of those genes had been previously evaluated in differentiation between normal and severe emphysema lung. qRT-PCR confirmed the direction of change in expression in 29 of the 51 genes and 11 of those validated, remaining significant at p < 0.05. Biological replication in an independent cohort confirmed the altered expression of eight genes, with seven genes differentially expressed by greater than 1.3 fold, identifying these as candidate determinants of emphysema severity. Gene expression profiling of lung from emphysema patients identified seven candidate genes associated with emphysema severity including COL6A3, SERPINF1, ZNHIT6, NEDD4, CDKN2A, NRN1 and GSTM3. PMID:19723343

  10. Laboratory evaluation of the IriScan prototype biometric identifier

    SciTech Connect

    Bouchier, F.; Ahrens, J.S.; Wells, G.

    1996-04-01

    One thing that all access control applications have in common is the need to identify those individuals authorized to gain access to an area. Traditionally, the identification is based on something that person possesses, such as a key or badge, or something they know, such as a PIN or password. Biometric identifiers make their decisions based on the physiological or behavioral characteristics of individuals. The potential of biometrics devices to positively identify individuals has made them attractive for use in access control and computer security applications. However, no systems perform perfectly, so it is important to understand what a biometric device`s performance is under real world conditions before deciding to implement one in an access control system. This paper will describe the evaluation of a prototype biometric identifier provided by IriScan Incorporated. This identifier was developed to recognize individual human beings based on the distinctive visual characteristics of the irises of their eyes. The main goal of the evaluation was to determine whether the system has potential as an access control device within the Department of Energy (DOE). The primary interest was an estimate of the accuracy of the system in terms of false accept and false reject rates. Data was also collected to estimate throughput time and user acceptability. The performance of the system during the test will be discussed. Lessons learned during the test which may aid in further testing and simplify implementation of a production system will also be discussed.

  11. Parameter identifiability of power-law biochemical system models.

    PubMed

    Srinath, Sridharan; Gunawan, Rudiyanto

    2010-09-01

    Mathematical modeling has become an integral component in biotechnology, in which these models are frequently used to design and optimize bioprocesses. Canonical models, like power-laws within the Biochemical Systems Theory, offer numerous mathematical and numerical advantages, including built-in flexibility to simulate general nonlinear behavior. The construction of such models relies on the estimation of unknown case-specific model parameters by way of experimental data fitting, also known as inverse modeling. Despite the large number of publications on this topic, this task remains the bottleneck in canonical modeling of biochemical systems. The focus of this paper concerns with the question of identifiability of power-law models from dynamic data, that is, whether the parameter values can be uniquely and accurately identified from time-series data. Existing and newly developed parameter identifiability methods were applied to two power-law models of biochemical systems, and the results pointed to the lack of parametric identifiability as the root cause of the difficulty faced in the inverse modeling. Despite the focus on power-law models, the analyses and conclusions are extendable to other canonical models, and the issue of parameter identifiability is expected to be a common problem in biochemical system modeling. PMID:20197073

  12. Analysis of gene expression profile identifies potential biomarkers for atherosclerosis.

    PubMed

    Liu, Luran; Liu, Yan; Liu, Chang; Zhang, Zhuobo; Du, Yaojun; Zhao, Hao

    2016-10-01

    The present study aimed to identify potential biomarkers for atherosclerosis via analysis of gene expression profiles. The microarray dataset no. GSE20129 was downloaded from the Gene Expression Omnibus database. A total of 118 samples from the peripheral blood of female patients was used, including 47 atherosclerotic and 71 non‑atherosclerotic patients. The differentially expressed genes (DEGs) in the atherosclerosis samples were identified using the Limma package. Gene ontology term and Kyoto Encyclopedia of Genes and Genomes pathway analyses for DEGs were performed using the Database for Annotation, Visualization and Integrated Discovery tool. The recursive feature elimination (RFE) algorithm was applied for feature selection via iterative classification, and support vector machine classifier was used for the validation of prediction accuracy. A total of 430 DEGs in the atherosclerosis samples were identified, including 149 up‑ and 281 downregulated genes. Subsequently, the RFE algorithm was used to identify 11 biomarkers, whose receiver operating characteristic curves had an area under curve of 0.92, indicating that the identified 11 biomarkers were representative. The present study indicated that APH1B, JAM3, FBLN2, CSAD and PSTPIP2 may have important roles in the progression of atherosclerosis in females and may be potential biomarkers for early diagnosis and prognosis as well as treatment targets for this disease. PMID:27573188

  13. Effectively identifying user profiles in network and host metrics

    NASA Astrophysics Data System (ADS)

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

    2010-04-01

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

  14. Early Hemostatic Responses to Trauma Identified Using Hierarchical Clustering Analysis

    PubMed Central

    White, N.J.; Contaifer, D.; Martin, E.J.; Newton, J.C.; Mohammed, B.M.; Bostic, J.L.; Brophy, G.M.; Spiess, B.D.; Pusateri, A.E.; Ward, K.R.; Brophy, D.F.

    2015-01-01

    Background Trauma-induced coagulopathy is a complex multifactorial hemostatic response that is poorly understood. Objectives Identify distinct hemostatic responses to trauma and identify key components of the hemostatic system that vary between responses. Patients/Methods Cross-sectional observational study of adult trauma patients at an urban Level I trauma center Emergency Department. Hierarchical clustering analysis was used to identify distinct clusters of similar subjects using vital signs, injury/shock severity, and by comprehensive assessment of coagulation, clot formation, platelet function, and thrombin generation. Results Of 84 total trauma patients included in the model, three distinct trauma clusters were identified. Cluster 1 (N=57) displayed platelet activation, preserved peak thrombin generation, plasma coagulation dysfunction, moderately decreased fibrinogen concentration, and normal clot formation relative to healthy controls. Cluster 2 (N=18) displayed platelet activation, preserved peak thrombin generation, and preserved fibrinogen concentration with normal clot formation. Cluster 3 (N=9) was the most severely injured and shocked and displayed a strong inflammatory and bleeding phenotype. Platelet dysfunction, thrombin inhibition, plasma coagulation dysfunction, and decreased fibrinogen concentration were present in this cluster. Fibrinolytic activation was present in all clusters, but increased more so in Cluster 3. Trauma clusters were different most noticeably in their relative fibrinogen concentration, peak thrombin generation, and platelet-induced clot contraction. Conclusions Hierarchical clustering analysis identified 3 distinct hemostatic responses to trauma. Further insight into the underlying hemostatic mechanisms responsible for these responses is needed. PMID:25816845

  15. Analysis of gene expression profile identifies potential biomarkers for atherosclerosis

    PubMed Central

    Liu, Luran; Liu, Yan; Liu, Chang; Zhang, Zhuobo; Du, Yaojun; Zhao, Hao

    2016-01-01

    The present study aimed to identify potential biomarkers for atherosclerosis via analysis of gene expression profiles. The microarray dataset no. GSE20129 was downloaded from the Gene Expression Omnibus database. A total of 118 samples from the peripheral blood of female patients was used, including 47 atherosclerotic and 71 non-atherosclerotic patients. The differentially expressed genes (DEGs) in the atherosclerosis samples were identified using the Limma package. Gene ontology term and Kyoto Encyclopedia of Genes and Genomes pathway analyses for DEGs were performed using the Database for Annotation, Visualization and Integrated Discovery tool. The recursive feature elimination (RFE) algorithm was applied for feature selection via iterative classification, and support vector machine classifier was used for the validation of prediction accuracy. A total of 430 DEGs in the atherosclerosis samples were identified, including 149 up- and 281 downregulated genes. Subsequently, the RFE algorithm was used to identify 11 biomarkers, whose receiver operating characteristic curves had an area under curve of 0.92, indicating that the identified 11 biomarkers were representative. The present study indicated that APH1B, JAM3, FBLN2, CSAD and PSTPIP2 may have important roles in the progression of atherosclerosis in females and may be potential biomarkers for early diagnosis and prognosis as well as treatment targets for this disease. PMID:27573188

  16. GTA: a game theoretic approach to identifying cancer subnetwork markers.

    PubMed

    Farahmand, S; Goliaei, S; Ansari-Pour, N; Razaghi-Moghadam, Z

    2016-03-01

    The identification of genetic markers (e.g. genes, pathways and subnetworks) for cancer has been one of the most challenging research areas in recent years. A subset of these studies attempt to analyze genome-wide expression profiles to identify markers with high reliability and reusability across independent whole-transcriptome microarray datasets. Therefore, the functional relationships of genes are integrated with their expression data. However, for a more accurate representation of the functional relationships among genes, utilization of the protein-protein interaction network (PPIN) seems to be necessary. Herein, a novel game theoretic approach (GTA) is proposed for the identification of cancer subnetwork markers by integrating genome-wide expression profiles and PPIN. The GTA method was applied to three distinct whole-transcriptome breast cancer datasets to identify the subnetwork markers associated with metastasis. To evaluate the performance of our approach, the identified subnetwork markers were compared with gene-based, pathway-based and network-based markers. We show that GTA is not only capable of identifying robust metastatic markers, it also provides a higher classification performance. In addition, based on these GTA-based subnetworks, we identified a new bonafide candidate gene for breast cancer susceptibility. PMID:26750920

  17. Utilizing signature-score to identify oncogenic pathways of cholangiocarcinoma

    PubMed Central

    Hsiao, Tzu-Hung; Chen, Hung-I Harry; Lu, Jo-Yang; Lin, Pei-Ying; Keller, Charles; Comerford, Sarah; Tomlinson, Gail E.; Chen, Yidong

    2013-01-01

    Extracting maximal information from gene signature sets (GSSs) via microarray-based transcriptional profiling involves assigning function to up and down regulated genes. Here we present a novel sample scoring method called Signature-score (S-score) which can be used to quantify the expression pattern of tumor samples from previously identified gene signature sets. A simulation result demonstrated an improved accuracy and robustness by S-score method comparing with other scoring methods. By applying the S-score method to cholangiocarcinoma (CAC), an aggressive hepatic cancer that arises from bile ducts cells, we identified enriched oncogenic pathways in two large CAC data sets. Thirteen pathways were enriched in CAC compared with normal liver and bile duct. Moreover, using S-score, we were able to dissect correlations between CAC-associated oncogenic pathways and Gene Ontology function. Two major oncogenic clusters and associated functions were identified. Cluster 1, which included beta-catenin and Ras, showed a positive correlation with the cell cycle, while cluster 2, which included TGF-beta, cytokeratin 19 and EpCAM was inversely correlated with immune function. We also used S-score to identify pathways that are differentially expressed in CAC and hepatocellular carcinoma (HCC), the more common subtype of liver cancer. Our results demonstrate the utility and effectiveness of S-score in assigning functional roles to tumor-associated gene signature sets and in identifying potential therapeutic targets for specific liver cancer subtypes. PMID:23905013

  18. Using local operator fluctuations to identify wave function improvements.

    PubMed

    Williams, Kiel T; Wagner, Lucas K

    2016-07-01

    A method is developed that allows analysis of quantum Monte Carlo simulations to identify errors in trial wave functions. The purpose of this method is to allow for the systematic improvement of variational wave functions by identifying degrees of freedom that are not well described by an initial trial state. We provide proof of concept implementations of this method by identifying the need for a Jastrow correlation factor and implementing a selected multideterminant wave function algorithm for small dimers that systematically decreases the variational energy. Selection of the two-particle excitations is done using the quantum Monte Carlo method within the presence of a Jastrow correlation factor and without the need to explicitly construct the determinants. We also show how this technique can be used to design compact wave functions for transition metal systems. This method may provide a route to analyze and systematically improve descriptions of complex quantum systems in a scalable way. PMID:27575232

  19. Identifiability in biobanks: models, measures, and mitigation strategies

    PubMed Central

    Loukides, Grigorios; Benitez, Kathleen; Clayton, Ellen Wright

    2013-01-01

    The collection and sharing of person-specific biospecimens has raised significant questions regarding privacy. In particular, the question of identifiability, or the degree to which materials stored in biobanks can be linked to the name of the individuals from which they were derived, is under scrutiny. The goal of this paper is to review the extent to which biospecimens and affiliated data can be designated as identifiable. To achieve this goal, we summarize recent research in identifiability assessment for DNA sequence data, as well as associated demographic and clinical data, shared via biobanks. We demonstrate the variability of the degree of risk, the factors that contribute to this variation, and potential ways to mitigate and manage such risk. Finally, we discuss the policy implications of these findings, particularly as they pertain to biobank security and access policies. We situate our review in the context of real data sharing scenarios and biorepositories. PMID:21739176

  20. A Study of Scientometric Methods to Identify Emerging Technologies

    SciTech Connect

    Abercrombie, Robert K; Udoeyop, Akaninyene W

    2011-01-01

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

  1. Proteomic and Genetic Approaches Identify Syk as an AML Target

    PubMed Central

    Hahn, Cynthia K.; Berchuck, Jacob E.; Ross, Kenneth N.; Kakoza, Rose M.; Clauser, Karl; Schinzel, Anna C.; Ross, Linda; Galinsky, Ilene; Davis, Tina N.; Silver, Serena J.; Root, David E.; Stone, Richard M.; DeAngelo, Daniel J.; Carroll, Martin; Hahn, William C.; Carr, Steven A.; Golub, Todd R.; Kung, Andrew L.; Stegmaier, Kimberly

    2009-01-01

    SUMMARY Cell-based screening can facilitate rapid identification of compounds inducing complex cellular phenotypes. Advancing a compound toward the clinic, however, generally requires identification of precise mechanisms of action. We previously found that epidermal growth factor receptor (EGFR) inhibitors induce acute myeloid leukemia (AML) differentiation via a non-EGFR mechanism. In this report, we integrated proteomic and RNAi-based strategies to identify their off-target anti-AML mechanism. These orthogonal approaches identified Syk as a target in AML. Genetic and pharmacological inactivation of Syk with a drug in clinical trial for other indications promoted differentiation of AML cells and attenuated leukemia growth in vivo. These results demonstrate the power of integrating diverse chemical, proteomic, and genomic screening approaches to identify therapeutic strategies for cancer. PMID:19800574

  2. Identifying splicing regulatory elements with de Bruijn graphs.

    PubMed

    Badr, Eman; Heath, Lenwood S

    2014-12-01

    Splicing regulatory elements (SREs) are short, degenerate sequences on pre-mRNA molecules that enhance or inhibit the splicing process via the binding of splicing factors, proteins that regulate the functioning of the spliceosome. Existing methods for identifying SREs in a genome are either experimental or computational. Here, we propose a formalism based on de Bruijn graphs that combines genomic structure, word count enrichment analysis, and experimental evidence to identify SREs found in exons. In our approach, SREs are not restricted to a fixed length (i.e., k-mers, for a fixed k). As a result, we identify 2001 putative exonic enhancers and 3080 putative exonic silencers for human genes, with lengths varying from 6 to 15 nucleotides. Many of the predicted SREs overlap with experimentally verified binding sites. Our model provides a novel method to predict variable length putative regulatory elements computationally for further experimental investigation.

  3. Identifying, studying and making good use of macromolecular crystals

    PubMed Central

    Calero, Guillermo; Cohen, Aina E.; Luft, Joseph R.; Newman, Janet; Snell, Edward H.

    2014-01-01

    Structural biology has contributed tremendous knowledge to the understanding of life on the molecular scale. The Protein Data Bank, a depository of this structural knowledge, currently contains over 100 000 protein structures, with the majority stemming from X-ray crystallography. As the name might suggest, crystallography requires crystals. As detectors become more sensitive and X-ray sources more intense, the notion of a crystal is gradually changing from one large enough to embellish expensive jewellery to objects that have external dimensions of the order of the wavelength of visible light. Identifying these crystals is a prerequisite to their study. This paper discusses developments in identifying these crystals during crystallization screening and distinguishing them from other potential outcomes. The practical aspects of ensuring that once a crystal is identified it can then be positioned in the X-ray beam for data collection are also addressed. PMID:25084371

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

    PubMed

    Levinson, Sarah; Cagan, Ross L

    2016-09-13

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

  5. Identifying interactions between chemical entities in biomedical text.

    PubMed

    Lamurias, Andre; Ferreira, João D; Couto, Francisco M

    2014-01-01

    Interactions between chemical compounds described in biomedical text can be of great importance to drug discovery and design, as well as pharmacovigilance. We developed a novel system, \\"Identifying Interactions between Chemical Entities\\" (IICE), to identify chemical interactions described in text. Kernel-based Support Vector Machines first identify the interactions and then an ensemble classifier validates and classifies the type of each interaction. This relation extraction module was evaluated with the corpus released for the DDI Extraction task of SemEval 2013, obtaining results comparable to state-of-the-art methods for this type of task. We integrated this module with our chemical named entity recognition module and made the whole system available as a web tool at www.lasige.di.fc.ul.pt/webtools/iice. PMID:25339081

  6. Identifying, studying and making good use of macromolecular crystals.

    PubMed

    Calero, Guillermo; Cohen, Aina E; Luft, Joseph R; Newman, Janet; Snell, Edward H

    2014-08-01

    Structural biology has contributed tremendous knowledge to the understanding of life on the molecular scale. The Protein Data Bank, a depository of this structural knowledge, currently contains over 100,000 protein structures, with the majority stemming from X-ray crystallography. As the name might suggest, crystallography requires crystals. As detectors become more sensitive and X-ray sources more intense, the notion of a crystal is gradually changing from one large enough to embellish expensive jewellery to objects that have external dimensions of the order of the wavelength of visible light. Identifying these crystals is a prerequisite to their study. This paper discusses developments in identifying these crystals during crystallization screening and distinguishing them from other potential outcomes. The practical aspects of ensuring that once a crystal is identified it can then be positioned in the X-ray beam for data collection are also addressed. PMID:25084371

  7. Agreement among response to intervention criteria for identifying responder status

    PubMed Central

    Barth, Amy E.; Stuebing, Karla K.; Anthony, Jason L.; Denton, Carolyn A.; Mathes, Patricia G.; Fletcher, Jack M.; Francis, David J.

    2008-01-01

    In order to better understand the extent to which operationalizations of response to intervention (RTI) overlap and agree in identifying adequate and inadequate responders, an existing database of 399 first grade students was evaluated in relation to cut-points, measures, and methods frequently cited for the identification of inadequate responders to instruction. A series of 543 2×2 measures of association (808 total comparisons) were computed to address the agreement of different operationalizations of RTI. The results indicate that agreement is generally poor and that different methods tend to identify different students as inadequate responders, although agreement for identifying adequate responders is higher. Approaches to the assessment of responder status must use multiple criteria and avoid formulaic decision making. PMID:19081758

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

    NASA Astrophysics Data System (ADS)

    Ma, Ling-ling; Ma, Chuang; Zhang, Hai-Feng; Wang, Bing-Hong

    2016-06-01

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

  9. Waveform correlation methods for identifying populations of calibration events

    SciTech Connect

    Harris, D.B.

    1997-07-01

    An approach for systematically screening large volumes of continuous data for repetitive events identified as mining explosions on basis of temporal and amplitude population characteristics. The method extends event clustering through waveform correlation with a new source-region-specific detector. The new signal subspace detector generalizes the matched filter and can be used to increase the number of events associated with a given cluster, thereby increasing the reliability of diagnostic cluster population characteristics. The method can be applied to obtain bootstrap ground truth explosion waveforms for testing discriminants, where actual ground truth is absent. The same events, if associated with to a particular mine, may help calibrate velocity models. The method may also assist earthquake hazard risk assessment by providing what amounts to blasting logs for identified mines. The cluster event lists can be reconciled against earthquake catalogs to screen explosions, otherwise hard to identify from the catalogs.

  10. Identifying splicing regulatory elements with de Bruijn graphs.

    PubMed

    Badr, Eman; Heath, Lenwood S

    2014-12-01

    Splicing regulatory elements (SREs) are short, degenerate sequences on pre-mRNA molecules that enhance or inhibit the splicing process via the binding of splicing factors, proteins that regulate the functioning of the spliceosome. Existing methods for identifying SREs in a genome are either experimental or computational. Here, we propose a formalism based on de Bruijn graphs that combines genomic structure, word count enrichment analysis, and experimental evidence to identify SREs found in exons. In our approach, SREs are not restricted to a fixed length (i.e., k-mers, for a fixed k). As a result, we identify 2001 putative exonic enhancers and 3080 putative exonic silencers for human genes, with lengths varying from 6 to 15 nucleotides. Many of the predicted SREs overlap with experimentally verified binding sites. Our model provides a novel method to predict variable length putative regulatory elements computationally for further experimental investigation. PMID:25393830

  11. Using local operator fluctuations to identify wave function improvements

    NASA Astrophysics Data System (ADS)

    Williams, Kiel T.; Wagner, Lucas K.

    2016-07-01

    A method is developed that allows analysis of quantum Monte Carlo simulations to identify errors in trial wave functions. The purpose of this method is to allow for the systematic improvement of variational wave functions by identifying degrees of freedom that are not well described by an initial trial state. We provide proof of concept implementations of this method by identifying the need for a Jastrow correlation factor and implementing a selected multideterminant wave function algorithm for small dimers that systematically decreases the variational energy. Selection of the two-particle excitations is done using the quantum Monte Carlo method within the presence of a Jastrow correlation factor and without the need to explicitly construct the determinants. We also show how this technique can be used to design compact wave functions for transition metal systems. This method may provide a route to analyze and systematically improve descriptions of complex quantum systems in a scalable way.

  12. Identifying Differentially Abundant Metabolic Pathways in Metagenomic Datasets

    NASA Astrophysics Data System (ADS)

    Liu, Bo; Pop, Mihai

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

  13. Spectral Library Searching To Identify Cross-Linked Peptides.

    PubMed

    Schweppe, Devin K; Chavez, Juan D; Navare, Arti T; Wu, Xia; Ruiz, Bianca; Eng, Jimmy K; Lam, Henry; Bruce, James E

    2016-05-01

    Methods harnessing protein cross-linking and mass spectrometry (XL-MS) offer high-throughput means to identify protein-protein interactions (PPIs) and structural interfaces of protein complexes. Yet, specialized data dependent methods and search algorithms are often required to confidently assign peptide identifications to spectra. To improve the efficiency of matching high confidence spectra, we developed a spectral library based approach to search cross-linked peptide data derived from Protein Interaction Reporter (PIR) methods using the spectral library search algorithm, SpectraST. Spectral library matching of cross-linked peptide data from query spectra increased the absolute number of confident peptide relationships matched to spectra and thereby the number of PPIs identified. By matching library spectra from bona fide, previously established PIR-cross-linked peptide relationships, spectral library searching reduces the need for continued, complex mass spectrometric methods to identify peptide relationships, increases coverage of relationship identifications, and improves the accessibility of XL-MS technologies.

  14. Modern Matrons: can they be easily identified by hospital patients?

    PubMed

    Bufton, Sally

    The Modern Matron was introduced into hospital Trusts in April 2002 to improve the basics of patient care. They were to be easily identifiable, highly visible and authoritative figures. This article reports on a quantitative study done to ascertain if patients can identify the Modern Matron in one acute NHS Trust. A researcher-developed questionnaire was sent to 20 Modern Matrons and a different questionnaire was distributed to 72 randomly selected patients. The results demonstrated that only 5% of patients surveyed were able to correctly identify the Modern Matron by their uniform. This may be explained by the response from the Modern Matrons when asked how much time was spent with patients; 67% of their normal working day was taken up with management of staff, paperwork and meetings, leaving very little direct patient time.

  15. Feline polycystic kidney disease mutation identified in PKD1.

    PubMed

    Lyons, Leslie A; Biller, David S; Erdman, Carolyn A; Lipinski, Monika J; Young, Amy E; Roe, Bruce A; Qin, Baifang; Grahn, Robert A

    2004-10-01

    Autosomal dominant polycystic kidney disease (ADPKD) is a commonly inherited disorder in humans that causes the formation of fluid-filled renal cysts, often leading to renal failure. PKD1 mutations cause 85% of ADPKD. Feline PKD is autosomal dominant and has clinical presentations similar to humans. PKD affects approximately 38% of Persian cats worldwide, which is approximately 6% of cats, making it the most prominent inherited feline disease. Previous analyses have shown significant linkage between the PKD phenotype and microsatellite markers linked to the feline homolog for PKD1. In this report, the feline PKD1 gene was scanned for causative mutations and a C>A transversion was identified at c.10063 (human ref NM_000296) in exon 29, resulting in a stop mutation at position 3284, which suggests a loss of approximately 25% of the C-terminus of the protein. The same mutation has not been identified in humans, although similar regions of the protein are truncated. The C>A transversion has been identified in the heterozygous state in 48 affected cats examined, including 41 Persians, a Siamese, and several other breeds that have been known to outcross with Persians. In addition, the mutation is segregating concordantly in all available PKD families. No unaffected cats have been identified with the mutation. No homozygous cats have been identified, supporting the suggestion that the mutation is embryonic lethal. These data suggest that the stop mutation causes feline PKD, providing a test to identify cats that will develop PKD and demonstrating that the domestic cat is an ideal model for human PKD. PMID:15466259

  16. Intraoperative Near-Infrared Imaging Can Identify Pulmonary Nodules

    PubMed Central

    Okusanya, Olugbenga T.; Holt, David; Heitjan, Daniel; Deshpande, Charuhas; Venegas, Ollin; Jiang, Jack; Judy, Ryan; DeJesus, Elizabeth; Madajewski, Brian; Oh, Kenny; Albelda, Steven M.; Nie, Shuming; Singhal, Sunil

    2014-01-01

    Background Over 80,000 people undergo pulmonary resection for a lung nodule in the United States each year. Small nodules are frequently missed or difficult to find despite preoperative imaging. We hypothesized that near-infrared (NIR) imaging technology could be used to identify and locate lung nodules during surgery. Methods We enrolled 18 patients who were diagnosed with a pulmonary nodule that required resection. All patients had a fine-cut 1mm computed tomography scan preoperatively. The patients were given systemic 5 mg/kg indocyanine green (ICG) and then underwent an open thoracotomy 24 hours later. NIR imaging was used to identify the primary nodule and search for additional nodules that were not found by visual inspection or manual palpation of the ipsilateral lung. Results Manual palpation and visual inspection identified all 18 primary pulmonary nodules and no additional lesions. Intraoperative NIR imaging detected 16 out of the 18 primary nodules. NIR imaging also identified 5 additional subcentimeter nodules: 3 metastatic adenocarcinomas and 2 metastatic sarcomas. This technology could identify nodules as small as 0.2 cm and as deep as 1.3 cm from the pleural surface. This approach discovered 3 nodules that were in different lobes than the primary tumor. Nodule fluorescence was independent of size, metabolic activity, histology, tumor grade and vascularity. Conclusions This is the first-in-human demonstration of identifying pulmonary nodules during Thoracic surgery with NIR imaging without a priori knowledge of their location or existence. NIR imaging can detect pulmonary nodules during lung resections that are poorly visualized on computed tomography and difficult to discriminate on finger palpation. PMID:25106680

  17. Advance care planning: identifying system-specific barriers and facilitators

    PubMed Central

    Hagen, N.A.; Howlett, J.; Sharma, N.C.; Biondo, P.; Holroyd-Leduc, J.; Fassbender, K.; Simon, J.

    2015-01-01

    Background Advance care planning (acp) is an important process in health care today. How to prospectively identify potential local barriers and facilitators to uptake of acp across a complex, multi-sector, publicly funded health care system and how to develop specific mitigating strategies have not been well characterized. Methods We surveyed a convenience sample of clinical and administrative health care opinion leaders across the province of Alberta to characterize system-specific barriers and facilitators to uptake of acp. The survey was based on published literature about the barriers to and facilitators of acp and on the Michie Theoretical Domains Framework. Results Of 88 surveys, 51 (58%) were returned. The survey identified system-specific barriers that could challenge uptake of acp. The factors were categorized into four main domains. Three examples of individual system-specific barriers were “insufficient public engagement and misunderstanding,” “conflict among different provincial health service initiatives,” and “lack of infrastructure.” Local system-specific barriers and facilitators were subsequently explored through a semi-structured informal discussion group involving key informants. The group identified approaches to mitigate specific barriers. Conclusions Uptake of acp is a priority for many health care systems, but bringing about change in multi-sector health care systems is complex. Identifying system-specific barriers and facilitators to the uptake of innovation are important elements of successful knowledge translation. We developed and successfully used a simple and inexpensive process to identify local system-specific barriers and enablers to uptake of acp, and to identify specific mitigating strategies. PMID:26300673

  18. Recent developments in methods for identifying reaction coordinates.

    PubMed

    Li, Wenjin; Ma, Ao

    2014-01-01

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

  19. A selection system for identifying accessible sites in target RNAs.

    PubMed Central

    Pan, W H; Devlin, H F; Kelley, C; Isom, H C; Clawson, G A

    2001-01-01

    Although ribozymes offer tremendous potential for posttranscriptionally controlling expression of targeted genes, their utility is often limited by the accessibility of the targeted regions within the RNA transcripts. Here we describe a method that identifies RNA regions that are accessible to oligonucleotides. Based on this selection protocol, we show that construction of hammerhead ribozymes targeted to the identified regions results in catalytic activities that are consistently and substantially greater than those of ribozymes designed on the basis of computer modeling. Identification of accessible sites should also be widely applicable to design of antisense oligonucleotides and DNAzymes. PMID:11345439

  20. Using ILP to Identify Pathway Activation Patterns in Systems Biology

    PubMed Central

    Neaves, Samuel R; Millard, Louise A C; Tsoka, Sophia

    2016-01-01

    We show a logical aggregation method that, combined with propositionalization methods, can construct novel structured biological features from gene expression data. We do this to gain understanding of pathway mechanisms, for instance, those associated with a particular disease. We illustrate this method on the task of distinguishing between two types of lung cancer; Squamous Cell Carcinoma (SCC) and Adenocarcinoma (AC). We identify pathway activation patterns in pathways previously implicated in the development of cancers. Our method identified a model with comparable predictive performance to the winning algorithm of a recent challenge, while providing biologically relevant explanations that may be useful to a biologist. PMID:27478883

  1. Identifying approximate linear models for simple nonlinear systems

    NASA Technical Reports Server (NTRS)

    Horta, L. G.; Juang, J.-N.

    1985-01-01

    This paper addresses the identification (realization) of approximate linear models from response data for certain nonlinear dynamic systems. Response characteristics for several typical nonlinear joints are analyzed mathematically and represented by series expansions. The parameters of the series expansion are then compared with the modal parameters of a linear model identified by the Eigensystem Realization Algorithm. The agreement of the identified model and the analytically derived representation is excellent for the cases studied. Also laboratory data from a model which exhibited stiffening behavior was analyzed using the Eigensystem Realization algorithm and Fast Fourier Transform. The laboratory experiment demonstrated the ability of the technique to recover the model characteristics using real data.

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

    PubMed

    Yee, Chia Choon

    2002-01-01

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

  3. PlateRunner: A Search Engine to Identify EMR Boilerplates.

    PubMed

    Divita, Guy; Workman, T Elizabeth; Carter, Marjorie E; Redd, Andrew; Samore, Matthew H; Gundlapalli, Adi V

    2016-01-01

    Medical text contains boilerplated content, an artifact of pull-down forms from EMRs. Boilerplated content is the source of challenges for concept extraction on clinical text. This paper introduces PlateRunner, a search engine on boilerplates from the US Department of Veterans Affairs (VA) EMR. Boilerplates containing concepts should be identified and reviewed to recognize challenging formats, identify high yield document titles, and fine tune section zoning. This search engine has the capability to filter negated and asserted concepts, save and search query results. This tool can save queries, search results, and documents found for later analysis.

  4. Systems and Techniques for Identifying and Avoiding Ice

    NASA Technical Reports Server (NTRS)

    Hansman, R. John

    1995-01-01

    In-flight icing is one of the most difficult aviation weather hazards facing general aviation. Because most aircraft in the general aviation category are not certified for flight into known icing conditions, techniques for identifying and avoiding in-flight ice are important to maintain safety while increasing the utility and dispatch capability which is part of the AGATE vision. This report summarizes a brief study effort which: (1) Reviewed current ice identification, forecasting, and avoidance techniques; (2) Assessed feasibility of improved forecasting and ice avoidance procedures; and (3) Identified key issues for the development of improved capability with regard to in-flight icing.

  5. Applications for unique identifiers in the geological sciences

    NASA Astrophysics Data System (ADS)

    Klump, J.; Lehnert, K. A.

    2012-12-01

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

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

    PubMed

    Carroll, Roberta

    2016-01-01

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

  7. Identifiability of PBPK Models with Applications to Dimethylarsinic Acid Exposure

    EPA Science Inventory

    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 diff...

  8. The Use of Citation Counting to Identify Research Trends

    ERIC Educational Resources Information Center

    Rothman, Harry; Woodhead, Michael

    1971-01-01

    The analysis and application of manpower statistics to identify some long-term international research trends in economic entomology and pest conrol are described. Movements in research interests, particularly towards biological methods of control, correlations between these sectors, and the difficulties encountered in the construction of a…

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

    ERIC Educational Resources Information Center

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

    2001-01-01

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

  10. Identifying Psychopathy Subtypes on the Basis of Personality Structure

    ERIC Educational Resources Information Center

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

    2004-01-01

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

  11. Identifying Exemplary Criteria to Evaluate Studio Products in Art Education

    ERIC Educational Resources Information Center

    Sabol, F. Robert

    2006-01-01

    Assessments have become commonplace in every art program in the country. They depend on guidelines often called "criteria," which is described as "characteristics of something by which its quality can be judged or a decision about it [the quality of the object] can be made." Art teachers routinely struggle to identify criteria that capture the…

  12. GENE EXPRESSION PROFILING TO IDENTIFY MECHANISMS OF MALE REPRODUCTIVE TOXICITY

    EPA Science Inventory

    Gene Expression Profiling to Identify Mechanisms of Male Reproductive Toxicity
    David J. Dix
    National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, 27711, USA.
    Ab...

  13. Identifying the Enemy: Social Categorization and National Security Policy

    ERIC Educational Resources Information Center

    Unsworth, Kristene

    2010-01-01

    This dissertation seeks to understand the interplay between informal articulations of social categories and formal instantiations of those categories in official language. Specifically, it explores the process of social categorization as it is used to identify threats to national security. The research employed a qualitative, document-based,…

  14. 44 CFR 9.10 - Identify impacts of proposed actions.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ..., DEPARTMENT OF HOMELAND SECURITY GENERAL FLOODPLAIN MANAGEMENT AND PROTECTION OF WETLANDS § 9.10 Identify... adverse impacts associated with the occupancy and modification of floodplains and wetlands and the potential direct and indirect support of floodplain and wetland development that could result from...

  15. 44 CFR 9.10 - Identify impacts of proposed actions.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ..., DEPARTMENT OF HOMELAND SECURITY GENERAL FLOODPLAIN MANAGEMENT AND PROTECTION OF WETLANDS § 9.10 Identify... adverse impacts associated with the occupancy and modification of floodplains and wetlands and the potential direct and indirect support of floodplain and wetland development that could result from...

  16. 44 CFR 9.10 - Identify impacts of proposed actions.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ..., DEPARTMENT OF HOMELAND SECURITY GENERAL FLOODPLAIN MANAGEMENT AND PROTECTION OF WETLANDS § 9.10 Identify... adverse impacts associated with the occupancy and modification of floodplains and wetlands and the potential direct and indirect support of floodplain and wetland development that could result from...

  17. 44 CFR 9.10 - Identify impacts of proposed actions.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ..., DEPARTMENT OF HOMELAND SECURITY GENERAL FLOODPLAIN MANAGEMENT AND PROTECTION OF WETLANDS § 9.10 Identify... adverse impacts associated with the occupancy and modification of floodplains and wetlands and the potential direct and indirect support of floodplain and wetland development that could result from...

  18. 44 CFR 9.10 - Identify impacts of proposed actions.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ..., DEPARTMENT OF HOMELAND SECURITY GENERAL FLOODPLAIN MANAGEMENT AND PROTECTION OF WETLANDS § 9.10 Identify... adverse impacts associated with the occupancy and modification of floodplains and wetlands and the potential direct and indirect support of floodplain and wetland development that could result from...

  19. Identifying structures of continuously-varying weighted networks

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

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

    SciTech Connect

    Schreck, Carl

    1993-03-01

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