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Sample records for microbial genotyping schemes

  1. An Affymetrix Microarray Design for Microbial Genotyping

    Science.gov (United States)

    2009-10-01

    les échantillons qui ne se prêtent pas aux méthodes culturales de la microbiologie classique. La puce à ADN est une technologie qui permet la... area of microbial genotyping there are multiple platforms that can identify one or a few microbial targets in a single assay iteration. For most

  2. Synthetic microbial ecology and the dynamic interplay between microbial genotypes.

    Science.gov (United States)

    Dolinšek, Jan; Goldschmidt, Felix; Johnson, David R

    2016-11-01

    Assemblages of microbial genotypes growing together can display surprisingly complex and unexpected dynamics and result in community-level functions and behaviors that are not readily expected from analyzing each genotype in isolation. This complexity has, at least in part, inspired a discipline of synthetic microbial ecology. Synthetic microbial ecology focuses on designing, building and analyzing the dynamic behavior of ‘ecological circuits’ (i.e. a set of interacting microbial genotypes) and understanding how community-level properties emerge as a consequence of those interactions. In this review, we discuss typical objectives of synthetic microbial ecology and the main advantages and rationales of using synthetic microbial assemblages. We then summarize recent findings of current synthetic microbial ecology investigations. In particular, we focus on the causes and consequences of the interplay between different microbial genotypes and illustrate how simple interactions can create complex dynamics and promote unexpected community-level properties. We finally propose that distinguishing between active and passive interactions and accounting for the pervasiveness of competition can improve existing frameworks for designing and predicting the dynamics of microbial assemblages.

  3. Transforming microbial genotyping: a robotic pipeline for genotyping bacterial strains.

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    Brian O'Farrell

    Full Text Available Microbial genotyping increasingly deals with large numbers of samples, and data are commonly evaluated by unstructured approaches, such as spread-sheets. The efficiency, reliability and throughput of genotyping would benefit from the automation of manual manipulations within the context of sophisticated data storage. We developed a medium- throughput genotyping pipeline for MultiLocus Sequence Typing (MLST of bacterial pathogens. This pipeline was implemented through a combination of four automated liquid handling systems, a Laboratory Information Management System (LIMS consisting of a variety of dedicated commercial operating systems and programs, including a Sample Management System, plus numerous Python scripts. All tubes and microwell racks were bar-coded and their locations and status were recorded in the LIMS. We also created a hierarchical set of items that could be used to represent bacterial species, their products and experiments. The LIMS allowed reliable, semi-automated, traceable bacterial genotyping from initial single colony isolation and sub-cultivation through DNA extraction and normalization to PCRs, sequencing and MLST sequence trace evaluation. We also describe robotic sequencing to facilitate cherrypicking of sequence dropouts. This pipeline is user-friendly, with a throughput of 96 strains within 10 working days at a total cost of 200,000 items were processed by two to three people. Our sophisticated automated pipeline can be implemented by a small microbiology group without extensive external support, and provides a general framework for semi-automated bacterial genotyping of large numbers of samples at low cost.

  4. Plant genotype, microbial recruitment and nutritional security.

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    Patel, Jai S; Singh, Akanksha; Singh, Harikesh B; Sarma, Birinchi K

    2015-01-01

    Agricultural food products with high nutritional value should always be preferred over food products with low nutritional value. Efforts are being made to increase nutritional value of food by incorporating dietary supplements to the food products. The same is more desirous if the nutritional value of food is increased under natural environmental conditions especially in agricultural farms. Fragmented researches have demonstrated possibilities in achieving the same. The rhizosphere is vital in this regard for not only health and nutritional status of plants but also for the microorganisms colonizing the rhizosphere. Remarkably robust composition of plant microbiome with respect to other soil environments clearly suggests the role of a plant host in discriminating its colonizers (Zancarini et al., 2012). A large number of biotic and abiotic factors are believed to manipulate the microbial communities in the rhizosphere. However, plant genotype has proven to be the key in giving the final shape of the rhizosphere microbiome (Berendsen et al., 2012; Marques et al., 2014).

  5. A Microbial Assessment Scheme to measure microbial performance of Food Safety Management Systems.

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    Jacxsens, L; Kussaga, J; Luning, P A; Van der Spiegel, M; Devlieghere, F; Uyttendaele, M

    2009-08-31

    A Food Safety Management System (FSMS) implemented in a food processing industry is based on Good Hygienic Practices (GHP), Hazard Analysis Critical Control Point (HACCP) principles and should address both food safety control and assurance activities in order to guarantee food safety. One of the most emerging challenges is to assess the performance of a present FSMS. The objective of this work is to explain the development of a Microbial Assessment Scheme (MAS) as a tool for a systematic analysis of microbial counts in order to assess the current microbial performance of an implemented FSMS. It is assumed that low numbers of microorganisms and small variations in microbial counts indicate an effective FSMS. The MAS is a procedure that defines the identification of critical sampling locations, the selection of microbiological parameters, the assessment of sampling frequency, the selection of sampling method and method of analysis, and finally data processing and interpretation. Based on the MAS assessment, microbial safety level profiles can be derived, indicating which microorganisms and to what extent they contribute to food safety for a specific food processing company. The MAS concept is illustrated with a case study in the pork processing industry, where ready-to-eat meat products are produced (cured, cooked ham and cured, dried bacon).

  6. Genotyping of B. licheniformis based on a novel multi-locus sequence typing (MLST scheme

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    Madslien Elisabeth H

    2012-10-01

    Full Text Available Abstract Background Bacillus licheniformis has for many years been used in the industrial production of enzymes, antibiotics and detergents. However, as a producer of dormant heat-resistant endospores B. licheniformis might contaminate semi-preserved foods. The aim of this study was to establish a robust and novel genotyping scheme for B. licheniformis in order to reveal the evolutionary history of 53 strains of this species. Furthermore, the genotyping scheme was also investigated for its use to detect food-contaminating strains. Results A multi-locus sequence typing (MLST scheme, based on the sequence of six house-keeping genes (adk, ccpA, recF, rpoB, spo0A and sucC of 53 B. licheniformis strains from different sources was established. The result of the MLST analysis supported previous findings of two different subgroups (lineages within this species, named “A” and “B” Statistical analysis of the MLST data indicated a higher rate of recombination within group “A”. Food isolates were widely dispersed in the MLST tree and could not be distinguished from the other strains. However, the food contaminating strain B. licheniformis NVH1032, represented by a unique sequence type (ST8, was distantly related to all other strains. Conclusions In this study, a novel and robust genotyping scheme for B. licheniformis was established, separating the species into two subgroups. This scheme could be used for further studies of evolution and population genetics in B. licheniformis.

  7. A multi locus variable number of tandem repeat analysis (MLVA scheme for Streptococcus agalactiae genotyping

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    Mereghetti Laurent

    2011-07-01

    Full Text Available Abstract Background Multilocus sequence typing (MLST is currently the reference method for genotyping Streptococcus agalactiae strains, the leading cause of infectious disease in newborns and a major cause of disease in immunocompromised children and adults. We describe here a genotyping method based on multiple locus variable number of tandem repeat (VNTR analysis (MLVA applied to a population of S. agalactiae strains of various origins characterized by MLST and serotyping. Results We studied a collection of 186 strains isolated from humans and cattle and three reference strains (A909, NEM316 and 2603 V/R. Among 34 VNTRs, 6 polymorphic VNTRs loci were selected for use in genotyping of the bacterial population. The MLVA profile consists of a series of allele numbers, corresponding to the number of repeats at each VNTR locus. 98 MLVA genotypes were obtained compared to 51 sequences types generated by MLST. The MLVA scheme generated clusters which corresponded well to the main clonal complexes obtained by MLST. However it provided a higher discriminatory power. The diversity index obtained with MLVA was 0.960 compared to 0.881 with MLST for this population of strains. Conclusions The MLVA scheme proposed here is a rapid, cheap and easy genotyping method generating results suitable for exchange and comparison between different laboratories and for the epidemiologic surveillance of S. agalactiae and analyses of outbreaks.

  8. Features of Variable Number of Tandem Repeats in Yersinia pestis and the Development of a Hierarchical Genotyping Scheme.

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    Yanjun Li

    Full Text Available Variable number of tandem repeats (VNTRs that are widely distributed in the genome of Yersinia pestis proved to be useful markers for the genotyping and source-tracing of this notorious pathogen. In this study, we probed into the features of VNTRs in the Y. pestis genome and developed a simple hierarchical genotyping system based on optimized VNTR loci.Capillary electrophoresis was used in this study for multi-locus VNTR analysis (MLVA in 956 Y. pestis strains. The general features and genetic diversities of 88 VNTR loci in Y. pestis were analyzed with BioNumerics, and a "14+12" loci-based hierarchical genotyping system, which is compatible with single nucleotide polymorphism-based phylogenic analysis, was established.Appropriate selection of target loci reduces the impact of homoplasies caused by the rapid mutation rates of VNTR loci. The optimized "14+12" loci are highly discriminative in genotyping and source-tracing Y. pestis for molecular epidemiological or microbial forensic investigations with less time and lower cost. An MLVA genotyping datasets of representative strains will improve future research on the source-tracing and microevolution of Y. pestis.

  9. Microbe-ID: An open source toolbox for microbial genotyping and species identification

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    Development of tools to identify species, genotypes, or novel strains of invasive organisms is critical for monitoring emergence and implementing rapid response measures. Molecular markers, although critical to identifying species or genotypes, require bioinformatic tools for analysis. However, user...

  10. Microbial counts of food contact surfaces at schools depending on a feeding scheme

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    Nthabiseng Nhlapo

    2014-11-01

    Full Text Available The prominence of disease transmission between individuals in confined environments is a concern, particularly in the educational environment. With respect to school feeding schemes, food contact surfaces have been shown to be potential vehicles of foodborne pathogens. The aim of this study was to assess the cleanliness of the surfaces that come into contact with food that is provided to children through the National School Nutrition Programme in central South Africa. In each school under study, microbiological samples were collected from the preparation surface and the dominant hand and apron of the food handler. The samples were analysed for total viable counts, coliforms, Escherichia coli, Staphylococcus aureus and yeasts and moulds. The criteria specified in the British Columbia Guide for Environmental Health Officers were used to evaluate the results. Total viable counts were high for all surfaces, with the majority of colonies being too numerous to count (over 100 colonies per plate. Counts of organisms were relatively low, with 20% of the surfaces producing unsatisfactory enumeration of S. aureus and E. coli and 30% unsatisfactory for coliforms. Yeast and mould produced 50% and 60% unsatisfactory counts from preparation surfaces and aprons, respectively. Statistically significant differences could not be established amongst microbial counts of the surfaces, which suggests cross-contamination may have occurred. Contamination may be attributed to foodstuffs and animals in the vicinity of the preparation area rather than to the food handlers, because hands had the lowest counts of enumerated organisms amongst the analysed surfaces.

  11. Intergenerational response to the endocrine disruptor vinclozolin is influenced by maternal genotype and crossing scheme.

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    Pietryk, Edward W; Clement, Kiristin; Elnagheeb, Marwa; Kuster, Ryan; Kilpatrick, Kayla; Love, Michael I; Ideraabdullah, Folami Y

    2018-03-10

    In utero exposure to vinclozolin (VIN), an antiandrogenic fungicide, is linked to multigenerational phenotypic and epigenetic effects. Mechanisms remain unclear. We assessed the role of antiandrogenic activity and DNA sequence context by comparing effects of VIN vs. M2 (metabolite with greater antiandrogenic activity) and wild-type C57BL/6 (B6) mice vs. mice carrying mutations at the previously reported VIN-responsive H19/Igf2 locus. First generation offspring from VIN-treated 8nrCG mutant dams exhibited increased body weight and decreased sperm ICR methylation. Second generation pups sired by affected males exhibited decreased neonatal body weight but only when dam was unexposed. Offspring from M2 treatments, B6 dams, 8nrCG sires or additional mutant lines were not similarly affected. Therefore, pup response to VIN over two generations detected here was an 8nrCG-specific maternal effect, independent of antiandrogenic activity. These findings demonstrate that maternal effects and crossing scheme play a major role in multigenerational response to in utero exposures. Copyright © 2018 Elsevier Inc. All rights reserved.

  12. Testing GxG interactions between coinfecting microbial parasite genotypes within hosts

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    Rebecca D Schulte

    2014-05-01

    Full Text Available Host-parasite interactions represent one of the strongest selection pressures in nature. They are often governed by genotype-specific (GxG interactions resulting in host genotypes that differ in resistance and parasite genotypes that differ in virulence depending on the antagonist’s genotype. Another type of GxG interactions, which is often neglected but which certainly influences host-parasite interactions, are those between coinfecting parasite genotypes. Mechanistically, within-host parasite interactions may range from competition for limited host resources to cooperation for more efficient host exploitation. The exact type of interaction, i.e. whether competitive or cooperative, is known to affect life-history traits such as virulence. However, the latter has been shown for chosen genotype combinations only, not considering whether the specific genotype combination per se may influence the interaction (i.e. GxG interactions. Here, we want to test for the presence of GxG interactions between coinfections of the bacterium Bacillus thuringiensis infecting the nematode Caenorhabditis elegans by combining two non-pathogenic and five pathogenic strains in all possible ways. Furthermore, we evaluate whether the type of interaction, reflected by the direction of virulence change of multiple compared to single infections, is genotype-specific. Generally, we found no indication for GxG interactions between non-pathogenic and pathogenic bacterial strains, indicating that virulence of pathogenic strains is equally affected by both non-pathogenic strains. Specific genotype combinations, however, differ in the strength of virulence change, indicating that the interaction type between coinfecting parasite strains and thus the virulence mechanism is specific for different genotype combinations. Such interactions are expected to influence host-parasite interactions and to have strong implications for coevolution.

  13. Inflammatory bowel diseases phenotype, C. difficile and NOD2 genotype are associated with shifts in human ileum associated microbial composition.

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    Ellen Li

    Full Text Available We tested the hypothesis that Crohn's disease (CD-related genetic polymorphisms involved in host innate immunity are associated with shifts in human ileum-associated microbial composition in a cross-sectional analysis of human ileal samples. Sanger sequencing of the bacterial 16S ribosomal RNA (rRNA gene and 454 sequencing of 16S rRNA gene hypervariable regions (V1-V3 and V3-V5, were conducted on macroscopically disease-unaffected ileal biopsies collected from 52 ileal CD, 58 ulcerative colitis and 60 control patients without inflammatory bowel diseases (IBD undergoing initial surgical resection. These subjects also were genotyped for the three major NOD2 risk alleles (Leu1007fs, R708W, G908R and the ATG16L1 risk allele (T300A. The samples were linked to clinical metadata, including body mass index, smoking status and Clostridia difficile infection. The sequences were classified into seven phyla/subphyla categories using the Naïve Bayesian Classifier of the Ribosome Database Project. Centered log ratio transformation of six predominant categories was included as the dependent variable in the permutation based MANCOVA for the overall composition with stepwise variable selection. Polymerase chain reaction (PCR assays were conducted to measure the relative frequencies of the Clostridium coccoides - Eubacterium rectales group and the Faecalibacterium prausnitzii spp. Empiric logit transformations of the relative frequencies of these two microbial groups were included in permutation-based ANCOVA. Regardless of sequencing method, IBD phenotype, Clostridia difficile and NOD2 genotype were selected as associated (FDR ≤ 0.05 with shifts in overall microbial composition. IBD phenotype and NOD2 genotype were also selected as associated with shifts in the relative frequency of the C. coccoides--E. rectales group. IBD phenotype, smoking and IBD medications were selected as associated with shifts in the relative frequency of F. prausnitzii spp. These

  14. Inflammatory bowel diseases phenotype, C. difficile and NOD2 genotype are associated with shifts in human ileum associated microbial composition.

    Science.gov (United States)

    Li, Ellen; Hamm, Christina M; Gulati, Ajay S; Sartor, R Balfour; Chen, Hongyan; Wu, Xiao; Zhang, Tianyi; Rohlf, F James; Zhu, Wei; Gu, Chi; Robertson, Charles E; Pace, Norman R; Boedeker, Edgar C; Harpaz, Noam; Yuan, Jeffrey; Weinstock, George M; Sodergren, Erica; Frank, Daniel N

    2012-01-01

    We tested the hypothesis that Crohn's disease (CD)-related genetic polymorphisms involved in host innate immunity are associated with shifts in human ileum-associated microbial composition in a cross-sectional analysis of human ileal samples. Sanger sequencing of the bacterial 16S ribosomal RNA (rRNA) gene and 454 sequencing of 16S rRNA gene hypervariable regions (V1-V3 and V3-V5), were conducted on macroscopically disease-unaffected ileal biopsies collected from 52 ileal CD, 58 ulcerative colitis and 60 control patients without inflammatory bowel diseases (IBD) undergoing initial surgical resection. These subjects also were genotyped for the three major NOD2 risk alleles (Leu1007fs, R708W, G908R) and the ATG16L1 risk allele (T300A). The samples were linked to clinical metadata, including body mass index, smoking status and Clostridia difficile infection. The sequences were classified into seven phyla/subphyla categories using the Naïve Bayesian Classifier of the Ribosome Database Project. Centered log ratio transformation of six predominant categories was included as the dependent variable in the permutation based MANCOVA for the overall composition with stepwise variable selection. Polymerase chain reaction (PCR) assays were conducted to measure the relative frequencies of the Clostridium coccoides - Eubacterium rectales group and the Faecalibacterium prausnitzii spp. Empiric logit transformations of the relative frequencies of these two microbial groups were included in permutation-based ANCOVA. Regardless of sequencing method, IBD phenotype, Clostridia difficile and NOD2 genotype were selected as associated (FDR ≤ 0.05) with shifts in overall microbial composition. IBD phenotype and NOD2 genotype were also selected as associated with shifts in the relative frequency of the C. coccoides--E. rectales group. IBD phenotype, smoking and IBD medications were selected as associated with shifts in the relative frequency of F. prausnitzii spp. These results indicate

  15. Microbial Performance of Food Safety Control and Assurance Activities in a Fresh Produce Processing Sector Measured Using a Microbial Assessment Scheme and Statistical Modeling

    DEFF Research Database (Denmark)

    Njage, Patrick Murigu Kamau; Sawe, Chemutai Tonui; Onyango, Cecilia Moraa

    2017-01-01

    assessment scheme and statistical modeling were used to systematically assess the microbial performance of core control and assurance activities in five Kenyan fresh produce processing and export companies. Generalized linear mixed models and correlated random-effects joint models for multivariate clustered...... the maximum safety level for environmental samples. Escherichia coli was detected in five of the six CSLs, including the final product. Among the processing-environment samples, the hand or glove swabs of personnel revealed a higher level of predicted contamination with E. coli, and 80% of the factories were...... of contamination with coliforms in water at the inlet than in the final rinse water. Four (80%) of the five assessed processors had poor to unacceptable counts of Enterobacteriaceae on processing surfaces. Personnel-, equipment-, and product-related hygiene measures to improve the performance of preventive...

  16. Dietary fat sources affect feed intake, digestibility, rumen microbial populations, energy partition and methane emissions in different beef cattle genotypes.

    Science.gov (United States)

    Kaewpila, C; Sommart, K; Mitsumori, M

    2018-03-20

    The mitigation of enteric methane emission in beef cattle production is important for reducing feed energy loss and increasing environmental sustainability. The main objective of this study was to evaluate the effect of different oilseeds included in fermented total mixed rations (whole soyabean seed (SBS, control), whole kapok seed (KPS) and cracked oil palm fruit (OPF)) on feed intake, digestibility, rumen microbial populations, energy partition and methane emissions in different cattle genotypes (Charolais crossbred v. Japanese Black crossbred). Three Charolais crossbred and three Japanese Black crossbred bulls were studied in a replicated 3×3 Latin square experimental design; genotypes were analysed in separate squares including three periods of 21 days each and three dietary oilseed treatments fed ad libitum. The cattle were placed in a metabolic cage equipped with a ventilated head box respiration system for evaluating digestibility and energy balance. As compared with Charolais crossbred individuals, Japanese Black crossbred bulls showed consistently lower dry matter intake (15.5%, P0.05) or diet (P>0.05) under the experimental conditions and ranged from 5.8% to 6.0% of gross energy intake. This value is lower than that reported by the Intergovernmental Panel on Climate Change (6.5%) for cattle fed with low-quality crop residues or by-products. Thus, our results imply that the Japanese Black crossbred cattle consume less feed and emits less enteric methane than the Charolais crossbred does, mainly owing to its lower ME requirement for maintenance. The OPF diet could be used to replace SBS for high beef production, although further studies are required to evaluate their application across a wide range of beef production systems.

  17. Genotype, soil type, and locale effects on reciprocal transplant vigor, endophyte growth, and microbial functional diversity of a narrow sagebrush hybrid zone in Salt Creek Canyon, Utah

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    Miglia, K.J.; McArthur, E.D.; Redman, R.S.; Rodriguez, R.J.; Zak, J.C.; Freeman, D.C.

    2007-01-01

    When addressing the nature of ecological adaptation and environmental factors limiting population ranges and contributing to speciation, it is important to consider not only the plant's genotype and its response to the environment, but also any close interactions that it has with other organisms, specifically, symbiotic microorganisms. To investigate this, soils and seedlings were reciprocally transplanted into common gardens of the big sagebrush hybrid zone in Salt Creek Canyon, Utah, to determine location and edaphic effects on the fitness of parental and hybrid plants. Endophytic symbionts and functional microbial diversity of indigenous and transplanted soils and sagebrush plants were also examined. Strong selection occurred against the parental genotypes in the middle hybrid zone garden in middle hybrid zone soil; F1 hybrids had the highest fitness under these conditions. Neither of the parental genotypes had superior fitness in their indigenous soils and habitats; rather F1 hybrids with the nonindigenous maternal parent were superiorly fit. Significant garden-by-soil type interactions indicate adaptation of both plant and soil microorganisms to their indigenous soils and habitats, most notably in the middle hybrid zone garden in middle hybrid zone soil. Contrasting performances of F1 hybrids suggest asymmetrical gene flow with mountain, rather than basin, big sagebrush acting as the maternal parent. We showed that the microbial community impacted the performance of parental and hybrid plants in different soils, likely limiting the ranges of the different genotypes.

  18. Phenotypic and genotypic anti-microbial resistance profiles of campylobacters from untreated feedlot cattle and their environment.

    Science.gov (United States)

    Minihan, D; Whyte, P; O'mahony, M; Cowley, D; O'halloran, F; Corcoran, D; Fanning, S; Collins, J D

    2006-05-01

    Anti-microbial resistance is an emerging public health issue. Farmed animals may act as reservoirs and potential sources of anti-microbial resistant Campylobacters. The aim of this study was to investigate the anti-microbial resistance profile of cattle and environmental Campylobacter isolates from normal untreated feedlot cattle, the role of the gyrA Thr-86-Ile mutation in ciprofloxacin-resistant Campylobacter jejuni isolates and the involvement of the tripartite CmeABC efflux system for multi-resistant C. jejuni isolates. The phenotypic anti-microbial resistance testing was carried out on 500 Campylobacter isolates (445 cattle isolates and 55 environmental isolates). In general, there was a higher level of anti-microbial resistance for the environmental isolates compared with the animal isolates, 45% of the animal isolates were resistant to one or more of the seven anti-microbials compared with 84% of the environmental isolates. The combined cattle and environmental Campylobacters had 34 (6.8%) isolates resistant to three or more of the seven anti-microbials tested on all isolates and 11 (2.2%) isolates were resistant to the seven anti-microbials. There was a substantial level of ciprofloxacin-resistant Campylobacters in both animal (8.5%) and environmental (21.8%) isolates. The gyrA Thr-86-Ile mutation was only present in five of 22 ciprofloxacin-resistant C. jejuni isolates investigated. No multi-drug-resistant associated mutation was detected in the CmeB or the CmeR regions investigated. In conclusion, our study observed a substantial level of Campylobacter anti-microbial resistance, highlighting the need for an active anti-microbial surveillance program for food animals in Ireland and the importance of the chosen sampling point can have on the findings of such a program.

  19. The role of arbuscular mycorrhizal fungi in grain production and nutrition of sorghum genotypes: Enhancing sustainability through plant-microbial partnership

    Science.gov (United States)

    The role of arbuscular mycorrhizal (AM) fungi and fertilization in sorghum grain production and quality was assessed for 3 hybrid genotypes, 2 open-pollinated African genotypes, and 1 open-pollinated Latin American genotype. The open-pollinated genotypes produced an average of 206% more vegetative b...

  20. Drivers of Microbial Risk for Direct Potable Reuse and de Facto Reuse Treatment Schemes: The Impacts of Source Water Quality and Blending

    Science.gov (United States)

    Chaudhry, Rabia M.; Hamilton, Kerry A.; Haas, Charles N.; Nelson, Kara L.

    2017-01-01

    Although reclaimed water for potable applications has many potential benefits, it poses concerns for chemical and microbial risks to consumers. We present a quantitative microbial risk assessment (QMRA) Monte Carlo framework to compare a de facto water reuse scenario (treated wastewater-impacted surface water) with four hypothetical Direct Potable Reuse (DPR) scenarios for Norovirus, Cryptosporidium, and Salmonella. Consumer microbial risks of surface source water quality (impacted by 0–100% treated wastewater effluent) were assessed. Additionally, we assessed risks for different blending ratios (0–100% surface water blended into advanced-treated DPR water) when source surface water consisted of 50% wastewater effluent. De facto reuse risks exceeded the yearly 10−4 infections risk benchmark while all modeled DPR risks were significantly lower. Contamination with 1% or more wastewater effluent in the source water, and blending 1% or more wastewater-impacted surface water into the advanced-treated DPR water drove the risk closer to the 10−4 benchmark. We demonstrate that de facto reuse by itself, or as an input into DPR, drives microbial risks more so than the advanced-treated DPR water. When applied using location-specific inputs, this framework can contribute to project design and public awareness campaigns to build legitimacy for DPR. PMID:28608808

  1. Drivers of Microbial Risk for Direct Potable Reuse and de Facto Reuse Treatment Schemes: The Impacts of Source Water Quality and Blending

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    Rabia M. Chaudhry

    2017-06-01

    Full Text Available Although reclaimed water for potable applications has many potential benefits, it poses concerns for chemical and microbial risks to consumers. We present a quantitative microbial risk assessment (QMRA Monte Carlo framework to compare a de facto water reuse scenario (treated wastewater-impacted surface water with four hypothetical Direct Potable Reuse (DPR scenarios for Norovirus, Cryptosporidium, and Salmonella. Consumer microbial risks of surface source water quality (impacted by 0–100% treated wastewater effluent were assessed. Additionally, we assessed risks for different blending ratios (0–100% surface water blended into advanced-treated DPR water when source surface water consisted of 50% wastewater effluent. De facto reuse risks exceeded the yearly 10−4 infections risk benchmark while all modeled DPR risks were significantly lower. Contamination with 1% or more wastewater effluent in the source water, and blending 1% or more wastewater-impacted surface water into the advanced-treated DPR water drove the risk closer to the 10−4 benchmark. We demonstrate that de facto reuse by itself, or as an input into DPR, drives microbial risks more so than the advanced-treated DPR water. When applied using location-specific inputs, this framework can contribute to project design and public awareness campaigns to build legitimacy for DPR.

  2. Drivers of Microbial Risk for Direct Potable Reuse and de Facto Reuse Treatment Schemes: The Impacts of Source Water Quality and Blending.

    Science.gov (United States)

    Chaudhry, Rabia M; Hamilton, Kerry A; Haas, Charles N; Nelson, Kara L

    2017-06-13

    Although reclaimed water for potable applications has many potential benefits, it poses concerns for chemical and microbial risks to consumers. We present a quantitative microbial risk assessment (QMRA) Monte Carlo framework to compare a de facto water reuse scenario (treated wastewater-impacted surface water) with four hypothetical Direct Potable Reuse (DPR) scenarios for Norovirus, Cryptosporidium , and Salmonella . Consumer microbial risks of surface source water quality (impacted by 0-100% treated wastewater effluent) were assessed. Additionally, we assessed risks for different blending ratios (0-100% surface water blended into advanced-treated DPR water) when source surface water consisted of 50% wastewater effluent. De facto reuse risks exceeded the yearly 10 -4 infections risk benchmark while all modeled DPR risks were significantly lower. Contamination with 1% or more wastewater effluent in the source water, and blending 1% or more wastewater-impacted surface water into the advanced-treated DPR water drove the risk closer to the 10 -4 benchmark. We demonstrate that de facto reuse by itself, or as an input into DPR, drives microbial risks more so than the advanced-treated DPR water. When applied using location-specific inputs, this framework can contribute to project design and public awareness campaigns to build legitimacy for DPR.

  3. Desmanthus GENOTYPES

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    JOSÉ HENRIQUE DE ALBUQUERQUE RANGEL

    2015-01-01

    Full Text Available Desmanthus is a genus of forage legumes with potential to improve pastures and livestock produc-tion on clay soils of dry tropical and subtropical regions such as the existing in Brazil and Australia. Despite this patterns of natural or enforced after-ripening of Desmanthus seeds have not been well established. Four year old seed banks of nine Desmanthus genotypes at James Cook University were accessed for their patterns of seed softe-ning in response to a range of temperatures. Persistent seed banks were found to exist under all of the studied ge-notypes. The largest seeds banks were found in the genotypes CPI 78373 and CPI 78382 and the smallest in the genotypes CPI’s 37143, 67643, and 83563. An increase in the percentage of softened seeds was correlated with higher temperatures, in two patterns of response: in some accessions seeds were not significantly affected by tempe-ratures below 80º C; and in others, seeds become soft when temperature rose to as little as 60 ºC. At 80 °C the heat started to depress germination. High seed production of Desmanthus associated with dependence of seeds on eleva-ted temperatures to softening can be a very important strategy for plants to survive in dry tropical regions.

  4. Colour schemes

    DEFF Research Database (Denmark)

    van Leeuwen, Theo

    2013-01-01

    This chapter presents a framework for analysing colour schemes based on a parametric approach that includes not only hue, value and saturation, but also purity, transparency, luminosity, luminescence, lustre, modulation and differentiation.......This chapter presents a framework for analysing colour schemes based on a parametric approach that includes not only hue, value and saturation, but also purity, transparency, luminosity, luminescence, lustre, modulation and differentiation....

  5. Tradable schemes

    NARCIS (Netherlands)

    J.K. Hoogland (Jiri); C.D.D. Neumann

    2000-01-01

    textabstractIn this article we present a new approach to the numerical valuation of derivative securities. The method is based on our previous work where we formulated the theory of pricing in terms of tradables. The basic idea is to fit a finite difference scheme to exact solutions of the pricing

  6. Additive operator-difference schemes splitting schemes

    CERN Document Server

    Vabishchevich, Petr N

    2013-01-01

    Applied mathematical modeling isconcerned with solving unsteady problems. This bookshows how toconstruct additive difference schemes to solve approximately unsteady multi-dimensional problems for PDEs. Two classes of schemes are highlighted: methods of splitting with respect to spatial variables (alternating direction methods) and schemes of splitting into physical processes. Also regionally additive schemes (domain decomposition methods)and unconditionally stable additive schemes of multi-component splitting are considered for evolutionary equations of first and second order as well as for sy

  7. Establishment of a genotyping scheme for Coxiella burnetii.

    NARCIS (Netherlands)

    Svraka, Sanela; Toman, Rudolf; Skultety, Ludovit; Slaba, Katarina; Homan, Wieger L

    2006-01-01

    Coxiella burnetii is the causative agent of Q fever. The bacterium is highly infectious and is classified as a category B biological weapon. The tools of molecular biology are of utmost importance in a rapid and unambiguous identification of C. burnetii in naturally occurring Q fever outbreaks, or

  8. Genotyping by PCR and High-Throughput Sequencing of Commercial Probiotic Products Reveals Composition Biases.

    Directory of Open Access Journals (Sweden)

    Wesley Morovic

    2016-11-01

    Full Text Available Recent advances in microbiome research have brought renewed focus on beneficial bacteria, many of which are available in food and dietary supplements. Although probiotics have historically been defined as microorganisms that convey health benefits when ingested in sufficient viable amounts, this description now includes the stipulation well defined strains, encompassing definitive taxonomy for consumer consideration and regulatory oversight. Here, we evaluated 52 commercial dietary supplements covering a range of labeled species, and determined their content using plate counting, targeted genotyping. Additionally, strain identities were assessed using methods recently published by the United States Pharmacopeial Convention. We also determined the relative abundance of individual bacteria by high-throughput sequencing (HTS of the 16S rRNA sequence using paired-end 2x250bp Illumina MiSeq technology. Using multiple methods, we tested the hypothesis that products do contain the quantitative amount of labeled bacteria, and qualitative list of labeled microbial species. We found that 17 samples (33% were below label claim for CFU prior to their expiration dates. A multiplexed-PCR scheme showed that only 30/52 (58% of the products contained a correctly labeled classification, with issues encompassing incorrect taxonomy, missing species and un-labeled species. The HTS revealed that many blended products consisted predominantly of Lactobacillus acidophilus and Bifidobacterium animalis subsp. lactis. These results highlight the need for reliable methods to qualitatively determine the correct taxonomy and quantitatively ascertain the relative amounts of mixed microbial populations in commercial probiotic products.

  9. Microbial biosensors

    International Nuclear Information System (INIS)

    Le Yu; Chen, Wilfred; Mulchandani, Ashok

    2006-01-01

    A microbial biosensor is an analytical device that couples microorganisms with a transducer to enable rapid, accurate and sensitive detection of target analytes in fields as diverse as medicine, environmental monitoring, defense, food processing and safety. The earlier microbial biosensors used the respiratory and metabolic functions of the microorganisms to detect a substance that is either a substrate or an inhibitor of these processes. Recently, genetically engineered microorganisms based on fusing of the lux, gfp or lacZ gene reporters to an inducible gene promoter have been widely applied to assay toxicity and bioavailability. This paper reviews the recent trends in the development and application of microbial biosensors. Current advances and prospective future direction in developing microbial biosensor have also been discussed

  10. Finite Boltzmann schemes

    NARCIS (Netherlands)

    Sman, van der R.G.M.

    2006-01-01

    In the special case of relaxation parameter = 1 lattice Boltzmann schemes for (convection) diffusion and fluid flow are equivalent to finite difference/volume (FD) schemes, and are thus coined finite Boltzmann (FB) schemes. We show that the equivalence is inherent to the homology of the

  11. In Vitro Conservation of Sweet Potato Genotypes

    Directory of Open Access Journals (Sweden)

    Maria de Fátima Arrigoni-Blank

    2014-01-01

    Full Text Available The aim of this study was to develop a protocol for the in vitro conservation of sweet potato genotypes using the slow growth technique. The first experiment was conducted in a 4×5×2 factorial scheme, testing four genotypes (IPB-007, IPB-052, IPB-072, and IPB-137, five concentrations of abscisic acid (ABA (0.0, 1.0, 2.0, 4.0, and 8.0 mg·L−1, and two temperatures (18 and 25°C. The second experiment was conducted in a 4×3×3 factorial scheme at 18°C, testing four genotypes (IPB-007, IPB-052, IPB-072, and IPB-137, three variations of MS salts (50, 75, and 100%, and three concentrations of sucrose (10, 20, and 30 g·L−1. Every three months, we evaluated the survival (%, shoot height, and shoot viability. In vitro conservation of the sweet potato genotypes IPB-052 and IPB-007 was obtained over three and six months, respectively, using MS medium plus 2.0 mg·L−1 of ABA at either 18 or 25°C. Genotypes IPB-072 and IPB-137 can be kept for three and six months, respectively, in MS medium without ABA at 18°C. It is possible to store IPB-052 and IPB-072 for six months and IPB-007 and IPB-137 for nine months using 30 g·L−1 of sucrose and 50% MS salts.

  12. Root phenotypic differences across a historical gradient of wheat genotypes alter soil rhizosphere communities and their impact on nitrogen cycling

    Science.gov (United States)

    Kallenbach, C.; Junaidi, D.; Fonte, S.; Byrne, P. F.; Wallenstein, M. D.

    2017-12-01

    Plants and soil microorganisms can exhibit coevolutionary relationships where, for example, in exchange for root carbon, rhizosphere microbes enhance plant fitness through improved plant nutrient availability. Organic agriculture relies heavily on these interactions to enhance crop nitrogen (N) availability. However, modern agriculture and breeding under high mineral N fertilization may have disrupted these interactions through alterations to belowground carbon inputs and associated impacts on the soil microbiome. As sustainability initiatives lead to a restoration of agricultural soil organic matter, modern crop cultivars may still be constrained by crop roots' ability to effectively support microbial-mediated N mineralization. We investigated how differences in root traits across a historical gradient of spring wheat genotypes influence the rhizosphere microbial community and effects on soil N and wheat yield. Five genotypes, representing wild (Wild), pre-Green Revolution (Old), and modern (Modern) wheat, were grown under greenhouse conditions in soils with and without compost to also compare genotype response to difference in native soil microbiomes and organic resource availability. We analyzed rhizosphere soils for microbial community composition, enzyme activities, inorganic N, and microbial biomass. Root length density, surface area, fine root volume and root:shoot ratio were higher in the Wild and Old genotype (Gypsum) compared to the two Modern genotypes (Psoil inorganic N, compared to Modern genotypes. However, under unamended soils, the microbial community and soil N were not affected by genotypes. We also relate how root traits and N cycling across genotypes correspond to microbial community composition. Our preliminary data suggest that the older wheat genotypes and their root traits are more effective at enhancing microbial N mineralization under organically managed soils. Thus, to optimize crop N availability from organic sources, breeding efforts

  13. APOE Genotyping, Cardiovascular Disease

    Science.gov (United States)

    ... Resources For Health Professionals Subscribe Search APOE Genotyping, Cardiovascular Disease Send Us Your Feedback Choose Topic At a ... help understand the role of genetic factors in cardiovascular disease . However, the testing is sometimes used in clinical ...

  14. Radiosensitivity of fingermillet genotypes

    Energy Technology Data Exchange (ETDEWEB)

    Raveendran, T S; Nagarajan, C; Appadurai, R; Prasad, M N; Sundaresan, N [Tamil Nadu Agricultural Univ., Coimbatore (India)

    1984-07-01

    Varietal differences in radiosensitivity were observed in a study involving 4 genotypes of fingermillet (Eleusine coracana (Linn.) Gaertn.) subjected to gamma-irradiation. Harder seeds were found to tolerate a higher dose of the mutagen.

  15. Microbial glycoproteomics

    DEFF Research Database (Denmark)

    Halim, Adnan; Anonsen, Jan Haug

    2017-01-01

    Mass spectrometry-based "-omics" technologies are important tools for global and detailed mapping of post-translational modifications. Protein glycosylation is an abundant and important post translational modification widespread throughout all domains of life. Characterization of glycoproteins...... and research in this area is rapidly accelerating. Here, we review recent developments in glycoproteomic technologies with a special focus on microbial protein glycosylation....

  16. Scheme Program Documentation Tools

    DEFF Research Database (Denmark)

    Nørmark, Kurt

    2004-01-01

    are separate and intended for different documentation purposes they are related to each other in several ways. Both tools are based on XML languages for tool setup and for documentation authoring. In addition, both tools rely on the LAML framework which---in a systematic way---makes an XML language available...... as named functions in Scheme. Finally, the Scheme Elucidator is able to integrate SchemeDoc resources as part of an internal documentation resource....

  17. Multiresolution signal decomposition schemes

    NARCIS (Netherlands)

    J. Goutsias (John); H.J.A.M. Heijmans (Henk)

    1998-01-01

    textabstract[PNA-R9810] Interest in multiresolution techniques for signal processing and analysis is increasing steadily. An important instance of such a technique is the so-called pyramid decomposition scheme. This report proposes a general axiomatic pyramid decomposition scheme for signal analysis

  18. Adaptive protection scheme

    Directory of Open Access Journals (Sweden)

    R. Sitharthan

    2016-09-01

    Full Text Available This paper aims at modelling an electronically coupled distributed energy resource with an adaptive protection scheme. The electronically coupled distributed energy resource is a microgrid framework formed by coupling the renewable energy source electronically. Further, the proposed adaptive protection scheme provides a suitable protection to the microgrid for various fault conditions irrespective of the operating mode of the microgrid: namely, grid connected mode and islanded mode. The outstanding aspect of the developed adaptive protection scheme is that it monitors the microgrid and instantly updates relay fault current according to the variations that occur in the system. The proposed adaptive protection scheme also employs auto reclosures, through which the proposed adaptive protection scheme recovers faster from the fault and thereby increases the consistency of the microgrid. The effectiveness of the proposed adaptive protection is studied through the time domain simulations carried out in the PSCAD⧹EMTDC software environment.

  19. Microbial xanthophylls.

    Science.gov (United States)

    Bhosale, Prakash; Bernstein, Paul S

    2005-09-01

    Xanthophylls are oxygenated carotenoids abundant in the human food supply. Lutein, zeaxanthin, and cryptoxanthin are major xanthophyll carotenoids in human plasma. The consumption of these xanthophylls is directly associated with reduction in the risk of cancers, cardiovascular disease, age-related macular degeneration, and cataract formation. Canthaxanthin and astaxanthin also have considerable importance in aquaculture for salmonid and crustacean pigmentation, and are of commercial interest for the pharmaceutical and food industries. Chemical synthesis is a major source for the heavy demand of xanthophylls in the consumer market; however, microbial producers also have potential as commercial sources. In this review, we discuss the biosynthesis, commercial utility, and major microbial sources of xanthophylls. We also present a critical review of current research and technologies involved in promoting microbes as potential commercial sources for mass production.

  20. High-throughput mouse genotyping using robotics automation.

    Science.gov (United States)

    Linask, Kaari L; Lo, Cecilia W

    2005-02-01

    The use of mouse models is rapidly expanding in biomedical research. This has dictated the need for the rapid genotyping of mutant mouse colonies for more efficient utilization of animal holding space. We have established a high-throughput protocol for mouse genotyping using two robotics workstations: a liquid-handling robot to assemble PCR and a microfluidics electrophoresis robot for PCR product analysis. This dual-robotics setup incurs lower start-up costs than a fully automated system while still minimizing human intervention. Essential to this automation scheme is the construction of a database containing customized scripts for programming the robotics workstations. Using these scripts and the robotics systems, multiple combinations of genotyping reactions can be assembled simultaneously, allowing even complex genotyping data to be generated rapidly with consistency and accuracy. A detailed protocol, database, scripts, and additional background information are available at http://dir.nhlbi.nih.gov/labs/ldb-chd/autogene/.

  1. Most of the benefits from genomic selection can be realised by genotyping a proportion of selection candidates

    DEFF Research Database (Denmark)

    Henryon, Mark; Berg, Peer; Sørensen, Anders Christian

    2012-01-01

    allocated to male and female candidates at ratios of 100:0, 75:25, 50:50, 25:75, and 0:100. For genotyped candidates, a direct-genomic value (DGV) was sampled with reliabilities 0.10, 0.50, and 0.90. Ten sires and 300 dams with the highest breeding values after genotyping were selected at each generation......We reasoned that there are diminishing marginal returns from genomic selection as the proportion of genotyped selection candidates is increased and breeding values based on a priori information are used to choose the candidates that are genotyped. We tested this premise by stochastic simulation...... of breeding schemes that resembled those used for pigs. We estimated rates of genetic gain and inbreeding realized by genomic selection in breeding schemes where candidates were phenotyped before genotyping and 0-100% of the candidates were genotyped based on predicted breeding values. Genotypings were...

  2. Threshold Signature Schemes Application

    Directory of Open Access Journals (Sweden)

    Anastasiya Victorovna Beresneva

    2015-10-01

    Full Text Available This work is devoted to an investigation of threshold signature schemes. The systematization of the threshold signature schemes was done, cryptographic constructions based on interpolation Lagrange polynomial, elliptic curves and bilinear pairings were examined. Different methods of generation and verification of threshold signatures were explored, the availability of practical usage of threshold schemes in mobile agents, Internet banking and e-currency was shown. The topics of further investigation were given and it could reduce a level of counterfeit electronic documents signed by a group of users.

  3. New paradigms for Salmonella source attribution based on microbial subtyping.

    Science.gov (United States)

    Mughini-Gras, Lapo; Franz, Eelco; van Pelt, Wilfrid

    2018-05-01

    Microbial subtyping is the most common approach for Salmonella source attribution. Typically, attributions are computed using frequency-matching models like the Dutch and Danish models based on phenotyping data (serotyping, phage-typing, and antimicrobial resistance profiling). Herewith, we critically review three major paradigms facing Salmonella source attribution today: (i) the use of genotyping data, particularly Multi-Locus Variable Number of Tandem Repeats Analysis (MLVA), which is replacing traditional Salmonella phenotyping beyond serotyping; (ii) the integration of case-control data into source attribution to improve risk factor identification/characterization; (iii) the investigation of non-food sources, as attributions tend to focus on foods of animal origin only. Population genetics models or simplified MLVA schemes may provide feasible options for source attribution, although there is a strong need to explore novel modelling options as we move towards whole-genome sequencing as the standard. Classical case-control studies are enhanced by incorporating source attribution results, as individuals acquiring salmonellosis from different sources have different associated risk factors. Thus, the more such analyses are performed the better Salmonella epidemiology will be understood. Reparametrizing current models allows for inclusion of sources like reptiles, the study of which improves our understanding of Salmonella epidemiology beyond food to tackle the pathogen in a more holistic way. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. CSR schemes in agribusiness

    DEFF Research Database (Denmark)

    Pötz, Katharina Anna; Haas, Rainer; Balzarova, Michaela

    2013-01-01

    of schemes that can be categorized on focus areas, scales, mechanisms, origins, types and commitment levels. Research limitations/implications – The findings contribute to conceptual and empirical research on existing models to compare and analyse CSR standards. Sampling technique and depth of analysis limit......Purpose – The rise of CSR followed a demand for CSR standards and guidelines. In a sector already characterized by a large number of standards, the authors seek to ask what CSR schemes apply to agribusiness, and how they can be systematically compared and analysed. Design....../methodology/approach – Following a deductive-inductive approach the authors develop a model to compare and analyse CSR schemes based on existing studies and on coding qualitative data on 216 CSR schemes. Findings – The authors confirm that CSR standards and guidelines have entered agribusiness and identify a complex landscape...

  5. Tabled Execution in Scheme

    Energy Technology Data Exchange (ETDEWEB)

    Willcock, J J; Lumsdaine, A; Quinlan, D J

    2008-08-19

    Tabled execution is a generalization of memorization developed by the logic programming community. It not only saves results from tabled predicates, but also stores the set of currently active calls to them; tabled execution can thus provide meaningful semantics for programs that seemingly contain infinite recursions with the same arguments. In logic programming, tabled execution is used for many purposes, both for improving the efficiency of programs, and making tasks simpler and more direct to express than with normal logic programs. However, tabled execution is only infrequently applied in mainstream functional languages such as Scheme. We demonstrate an elegant implementation of tabled execution in Scheme, using a mix of continuation-passing style and mutable data. We also show the use of tabled execution in Scheme for a problem in formal language and automata theory, demonstrating that tabled execution can be a valuable tool for Scheme users.

  6. Microbial effects

    International Nuclear Information System (INIS)

    Sharpe, V.J.

    1985-10-01

    The long term safety and integrity of radioactive waste disposal sites proposed for use by Ontario Hydro may be affected by the release of radioactive gases. Microbes mediate the primary pathways of waste degradation and hence an assessment of their potential to produce gaseous end products from the breakdown of low level waste was performed. Due to a number of unknown variables, assumptions were made regarding environmental and waste conditions that controlled microbial activity; however, it was concluded that 14 C and 3 H would be produced, albeit over a long time scale of about 1500 years for 14 C in the worst case situation

  7. Evaluating statistical cloud schemes

    OpenAIRE

    Grützun, Verena; Quaas, Johannes; Morcrette , Cyril J.; Ament, Felix

    2015-01-01

    Statistical cloud schemes with prognostic probability distribution functions have become more important in atmospheric modeling, especially since they are in principle scale adaptive and capture cloud physics in more detail. While in theory the schemes have a great potential, their accuracy is still questionable. High-resolution three-dimensional observational data of water vapor and cloud water, which could be used for testing them, are missing. We explore the potential of ground-based re...

  8. Gamma spectrometry; level schemes

    International Nuclear Information System (INIS)

    Blachot, J.; Bocquet, J.P.; Monnand, E.; Schussler, F.

    1977-01-01

    The research presented dealt with: a new beta emitter, isomer of 131 Sn; the 136 I levels fed through the radioactive decay of 136 Te (20.9s); the A=145 chain (β decay of Ba, La and Ce, and level schemes for 145 La, 145 Ce, 145 Pr); the A=47 chain (La and Ce, β decay, and the level schemes of 147 Ce and 147 Pr) [fr

  9. Scheme of energy utilities

    International Nuclear Information System (INIS)

    2002-04-01

    This scheme defines the objectives relative to the renewable energies and the rational use of the energy in the framework of the national energy policy. It evaluates the needs and the potentialities of the regions and preconizes the actions between the government and the territorial organizations. The document is presented in four parts: the situation, the stakes and forecasts; the possible actions for new measures; the scheme management and the regional contributions analysis. (A.L.B.)

  10. Potential of biofertilisers to improve performance of local genotype tomatoes

    Directory of Open Access Journals (Sweden)

    Carmen Puia

    2017-09-01

    Full Text Available Complex microbial communities in the plant rhizosphere are responsible for their success in ecosystems. Supplementary inoculation of soil with mycorrhizal fungi and rhizospheric bacteria may act as a plant growth-promoting factor. The present study aims to assess the potential use of biofertilisers on tomato as a way of increasing yield and stability of root exploration area. The experiment was set up in greenhouse, regarding the evaluation of growing dynamics of plants, mycorrhization level and obtained yield. The identification of effective inoculation variants can lead to a standardisation of technologies of growing for local plant genotypes. Data analysis was performed based on the ANOVA test, followed by Tukey HSD, principal component analysis and cluster analysis in order to identify the potential of bioproducts to stimulate the development of tomato plants. Application of bacterial biofertilisers does not stimulate enough the aboveground development of plants. An antagonistic reaction is visible between exogenous mycorrhizas and those specific in soil, acting slightly different for each genotype. Mycorrhizal level in root systems is more dependent on applied biofertilisers than on analyzed genotypes. For the variants without additional fertilisers, a high level of mycorrhization is visible only after 75 days from the transplantation. Based on results we can conclude that microbial active fertilisers may represent viable solutions to increase yield capacity and root exploration area for local tomato genotypes.

  11. Role of Genomic Typing in Taxonomy, Evolutionary Genetics, and Microbial Epidemiology

    OpenAIRE

    van Belkum, Alex; Struelens, Marc; de Visser, Arjan; Verbrugh, Henri; Tibayrenc, Michel

    2001-01-01

    Currently, genetic typing of microorganisms is widely used in several major fields of microbiological research. Taxonomy, research aimed at elucidation of evolutionary dynamics or phylogenetic relationships, population genetics of microorganisms, and microbial epidemiology all rely on genetic typing data for discrimination between genotypes. Apart from being an essential component of these fundamental sciences, microbial typing clearly affects several areas of applied microbiogical research. ...

  12. Role of genomic typing in taxonomy, evolutionary genetics, and microbial epidemiology.

    OpenAIRE

    Belkum, Alex; Struelens, M.; Visser, Arjan; Verbrugh, Henri; Tibayrench, M.

    2001-01-01

    textabstractCurrently, genetic typing of microorganisms is widely used in several major fields of microbiological research. Taxonomy, research aimed at elucidation of evolutionary dynamics or phylogenetic relationships, population genetics of microorganisms, and microbial epidemiology all rely on genetic typing data for discrimination between genotypes. Apart from being an essential component of these fundamental sciences, microbial typing clearly affects several areas of applied microbiologi...

  13. Towards Symbolic Encryption Schemes

    DEFF Research Database (Denmark)

    Ahmed, Naveed; Jensen, Christian D.; Zenner, Erik

    2012-01-01

    , namely an authenticated encryption scheme that is secure under chosen ciphertext attack. Therefore, many reasonable encryption schemes, such as AES in the CBC or CFB mode, are not among the implementation options. In this paper, we report new attacks on CBC and CFB based implementations of the well......Symbolic encryption, in the style of Dolev-Yao models, is ubiquitous in formal security models. In its common use, encryption on a whole message is specified as a single monolithic block. From a cryptographic perspective, however, this may require a resource-intensive cryptographic algorithm......-known Needham-Schroeder and Denning-Sacco protocols. To avoid such problems, we advocate the use of refined notions of symbolic encryption that have natural correspondence to standard cryptographic encryption schemes....

  14. Compact Spreader Schemes

    Energy Technology Data Exchange (ETDEWEB)

    Placidi, M.; Jung, J. -Y.; Ratti, A.; Sun, C.

    2014-07-25

    This paper describes beam distribution schemes adopting a novel implementation based on low amplitude vertical deflections combined with horizontal ones generated by Lambertson-type septum magnets. This scheme offers substantial compactness in the longitudinal layouts of the beam lines and increased flexibility for beam delivery of multiple beam lines on a shot-to-shot basis. Fast kickers (FK) or transverse electric field RF Deflectors (RFD) provide the low amplitude deflections. Initially proposed at the Stanford Linear Accelerator Center (SLAC) as tools for beam diagnostics and more recently adopted for multiline beam pattern schemes, RFDs offer repetition capabilities and a likely better amplitude reproducibility when compared to FKs, which, in turn, offer more modest financial involvements both in construction and operation. Both solutions represent an ideal approach for the design of compact beam distribution systems resulting in space and cost savings while preserving flexibility and beam quality.

  15. New analytic unitarization schemes

    International Nuclear Information System (INIS)

    Cudell, J.-R.; Predazzi, E.; Selyugin, O. V.

    2009-01-01

    We consider two well-known classes of unitarization of Born amplitudes of hadron elastic scattering. The standard class, which saturates at the black-disk limit includes the standard eikonal representation, while the other class, which goes beyond the black-disk limit to reach the full unitarity circle, includes the U matrix. It is shown that the basic properties of these schemes are independent of the functional form used for the unitarization, and that U matrix and eikonal schemes can be extended to have similar properties. A common form of unitarization is proposed interpolating between both classes. The correspondence with different nonlinear equations are also briefly examined.

  16. On coding genotypes for genetic markers with multiple alleles in genetic association study of quantitative traits

    Directory of Open Access Journals (Sweden)

    Wang Tao

    2011-09-01

    Full Text Available Abstract Background In genetic association study of quantitative traits using F∞ models, how to code the marker genotypes and interpret the model parameters appropriately is important for constructing hypothesis tests and making statistical inferences. Currently, the coding of marker genotypes in building F∞ models has mainly focused on the biallelic case. A thorough work on the coding of marker genotypes and interpretation of model parameters for F∞ models is needed especially for genetic markers with multiple alleles. Results In this study, we will formulate F∞ genetic models under various regression model frameworks and introduce three genotype coding schemes for genetic markers with multiple alleles. Starting from an allele-based modeling strategy, we first describe a regression framework to model the expected genotypic values at given markers. Then, as extension from the biallelic case, we introduce three coding schemes for constructing fully parameterized one-locus F∞ models and discuss the relationships between the model parameters and the expected genotypic values. Next, under a simplified modeling framework for the expected genotypic values, we consider several reduced one-locus F∞ models from the three coding schemes on the estimability and interpretation of their model parameters. Finally, we explore some extensions of the one-locus F∞ models to two loci. Several fully parameterized as well as reduced two-locus F∞ models are addressed. Conclusions The genotype coding schemes provide different ways to construct F∞ models for association testing of multi-allele genetic markers with quantitative traits. Which coding scheme should be applied depends on how convenient it can provide the statistical inferences on the parameters of our research interests. Based on these F∞ models, the standard regression model fitting tools can be used to estimate and test for various genetic effects through statistical contrasts with the

  17. 4. Payment Schemes

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 6; Issue 2. Electronic Commerce - Payment Schemes. V Rajaraman. Series Article Volume 6 Issue 2 February 2001 pp 6-13. Fulltext. Click here to view fulltext PDF. Permanent link: https://www.ias.ac.in/article/fulltext/reso/006/02/0006-0013 ...

  18. Contract saving schemes

    NARCIS (Netherlands)

    Ronald, R.; Smith, S.J.; Elsinga, M.; Eng, O.S.; Fox O'Mahony, L.; Wachter, S.

    2012-01-01

    Contractual saving schemes for housing are institutionalised savings programmes normally linked to rights to loans for home purchase. They are diverse types as they have been developed differently in each national context, but normally fall into categories of open, closed, compulsory, and ‘free

  19. Alternative reprocessing schemes evaluation

    International Nuclear Information System (INIS)

    1979-02-01

    This paper reviews the parameters which determine the inaccessibility of the plutonium in reprocessing plants. Among the various parameters, the physical and chemical characteristics of the materials, the various processing schemes and the confinement are considered. The emphasis is placed on that latter parameter, and the advantages of an increased confinement in the socalled PIPEX reprocessing plant type are presented

  20. Introduction to association schemes

    NARCIS (Netherlands)

    Seidel, J.J.

    1991-01-01

    The present paper gives an introduction to the theory of association schemes, following Bose-Mesner (1959), Biggs (1974), Delsarte (1973), Bannai-Ito (1984) and Brouwer-Cohen-Neumaier (1989). Apart from definitions and many examples, also several proofs and some problems are included. The paragraphs

  1. Reaction schemes of immunoanalysis

    International Nuclear Information System (INIS)

    Delaage, M.; Barbet, J.

    1991-01-01

    The authors apply a general theory for multiple equilibria to the reaction schemes of immunoanalysis, competition and sandwich. This approach allows the manufacturer to optimize the system and provide the user with interpolation functions for the standard curve and its first derivative as well, thus giving access to variance [fr

  2. Alternative health insurance schemes

    DEFF Research Database (Denmark)

    Keiding, Hans; Hansen, Bodil O.

    2002-01-01

    In this paper, we present a simple model of health insurance with asymmetric information, where we compare two alternative ways of organizing the insurance market. Either as a competitive insurance market, where some risks remain uninsured, or as a compulsory scheme, where however, the level...... competitive insurance; this situation turns out to be at least as good as either of the alternatives...

  3. Genomic selection strategies in breeding programs: Strong positive interaction between application of genotypic information and intensive use of young bulls on genetic gain

    DEFF Research Database (Denmark)

    Buch, Line Hjortø; Sørensen, Morten Kargo; Berg, Peer

    2012-01-01

    We tested the following hypotheses: (i) breeding schemes with genomic selection are superior to breeding schemes without genomic selection regarding annual genetic gain of the aggregate genotype (ΔGAG), annual genetic gain of the functional traits and rate of inbreeding per generation (ΔF), (ii......) a positive interaction exists between the use of genotypic information and a short generation interval on ΔGAG and (iii) the inclusion of an indicator trait in the selection index will only result in a negligible increase in ΔGAG if genotypic information about the breeding goal trait is known. We examined......, greater contributions of the functional trait to ΔGAG and lower ΔF than the two breeding schemes without genomic selection. Thus, the use of genotypic information may lead to more sustainable breeding schemes. In addition, a short generation interval increases the effect of using genotypic information...

  4. On Converting Secret Sharing Scheme to Visual Secret Sharing Scheme

    Directory of Open Access Journals (Sweden)

    Wang Daoshun

    2010-01-01

    Full Text Available Abstract Traditional Secret Sharing (SS schemes reconstruct secret exactly the same as the original one but involve complex computation. Visual Secret Sharing (VSS schemes decode the secret without computation, but each share is m times as big as the original and the quality of the reconstructed secret image is reduced. Probabilistic visual secret sharing (Prob.VSS schemes for a binary image use only one subpixel to share the secret image; however the probability of white pixels in a white area is higher than that in a black area in the reconstructed secret image. SS schemes, VSS schemes, and Prob. VSS schemes have various construction methods and advantages. This paper first presents an approach to convert (transform a -SS scheme to a -VSS scheme for greyscale images. The generation of the shadow images (shares is based on Boolean XOR operation. The secret image can be reconstructed directly by performing Boolean OR operation, as in most conventional VSS schemes. Its pixel expansion is significantly smaller than that of VSS schemes. The quality of the reconstructed images, measured by average contrast, is the same as VSS schemes. Then a novel matrix-concatenation approach is used to extend the greyscale -SS scheme to a more general case of greyscale -VSS scheme.

  5. Identification of zoonotic genotypes of Giardia duodenalis.

    Directory of Open Access Journals (Sweden)

    Hein Sprong

    Full Text Available Giardia duodenalis, originally regarded as a commensal organism, is the etiologic agent of giardiasis, a gastrointestinal disease of humans and animals. Giardiasis causes major public and veterinary health concerns worldwide. Transmission is either direct, through the faecal-oral route, or indirect, through ingestion of contaminated water or food. Genetic characterization of G. duodenalis isolates has revealed the existence of seven groups (assemblages A to G which differ in their host distribution. Assemblages A and B are found in humans and in many other mammals, but the role of animals in the epidemiology of human infection is still unclear, despite the fact that the zoonotic potential of Giardia was recognised by the WHO some 30 years ago. Here, we performed an extensive genetic characterization of 978 human and 1440 animal isolates, which together comprise 3886 sequences from 4 genetic loci. The data were assembled into a molecular epidemiological database developed by a European network of public and veterinary health Institutions. Genotyping was performed at different levels of resolution (single and multiple loci on the same dataset. The zoonotic potential of both assemblages A and B is evident when studied at the level of assemblages, sub-assemblages, and even at each single locus. However, when genotypes are defined using a multi-locus sequence typing scheme, only 2 multi-locus genotypes (MLG of assemblage A and none of assemblage B appear to have a zoonotic potential. Surprisingly, mixtures of genotypes in individual isolates were repeatedly observed. Possible explanations are the uptake of genetically different Giardia cysts by a host, or subsequent infection of an already infected host, likely without overt symptoms, with a different Giardia species, which may cause disease. Other explanations for mixed genotypes, particularly for assemblage B, are substantial allelic sequence heterogeneity and/or genetic recombination. Although the

  6. Selectively strippable paint schemes

    Science.gov (United States)

    Stein, R.; Thumm, D.; Blackford, Roger W.

    1993-03-01

    In order to meet the requirements of more environmentally acceptable paint stripping processes many different removal methods are under evaluation. These new processes can be divided into mechanical and chemical methods. ICI has developed a paint scheme with intermediate coat and fluid resistant polyurethane topcoat which can be stripped chemically in a short period of time with methylene chloride free and phenol free paint strippers.

  7. Microbial micropatches within microbial hotspots

    Science.gov (United States)

    Smith, Renee J.; Tobe, Shanan S.; Paterson, James S.; Seymour, Justin R.; Oliver, Rod L.; Mitchell, James G.

    2018-01-01

    The spatial distributions of organism abundance and diversity are often heterogeneous. This includes the sub-centimetre distributions of microbes, which have ‘hotspots’ of high abundance, and ‘coldspots’ of low abundance. Previously we showed that 300 μl abundance hotspots, coldspots and background regions were distinct at all taxonomic levels. Here we build on these results by showing taxonomic micropatches within these 300 μl microscale hotspots, coldspots and background regions at the 1 μl scale. This heterogeneity among 1 μl subsamples was driven by heightened abundance of specific genera. The micropatches were most pronounced within hotspots. Micropatches were dominated by Pseudomonas, Bacteroides, Parasporobacterium and Lachnospiraceae incertae sedis, with Pseudomonas and Bacteroides being responsible for a shift in the most dominant genera in individual hotspot subsamples, representing up to 80.6% and 47.3% average abundance, respectively. The presence of these micropatches implies the ability these groups have to create, establish themselves in, or exploit heterogeneous microenvironments. These genera are often particle-associated, from which we infer that these micropatches are evidence for sub-millimetre aggregates and the aquatic polymer matrix. These findings support the emerging paradigm that the microscale distributions of planktonic microbes are numerically and taxonomically heterogeneous at scales of millimetres and less. We show that microscale microbial hotspots have internal structure within which specific local nutrient exchanges and cellular interactions might occur. PMID:29787564

  8. Scalable Nonlinear Compact Schemes

    Energy Technology Data Exchange (ETDEWEB)

    Ghosh, Debojyoti [Argonne National Lab. (ANL), Argonne, IL (United States); Constantinescu, Emil M. [Univ. of Chicago, IL (United States); Brown, Jed [Univ. of Colorado, Boulder, CO (United States)

    2014-04-01

    In this work, we focus on compact schemes resulting in tridiagonal systems of equations, specifically the fifth-order CRWENO scheme. We propose a scalable implementation of the nonlinear compact schemes by implementing a parallel tridiagonal solver based on the partitioning/substructuring approach. We use an iterative solver for the reduced system of equations; however, we solve this system to machine zero accuracy to ensure that no parallelization errors are introduced. It is possible to achieve machine-zero convergence with few iterations because of the diagonal dominance of the system. The number of iterations is specified a priori instead of a norm-based exit criterion, and collective communications are avoided. The overall algorithm thus involves only point-to-point communication between neighboring processors. Our implementation of the tridiagonal solver differs from and avoids the drawbacks of past efforts in the following ways: it introduces no parallelization-related approximations (multiprocessor solutions are exactly identical to uniprocessor ones), it involves minimal communication, the mathematical complexity is similar to that of the Thomas algorithm on a single processor, and it does not require any communication and computation scheduling.

  9. Common genotypes of hepatitis B virus

    International Nuclear Information System (INIS)

    Idrees, M.; Khan, S.; Riazuddin, S.

    2004-01-01

    Objective: To find out the frequency of common genotypes of hepatitis-B virus (HBV). Subjects and Methods: HBV genotypes were determined in 112 HBV DNA positive sera by a simple and precise molecular genotyping system base on PCR using type-specific primers for the determination of genotypes of HBV A through H. Results: Four genotypes (A,B,C and D) out of total eight reported genotypes so far were identified. Genotypes A, B and C were predominant. HBV genotype C was the most predominant in this collection, appearing in 46 samples (41.7%). However, the genotypes of a total of 5 (4.46%) samples could not be determined with the present genotyping system. Mixed genotypes were seen in 8(7.14% HBV) isolates. Five of these were infected with genotypes A/D whereas two were with genotypes C/D. One patient was infected with 4 genotypes (A/B/C/D). Genotype A (68%) was predominant in Sindh genotype C was most predominant in North West Frontier Province (NWFP) (68.96) whereas genotype C and B were dominant in Punjab (39.65% and 25.86% respectively). Conclusion: All the four common genotypes of HBV found worldwide (A,B,C and D) were isolated. Genotype C is the predominant Genotypes B and C are predominant in Punjab and N.W.F.P. whereas genotype A is predominant in Sindh. (author)

  10. HBV genotypic variability in Cuba.

    Directory of Open Access Journals (Sweden)

    Carmen L Loureiro

    Full Text Available The genetic diversity of HBV in human population is often a reflection of its genetic admixture. The aim of this study was to explore the genotypic diversity of HBV in Cuba. The S genomic region of Cuban HBV isolates was sequenced and for selected isolates the complete genome or precore-core sequence was analyzed. The most frequent genotype was A (167/250, 67%, mainly A2 (149, 60% but also A1 and one A4. A total of 77 isolates were classified as genotype D (31%, with co-circulation of several subgenotypes (56 D4, 2 D1, 5 D2, 7 D3/6 and 7 D7. Three isolates belonged to genotype E, two to H and one to B3. Complete genome sequence analysis of selected isolates confirmed the phylogenetic analysis performed with the S region. Mutations or polymorphisms in precore region were more common among genotype D compared to genotype A isolates. The HBV genotypic distribution in this Caribbean island correlates with the Y lineage genetic background of the population, where a European and African origin prevails. HBV genotypes E, B3 and H isolates might represent more recent introductions.

  11. HBV Genotypic Variability in Cuba

    Science.gov (United States)

    Loureiro, Carmen L.; Aguilar, Julio C.; Aguiar, Jorge; Muzio, Verena; Pentón, Eduardo; Garcia, Daymir; Guillen, Gerardo; Pujol, Flor H.

    2015-01-01

    The genetic diversity of HBV in human population is often a reflection of its genetic admixture. The aim of this study was to explore the genotypic diversity of HBV in Cuba. The S genomic region of Cuban HBV isolates was sequenced and for selected isolates the complete genome or precore-core sequence was analyzed. The most frequent genotype was A (167/250, 67%), mainly A2 (149, 60%) but also A1 and one A4. A total of 77 isolates were classified as genotype D (31%), with co-circulation of several subgenotypes (56 D4, 2 D1, 5 D2, 7 D3/6 and 7 D7). Three isolates belonged to genotype E, two to H and one to B3. Complete genome sequence analysis of selected isolates confirmed the phylogenetic analysis performed with the S region. Mutations or polymorphisms in precore region were more common among genotype D compared to genotype A isolates. The HBV genotypic distribution in this Caribbean island correlates with the Y lineage genetic background of the population, where a European and African origin prevails. HBV genotypes E, B3 and H isolates might represent more recent introductions. PMID:25742179

  12. ESCAP mobile training scheme.

    Science.gov (United States)

    Yasas, F M

    1977-01-01

    In response to a United Nations resolution, the Mobile Training Scheme (MTS) was set up to provide training to the trainers of national cadres engaged in frontline and supervisory tasks in social welfare and rural development. The training is innovative in its being based on an analysis of field realities. The MTS team consisted of a leader, an expert on teaching methods and materials, and an expert on action research and evaluation. The country's trainers from different departments were sent to villages to work for a short period and to report their problems in fulfilling their roles. From these grass roots experiences, they made an analysis of the job, determining what knowledge, attitude and skills it required. Analysis of daily incidents and problems were used to produce indigenous teaching materials drawn from actual field practice. How to consider the problems encountered through government structures for policy making and decisions was also learned. Tasks of the students were to identify the skills needed for role performance by job analysis, daily diaries and project histories; to analyze the particular community by village profiles; to produce indigenous teaching materials; and to practice the role skills by actual role performance. The MTS scheme was tried in Nepal in 1974-75; 3 training programs trained 25 trainers and 51 frontline workers; indigenous teaching materials were created; technical papers written; and consultations were provided. In Afghanistan the scheme was used in 1975-76; 45 participants completed the training; seminars were held; and an ongoing Council was created. It is hoped that the training program will be expanded to other countries.

  13. Bonus schemes and trading activity

    NARCIS (Netherlands)

    Pikulina, E.S.; Renneboog, L.D.R.; ter Horst, J.R.; Tobler, P.N.

    2014-01-01

    Little is known about how different bonus schemes affect traders' propensity to trade and which bonus schemes improve traders' performance. We study the effects of linear versus threshold bonus schemes on traders' behavior. Traders buy and sell shares in an experimental stock market on the basis of

  14. Succesful labelling schemes

    DEFF Research Database (Denmark)

    Juhl, Hans Jørn; Stacey, Julia

    2001-01-01

    . In the spring of 2001 MAPP carried out an extensive consumer study with special emphasis on the Nordic environmentally friendly label 'the swan'. The purpose was to find out how much consumers actually know and use various labelling schemes. 869 households were contacted and asked to fill in a questionnaire...... it into consideration when I go shopping. The respondent was asked to pick the most suitable answer, which described her use of each label. 29% - also called 'the labelling blind' - responded that they basically only knew the recycling label and the Government controlled organic label 'Ø-mærket'. Another segment of 6...

  15. Scheme of stepmotor control

    International Nuclear Information System (INIS)

    Grashilin, V.A.; Karyshev, Yu.Ya.

    1982-01-01

    A 6-cycle scheme of step motor is described. The block-diagram and the basic circuit of the step motor control are presented. The step motor control comprises a pulse shaper, electronic commutator and power amplifiers. The step motor supply from 6-cycle electronic commutator provides for higher reliability and accuracy than from 3-cycle commutator. The control of step motor work is realised by the program given by the external source of control signals. Time-dependent diagrams for step motor control are presented. The specifications of the step-motor is given

  16. A Microbial Assessment Scheme to measure microbial performance of Food Safety Management Systems

    NARCIS (Netherlands)

    Jacxsens, L.; Kussaga, J.; Luning, P.A.; Spiegel, van der M.; Devlieghere, F.; Uyttendaele, M.

    2009-01-01

    A Food Safety Management System (FSMS) implemented in a food processing industry is based on Good Hygienic Practices (GHP), Hazard Analysis Critical Control Point (HACCP) principles and should address both food safety control and assurance activities in order to guarantee food safety. One of the

  17. Alternation of cowpea genotypes affects the biology of Callosobruchus maculatus (fabr. (Coleoptera: Bruchidae

    Directory of Open Access Journals (Sweden)

    Lima Marcileyne Pessôa Leite de

    2004-01-01

    Full Text Available Callosobruchus maculatus (Fabr. is an important pest in stored cowpea, Vigna unguiculata (L. Walp., with ample distribution in tropical and subtropical regions. The effect of alternation of cowpea genotypes, susceptible (S and resistant (R, on the biology of (C. maculatus was studied after four generations. A no-choice test was carried out in a completely randomized design, factorial scheme, with five treatments, four host combinations (RR, RS, SR and SS and five replications. Each replication consisted of 30 grains of each genotype infested by two insect couples. The number of eggs per female was not different within or between combinations, evidencing that the genotypes and their alternation did not affect C. maculatus fecundity. Egg viability, however, varied between genotypes and between combinations. In combination RR, the longest duration of the immature stage was verified for genotype IT89KD-245; in addition, all genotypes presented the smallest survival for the same stage, resulting in a higher mortality of the pest. The resistance index categorized combination RR as moderately resistant for genotypes IT89KD-245, BR14-Mulato and BR17-Gurguéia, and as susceptible (S only for IT89KD-260, demonstrating that these combinations were not very adequate for the development of C. maculatus, a fact that was confirmed by the better performance of the pest on the genotype from combination SS, and because of a reduction in its performance when it returned to resistant genotypes.

  18. 11 Soil Microbial Biomass

    African Journals Online (AJOL)

    186–198. Insam H. (1990). Are the soil microbial biomass and basal respiration governed by the climatic regime? Soil. Biol. Biochem. 22: 525–532. Insam H. D. and Domsch K. H. (1989). Influence of microclimate on soil microbial biomass. Soil Biol. Biochem. 21: 211–21. Jenkinson D. S. (1988). Determination of microbial.

  19. Molecular microbial ecology manual

    NARCIS (Netherlands)

    Kowalchuk, G.A.; Bruijn, de F.J.; Head, I.M.; Akkermans, A.D.L.

    2004-01-01

    The field of microbial ecology has been revolutionized in the past two decades by the introduction of molecular methods into the toolbox of the microbial ecologist. This molecular arsenal has helped to unveil the enormity of microbial diversity across the breadth of the earth's ecosystems, and has

  20. Microbial Rechargeable Battery

    NARCIS (Netherlands)

    Molenaar, Sam D.; Mol, Annemerel R.; Sleutels, Tom H.J.A.; Heijne, Ter Annemiek; Buisman, Cees J.N.

    2016-01-01

    Bioelectrochemical systems hold potential for both conversion of electricity into chemicals through microbial electrosynthesis (MES) and the provision of electrical power by oxidation of organics using microbial fuel cells (MFCs). This study provides a proof of concept for a microbial

  1. Childhood microbial keratitis

    Directory of Open Access Journals (Sweden)

    Abdullah G Al Otaibi

    2012-01-01

    Conclusion: Children with suspected microbial keratitis require comprehensive evaluation and management. Early recognition, identifying the predisposing factors and etiological microbial organisms, and instituting appropriate treatment measures have a crucial role in outcome. Ocular trauma was the leading cause of childhood microbial keratitis in our study.

  2. Packet reversed packet combining scheme

    International Nuclear Information System (INIS)

    Bhunia, C.T.

    2006-07-01

    The packet combining scheme is a well defined simple error correction scheme with erroneous copies at the receiver. It offers higher throughput combined with ARQ protocols in networks than that of basic ARQ protocols. But packet combining scheme fails to correct errors when the errors occur in the same bit locations of two erroneous copies. In the present work, we propose a scheme that will correct error if the errors occur at the same bit location of the erroneous copies. The proposed scheme when combined with ARQ protocol will offer higher throughput. (author)

  3. A full quantum network scheme

    International Nuclear Information System (INIS)

    Ma Hai-Qiang; Wei Ke-Jin; Yang Jian-Hui; Li Rui-Xue; Zhu Wu

    2014-01-01

    We present a full quantum network scheme using a modified BB84 protocol. Unlike other quantum network schemes, it allows quantum keys to be distributed between two arbitrary users with the help of an intermediary detecting user. Moreover, it has good expansibility and prevents all potential attacks using loopholes in a detector, so it is more practical to apply. Because the fiber birefringence effects are automatically compensated, the scheme is distinctly stable in principle and in experiment. The simple components for every user make our scheme easier for many applications. The experimental results demonstrate the stability and feasibility of this scheme. (general)

  4. Echinococcus granulosus genotypes in Iran

    Science.gov (United States)

    Sharafi, Seyedeh Maryam; Rostami-Nejad, Mohammad; Moazeni, Mohammad; Yousefi, Morteza; Saneie, Behnam; Hosseini-Safa, Ahmad

    2014-01-01

    Hydatidosis, caused by Echinococcus granulosus is one of the most important zoonotic diseases, throughout most parts of the world. Hydatidosis is endemic in Iran and responsible for approximately 1% of admission to surgical wards. There are extensive genetic variations within E. granulosus and 10 different genotypes (G1–G10) within this parasite have been reported. Identification of strains is important for improvement of control and prevention of the disease. No new review article presented the situation of Echinococcus granulosus genotypes in Iran in the recent years; therefore in this paper we reviewed the different studies regarding Echinococcus granulosus genotypes in Iran. PMID:24834298

  5. Genotyping common and rare variation using overlapping pool sequencing

    Directory of Open Access Journals (Sweden)

    Pasaniuc Bogdan

    2011-07-01

    Full Text Available Abstract Background Recent advances in sequencing technologies set the stage for large, population based studies, in which the ANA or RNA of thousands of individuals will be sequenced. Currently, however, such studies are still infeasible using a straightforward sequencing approach; as a result, recently a few multiplexing schemes have been suggested, in which a small number of ANA pools are sequenced, and the results are then deconvoluted using compressed sensing or similar approaches. These methods, however, are limited to the detection of rare variants. Results In this paper we provide a new algorithm for the deconvolution of DNA pools multiplexing schemes. The presented algorithm utilizes a likelihood model and linear programming. The approach allows for the addition of external data, particularly imputation data, resulting in a flexible environment that is suitable for different applications. Conclusions Particularly, we demonstrate that both low and high allele frequency SNPs can be accurately genotyped when the DNA pooling scheme is performed in conjunction with microarray genotyping and imputation. Additionally, we demonstrate the use of our framework for the detection of cancer fusion genes from RNA sequences.

  6. Modified Aggressive Packet Combining Scheme

    International Nuclear Information System (INIS)

    Bhunia, C.T.

    2010-06-01

    In this letter, a few schemes are presented to improve the performance of aggressive packet combining scheme (APC). To combat error in computer/data communication networks, ARQ (Automatic Repeat Request) techniques are used. Several modifications to improve the performance of ARQ are suggested by recent research and are found in literature. The important modifications are majority packet combining scheme (MjPC proposed by Wicker), packet combining scheme (PC proposed by Chakraborty), modified packet combining scheme (MPC proposed by Bhunia), and packet reversed packet combining (PRPC proposed by Bhunia) scheme. These modifications are appropriate for improving throughput of conventional ARQ protocols. Leung proposed an idea of APC for error control in wireless networks with the basic objective of error control in uplink wireless data network. We suggest a few modifications of APC to improve its performance in terms of higher throughput, lower delay and higher error correction capability. (author)

  7. Transmission usage cost allocation schemes

    International Nuclear Information System (INIS)

    Abou El Ela, A.A.; El-Sehiemy, R.A.

    2009-01-01

    This paper presents different suggested transmission usage cost allocation (TCA) schemes to the system individuals. Different independent system operator (ISO) visions are presented using the proportional rata and flow-based TCA methods. There are two proposed flow-based TCA schemes (FTCA). The first FTCA scheme generalizes the equivalent bilateral exchanges (EBE) concepts for lossy networks through two-stage procedure. The second FTCA scheme is based on the modified sensitivity factors (MSF). These factors are developed from the actual measurements of power flows in transmission lines and the power injections at different buses. The proposed schemes exhibit desirable apportioning properties and are easy to implement and understand. Case studies for different loading conditions are carried out to show the capability of the proposed schemes for solving the TCA problem. (author)

  8. Nephele: genotyping via complete composition vectors and MapReduce

    Directory of Open Access Journals (Sweden)

    Mardis Scott

    2011-08-01

    Full Text Available Abstract Background Current sequencing technology makes it practical to sequence many samples of a given organism, raising new challenges for the processing and interpretation of large genomics data sets with associated metadata. Traditional computational phylogenetic methods are ideal for studying the evolution of gene/protein families and using those to infer the evolution of an organism, but are less than ideal for the study of the whole organism mainly due to the presence of insertions/deletions/rearrangements. These methods provide the researcher with the ability to group a set of samples into distinct genotypic groups based on sequence similarity, which can then be associated with metadata, such as host information, pathogenicity, and time or location of occurrence. Genotyping is critical to understanding, at a genomic level, the origin and spread of infectious diseases. Increasingly, genotyping is coming into use for disease surveillance activities, as well as for microbial forensics. The classic genotyping approach has been based on phylogenetic analysis, starting with a multiple sequence alignment. Genotypes are then established by expert examination of phylogenetic trees. However, these traditional single-processor methods are suboptimal for rapidly growing sequence datasets being generated by next-generation DNA sequencing machines, because they increase in computational complexity quickly with the number of sequences. Results Nephele is a suite of tools that uses the complete composition vector algorithm to represent each sequence in the dataset as a vector derived from its constituent k-mers by passing the need for multiple sequence alignment, and affinity propagation clustering to group the sequences into genotypes based on a distance measure over the vectors. Our methods produce results that correlate well with expert-defined clades or genotypes, at a fraction of the computational cost of traditional phylogenetic methods run on

  9. Microbial electrosynthetic cells

    Energy Technology Data Exchange (ETDEWEB)

    May, Harold D.; Marshall, Christopher W.; Labelle, Edward V.

    2018-01-30

    Methods are provided for microbial electrosynthesis of H.sub.2 and organic compounds such as methane and acetate. Method of producing mature electrosynthetic microbial populations by continuous culture is also provided. Microbial populations produced in accordance with the embodiments as shown to efficiently synthesize H.sub.2, methane and acetate in the presence of CO.sub.2 and a voltage potential. The production of biodegradable and renewable plastics from electricity and carbon dioxide is also disclosed.

  10. Coordinated renewable energy support schemes

    DEFF Research Database (Denmark)

    Morthorst, P.E.; Jensen, S.G.

    2006-01-01

    . The first example covers countries with regional power markets that also regionalise their support schemes, the second countries with separate national power markets that regionalise their support schemes. The main findings indicate that the almost ideal situation exists if the region prior to regionalising...

  11. CANONICAL BACKWARD DIFFERENTIATION SCHEMES FOR ...

    African Journals Online (AJOL)

    This paper describes a new nonlinear backward differentiation schemes for the numerical solution of nonlinear initial value problems of first order ordinary differential equations. The schemes are based on rational interpolation obtained from canonical polynomials. They are A-stable. The test problems show that they give ...

  12. Microbial interactions: ecology in a molecular perspective.

    Science.gov (United States)

    Braga, Raíssa Mesquita; Dourado, Manuella Nóbrega; Araújo, Welington Luiz

    2016-12-01

    The microorganism-microorganism or microorganism-host interactions are the key strategy to colonize and establish in a variety of different environments. These interactions involve all ecological aspects, including physiochemical changes, metabolite exchange, metabolite conversion, signaling, chemotaxis and genetic exchange resulting in genotype selection. In addition, the establishment in the environment depends on the species diversity, since high functional redundancy in the microbial community increases the competitive ability of the community, decreasing the possibility of an invader to establish in this environment. Therefore, these associations are the result of a co-evolution process that leads to the adaptation and specialization, allowing the occupation of different niches, by reducing biotic and abiotic stress or exchanging growth factors and signaling. Microbial interactions occur by the transference of molecular and genetic information, and many mechanisms can be involved in this exchange, such as secondary metabolites, siderophores, quorum sensing system, biofilm formation, and cellular transduction signaling, among others. The ultimate unit of interaction is the gene expression of each organism in response to an environmental (biotic or abiotic) stimulus, which is responsible for the production of molecules involved in these interactions. Therefore, in the present review, we focused on some molecular mechanisms involved in the microbial interaction, not only in microbial-host interaction, which has been exploited by other reviews, but also in the molecular strategy used by different microorganisms in the environment that can modulate the establishment and structuration of the microbial community. Copyright © 2016 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

  13. Leaf N resorption efficiency and litter N mineralization rate have a genotypic tradeoff in a silver birch population.

    Science.gov (United States)

    Mikola, Juha; Silfver, Tarja; Paaso, Ulla; Possen, Boy J M H; Rousi, Matti

    2018-02-07

    Plants enhance N use efficiency by resorbing N from senescing leaves. This can affect litter N mineralization rate due to the C:N-ratio requirements of microbial growth. We examined genotypic links between leaf N resorption and litter mineralization by collecting leaves and litter from 19 Betula pendula genotypes and following the N release of litter patches on forest ground. We found significant genotypic variation for N resorption efficiency, litter N concentration, cumulative three-year patch N-input and litter N release with high broad-sense heritabilities (H 2  = 0.28-0.65). The genotype means of N resorption efficiency varied from 46% to 65% and correlated negatively with the genotype means of litter N concentration, cumulative patch N-input and litter N release. NH 4 + yield under patches had a positive genotypic correlation with the cumulative patch N-input. During the first year of litter decomposition, genotypes varied from N immobilization (max 2.71 mg/g dry litter) to N release (max 1.41 mg/g dry litter), creating a genotypic tradeoff between the N conserved by resorption and the N available for root uptake during the growing season. We speculate that this tradeoff is one likely reason for the remarkably wide genotypic range of N resorption efficiencies in our birch population. © 2018 by the Ecological Society of America.

  14. Astrobiology and Microbial Diversity Websites at MBL

    Science.gov (United States)

    Bahr, M.; Bordenstein, S. R.

    2006-12-01

    The NASA Astrobiology Institute (NAI) mission is to study the origin, evolution and future of life in the Universe. The MBL Astrobiology team explores the evolution and interaction of genomes of diverse organisms that play significant roles in environmental biology over evolutionary time scales. Communication about our research includes the personal contact of teacher workshops, and the development of web-based resources. Microbial Life Educational Resources (MLER) provides an expanding internet resource about the ecology, diversity and evolution for students, K-12 teachers, university faculty, and the general public. MLER includes websites, PowerPoint presentations, teaching activities, data sets, and other useful materials for creating or enhancing courses related to astrobiology. Our second site, micro*scope (http://microscope.mbl.edu), has images of microbes, classification schemes, descriptions of organisms, talks and other educational resources to improve awareness of the biodiversity of our microbial partners.

  15. Microbial accumulation of uranium

    International Nuclear Information System (INIS)

    Zhang Wei; Dong Faqin; Dai Qunwei

    2005-01-01

    The mechanism of microbial accumulation of uranium and the effects of some factors (including pH, initial uranium concentration, pretreatment of bacteria, and so on) on microbial accumulation of uranium are discussed briefly. The research direction and application prospect are presented. (authors)

  16. MICROBIAL FUEL CELL

    DEFF Research Database (Denmark)

    2008-01-01

    A novel microbial fuel cell construction for the generation of electrical energy. The microbial fuel cell comprises: (i) an anode electrode, (ii) a cathode chamber, said cathode chamber comprising an in let through which an influent enters the cathode chamber, an outlet through which an effluent...

  17. Microbial control of pollution

    Energy Technology Data Exchange (ETDEWEB)

    Fry, J C; Gadd, G M; Herbert, R A; Jones, C W; Watson-Craik, I A [eds.

    1992-01-01

    12 papers are presented on the microbial control of pollution. Topics covered include: bioremediation of oil spills; microbial control of heavy metal pollution; pollution control using microorganisms and magnetic separation; degradation of cyanide and nitriles; nitrogen removal from water and waste; and land reclamation and restoration.

  18. hybrid modulation scheme fo rid modulation scheme fo dulation

    African Journals Online (AJOL)

    eobe

    control technique is done through simulations and ex control technique .... HYBRID MODULATION SCHEME FOR CASCADED H-BRIDGE INVERTER CELLS. C. I. Odeh ..... and OR operations. Referring to ... MATLAB/SIMULINK environment.

  19. FTO genotype and weight loss

    DEFF Research Database (Denmark)

    Livingstone, Katherine M; Celis-Morales, Carlos; Papandonatos, George D

    2016-01-01

    : Ovid Medline, Scopus, Embase, and Cochrane from inception to November 2015. ELIGIBILITY CRITERIA FOR STUDY SELECTION: Randomised controlled trials in overweight or obese adults reporting reduction in body mass index, body weight, or waist circumference by FTO genotype (rs9939609 or a proxy) after...

  20. FTO genotype and weight loss

    DEFF Research Database (Denmark)

    Livingstone, Katherine M; Celis-Morales, Carlos; Papandonatos, George D

    2016-01-01

    OBJECTIVE: To assess the effect of the FTO genotype on weight loss after dietary, physical activity, or drug based interventions in randomised controlled trials. DESIGN: Systematic review and random effects meta-analysis of individual participant data from randomised controlled trials. DATA SOURC...

  1. Good governance for pension schemes

    CERN Document Server

    Thornton, Paul

    2011-01-01

    Regulatory and market developments have transformed the way in which UK private sector pension schemes operate. This has increased demands on trustees and advisors and the trusteeship governance model must evolve in order to remain fit for purpose. This volume brings together leading practitioners to provide an overview of what today constitutes good governance for pension schemes, from both a legal and a practical perspective. It provides the reader with an appreciation of the distinctive characteristics of UK occupational pension schemes, how they sit within the capital markets and their social and fiduciary responsibilities. Providing a holistic analysis of pension risk, both from the trustee and the corporate perspective, the essays cover the crucial role of the employer covenant, financing and investment risk, developments in longevity risk hedging and insurance de-risking, and best practice scheme administration.

  2. Optimum RA reactor fuelling scheme

    International Nuclear Information System (INIS)

    Strugar, P.; Nikolic, V.

    1965-10-01

    Ideal reactor refueling scheme can be achieved only by continuous fuel elements movement in the core, which is not possible, and thus approximations are applied. One of the possible approximations is discontinuous movement of fuel elements groups in radial direction. This enables higher burnup especially if axial exchange is possible. Analysis of refueling schemes in the RA reactor core and schemes with mixing the fresh and used fuel elements show that 30% higher burnup can be achieved by applying mixing, and even 40% if reactivity due to decrease in experimental space is taken into account. Up to now, mean burnup of 4400 MWd/t has been achieved, and the proposed fueling scheme with reduction of experimental space could achieve mean burnup of 6300 MWd/t which means about 25 Mwd/t per fuel channel [sr

  3. A Novel Iris Segmentation Scheme

    Directory of Open Access Journals (Sweden)

    Chen-Chung Liu

    2014-01-01

    Full Text Available One of the key steps in the iris recognition system is the accurate iris segmentation from its surrounding noises including pupil, sclera, eyelashes, and eyebrows of a captured eye-image. This paper presents a novel iris segmentation scheme which utilizes the orientation matching transform to outline the outer and inner iris boundaries initially. It then employs Delogne-Kåsa circle fitting (instead of the traditional Hough transform to further eliminate the outlier points to extract a more precise iris area from an eye-image. In the extracted iris region, the proposed scheme further utilizes the differences in the intensity and positional characteristics of the iris, eyelid, and eyelashes to detect and delete these noises. The scheme is then applied on iris image database, UBIRIS.v1. The experimental results show that the presented scheme provides a more effective and efficient iris segmentation than other conventional methods.

  4. Numerical schemes for explosion hazards

    International Nuclear Information System (INIS)

    Therme, Nicolas

    2015-01-01

    In nuclear facilities, internal or external explosions can cause confinement breaches and radioactive materials release in the environment. Hence, modeling such phenomena is crucial for safety matters. Blast waves resulting from explosions are modeled by the system of Euler equations for compressible flows, whereas Navier-Stokes equations with reactive source terms and level set techniques are used to simulate the propagation of flame front during the deflagration phase. The purpose of this thesis is to contribute to the creation of efficient numerical schemes to solve these complex models. The work presented here focuses on two major aspects: first, the development of consistent schemes for the Euler equations, then the buildup of reliable schemes for the front propagation. In both cases, explicit in time schemes are used, but we also introduce a pressure correction scheme for the Euler equations. Staggered discretization is used in space. It is based on the internal energy formulation of the Euler system, which insures its positivity and avoids tedious discretization of the total energy over staggered grids. A discrete kinetic energy balance is derived from the scheme and a source term is added in the discrete internal energy balance equation to preserve the exact total energy balance at the limit. High order methods of MUSCL type are used in the discrete convective operators, based solely on material velocity. They lead to positivity of density and internal energy under CFL conditions. This ensures that the total energy cannot grow and we can furthermore derive a discrete entropy inequality. Under stability assumptions of the discrete L8 and BV norms of the scheme's solutions one can prove that a sequence of converging discrete solutions necessarily converges towards the weak solution of the Euler system. Besides it satisfies a weak entropy inequality at the limit. Concerning the front propagation, we transform the flame front evolution equation (the so called

  5. Breeding schemes in reindeer husbandry

    Directory of Open Access Journals (Sweden)

    Lars Rönnegård

    2003-04-01

    Full Text Available The objective of the paper was to investigate annual genetic gain from selection (G, and the influence of selection on the inbreeding effective population size (Ne, for different possible breeding schemes within a reindeer herding district. The breeding schemes were analysed for different proportions of the population within a herding district included in the selection programme. Two different breeding schemes were analysed: an open nucleus scheme where males mix and mate between owner flocks, and a closed nucleus scheme where the males in non-selected owner flocks are culled to maximise G in the whole population. The theory of expected long-term genetic contributions was used and maternal effects were included in the analyses. Realistic parameter values were used for the population, modelled with 5000 reindeer in the population and a sex ratio of 14 adult females per male. The standard deviation of calf weights was 4.1 kg. Four different situations were explored and the results showed: 1. When the population was randomly culled, Ne equalled 2400. 2. When the whole population was selected on calf weights, Ne equalled 1700 and the total annual genetic gain (direct + maternal in calf weight was 0.42 kg. 3. For the open nucleus scheme, G increased monotonically from 0 to 0.42 kg as the proportion of the population included in the selection programme increased from 0 to 1.0, and Ne decreased correspondingly from 2400 to 1700. 4. In the closed nucleus scheme the lowest value of Ne was 1300. For a given proportion of the population included in the selection programme, the difference in G between a closed nucleus scheme and an open one was up to 0.13 kg. We conclude that for mass selection based on calf weights in herding districts with 2000 animals or more, there are no risks of inbreeding effects caused by selection.

  6. Hepatitis C Virus: Virology and Genotypes

    KAUST Repository

    Abdelaziz, Ahmed

    2017-01-01

    Hepatitis C virus (HCV) is a major causative agent of chronic liver disease worldwide. HCV is characterized by genetic heterogeneity, with at least six genotypes identified. The geographic distribution of genotypes has shown variations in different

  7. Genotyping cows for the reference increase reliability of genomic prediction in a small breed

    DEFF Research Database (Denmark)

    Thomasen, Jørn Rind; Sørensen, Anders Christian; Lund, Mogens Sandø

    2013-01-01

    We hypothesized that adding cows to the reference population in a breed with a small number of reference bulls would increase reliabilities of genomic breeding values and genetic gain. We tested this premise by comparing two strategies for maintaining the reference population for genetic gain......, inbreeding and reliabilities of genomic predictions: 1) Adding 60 progeny tested bulls each year (B), and 2) in addition to 60 progeny tested bulls, adding 2,000 genotyped cows per year (C). Two breeding schemes were tested: 1) A turbo scheme (T) with only genotyped young bulls used intensively, and 2...... compared to the H-B, at the same level of ∆F. T-C yielded 15% higher ∆G compared t o T-B. Changing the breeding scheme from H-B to H-C increased ∆G by 5.5%. The lowest ∆F was observed with genotyping of cows. Reliabilities of GEBV in the C schemes showed a steep increase in reliability during the first...

  8. Response of cactus pear genotypes to different crop densities

    Directory of Open Access Journals (Sweden)

    Lucas Aroaldo Dantas Cavalcante

    2014-09-01

    Full Text Available Considering the importance of cactus pear as an alimentary alternative for the herd of cattle of the Brazilian semiarid region and the effect of crop spacing among plants, this study aimed to evaluate the morphometry, yield and chemical-bromatological composition of cactus pear genotypes, under different cropping densities. The experimental design was completely randomized blocks, in a 3x4 factorial scheme. Treatments consisted of a combination of three cactus pear genotypes (Gigante, Redonda and Miúda and four cropping densities (10,000 plants ha-1; 20,000 plants ha-1; 40,000 plants ha-1; and 80,000 plants ha-1, with three replications. The cactus pear genotypes reacted differently, regarding morphometry, yield and chemical-bromatological composition, and, regardless of the species, the denser planting increased yield (tons ha-1. The Miúda palm presented the highest dry matter yield and consequently the greater accumulation of total digestible nutrients, raw protein and water per hectare, as well as the highest in vitro dry matter digestibility.

  9. Genotype x environment interaction and optimum resource ...

    African Journals Online (AJOL)

    ... x E) interaction and to determine the optimum resource allocation for cassava yield trials. The effects of environment, genotype and G x E interaction were highly significant for all yield traits. Variations due to G x E interaction were greater than those due to genotypic differences for all yield traits. Genotype x location x year ...

  10. Evolution of microbial pathogens

    National Research Council Canada - National Science Library

    DiRita, Victor J; Seifert, H. Steven

    2006-01-01

    ... A. Hogan vvi ■ CONTENTS 8. Evolution of Pathogens in Soil Rachel Muir and Man-Wah Tan / 131 9. Experimental Models of Symbiotic Host-Microbial Relationships: Understanding the Underpinnings of ...

  11. Genetic Divergence in Sugarcane Genotypes

    OpenAIRE

    Tahir, Mohammad; Rahman, Hidayatur; Gul, Rahmani; Ali, Amjad; Khalid, Muhammad

    2012-01-01

    To assess genetic divergence of sugarcane germplasm, an experiment comprising 25 sugarcane genotypes was conducted at Sugar Crops Research Institute (SCRI), Mardan, Khyber Pakhtunkhwa, Pakistan, in quadruple lattice design during 2008-09. Among the 14 parameters evaluated, majority exhibited significant differences while some showed nonsignificant mean squares. The initial correlation matrix revealed medium to high correlations. Principal Component Analysis (PCA) showed that there were two pr...

  12. Synthetic Electric Microbial Biosensors

    Science.gov (United States)

    2017-06-10

    domains and DNA-binding domains into a single protein for deregulation of down stream genes of have been favored [10]. Initially experiments with... Germany DISTRIBUTION A. Approved for public release: distribution unlimited.   Talk title: “Synthetic biology based microbial biosensors for the...toolbox” in Heidelberg, Germany Poster title: “Anaerobic whole cell microbial biosensors” Link: http://phdsymposium.embl.org/#home   September, 2014

  13. Association Between Early Childhood Caries and Colonization with Streptococcus mutans Genotypes From Mothers.

    Science.gov (United States)

    Childers, Noel K; Momeni, Stephanie S; Whiddon, Jennifer; Cheon, Kyounga; Cutter, Gary R; Wiener, Howard W; Ghazal, Tariq S; Ruby, John D; Moser, Stephen A

    2017-03-15

    The purpose of this study was to evaluate Streptococcus mutans genotypes (GT) between mother and child (M-C) in a high caries risk cohort to explore the association with early childhood caries (ECC). Sixty-nine infants (each approximately one year old) had periodic oral examinations (dmfs) and microbial samples collected from dental plaque, saliva, and other oral surfaces. Their mothers had an examination and plaque collected. S mutans isolates were genotyped using repetitive extragenic palindromic-PCR (rep-PCR). Statistical analyses were conducted for associations of S mutans in M-C dyads with caries outcomes. Twenty-seven S mutans genotypes (GT) from 3,414 isolates were identified. M-C were categorized as GT match (n equals 40) or no-match (n equals 29). When modeling the severity of ECC at 36 months (approximately four years old), the estimated dmfs in the match group was 2.61 times that of the no-match group (P=.014). Colonization of children with Streptococcus mutans genotypes that matched with mothers was shown to be highly associated with early childhood caries. Although the data suggest vertical transmission of S mutans in 40 of 69 children that shared GT with their mother, it is possible that other individuals transmitted the S mutans. Nonetheless, these findings support the importance of the mother's oral microbial status as a contributing influence to their children's oral health.

  14. Microbial bioinformatics 2020.

    Science.gov (United States)

    Pallen, Mark J

    2016-09-01

    Microbial bioinformatics in 2020 will remain a vibrant, creative discipline, adding value to the ever-growing flood of new sequence data, while embracing novel technologies and fresh approaches. Databases and search strategies will struggle to cope and manual curation will not be sustainable during the scale-up to the million-microbial-genome era. Microbial taxonomy will have to adapt to a situation in which most microorganisms are discovered and characterised through the analysis of sequences. Genome sequencing will become a routine approach in clinical and research laboratories, with fresh demands for interpretable user-friendly outputs. The "internet of things" will penetrate healthcare systems, so that even a piece of hospital plumbing might have its own IP address that can be integrated with pathogen genome sequences. Microbiome mania will continue, but the tide will turn from molecular barcoding towards metagenomics. Crowd-sourced analyses will collide with cloud computing, but eternal vigilance will be the price of preventing the misinterpretation and overselling of microbial sequence data. Output from hand-held sequencers will be analysed on mobile devices. Open-source training materials will address the need for the development of a skilled labour force. As we boldly go into the third decade of the twenty-first century, microbial sequence space will remain the final frontier! © 2016 The Author. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  15. Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution

    NARCIS (Netherlands)

    Bachmann, H.; Starrenburg, M.J.C.; Molenaar, D.; Kleerebezem, M.; Hylckama Vlieg, van J.E.T.

    2012-01-01

    Experimental evolution is a powerful approach to unravel how selective forces shape microbial genotypes and phenotypes. To this date, the available examples focus on the adaptation to conditions specific to the laboratory. The lactic acid bacterium Lactococcus lactis naturally occurs on plants and

  16. Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution.

    NARCIS (Netherlands)

    Bachmann, H.; Starrenburg, M.J.; Molenaar, D.; Kleerebezem, M.; van Hylckama Vlieg, J.E.T.

    2012-01-01

    Experimental evolution is a powerful approach to unravel how selective forces shape microbial genotypes and phenotypes. To this date, the available examples focus on the adaptation to conditions specific to the laboratory. The lactic acid bacterium Lactococcus lactis naturally occurs on plants and

  17. Multiuser switched diversity scheduling schemes

    KAUST Repository

    Shaqfeh, Mohammad; Alnuweiri, Hussein M.; Alouini, Mohamed-Slim

    2012-01-01

    Multiuser switched-diversity scheduling schemes were recently proposed in order to overcome the heavy feedback requirements of conventional opportunistic scheduling schemes by applying a threshold-based, distributed, and ordered scheduling mechanism. The main idea behind these schemes is that slight reduction in the prospected multiuser diversity gains is an acceptable trade-off for great savings in terms of required channel-state-information feedback messages. In this work, we characterize the achievable rate region of multiuser switched diversity systems and compare it with the rate region of full feedback multiuser diversity systems. We propose also a novel proportional fair multiuser switched-based scheduling scheme and we demonstrate that it can be optimized using a practical and distributed method to obtain the feedback thresholds. We finally demonstrate by numerical examples that switched-diversity scheduling schemes operate within 0.3 bits/sec/Hz from the ultimate network capacity of full feedback systems in Rayleigh fading conditions. © 2012 IEEE.

  18. Nonlinear secret image sharing scheme.

    Science.gov (United States)

    Shin, Sang-Ho; Lee, Gil-Je; Yoo, Kee-Young

    2014-01-01

    Over the past decade, most of secret image sharing schemes have been proposed by using Shamir's technique. It is based on a linear combination polynomial arithmetic. Although Shamir's technique based secret image sharing schemes are efficient and scalable for various environments, there exists a security threat such as Tompa-Woll attack. Renvall and Ding proposed a new secret sharing technique based on nonlinear combination polynomial arithmetic in order to solve this threat. It is hard to apply to the secret image sharing. In this paper, we propose a (t, n)-threshold nonlinear secret image sharing scheme with steganography concept. In order to achieve a suitable and secure secret image sharing scheme, we adapt a modified LSB embedding technique with XOR Boolean algebra operation, define a new variable m, and change a range of prime p in sharing procedure. In order to evaluate efficiency and security of proposed scheme, we use the embedding capacity and PSNR. As a result of it, average value of PSNR and embedding capacity are 44.78 (dB) and 1.74t⌈log2 m⌉ bit-per-pixel (bpp), respectively.

  19. Multiuser switched diversity scheduling schemes

    KAUST Repository

    Shaqfeh, Mohammad

    2012-09-01

    Multiuser switched-diversity scheduling schemes were recently proposed in order to overcome the heavy feedback requirements of conventional opportunistic scheduling schemes by applying a threshold-based, distributed, and ordered scheduling mechanism. The main idea behind these schemes is that slight reduction in the prospected multiuser diversity gains is an acceptable trade-off for great savings in terms of required channel-state-information feedback messages. In this work, we characterize the achievable rate region of multiuser switched diversity systems and compare it with the rate region of full feedback multiuser diversity systems. We propose also a novel proportional fair multiuser switched-based scheduling scheme and we demonstrate that it can be optimized using a practical and distributed method to obtain the feedback thresholds. We finally demonstrate by numerical examples that switched-diversity scheduling schemes operate within 0.3 bits/sec/Hz from the ultimate network capacity of full feedback systems in Rayleigh fading conditions. © 2012 IEEE.

  20. Electrical Injection Schemes for Nanolasers

    DEFF Research Database (Denmark)

    Lupi, Alexandra; Chung, Il-Sug; Yvind, Kresten

    2014-01-01

    Three electrical injection schemes based on recently demonstrated electrically pumped photonic crystal nanolasers have been numerically investigated: 1) a vertical p-i-n junction through a post structure; 2) a lateral p-i-n junction with a homostructure; and 3) a lateral p-i-n junction....... For this analysis, the properties of different schemes, i.e., electrical resistance, threshold voltage, threshold current, and internal efficiency as energy requirements for optical interconnects are compared and the physics behind the differences is discussed....

  1. Signal multiplexing scheme for LINAC

    International Nuclear Information System (INIS)

    Sujo, C.I.; Mohan, Shyam; Joshi, Gopal; Singh, S.K.; Karande, Jitendra

    2004-01-01

    For the proper operation of the LINAC some signals, RF (radio frequency) as well as LF (low frequency) have to be available at the Master Control Station (MCS). These signals are needed to control, calibrate and characterize the RF fields in the resonators. This can be achieved by proper multiplexing of various signals locally and then routing the selected signals to the MCS. A multiplexing scheme has been designed and implemented, which will allow the signals from the selected cavity to the MCS. High isolation between channels and low insertion loss for a given signal are important issues while selecting the multiplexing scheme. (author)

  2. Capacity-achieving CPM schemes

    OpenAIRE

    Perotti, Alberto; Tarable, Alberto; Benedetto, Sergio; Montorsi, Guido

    2008-01-01

    The pragmatic approach to coded continuous-phase modulation (CPM) is proposed as a capacity-achieving low-complexity alternative to the serially-concatenated CPM (SC-CPM) coding scheme. In this paper, we first perform a selection of the best spectrally-efficient CPM modulations to be embedded into SC-CPM schemes. Then, we consider the pragmatic capacity (a.k.a. BICM capacity) of CPM modulations and optimize it through a careful design of the mapping between input bits and CPM waveforms. The s...

  3. Mixed models identify physic nut genotypes adapted to environments with different phosphorus availability.

    Science.gov (United States)

    Teodoro, P E; Laviola, B G; Martins, L D; Amaral, J F T; Rodrigues, W N

    2016-08-19

    The aim of this study was to screen physic nut (Jatropha curcas) genotypes that differ in their phosphorous (P) use, using mixed models. The experiment was conducted in a greenhouse located in the experimental area of the Centro de Ciências Agrárias of the Universidade Federal do Espírito Santo, in Alegre, ES, Brazil. The experiment was arranged in a randomized block design, using a 10 x 3-factorial scheme, including ten physic nut genotypes and two environments that differed in their levels of soil P availability (10 and 60 mg/dm 3 ), each with four replications. After 100 days of cultivation, we evaluated the plant height, stem diameter, root volume, root dry matter, aerial part dry matter, total dry matter, as well as the efficiency of absorption, and use. The parameters were estimated for combined selection while considering the studied parameters: stability and adaptability for both environments were obtained using the harmonic mean of the relative performance of the predicted genotypic values. High genotype by environment interactions were observed for most physic nut traits, indicating considerable influences of P availability on the phenotypic value. The genotype Paraíso simultaneously presented high adaptability and stability for aerial part dry matter, total dry matter, and P translocation efficiency. The genotype CNPAE-C2 showed a positive response to P fertilization by increasing both the total and aerial part dry matter.

  4. Deep subsurface microbial processes

    Science.gov (United States)

    Lovley, D.R.; Chapelle, F.H.

    1995-01-01

    Information on the microbiology of the deep subsurface is necessary in order to understand the factors controlling the rate and extent of the microbially catalyzed redox reactions that influence the geophysical properties of these environments. Furthermore, there is an increasing threat that deep aquifers, an important drinking water resource, may be contaminated by man's activities, and there is a need to predict the extent to which microbial activity may remediate such contamination. Metabolically active microorganisms can be recovered from a diversity of deep subsurface environments. The available evidence suggests that these microorganisms are responsible for catalyzing the oxidation of organic matter coupled to a variety of electron acceptors just as microorganisms do in surface sediments, but at much slower rates. The technical difficulties in aseptically sampling deep subsurface sediments and the fact that microbial processes in laboratory incubations of deep subsurface material often do not mimic in situ processes frequently necessitate that microbial activity in the deep subsurface be inferred through nonmicrobiological analyses of ground water. These approaches include measurements of dissolved H2, which can predict the predominant microbially catalyzed redox reactions in aquifers, as well as geochemical and groundwater flow modeling, which can be used to estimate the rates of microbial processes. Microorganisms recovered from the deep subsurface have the potential to affect the fate of toxic organics and inorganic contaminants in groundwater. Microbial activity also greatly influences 1 the chemistry of many pristine groundwaters and contributes to such phenomena as porosity development in carbonate aquifers, accumulation of undesirably high concentrations of dissolved iron, and production of methane and hydrogen sulfide. Although the last decade has seen a dramatic increase in interest in deep subsurface microbiology, in comparison with the study of

  5. Reassessment of MLST schemes for Leptospira spp. typing worldwide.

    Science.gov (United States)

    Varni, Vanina; Ruybal, Paula; Lauthier, Juan José; Tomasini, Nicolás; Brihuega, Bibiana; Koval, Ariel; Caimi, Karina

    2014-03-01

    Leptospirosis is a neglected zoonosis of global importance. Several multilocus sequence typing (MLST) methods have been developed for Leptospira spp., the causative agent of leptospirosis. In this study we reassessed the most commonly used MLST schemes in a set of worldwide isolates, in order to select the loci that achieve the maximum power of discrimination for typing Leptospira spp. Global eBURST algorithm was used to detect clonal complexes among STs and phylogenetic relationships among concatenated and individual sequences were inferred through maximum likelihood (ML) analysis. The evaluation of 12 loci combined to type a subset of strains rendered 57 different STs. Seven of these loci were selected into a final scheme upon studying the number of alleles and polymorphisms, the typing efficiency, the discriminatory power and the ratio dN/dS per nucleotide site for each locus. This new 7-locus scheme was applied to a wider collection of worldwide strains. The ML tree constructed from concatenated sequences of the 7 loci identified 6 major clusters corresponding to 6 Leptospira species. Global eBURST established 8 CCs, which showed that genotypes were clearly related by geographic origin and host. ST52 and ST47, represented mostly by Argentinian isolates, grouped the higher number of isolates. These isolates were serotyped as serogroups Pomona and Icterohaemorrhagiae, showing a unidirectional correlation in which the isolates with the same ST belong to the same serogroup. In summary, this scheme combines the best loci from the most widely used MLST schemes for Leptospira spp. and supports worldwide strains classification. The Argentinian isolates exhibited congruence between allelic profile and serogroup, providing an alternative to serological methods. Published by Elsevier B.V.

  6. [Investigation of the safety of microbial biotechnological products and their hygienic regulation].

    Science.gov (United States)

    Omel'ianets', T H; Kovalenko, N K; Holovach, T M

    2008-01-01

    Peculiarities of influence of microbial preparations based on microorganisms of different taxonomic groups on the warm-blooded organisms are considered, that is necessary to take into account when developing the strategy of toxico-hygienic studying of these preparations and when substanting hygienic standards in industrial objects and in the environment. The possibility to simplify the methodical scheme of the toxicological estimation and the hygienic regulation of microbial preparations on the basis of soil nitrogen-fixing microorganisms is discussed.

  7. Assessment of tillage systems in organic farming: influence of soil structure on microbial biomass. First results

    OpenAIRE

    Vian, Jean François; Peigné, Joséphine; Chaussod, Rémi; Roger-Estrade, Jean

    2007-01-01

    Soil tillage modifies environmental conditions of soil microorganisms and their ability to release nitrogen. We compare the influence of reduced tillage (RT) and mouldboard ploughing (MP) on the soil microbial functioning in organic farming. In order to connect soil structure generated by these tillage systems on the soil microbial biomass we adopt a particular sampling scheme based on the morphological characterisation of the soil structure by the description of the soil profile. This method...

  8. Microbial conversion technologies

    Energy Technology Data Exchange (ETDEWEB)

    Lau, P. [National Research Council of Canada, Ottawa, ON (Canada). Bioconversion and Sustainable Development

    2006-07-01

    Microbes are a biomass and an valuable resource. This presentation discussed microbial conversion technologies along with background information on microbial cells, their characteristics and microbial diversity. Untapped opportunities for microbial conversion were identified. Metagenomic and genome mining approaches were also discussed, as they can provide access to uncultivated or unculturable microorganisms in communal populations and are an unlimited resource for biocatalysts, novel genes and metabolites. Genome mining was seen as an economical approach. The presentation also emphasized that the development of microbial biorefineries would require significant insights into the relevant microorganisms and that biocatalysts were the ultimate in sustainability. In addition, the presentation discussed the natural fibres initiative for biochemicals and biomaterials. Anticipated outputs were identified and work in progress of a new enzyme-retting cocktail to provide diversity and/or consistency in fibre characteristics for various applications were also presented. It was concluded that it is necessary to leverage understanding of biological processes to produce bioproducts in a clean and sustainable manner. tabs., figs.

  9. On 165Ho level scheme

    International Nuclear Information System (INIS)

    Ardisson, Claire; Ardisson, Gerard.

    1976-01-01

    A 165 Ho level scheme was constructed which led to the interpretation of sixty γ rays belonging to the decay of 165 Dy. A new 702.9keV level was identified to be the 5/2 - member of the 1/2 ) 7541{ Nilsson orbit. )] [fr

  10. Homogenization scheme for acoustic metamaterials

    KAUST Repository

    Yang, Min; Ma, Guancong; Wu, Ying; Yang, Zhiyu; Sheng, Ping

    2014-01-01

    the scattering amplitudes. We verify our scheme by applying it to three different examples: a layered lattice, a two-dimensional hexagonal lattice, and a decorated-membrane system. It is shown that the predicted characteristics and wave fields agree almost

  11. Homogenization scheme for acoustic metamaterials

    KAUST Repository

    Yang, Min

    2014-02-26

    We present a homogenization scheme for acoustic metamaterials that is based on reproducing the lowest orders of scattering amplitudes from a finite volume of metamaterials. This approach is noted to differ significantly from that of coherent potential approximation, which is based on adjusting the effective-medium parameters to minimize scatterings in the long-wavelength limit. With the aid of metamaterials’ eigenstates, the effective parameters, such as mass density and elastic modulus can be obtained by matching the surface responses of a metamaterial\\'s structural unit cell with a piece of homogenized material. From the Green\\'s theorem applied to the exterior domain problem, matching the surface responses is noted to be the same as reproducing the scattering amplitudes. We verify our scheme by applying it to three different examples: a layered lattice, a two-dimensional hexagonal lattice, and a decorated-membrane system. It is shown that the predicted characteristics and wave fields agree almost exactly with numerical simulations and experiments and the scheme\\'s validity is constrained by the number of dominant surface multipoles instead of the usual long-wavelength assumption. In particular, the validity extends to the full band in one dimension and to regimes near the boundaries of the Brillouin zone in two dimensions.

  12. New practicable Siberian Snake schemes

    International Nuclear Information System (INIS)

    Steffen, K.

    1983-07-01

    Siberian Snake schemes can be inserted in ring accelerators for making the spin tune almost independent of energy. Two such schemes are here suggested which lend particularly well to practical application over a wide energy range. Being composed of horizontal and vertical bending magnets, the proposed snakes are designed to have a small maximum beam excursion in one plane. By applying in this plane a bending correction that varies with energy, they can be operated at fixed geometry in the other plane where most of the bending occurs, thus avoiding complicated magnet motion or excessively large magnet apertures that would otherwise be needed for large energy variations. The first of the proposed schemes employs a pair of standard-type Siberian Snakes, i.e. of the usual 1st and 2nd kind which rotate the spin about the longitudinal and the transverse horizontal axis, respectively. The second scheme employs a pair of novel-type snakes which rotate the spin about either one of the horizontal axes that are at 45 0 to the beam direction. In obvious reference to these axes, they are called left-pointed and right-pointed snakes. (orig.)

  13. Nonlinear Secret Image Sharing Scheme

    Directory of Open Access Journals (Sweden)

    Sang-Ho Shin

    2014-01-01

    efficiency and security of proposed scheme, we use the embedding capacity and PSNR. As a result of it, average value of PSNR and embedding capacity are 44.78 (dB and 1.74tlog2⁡m bit-per-pixel (bpp, respectively.

  14. Decoding noises in HIV computational genotyping.

    Science.gov (United States)

    Jia, MingRui; Shaw, Timothy; Zhang, Xing; Liu, Dong; Shen, Ye; Ezeamama, Amara E; Yang, Chunfu; Zhang, Ming

    2017-11-01

    Lack of a consistent and reliable genotyping system can critically impede HIV genomic research on pathogenesis, fitness, virulence, drug resistance, and genomic-based healthcare and treatment. At present, mis-genotyping, i.e., background noises in molecular genotyping, and its impact on epidemic surveillance is unknown. For the first time, we present a comprehensive assessment of HIV genotyping quality. HIV sequence data were retrieved from worldwide published records, and subjected to a systematic genotyping assessment pipeline. Results showed that mis-genotyped cases occurred at 4.6% globally, with some regional and high-risk population heterogeneities. Results also revealed a consistent mis-genotyping pattern in gp120 in all studied populations except the group of men who have sex with men. Our study also suggests novel virus diversities in the mis-genotyped cases. Finally, this study reemphasizes the importance of implementing a standardized genotyping pipeline to avoid genotyping disparity and to advance our understanding of virus evolution in various epidemiological settings. Copyright © 2017 Elsevier Inc. All rights reserved.

  15. Applications of blood group genotyping

    Directory of Open Access Journals (Sweden)

    Mariza A. Mota

    2006-03-01

    Full Text Available Introduction: The determination of blood group polymorphism atthe genomic level facilitates the resolution of clinical problemsthat cannot be addressed by hemagglutination. They are useful to(a determine antigen types for which currently available antibodiesare weakly reactive; (b type patients who have been recentlytransfused; (c identify fetuses at risk for hemolytic disease of thenewborn; and (d to increase the reliability of repositories of antigennegative RBCs for transfusion. Objectives: This review assessedthe current applications of blood group genotyping in transfusionmedicine and hemolytic disease of the newborn. Search strategy:Blood group genotyping studies and reviews were searched ingeneral database (MEDLINE and references were reviewed.Selection criteria: All published data and reviews were eligible forinclusion provided they reported results for molecular basis ofblood group antigens, DNA analysis for blood group polymorphisms,determination of fetal group status and applications of blood groupgenotyping in blood transfusion. Data collection: All data werecollected based on studies and reviews of blood grouppolymorphisms and their clinical applications.

  16. Lineage-specific responses of microbial communities to environmental change.

    Science.gov (United States)

    Youngblut, Nicholas D; Shade, Ashley; Read, Jordan S; McMahon, Katherine D; Whitaker, Rachel J

    2013-01-01

    A great challenge facing microbial ecology is how to define ecologically relevant taxonomic units. To address this challenge, we investigated how changing the definition of operational taxonomic units (OTUs) influences the perception of ecological patterns in microbial communities as they respond to a dramatic environmental change. We used pyrosequenced tags of the bacterial V2 16S rRNA region, as well as clone libraries constructed from the cytochrome oxidase C gene ccoN, to provide additional taxonomic resolution for the common freshwater genus Polynucleobacter. At the most highly resolved taxonomic scale, we show that distinct genotypes associated with the abundant Polynucleobacter lineages exhibit divergent spatial patterns and dramatic changes over time, while the also abundant Actinobacteria OTUs are highly coherent. This clearly demonstrates that different bacterial lineages demand different taxonomic definitions to capture ecological patterns. Based on the temporal distribution of highly resolved taxa in the hypolimnion, we demonstrate that change in the population structure of a single genotype can provide additional insight into the mechanisms of community-level responses. These results highlight the importance and feasibility of examining ecological change in microbial communities across taxonomic scales while also providing valuable insight into the ecological characteristics of ecologically coherent groups in this system.

  17. Grain yield stability of early maize genotypes

    Directory of Open Access Journals (Sweden)

    Chitra Bahadur Kunwar

    2016-12-01

    Full Text Available The objective of this study was to estimate grain yield stability of early maize genotypes. Five early maize genotypes namely Pool-17, Arun1EV, Arun-4, Arun-2 and Farmer’s variety were evaluated using Randomized Complete Block Design along with three replications at four different locations namely Rampur, Rajahar, Pakhribas and Kabre districts of Nepal during summer seasons of three consecutive years from 2010 to 2012 under farmer’s fields. Genotype and genotype × environment (GGE biplot was used to identify superior genotype for grain yield and stability pattern. The genotypes Arun-1 EV and Arun-4 were better adapted for Kabre and Pakhribas where as pool-17 for Rajahar environments. The overall findings showed that Arun-1EV was more stable followed by Arun-2 therefore these two varieties can be recommended to farmers for cultivation in both environments.

  18. Diet dominates host genotype in shaping the murine gut microbiota

    Science.gov (United States)

    Carmody, Rachel N.; Gerber, Georg K.; Luevano, Jesus M.; Gatti, Daniel M.; Somes, Lisa; Svenson, Karen L.; Turnbaugh, Peter J.

    2014-01-01

    SUMMARY Mammals exhibit marked inter-individual variations in their gut microbiota, but it remains unclear if this is primarily driven by host genetics or by extrinsic factors like dietary intake. To address this, we examined the effect of dietary perturbations on the gut microbiota of five inbred mouse strains, mice deficient for genes relevant to host-microbial interactions (MyD88−/−, NOD2−/−, ob/ob, and Rag1−/−), and >200 outbred mice. In each experiment, consumption of a high-fat, high-sugar diet reproducibly altered the gut microbiota despite differences in host genotype. The gut microbiota exhibited a linear dose response to dietary perturbations, taking an average of 3.5 days for each diet-responsive bacterial groups to reach a new steady state. Repeated dietary shifts demonstrated that most changes to the gut microbiota are reversible, while also uncovering bacteria whose abundance depends on prior consumption. These results emphasize the dominant role that diet plays in shaping inter-individual variations in host-associated microbial communities. PMID:25532804

  19. EVA Suit Microbial Leakage Investigation

    Data.gov (United States)

    National Aeronautics and Space Administration — The objective of this project is to collect microbial samples from various EVA suits to determine how much microbial contamination is typically released during...

  20. Elevated temperature alters carbon cycling in a model microbial community

    Science.gov (United States)

    Mosier, A.; Li, Z.; Thomas, B. C.; Hettich, R. L.; Pan, C.; Banfield, J. F.

    2013-12-01

    Earth's climate is regulated by biogeochemical carbon exchanges between the land, oceans and atmosphere that are chiefly driven by microorganisms. Microbial communities are therefore indispensible to the study of carbon cycling and its impacts on the global climate system. In spite of the critical role of microbial communities in carbon cycling processes, microbial activity is currently minimally represented or altogether absent from most Earth System Models. Method development and hypothesis-driven experimentation on tractable model ecosystems of reduced complexity, as presented here, are essential for building molecularly resolved, benchmarked carbon-climate models. Here, we use chemoautotropic acid mine drainage biofilms as a model community to determine how elevated temperature, a key parameter of global climate change, regulates the flow of carbon through microbial-based ecosystems. This study represents the first community proteomics analysis using tandem mass tags (TMT), which enable accurate, precise, and reproducible quantification of proteins. We compare protein expression levels of biofilms growing over a narrow temperature range expected to occur with predicted climate changes. We show that elevated temperature leads to up-regulation of proteins involved in amino acid metabolism and protein modification, and down-regulation of proteins involved in growth and reproduction. Closely related bacterial genotypes differ in their response to temperature: Elevated temperature represses carbon fixation by two Leptospirillum genotypes, whereas carbon fixation is significantly up-regulated at higher temperature by a third closely related genotypic group. Leptospirillum group III bacteria are more susceptible to viral stress at elevated temperature, which may lead to greater carbon turnover in the microbial food web through the release of viral lysate. Overall, this proteogenomics approach revealed the effects of climate change on carbon cycling pathways and other

  1. Heterogeneous recombination among Hepatitis B virus genotypes.

    Science.gov (United States)

    Castelhano, Nadine; Araujo, Natalia M; Arenas, Miguel

    2017-10-01

    The rapid evolution of Hepatitis B virus (HBV) through both evolutionary forces, mutation and recombination, allows this virus to generate a large variety of adapted variants at both intra and inter-host levels. It can, for instance, generate drug resistance or the diverse viral genotypes that currently exist in the HBV epidemics. Concerning the latter, it is known that recombination played a major role in the emergence and genetic diversification of novel genotypes. In this regard, the quantification of viral recombination in each genotype can provide relevant information to devise expectations about the evolutionary trends of the epidemic. Here we measured the amount of this evolutionary force by estimating global and local recombination rates in >4700 HBV complete genome sequences corresponding to nine (A to I) HBV genotypes. Counterintuitively, we found that genotype E presents extremely high levels of recombination, followed by genotypes B and C. On the other hand, genotype G presents the lowest level, where recombination is almost negligible. We discuss these findings in the light of known characteristics of these genotypes. Additionally, we present a phylogenetic network to depict the evolutionary history of the studied HBV genotypes. This network clearly classified all genotypes into specific groups and indicated that diverse pairs of genotypes are derived from a common ancestor (i.e., C-I, D-E and, F-H) although still the origin of this virus presented large uncertainty. Altogether we conclude that the amount of observed recombination is heterogeneous among HBV genotypes and that this heterogeneity can influence on the future expansion of the epidemic. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. Hepatitis C virus genotypes in Myanmar.

    Science.gov (United States)

    Win, Nan Nwe; Kanda, Tatsuo; Nakamoto, Shingo; Yokosuka, Osamu; Shirasawa, Hiroshi

    2016-07-21

    Myanmar is adjacent to India, Bangladesh, Thailand, Laos and China. In Myanmar, the prevalence of hepatitis C virus (HCV) infection is 2%, and HCV infection accounts for 25% of hepatocellular carcinoma. In this study, we reviewed the prevalence of HCV genotypes in Myanmar. HCV genotypes 1, 3 and 6 were observed in volunteer blood donors in and around the Myanmar city of Yangon. Although there are several reports of HCV genotype 6 and its variants in Myanmar, the distribution of the HCV genotypes has not been well documented in areas other than Yangon. Previous studies showed that treatment with peginterferon and a weight-based dose of ribavirin for 24 or 48 wk could lead to an 80%-100% sustained virological response (SVR) rates in Myanmar. Current interferon-free treatments could lead to higher SVR rates (90%-95%) in patients infected with almost all HCV genotypes other than HCV genotype 3. In an era of heavy reliance on direct-acting antivirals against HCV, there is an increasing need to measure HCV genotypes, and this need will also increase specifically in Myanmar. Current available information of HCV genotypes were mostly from Yangon and other countries than Myanmar. The prevalence of HCV genotypes in Myanmar should be determined.

  3. Hepatitis C Virus: Virology and Genotypes

    KAUST Repository

    Abdelaziz, Ahmed

    2017-12-01

    Hepatitis C virus (HCV) is a major causative agent of chronic liver disease worldwide. HCV is characterized by genetic heterogeneity, with at least six genotypes identified. The geographic distribution of genotypes has shown variations in different parts of the world over the past decade because of variations in population structure, immigration, and routes of transmission. Genotype differences are of epidemiologic interest and help the study of viral transmission dynamics to trace the source of HCV infection in a given population. HCV genotypes are also of considerable clinical importance because they affect response to antiviral therapy and represent a challenging obstacle for vaccine development.

  4. Molecular ecology of microbial mats

    NARCIS (Netherlands)

    Bolhuis, H.; Cretoiu, M.S.; Stal, L.J.

    2014-01-01

    Phototrophic microbial mats are ideal model systems for ecological and evolutionary analysis of highly diverse microbial communities. Microbial mats are small-scale, nearly closed, and self-sustaining benthic ecosystems that comprise the major element cycles, trophic levels, and food webs. The steep

  5. Support Schemes and Ownership Structures

    DEFF Research Database (Denmark)

    Ropenus, Stephanie; Schröder, Sascha Thorsten; Costa, Ana

    , Denmark, France and Portugal. Another crucial aspect for the diffusion of the mCHP technology is possible ownership structures. These may range from full consumer ownership to ownership by utilities and energy service companies, which is discussed in Section 6. Finally, a conclusion (Section 7) wraps up......In recent years, fuel cell based micro‐combined heat and power has received increasing attention due to its potential contribution to energy savings, efficiency gains, customer proximity and flexibility in operation and capacity size. The FC4Home project assesses technical and economic aspects...... of support scheme simultaneously affects risk and technological development, which is the focus of Section 4. Subsequent to this conceptual overview, Section 5 takes a glance at the national application of support schemes for mCHP in practice, notably in the three country cases of the FC4Home project...

  6. [PICS: pharmaceutical inspection cooperation scheme].

    Science.gov (United States)

    Morénas, J

    2009-01-01

    The pharmaceutical inspection cooperation scheme (PICS) is a structure containing 34 participating authorities located worldwide (October 2008). It has been created in 1995 on the basis of the pharmaceutical inspection convention (PIC) settled by the European free trade association (EFTA) in1970. This scheme has different goals as to be an international recognised body in the field of good manufacturing practices (GMP), for training inspectors (by the way of an annual seminar and experts circles related notably to active pharmaceutical ingredients [API], quality risk management, computerized systems, useful for the writing of inspection's aide-memoires). PICS is also leading to high standards for GMP inspectorates (through regular crossed audits) and being a room for exchanges on technical matters between inspectors but also between inspectors and pharmaceutical industry.

  7. Project financing renewable energy schemes

    International Nuclear Information System (INIS)

    Brandler, A.

    1993-01-01

    The viability of many Renewable Energy projects is critically dependent upon the ability of these projects to secure the necessary financing on acceptable terms. The principal objective of the study was to provide an overview to project developers of project financing techniques and the conditions under which project finance for Renewable Energy schemes could be raised, focussing on the potential sources of finance, the typical project financing structures that could be utilised for Renewable Energy schemes and the risk/return and security requirements of lenders, investors and other potential sources of financing. A second objective is to describe the appropriate strategy and tactics for developers to adopt in approaching the financing markets for such projects. (author)

  8. Network Regulation and Support Schemes

    DEFF Research Database (Denmark)

    Ropenus, Stephanie; Schröder, Sascha Thorsten; Jacobsen, Henrik

    2009-01-01

    -in tariffs to market-based quota systems, and network regulation approaches, comprising rate-of-return and incentive regulation. National regulation and the vertical structure of the electricity sector shape the incentives of market agents, notably of distributed generators and network operators......At present, there exists no explicit European policy framework on distributed generation. Various Directives encompass distributed generation; inherently, their implementation is to the discretion of the Member States. The latter have adopted different kinds of support schemes, ranging from feed....... This article seeks to investigate the interactions between the policy dimensions of support schemes and network regulation and how they affect the deployment of distributed generation. Firstly, a conceptual analysis examines how the incentives of the different market agents are affected. In particular...

  9. Distance labeling schemes for trees

    DEFF Research Database (Denmark)

    Alstrup, Stephen; Gørtz, Inge Li; Bistrup Halvorsen, Esben

    2016-01-01

    We consider distance labeling schemes for trees: given a tree with n nodes, label the nodes with binary strings such that, given the labels of any two nodes, one can determine, by looking only at the labels, the distance in the tree between the two nodes. A lower bound by Gavoille et al. [Gavoille...... variants such as, for example, small distances in trees [Alstrup et al., SODA, 2003]. We improve the known upper and lower bounds of exact distance labeling by showing that 1/4 log2(n) bits are needed and that 1/2 log2(n) bits are sufficient. We also give (1 + ε)-stretch labeling schemes using Theta...

  10. Small-scale classification schemes

    DEFF Research Database (Denmark)

    Hertzum, Morten

    2004-01-01

    Small-scale classification schemes are used extensively in the coordination of cooperative work. This study investigates the creation and use of a classification scheme for handling the system requirements during the redevelopment of a nation-wide information system. This requirements...... classification inherited a lot of its structure from the existing system and rendered requirements that transcended the framework laid out by the existing system almost invisible. As a result, the requirements classification became a defining element of the requirements-engineering process, though its main...... effects remained largely implicit. The requirements classification contributed to constraining the requirements-engineering process by supporting the software engineers in maintaining some level of control over the process. This way, the requirements classification provided the software engineers...

  11. Anaerobic microbial dehalogenation

    NARCIS (Netherlands)

    Smidt, H.; Vos, de W.M.

    2004-01-01

    The natural production and anthropogenic release of halogenated hydrocarbons into the environment has been the likely driving force for the evolution of an unexpectedly high microbial capacity to dehalogenate different classes of xenobiotic haloorganics. This contribution provides an update on the

  12. Diazotrophic microbial mats

    NARCIS (Netherlands)

    Severin, I.; Stal, L.J.; Seckbach, J.; Oren, A.

    2010-01-01

    Microbial mats have been the focus of scientific research for a few decades. These small-scale ecosystems are examples of versatile benthic communities of microorganisms, usually dominated by phototrophic bacteria (e.g., Krumbein et al., 1977; Jørgensen et al., 1983). They develop as vertically

  13. Microbial Energy Conversion

    Energy Technology Data Exchange (ETDEWEB)

    Buckley, Merry [American Society for Microbiology (ASM), Washington, DC (United States); Wall, Judy D. [Univ. of Missouri, Columbia, MO (United States)

    2006-10-01

    The American Academy of Microbiology convened a colloquium March 10-12, 2006, in San Francisco, California, to discuss the production of energy fuels by microbial conversions. The status of research into various microbial energy technologies, the advantages and disadvantages of each of these approaches, research needs in the field, and education and training issues were examined, with the goal of identifying routes for producing biofuels that would both decrease the need for fossil fuels and reduce greenhouse gas emissions. Currently, the choices for providing energy are limited. Policy makers and the research community must begin to pursue a broader array of potential energy technologies. A diverse energy portfolio that includes an assortment of microbial energy choices will allow communities and consumers to select the best energy solution for their own particular needs. Funding agencies and governments alike need to prepare for future energy needs by investing both in the microbial energy technologies that work today and in the untested technologies that will serve the world’s needs tomorrow. More mature bioprocesses, such as ethanol production from starchy materials and methane from waste digestors, will find applications in the short term. However, innovative techniques for liquid fuel or biohydrogen production are among the longer term possibilities that should also be vigorously explored, starting now. Microorganisms can help meet human energy needs in any of a number of ways. In their most obvious role in energy conversion, microorganisms can generate fuels, including ethanol, hydrogen, methane, lipids, and butanol, which can be burned to produce energy. Alternatively, bacteria can be put to use in microbial fuel cells, where they carry out the direct conversion of biomass into electricity. Microorganisms may also be used some day to make oil and natural gas technologies more efficient by sequestering carbon or by assisting in the recovery of oil and

  14. Microbial electrosynthesis of biochemicals

    NARCIS (Netherlands)

    Bajracharya, S.

    2016-01-01

    Microbial electrosynthesis (MES) is an electricity-driven production of chemicals from low-value waste using microorganisms as biocatalysts. MES from CO2 comprises conversion of CO2 to multi-carbon compounds employing microbes at the cathode which use electricity as an energy source. This thesis

  15. Cambridge community Optometry Glaucoma Scheme.

    Science.gov (United States)

    Keenan, Jonathan; Shahid, Humma; Bourne, Rupert R; White, Andrew J; Martin, Keith R

    2015-04-01

    With a higher life expectancy, there is an increased demand for hospital glaucoma services in the United Kingdom. The Cambridge community Optometry Glaucoma Scheme (COGS) was initiated in 2010, where new referrals for suspected glaucoma are evaluated by community optometrists with a special interest in glaucoma, with virtual electronic review and validation by a consultant ophthalmologist with special interest in glaucoma. 1733 patients were evaluated by this scheme between 2010 and 2013. Clinical assessment is performed by the optometrist at a remote site. Goldmann applanation tonometry, pachymetry, monoscopic colour optic disc photographs and automated Humphrey visual field testing are performed. A clinical decision is made as to whether a patient has glaucoma or is a suspect, and referred on or discharged as a false positive referral. The clinical findings, optic disc photographs and visual field test results are transmitted electronically for virtual review by a consultant ophthalmologist. The number of false positive referrals from initial referral into the scheme. Of the patients, 46.6% were discharged at assessment and a further 5.7% were discharged following virtual review. Of the patients initially discharged, 2.8% were recalled following virtual review. Following assessment at the hospital, a further 10.5% were discharged after a single visit. The COGS community-based glaucoma screening programme is a safe and effective way of evaluating glaucoma referrals in the community and reducing false-positive referrals for glaucoma into the hospital system. © 2014 Royal Australian and New Zealand College of Ophthalmologists.

  16. New schemes for particle accelerators

    International Nuclear Information System (INIS)

    Nishida, Y.

    1985-01-01

    In the present paper, the authors propose new schemes for realizing the v/sub p/xB accelerator, by using no plasma system for producing the strong longitudinal waves. The first method is to use a grating for obtaining extended interaction of an electron beam moving along the grating surface with light beam incident also along the surface. Here, the light beam propagates obliquely to the grating grooves for producing strong electric field, and the electron beam propagates in parallel to the light beam. The static magnetic field is applied perpendicularly to the grating surface. In the present system, the beam interacts synchronously with the p-polarized wave which has the electric field be parallel to the grating surface. Another conventional scheme is to use a delay circuit. Here, the light beam propagates obliquely between a pair of array of conductor fins or slots. The phase velocity of the spatial harmonics in the y-direction (right angle to the array of slots) is slower than the speed of light. With the aid of powerful laser light or microwave source, it should be possible to miniaturise linacs by using the v/sub p/xB effect and schemes proposed here

  17. A Memory Efficient Network Encryption Scheme

    Science.gov (United States)

    El-Fotouh, Mohamed Abo; Diepold, Klaus

    In this paper, we studied the two widely used encryption schemes in network applications. Shortcomings have been found in both schemes, as these schemes consume either more memory to gain high throughput or low memory with low throughput. The need has aroused for a scheme that has low memory requirements and in the same time possesses high speed, as the number of the internet users increases each day. We used the SSM model [1], to construct an encryption scheme based on the AES. The proposed scheme possesses high throughput together with low memory requirements.

  18. An Arbitrated Quantum Signature Scheme without Entanglement*

    International Nuclear Information System (INIS)

    Li Hui-Ran; Luo Ming-Xing; Peng Dai-Yuan; Wang Xiao-Jun

    2017-01-01

    Several quantum signature schemes are recently proposed to realize secure signatures of quantum or classical messages. Arbitrated quantum signature as one nontrivial scheme has attracted great interests because of its usefulness and efficiency. Unfortunately, previous schemes cannot against Trojan horse attack and DoS attack and lack of the unforgeability and the non-repudiation. In this paper, we propose an improved arbitrated quantum signature to address these secure issues with the honesty arbitrator. Our scheme takes use of qubit states not entanglements. More importantly, the qubit scheme can achieve the unforgeability and the non-repudiation. Our scheme is also secure for other known quantum attacks . (paper)

  19. Evaluation of the Abbott Real Time HCV genotype II assay for Hepatitis C virus genotyping.

    Science.gov (United States)

    Sariguzel, Fatma Mutlu; Berk, Elife; Gokahmetoglu, Selma; Ercal, Baris Derya; Celik, Ilhami

    2015-01-01

    The determination of HCV genotypes and subtypes is very important for the selection of antiviral therapy and epidemiological studies. The aim of this study was to evaluate the performance of Abbott Real Time HCV Genotype II assay in HCV genotyping of HCV infected patients in Kayseri, Turkey. One hundred patients with chronic hepatitis C admitted to our hospital were evaluated between June 2012 and December 2012, HCV RNA levels were determined by the COBAS® AmpliPrep/COBAS® TaqMan® 48 HCV test. HCV genotyping was investigated by the Abbott Real Time HCV Genotype II assay. With the exception of genotype 1, subtypes of HCV genotypes could not be determined by Abbott assay. Sequencing analysis was used as the reference method. Genotypes 1, 2, 3 and 4 were observed in 70, 4, 2 and 24 of the 100 patients, respectively, by two methods. The concordance between the two systems to determine HCV major genotypes was 100%. Of 70 patients with genotype 1, 66 showed infection with subtype 1b and 4 with subtype 1a by Abbott Real Time HCV Genotype II assay. Using sequence analysis, 61 showed infection with subtype 1b and 9 with subtype 1a. In determining of HCV genotype 1 subtypes, the difference between the two methods was not statistically significant (P>0.05). HCV genotype 4 and 3 samples were found to be subtype 4d and 3a, respectively, by sequence analysis. There were four patients with genotype 2. Sequence analysis revealed that two of these patients had type 2a and the other two had type 2b. The Abbott Real Time HCV Genotype II assay yielded results consistent with sequence analysis. However, further optimization of the Abbott Real Time HCV Genotype II assay for subtype identification of HCV is required.

  20. Genotyping isolates of the entomopathogenic fungus Beauveria ...

    African Journals Online (AJOL)

    Multi-locus denaturing gradient gel electrophoresis (DGGE) analysis was developed to investigate the genotypes of Beauveria bassiana sensu lato. ... These results demonstrated that multi-locus DGGE is a potentially useful molecular marker for genotyping, identifying and tracking the fates of experimentally released ...

  1. Genetic relationship among Musa genotypes revealed by ...

    African Journals Online (AJOL)

    enoh

    2012-03-29

    Mar 29, 2012 ... A banana germplasm was established containing 44 Musa genotypes collected from various locations in Malaysia. To detect their genetic variation and to rule out duplicates among cultivar, microsatellite markers were used in their analysis. The microsatellite profiles of 44 Musa genotypes of various origins.

  2. PHENOLOGICAL CHARACTERISTICS OF GENOTYPES FROM CATTLEY GUAVA AND GUAVA TREES SUBMITTED TO FRUCTIFICATION PRUNING

    Directory of Open Access Journals (Sweden)

    CINTIA APARECIDA BREMENKAMP

    Full Text Available ABSTRACT Psidium cattleianum Sabine is a species from the Myrtaceae family that serves as an option for the native fruits cultivation, besides being considered a source of resistance to the Meloidogyne enterolobii nematode. Although cattley guava trees from this species produce flower buds in young branches, there are no reports of response to fructification pruning or phenological synchronism with the guava tree. The objective of this paper was the comparative evaluation of the genotype response of strawberry guava trees and guava cultivars to fructification pruning, thus, describing the phenology of both species under the same cultivation conditions. The experiment was conducted under an entirely randomized outline, in 7x2 factorial scheme, being evaluated seven genotypes (three from strawberry guava and four from guava trees, and with pruning performed in two seasons (May 2012 and March 2013, with three repetitions. Fructification pruning was executed by a lopping on all mature branches, from the last growth flow in the woody branch region. Were evaluated budding characteristics and fruit harvesting, as well as number of days from pruning to the observation of the phenological event. Cattley guava tree pruning stimulated fructification of all three genotypes after pruning done on May and two genotypes after the March’s pruning. There has been a sync between the guava cultivars’ flowering and both strawberry guava trees genotypes, when those were pruned on May.

  3. Decoupling schemes for the SSC Collider

    International Nuclear Information System (INIS)

    Cai, Y.; Bourianoff, G.; Cole, B.; Meinke, R.; Peterson, J.; Pilat, F.; Stampke, S.; Syphers, M.; Talman, R.

    1993-05-01

    A decoupling system is designed for the SSC Collider. This system can accommodate three decoupling schemes by using 44 skew quadrupoles in the different configurations. Several decoupling schemes are studied and compared in this paper

  4. Renormalization scheme-invariant perturbation theory

    International Nuclear Information System (INIS)

    Dhar, A.

    1983-01-01

    A complete solution to the problem of the renormalization scheme dependence of perturbative approximants to physical quantities is presented. An equation is derived which determines any physical quantity implicitly as a function of only scheme independent variables. (orig.)

  5. Wireless Broadband Access and Accounting Schemes

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    In this paper, we propose two wireless broadband access and accounting schemes. In both schemes, the accounting system adopts RADIUS protocol, but the access system adopts SSH and SSL protocols respectively.

  6. Tightly Secure Signatures From Lossy Identification Schemes

    OpenAIRE

    Abdalla , Michel; Fouque , Pierre-Alain; Lyubashevsky , Vadim; Tibouchi , Mehdi

    2015-01-01

    International audience; In this paper, we present three digital signature schemes with tight security reductions in the random oracle model. Our first signature scheme is a particularly efficient version of the short exponent discrete log-based scheme of Girault et al. (J Cryptol 19(4):463–487, 2006). Our scheme has a tight reduction to the decisional short discrete logarithm problem, while still maintaining the non-tight reduction to the computational version of the problem upon which the or...

  7. Millstone: software for multiplex microbial genome analysis and engineering.

    Science.gov (United States)

    Goodman, Daniel B; Kuznetsov, Gleb; Lajoie, Marc J; Ahern, Brian W; Napolitano, Michael G; Chen, Kevin Y; Chen, Changping; Church, George M

    2017-05-25

    Inexpensive DNA sequencing and advances in genome editing have made computational analysis a major rate-limiting step in adaptive laboratory evolution and microbial genome engineering. We describe Millstone, a web-based platform that automates genotype comparison and visualization for projects with up to hundreds of genomic samples. To enable iterative genome engineering, Millstone allows users to design oligonucleotide libraries and create successive versions of reference genomes. Millstone is open source and easily deployable to a cloud platform, local cluster, or desktop, making it a scalable solution for any lab.

  8. AFLP analysis of Genetic Diversity Among Different Jatropha curcas L. Genotypes from Africa and Ecuador

    Directory of Open Access Journals (Sweden)

    Konan, NO.

    2018-01-01

    Full Text Available Six populations amounting to a total number of seventy genotypes of Jatropha curcas L. originating from Africa (Senegal, Mali, Burkina Faso and Madagascar and Ecuador were investigated for genetic diversity using two AFLP primer combinations. The results revealed a high genetic diversity in the populations studied. The population with greatest genetic diversity was Madagascar (He = 0.2638 and I = 0.4066 and the least diverse was Senegal-Tamba (He = 0.1962 and I = 0.3079. AMOVA (analysis of molecular variance detected the highest proportion of variation within populations (81% of the total molecular variation. This may be attributed to the high level of allogamy observed in this species. The Nei's standard unbiased genetic distance (D between the populations ranged from 0.010 (Senegal-Tamba and Burkina Faso to 0.131 (Mali and Ecuador; the average was 0.063. Analysis of the genetic relationships among the 6 populations using both neighbor-joining cluster analysis and principal component analysis (PCoA showed five clusters with globally, groupings of i most of Burkina Faso and Senegal-Tamba genotypes, ii most of Mali and Senegal-Diobass genotypes , iii most of Madagascar and Ecuador genotypes, and iv some mixings of genotypes with different origins. Considering the distance existing between the different origins there are prospects to develop F1 hybrids. The greatest heterosis might be expected from crossing involving genotypes of cluster I and cluster V which group the more distant genotypes. Such crossing schemes might produce greater success in the production of genetic variability and might maximize the exploitation of heterosis and segregation.

  9. Toward fully automated genotyping: Genotyping microsatellite markers by deconvolution

    Energy Technology Data Exchange (ETDEWEB)

    Perlin, M.W.; Lancia, G.; See-Kiong, Ng [Carnegie Mellon Univ., Pittsburgh, PA (United States)

    1995-11-01

    Dense genetic linkage maps have been constructed for the human and mouse genomes, with average densities of 2.9 cM and 0.35 cM, respectively. These genetic maps are crucial for mapping both Mendelian and complex traits and are useful in clinical genetic diagnosis. Current maps are largely comprised of abundant, easily assayed, and highly polymorphic PCR-based microsatellite markers, primarily dinucleotide (CA){sub n} repeats. One key limitation of these length polymorphisms is the PCR stutter (or slippage) artifact that introduces additional stutter bands. With two (or more) closely spaced alleles, the stutter bands overlap, and it is difficult to accurately determine the correct alleles; this stutter phenomenon has all but precluded full automation, since a human must visually inspect the allele data. We describe here novel deconvolution methods for accurate genotyping that mathematically remove PCR stutter artifact from microsatellite markers. These methods overcome the manual interpretation bottleneck and thereby enable full automation of genetic map construction and use. New functionalities, including the pooling of DNAs and the pooling of markers, are described that may greatly reduce the associated experimentation requirements. 32 refs., 5 figs., 3 tabs.

  10. Comparative study of numerical schemes of TVD3, UNO3-ACM and optimized compact scheme

    Science.gov (United States)

    Lee, Duck-Joo; Hwang, Chang-Jeon; Ko, Duck-Kon; Kim, Jae-Wook

    1995-01-01

    Three different schemes are employed to solve the benchmark problem. The first one is a conventional TVD-MUSCL (Monotone Upwind Schemes for Conservation Laws) scheme. The second scheme is a UNO3-ACM (Uniformly Non-Oscillatory Artificial Compression Method) scheme. The third scheme is an optimized compact finite difference scheme modified by us: the 4th order Runge Kutta time stepping, the 4th order pentadiagonal compact spatial discretization with the maximum resolution characteristics. The problems of category 1 are solved by using the second (UNO3-ACM) and third (Optimized Compact) schemes. The problems of category 2 are solved by using the first (TVD3) and second (UNO3-ACM) schemes. The problem of category 5 is solved by using the first (TVD3) scheme. It can be concluded from the present calculations that the Optimized Compact scheme and the UN03-ACM show good resolutions for category 1 and category 2 respectively.

  11. Optimal Sales Schemes for Network Goods

    DEFF Research Database (Denmark)

    Parakhonyak, Alexei; Vikander, Nick

    consumers simultaneously, serve them all sequentially, or employ any intermediate scheme. We show that the optimal sales scheme is purely sequential, where each consumer observes all previous sales before choosing whether to buy himself. A sequential scheme maximizes the amount of information available...

  12. THROUGHPUT ANALYSIS OF EXTENDED ARQ SCHEMES

    African Journals Online (AJOL)

    PUBLICATIONS1

    ABSTRACT. Various Automatic Repeat Request (ARQ) schemes have been used to combat errors that befall in- formation transmitted in digital communication systems. Such schemes include simple ARQ, mixed mode ARQ and Hybrid ARQ (HARQ). In this study we introduce extended ARQ schemes and derive.

  13. Arbitrated quantum signature scheme with message recovery

    International Nuclear Information System (INIS)

    Lee, Hwayean; Hong, Changho; Kim, Hyunsang; Lim, Jongin; Yang, Hyung Jin

    2004-01-01

    Two quantum signature schemes with message recovery relying on the availability of an arbitrator are proposed. One scheme uses a public board and the other does not. However both schemes provide confidentiality of the message and a higher efficiency in transmission

  14. RAS screening in colorectal cancer: a comprehensive analysis of the results from the UK NEQAS colorectal cancer external quality assurance schemes (2009-2016).

    Science.gov (United States)

    Richman, Susan D; Fairley, Jennifer; Butler, Rachel; Deans, Zandra C

    2017-12-01

    Evidence strongly indicates that extended RAS testing should be undertaken in mCRC patients, prior to prescribing anti-EGFR therapies. With more laboratories implementing testing, the requirement for External Quality Assurance schemes increases, thus ensuring high standards of molecular analysis. Data was analysed from 15 United Kingdom National External Quality Assessment Service (UK NEQAS) for Molecular Genetics Colorectal cancer external quality assurance (EQA) schemes, delivered between 2009 and 2016. Laboratories were provided annually with nine colorectal tumour samples for genotyping. Information on methodology and extent of testing coverage was requested, and scores given for genotyping, interpretation and clerical accuracy. There has been a sixfold increase in laboratory participation (18 in 2009 to 108 in 2016). For RAS genotyping, fewer laboratories now use Roche cobas®, pyrosequencing and Sanger sequencing, with more moving to next generation sequencing (NGS). NGS is the most commonly employed technology for BRAF and PIK3CA mutation screening. KRAS genotyping errors were seen in ≤10% laboratories, until the 2014-2015 scheme, when there was an increase to 16.7%, corresponding to a large increase in scheme participants. NRAS genotyping errors peaked at 25.6% in the first 2015-2016 scheme but subsequently dropped to below 5%. Interpretation and clerical accuracy scores have been consistently good throughout. Within this EQA scheme, we have observed that the quality of molecular analysis for colorectal cancer has continued to improve, despite changes in the required targets, the volume of testing and the technologies employed. It is reassuring to know that laboratories clearly recognise the importance of participating in EQA schemes.

  15. Rumen microbial genomics

    International Nuclear Information System (INIS)

    Morrison, M.; Nelson, K.E.

    2005-01-01

    Improving microbial degradation of plant cell wall polysaccharides remains one of the highest priority goals for all livestock enterprises, including the cattle herds and draught animals of developing countries. The North American Consortium for Genomics of Fibrolytic Ruminal Bacteria was created to promote the sequencing and comparative analysis of rumen microbial genomes, offering the potential to fully assess the genetic potential in a functional and comparative fashion. It has been found that the Fibrobacter succinogenes genome encodes many more endoglucanases and cellodextrinases than previously isolated, and several new processive endoglucanases have been identified by genome and proteomic analysis of Ruminococcus albus, in addition to a variety of strategies for its adhesion to fibre. The ramifications of acquiring genome sequence data for rumen microorganisms are profound, including the potential to elucidate and overcome the biochemical, ecological or physiological processes that are rate limiting for ruminal fibre degradation. (author)

  16. Microbial Genomes Multiply

    Science.gov (United States)

    Doolittle, Russell F.

    2002-01-01

    The publication of the first complete sequence of a bacterial genome in 1995 was a signal event, underscored by the fact that the article has been cited more than 2,100 times during the intervening seven years. It was a marvelous technical achievement, made possible by automatic DNA-sequencing machines. The feat is the more impressive in that complete genome sequencing has now been adopted in many different laboratories around the world. Four years ago in these columns I examined the situation after a dozen microbial genomes had been completed. Now, with upwards of 60 microbial genome sequences determined and twice that many in progress, it seems reasonable to assess just what is being learned. Are new concepts emerging about how cells work? Have there been practical benefits in the fields of medicine and agriculture? Is it feasible to determine the genomic sequence of every bacterial species on Earth? The answers to these questions maybe Yes, Perhaps, and No, respectively.

  17. Degradation of microbial polyesters.

    Science.gov (United States)

    Tokiwa, Yutaka; Calabia, Buenaventurada P

    2004-08-01

    Microbial polyhydroxyalkanoates (PHAs), one of the largest groups of thermoplastic polyesters are receiving much attention as biodegradable substitutes for non-degradable plastics. Poly(D-3-hydroxybutyrate) (PHB) is the most ubiquitous and most intensively studied PHA. Microorganisms degrading these polyesters are widely distributed in various environments. Although various PHB-degrading microorganisms and PHB depolymerases have been studied and characterized, there are still many groups of microorganisms and enzymes with varying properties awaiting various applications. Distributions of PHB-degrading microorganisms, factors affecting the biodegradability of PHB, and microbial and enzymatic degradation of PHB are discussed in this review. We also propose an application of a new isolated, thermophilic PHB-degrading microorganism, Streptomyces strain MG, for producing pure monomers of PHA and useful chemicals, including D-3-hydroxycarboxylic acids such as D-3-hydroxybutyric acid, by enzymatic degradation of PHB.

  18. Global Microbial Identifier

    DEFF Research Database (Denmark)

    Wielinga, Peter; Hendriksen, Rene S.; Aarestrup, Frank Møller

    2017-01-01

    ) will likely also enable a much better understanding of the pathogenesis of the infection and the molecular basis of the host response to infection. But the full potential of these advances will only transpire if the data in this area become transferable and thereby comparable, preferably in open-source...... of microorganisms, for the identification of relevant genes and for the comparison of genomes to detect outbreaks and emerging pathogens. To harness the full potential of WGS, a shared global database of genomes linked to relevant metadata and the necessary software tools needs to be generated, hence the global...... microbial identifier (GMI) initiative. This tool will ideally be used in amongst others in the diagnosis of infectious diseases in humans and animals, in the identification of microorganisms in food and environment, and to track and trace microbial agents in all arenas globally. This will require...

  19. Genomic evaluations with many more genotypes

    Directory of Open Access Journals (Sweden)

    Wiggans George R

    2011-03-01

    Full Text Available Abstract Background Genomic evaluations in Holstein dairy cattle have quickly become more reliable over the last two years in many countries as more animals have been genotyped for 50,000 markers. Evaluations can also include animals genotyped with more or fewer markers using new tools such as the 777,000 or 2,900 marker chips recently introduced for cattle. Gains from more markers can be predicted using simulation, whereas strategies to use fewer markers have been compared using subsets of actual genotypes. The overall cost of selection is reduced by genotyping most animals at less than the highest density and imputing their missing genotypes using haplotypes. Algorithms to combine different densities need to be efficient because numbers of genotyped animals and markers may continue to grow quickly. Methods Genotypes for 500,000 markers were simulated for the 33,414 Holsteins that had 50,000 marker genotypes in the North American database. Another 86,465 non-genotyped ancestors were included in the pedigree file, and linkage disequilibrium was generated directly in the base population. Mixed density datasets were created by keeping 50,000 (every tenth of the markers for most animals. Missing genotypes were imputed using a combination of population haplotyping and pedigree haplotyping. Reliabilities of genomic evaluations using linear and nonlinear methods were compared. Results Differing marker sets for a large population were combined with just a few hours of computation. About 95% of paternal alleles were determined correctly, and > 95% of missing genotypes were called correctly. Reliability of breeding values was already high (84.4% with 50,000 simulated markers. The gain in reliability from increasing the number of markers to 500,000 was only 1.6%, but more than half of that gain resulted from genotyping just 1,406 young bulls at higher density. Linear genomic evaluations had reliabilities 1.5% lower than the nonlinear evaluations with 50

  20. REMINDER: Saved Leave Scheme (SLS)

    CERN Multimedia

    2003-01-01

    Transfer of leave to saved leave accounts Under the provisions of the voluntary saved leave scheme (SLS), a maximum total of 10 days'* annual and compensatory leave (excluding saved leave accumulated in accordance with the provisions of Administrative Circular No 22B) can be transferred to the saved leave account at the end of the leave year (30 September). We remind you that unused leave of all those taking part in the saved leave scheme at the closure of the leave year accounts is transferred automatically to the saved leave account on that date. Therefore, staff members have no administrative steps to take. In addition, the transfer, which eliminates the risk of omitting to request leave transfers and rules out calculation errors in transfer requests, will be clearly shown in the list of leave transactions that can be consulted in EDH from October 2003 onwards. Furthermore, this automatic leave transfer optimizes staff members' chances of benefiting from a saved leave bonus provided that they ar...

  1. Quantum Secure Communication Scheme with W State

    International Nuclear Information System (INIS)

    Wang Jian; Zhang Quan; Tang Chaojng

    2007-01-01

    We present a quantum secure communication scheme using three-qubit W state. It is unnecessary for the present scheme to use alternative measurement or Bell basis measurement. Compared with the quantum secure direct communication scheme proposed by Cao et al. [H.J. Cao and H.S. Song, Chin. Phys. Lett. 23 (2006) 290], in our scheme, the detection probability for an eavesdropper's attack increases from 8.3% to 25%. We also show that our scheme is secure for a noise quantum channel.

  2. Labeling schemes for bounded degree graphs

    DEFF Research Database (Denmark)

    Adjiashvili, David; Rotbart, Noy Galil

    2014-01-01

    We investigate adjacency labeling schemes for graphs of bounded degree Δ = O(1). In particular, we present an optimal (up to an additive constant) log n + O(1) adjacency labeling scheme for bounded degree trees. The latter scheme is derived from a labeling scheme for bounded degree outerplanar...... graphs. Our results complement a similar bound recently obtained for bounded depth trees [Fraigniaud and Korman, SODA 2010], and may provide new insights for closing the long standing gap for adjacency in trees [Alstrup and Rauhe, FOCS 2002]. We also provide improved labeling schemes for bounded degree...

  3. Developmental plasticity: re-conceiving the genotype.

    Science.gov (United States)

    Sultan, Sonia E

    2017-10-06

    In recent decades, the phenotype of an organism (i.e. its traits and behaviour) has been studied as the outcome of a developmental 'programme' coded in its genotype. This deterministic view is implicit in the Modern Synthesis approach to adaptive evolution as a sorting process among genetic variants. Studies of developmental pathways have revealed that genotypes are in fact differently expressed depending on environmental conditions. Accordingly, the genotype can be understood as a repertoire of potential developmental outcomes or norm of reaction. Reconceiving the genotype as an environmental response repertoire rather than a fixed developmental programme leads to three critical evolutionary insights. First, plastic responses to specific conditions often comprise functionally appropriate trait adjustments, resulting in an individual-level, developmental mode of adaptive variation. Second, because genotypes are differently expressed depending on the environment, the genetic diversity available to natural selection is itself environmentally contingent. Finally, environmental influences on development can extend across multiple generations via cytoplasmic and epigenetic factors transmitted to progeny individuals, altering their responses to their own, immediate environmental conditions and, in some cases, leading to inherited but non-genetic adaptations. Together, these insights suggest a more nuanced understanding of the genotype and its evolutionary role, as well as a shift in research focus to investigating the complex developmental interactions among genotypes, environments and previous environments.

  4. Genotype X/C recombinant (putative genotype I) of hepatitis B virus is rare in Hanoi, Vietnam--genotypes B4 and C1 predominate.

    Science.gov (United States)

    Phung, Thi Bich Thuy; Alestig, Erik; Nguyen, Thanh Liem; Hannoun, Charles; Lindh, Magnus

    2010-08-01

    There are eight known genotypes of hepatitis B virus, A-H, and several subgenotypes, with rather well-defined geographic distributions. HBV genotypes were evaluated in 153 serum samples from Hanoi, Vietnam. Of the 87 samples that could be genotyped, genotype B was found in 67 (77%) and genotype C in 19 (22%). All genotype C strains were of subgenotype C1, and the majority of genotype B strains were B4, while a few were B2. The genotype X/C recombinant strain, identified previously in Swedish patients of indigenous Vietnamese origin, was found in one sample. This variant, proposed to be classified as genotype I, has been found recently also by others in Vietnam and Laos. The current study indicates that the genotype X/C recombinant may represent approximately 1% of the HBV strains circulating in Vietnam. (c) 2010 Wiley-Liss, Inc.

  5. Linking microbial and ecosystem ecology using ecological stoichiometry: a synthesis of conceptual and empirical approaches

    Science.gov (United States)

    Hall, E.K.; Maixner, F.; Franklin, O.; Daims, H.; Richter, A.; Battin, T.

    2011-01-01

    Currently, one of the biggest challenges in microbial and ecosystem ecology is to develop conceptual models that organize the growing body of information on environmental microbiology into a clear mechanistic framework with a direct link to ecosystem processes. Doing so will enable development of testable hypotheses to better direct future research and increase understanding of key constraints on biogeochemical networks. Although the understanding of phenotypic and genotypic diversity of microorganisms in the environment is rapidly accumulating, how controls on microbial physiology ultimately affect biogeochemical fluxes remains poorly understood. We propose that insight into constraints on biogeochemical cycles can be achieved by a more rigorous evaluation of microbial community biomass composition within the context of ecological stoichiometry. Multiple recent studies have pointed to microbial biomass stoichiometry as an important determinant of when microorganisms retain or recycle mineral nutrients. We identify the relevant cellular components that most likely drive changes in microbial biomass stoichiometry by defining a conceptual model rooted in ecological stoichiometry. More importantly, we show how X-ray microanalysis (XRMA), nanoscale secondary ion mass spectroscopy (NanoSIMS), Raman microspectroscopy, and in situ hybridization techniques (for example, FISH) can be applied in concert to allow for direct empirical evaluation of the proposed conceptual framework. This approach links an important piece of the ecological literature, ecological stoichiometry, with the molecular front of the microbial revolution, in an attempt to provide new insight into how microbial physiology could constrain ecosystem processes.

  6. Fragment separator momentum compression schemes

    Energy Technology Data Exchange (ETDEWEB)

    Bandura, Laura, E-mail: bandura@anl.gov [Facility for Rare Isotope Beams (FRIB), 1 Cyclotron, East Lansing, MI 48824-1321 (United States); National Superconducting Cyclotron Lab, Michigan State University, 1 Cyclotron, East Lansing, MI 48824-1321 (United States); Erdelyi, Bela [Argonne National Laboratory, Argonne, IL 60439 (United States); Northern Illinois University, DeKalb, IL 60115 (United States); Hausmann, Marc [Facility for Rare Isotope Beams (FRIB), 1 Cyclotron, East Lansing, MI 48824-1321 (United States); Kubo, Toshiyuki [RIKEN Nishina Center, RIKEN, Wako (Japan); Nolen, Jerry [Argonne National Laboratory, Argonne, IL 60439 (United States); Portillo, Mauricio [Facility for Rare Isotope Beams (FRIB), 1 Cyclotron, East Lansing, MI 48824-1321 (United States); Sherrill, Bradley M. [National Superconducting Cyclotron Lab, Michigan State University, 1 Cyclotron, East Lansing, MI 48824-1321 (United States)

    2011-07-21

    We present a scheme to use a fragment separator and profiled energy degraders to transfer longitudinal phase space into transverse phase space while maintaining achromatic beam transport. The first order beam optics theory of the method is presented and the consequent enlargement of the transverse phase space is discussed. An interesting consequence of the technique is that the first order mass resolving power of the system is determined by the first dispersive section up to the energy degrader, independent of whether or not momentum compression is used. The fragment separator at the Facility for Rare Isotope Beams is a specific application of this technique and is described along with simulations by the code COSY INFINITY.

  7. Fragment separator momentum compression schemes

    International Nuclear Information System (INIS)

    Bandura, Laura; Erdelyi, Bela; Hausmann, Marc; Kubo, Toshiyuki; Nolen, Jerry; Portillo, Mauricio; Sherrill, Bradley M.

    2011-01-01

    We present a scheme to use a fragment separator and profiled energy degraders to transfer longitudinal phase space into transverse phase space while maintaining achromatic beam transport. The first order beam optics theory of the method is presented and the consequent enlargement of the transverse phase space is discussed. An interesting consequence of the technique is that the first order mass resolving power of the system is determined by the first dispersive section up to the energy degrader, independent of whether or not momentum compression is used. The fragment separator at the Facility for Rare Isotope Beams is a specific application of this technique and is described along with simulations by the code COSY INFINITY.

  8. Electrical injection schemes for nanolasers

    DEFF Research Database (Denmark)

    Lupi, Alexandra; Chung, Il-Sug; Yvind, Kresten

    2013-01-01

    The performance of injection schemes among recently demonstrated electrically pumped photonic crystal nanolasers has been investigated numerically. The computation has been carried out at room temperature using a commercial semiconductor simulation software. For the simulations two electrical...... of 3 InGaAsP QWs on an InP substrate has been chosen for the modeling. In the simulations the main focus is on the electrical and optical properties of the nanolasers i.e. electrical resistance, threshold voltage, threshold current and wallplug efficiency. In the current flow evaluation the lowest...... threshold current has been achieved with the lateral electrical injection through the BH; while the lowest resistance has been obtained from the current post structure even though this model shows a higher current threshold because of the lack of carrier confinement. Final scope of the simulations...

  9. Scheme of thinking quantum systems

    International Nuclear Information System (INIS)

    Yukalov, V I; Sornette, D

    2009-01-01

    A general approach describing quantum decision procedures is developed. The approach can be applied to quantum information processing, quantum computing, creation of artificial quantum intelligence, as well as to analyzing decision processes of human decision makers. Our basic point is to consider an active quantum system possessing its own strategic state. Processing information by such a system is analogous to the cognitive processes associated to decision making by humans. The algebra of probability operators, associated with the possible options available to the decision maker, plays the role of the algebra of observables in quantum theory of measurements. A scheme is advanced for a practical realization of decision procedures by thinking quantum systems. Such thinking quantum systems can be realized by using spin lattices, systems of magnetic molecules, cold atoms trapped in optical lattices, ensembles of quantum dots, or multilevel atomic systems interacting with electromagnetic field

  10. Yellow light for green scheme

    International Nuclear Information System (INIS)

    Morch, Stein

    2004-01-01

    The article asserts that there could be an investment boom for wind, hydro and bio power in a common Norwegian-Swedish market scheme for green certificates. The Swedish authorities are ready, and the Norwegian government is preparing a report to the Norwegian Parliament. What are the ambitions of Norway, and will hydro power be included? A green certificate market common to more countries have never before been established and requires the solution of many challenging problems. In Sweden, certificate support is expected to promote primarily bioenergy, wind power and small-scale hydro power. In Norway there is an evident potential for wind power, and more hydro power can be developed if desired

  11. Pomeranchuk conjecture and symmetry schemes

    Energy Technology Data Exchange (ETDEWEB)

    Galindo, A.; Morales, A.; Ruegg, H. [Junta de Energia Nuclear, Madrid (Spain); European Organization for Nuclear Research, Geneva (Switzerland); University of Geneva, Geneva (Switzerland)

    1963-01-15

    Pomeranchuk has conjectured that the cross-sections for charge-exchange processes vanish asymptotically as the energy tends to infinity. (By ''charge'' it is meant any internal quantum number, like electric charge, hypercharge, .. . ). It has been stated by several people that this conjecture implies equalities among the total cross-sections whenever any symmetry scheme is invoked for the strong interactions. But to our knowledge no explicit general proof of this statement has been given so far. We want to give this proof for any compact Lie group. We also prove, under certain assumptions, that the equality of the total cross-sections implies that s{sup -l} times the charge-exchange forward scattering absorptive amplitudes tend to zero as s -> ∞.

  12. Microbial Cell Dynamics Lab (MCDL)

    Data.gov (United States)

    Federal Laboratory Consortium — The Microbial Cell Dynamics Laboratory at PNNL enables scientists to study the molecular details of microbes under relevant environmental conditions. The MCDL seeks...

  13. Hepatitis B virus genotypes circulating in Brazil: molecular characterization of genotype F isolates

    Directory of Open Access Journals (Sweden)

    Virgolino Helaine A

    2007-11-01

    Full Text Available Abstract Background Hepatitis B virus (HBV isolates have been classified in eight genotypes, A to H, which exhibit distinct geographical distributions. Genotypes A, D and F are predominant in Brazil, a country formed by a miscegenated population, where the proportion of individuals from Caucasian, Amerindian and African origins varies by region. Genotype F, which is the most divergent, is considered indigenous to the Americas. A systematic molecular characterization of HBV isolates from different parts of the world would be invaluable in establishing HBV evolutionary origins and dispersion patterns. A large-scale study is needed to map the region-by-region distribution of the HBV genotypes in Brazil. Results Genotyping by PCR-RFLP of 303 HBV isolates from HBsAg-positive blood donors showed that at least two of the three genotypes, A, D, and F, co-circulate in each of the five geographic regions of Brazil. No other genotypes were identified. Overall, genotype A was most prevalent (48.5%, and most of these isolates were classified as subgenotype A1 (138/153; 90.2%. Genotype D was the most common genotype in the South (84.2% and Central (47.6% regions. The prevalence of genotype F was low (13% countrywide. Nucleotide sequencing of the S gene and a phylogenetic analysis of 32 HBV genotype F isolates showed that a great majority (28/32; 87.5% belonged to subgenotype F2, cluster II. The deduced serotype of 31 of 32 F isolates was adw4. The remaining isolate showed a leucine-to-isoleucine substitution at position 127. Conclusion The presence of genotypes A, D and F, and the absence of other genotypes in a large cohort of HBV infected individuals may reflect the ethnic origins of the Brazilian population. The high prevalence of isolates from subgenotype A1 (of African origin indicates that the African influx during the colonial slavery period had a major impact on the circulation of HBV genotype A currently found in Brazil. Although most genotype F

  14. Matroids and quantum-secret-sharing schemes

    International Nuclear Information System (INIS)

    Sarvepalli, Pradeep; Raussendorf, Robert

    2010-01-01

    A secret-sharing scheme is a cryptographic protocol to distribute a secret state in an encoded form among a group of players such that only authorized subsets of the players can reconstruct the secret. Classically, efficient secret-sharing schemes have been shown to be induced by matroids. Furthermore, access structures of such schemes can be characterized by an excluded minor relation. No such relations are known for quantum secret-sharing schemes. In this paper we take the first steps toward a matroidal characterization of quantum-secret-sharing schemes. In addition to providing a new perspective on quantum-secret-sharing schemes, this characterization has important benefits. While previous work has shown how to construct quantum-secret-sharing schemes for general access structures, these schemes are not claimed to be efficient. In this context the present results prove to be useful; they enable us to construct efficient quantum-secret-sharing schemes for many general access structures. More precisely, we show that an identically self-dual matroid that is representable over a finite field induces a pure-state quantum-secret-sharing scheme with information rate 1.

  15. Forensic SNP genotyping with SNaPshot

    DEFF Research Database (Denmark)

    Fondevila, M; Børsting, C; Phillips, C

    2017-01-01

    to routine STR profiling, use of SNaPshot is an important part of the development of SNP sets for a wide range of forensic applications with these markers, from genotyping highly degraded DNA with very short amplicons to the introduction of SNPs to ascertain the ancestry and physical characteristics......This review explores the key factors that influence the optimization, routine use, and profile interpretation of the SNaPshot single-base extension (SBE) system applied to forensic single-nucleotide polymorphism (SNP) genotyping. Despite being a mainly complimentary DNA genotyping technique...... of an unidentified contact trace donor. However, this technology, as resourceful as it is, displays several features that depart from the usual STR genotyping far enough to demand a certain degree of expertise from the forensic analyst before tackling the complex casework on which SNaPshot application provides...

  16. HMSRP Hawaiian Monk Seal Microsatellite Genotypes

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Currently ~2,400 Hawaiian monk seal specimens have been analyzed genetically, providing genotypes at 18 microsatellite loci. These data are organized by individual,...

  17. Global distribution of novel rhinovirus genotype

    DEFF Research Database (Denmark)

    Briese, Thomas; Renwick, Neil; Venter, Marietjie

    2008-01-01

    Global surveillance for a novel rhinovirus genotype indicated its association with community outbreaks and pediatric respiratory disease in Africa, Asia, Australia, Europe, and North America. Molecular dating indicates that these viruses have been circulating for at least 250 years Udgivelsesdato...

  18. Assessment of antibiotic susceptibilities, genotypic characteristics ...

    African Journals Online (AJOL)

    Jane

    2011-09-28

    Sep 28, 2011 ... Staphylococcus aureus and Salmonella Typhimurium ... This study was designed to evaluate the antibiotic susceptibilities, genotypic characteristics and ..... Distribution of reference and virulence genes among antibiotic-sensitive S. aureus (SAS), .... environmental factors such as temperature, water activity,.

  19. Hepatitis C Virus: Viral Quasispecies and Genotypes

    Directory of Open Access Journals (Sweden)

    Kyoko Tsukiyama-Kohara

    2017-12-01

    Full Text Available Hepatitis C virus (HCV mainly replicates in the cytoplasm, where it easily establishes persistent infection, resulting in chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. Due to its high rate of mutation, HCV forms viral quasispecies, categorized based on the highly variable regions in the envelope protein and nonstructural 5A protein. HCV possesses seven major genotypes, among which genotype 1 is the most prevalent globally. The distribution of HCV genotypes varies based on geography, and each genotype has a different sensitivity to interferon treatment. Recently-developed direct-acting antivirals (DAAs, which target viral proteases or polymerases, mediate drastically better antiviral effects than previous therapeutics. Although treatment with DAAs has led to the development of drug-resistant HCV mutants, the most recently approved DAAs show improved pan-genomic activity, with a higher barrier to viral resistance.

  20. Hepatitis C Virus: Viral Quasispecies and Genotypes.

    Science.gov (United States)

    Tsukiyama-Kohara, Kyoko; Kohara, Michinori

    2017-12-22

    Hepatitis C virus (HCV) mainly replicates in the cytoplasm, where it easily establishes persistent infection, resulting in chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. Due to its high rate of mutation, HCV forms viral quasispecies, categorized based on the highly variable regions in the envelope protein and nonstructural 5A protein. HCV possesses seven major genotypes, among which genotype 1 is the most prevalent globally. The distribution of HCV genotypes varies based on geography, and each genotype has a different sensitivity to interferon treatment. Recently-developed direct-acting antivirals (DAAs), which target viral proteases or polymerases, mediate drastically better antiviral effects than previous therapeutics. Although treatment with DAAs has led to the development of drug-resistant HCV mutants, the most recently approved DAAs show improved pan-genomic activity, with a higher barrier to viral resistance.

  1. Early seedling development of Medicago truncatula genotypes ...

    African Journals Online (AJOL)

    adel

    2014-01-08

    Jan 8, 2014 ... heat shock proteins; ABA, abscisic acid. Page 2. Amar et al. 323. Figure 1. Seed vigor of M. truncatula genotypes under different salt stress conditions. Results are means ..... (HSPs) that accumulate during seed late maturation.

  2. Hearing impairment in genotyped Wolfram syndrome patients.

    NARCIS (Netherlands)

    Plantinga, R.F.; Pennings, R.J.E.; Huygen, P.L.M.; Bruno, R.; Eller, P.; Barrett, T.G.; Vialettes, B.; Paquis-Fluklinger, V.; Lombardo, F.; Cremers, C.W.R.J.

    2008-01-01

    OBJECTIVES: Wolfram syndrome is a progressive neurodegenerative syndrome characterized by the features "DIDMOAD" (diabetes insipidus, diabetes mellitus, optic atrophy, and deafness). We sought to study the audiometric data of genotyped Wolfram syndrome patients with sensorineural hearing impairment.

  3. Existence of various human parvovirus B19 genotypes in Chinese plasma pools: genotype 1, genotype 3, putative intergenotypic recombinant variants and new genotypes.

    Science.gov (United States)

    Jia, Junting; Ma, Yuyuan; Zhao, Xiong; Huangfu, Chaoji; Zhong, Yadi; Fang, Chi; Fan, Rui; Lv, Maomin; Zhang, Jingang

    2016-09-17

    Human parvovirus B19 (B19V) is a frequent contaminant of blood and plasma-derived medicinal products. Three distinct genotypes of B19V have been identified. The distribution of the three B19V genotypes has been investigated in various regions or countries. However, in China, data on the existence of different B19V genotypes are limited. One hundred and eighteen B19V-DNA positive source plasma pool samples collected from three Chinese blood products manufacturers were analyzed. The subgenomic NS1/VP1u region junction of B19V was amplified by nested PCR. These amplified products were then cloned and subsequently sequenced. For genotyping, their phylogenetic inferences were constructed based on the NS1/VP1-unique region. Then putative recombination events were analyzed and identified. Phylogenetic analysis of 118 B19V sequences attributed 61.86 % to genotype 1a, 10.17 % to genotype 1b, and 17.80 % to genotype 3b. All the genotype 3b sequences obtained in this study grouped as a specific, closely related cluster with B19V strain D91.1. Four 1a/3b recombinants and 5 new atypical B19V variants with no recombination events were identified. There were at least 3 subtypes (1a, 1b and 3b) of B19V circulating in China. Furthermore, putative B19V 1a/3b recombinants and unclassified strains were identified as well. Such recombinant and unclassified strains may contribute to the genetic diversity of B19V and consequently complicate the B19V infection diagnosis and NAT screening. Further studies will be required to elucidate the biological significance of the recombinant and unclassified strains.

  4. Host Genome Influence on Gut Microbial Composition and Microbial Prediction of Complex Traits in Pigs.

    Science.gov (United States)

    Camarinha-Silva, Amelia; Maushammer, Maria; Wellmann, Robin; Vital, Marius; Preuss, Siegfried; Bennewitz, Jörn

    2017-07-01

    The aim of the present study was to analyze the interplay between gastrointestinal tract (GIT) microbiota, host genetics, and complex traits in pigs using extended quantitative-genetic methods. The study design consisted of 207 pigs that were housed and slaughtered under standardized conditions, and phenotyped for daily gain, feed intake, and feed conversion rate. The pigs were genotyped with a standard 60 K SNP chip. The GIT microbiota composition was analyzed by 16S rRNA gene amplicon sequencing technology. Eight from 49 investigated bacteria genera showed a significant narrow sense host heritability, ranging from 0.32 to 0.57. Microbial mixed linear models were applied to estimate the microbiota variance for each complex trait. The fraction of phenotypic variance explained by the microbial variance was 0.28, 0.21, and 0.16 for daily gain, feed conversion, and feed intake, respectively. The SNP data and the microbiota composition were used to predict the complex traits using genomic best linear unbiased prediction (G-BLUP) and microbial best linear unbiased prediction (M-BLUP) methods, respectively. The prediction accuracies of G-BLUP were 0.35, 0.23, and 0.20 for daily gain, feed conversion, and feed intake, respectively. The corresponding prediction accuracies of M-BLUP were 0.41, 0.33, and 0.33. Thus, in addition to SNP data, microbiota abundances are an informative source of complex trait predictions. Since the pig is a well-suited animal for modeling the human digestive tract, M-BLUP, in addition to G-BLUP, might be beneficial for predicting human predispositions to some diseases, and, consequently, for preventative and personalized medicine. Copyright © 2017 by the Genetics Society of America.

  5. Microbial products II

    Energy Technology Data Exchange (ETDEWEB)

    Pape, H; Rehm, H J [eds.

    1986-01-01

    The present volume deals mainly with compounds which have been detected as natural microbial products. Part 1 of this volume introduces the general aspects of the overproduction of metabolites and the concepts and genetics of secondary metabolism. Compounds such as nucleosides, nucleotides, coenzymes, vitamins and lipids are dealt with in part 2. Part 3 then is devoted to products and antibiotics with uses im medicine, veterinary medicine, plant protection and metabolites with antitumor activity. Several secondary metabolites have found uses in human and animal health care. With 244 figs., 109 tabs.

  6. Microbial bebop: creating music from complex dynamics in microbial ecology.

    Directory of Open Access Journals (Sweden)

    Peter Larsen

    Full Text Available In order for society to make effective policy decisions on complex and far-reaching subjects, such as appropriate responses to global climate change, scientists must effectively communicate complex results to the non-scientifically specialized public. However, there are few ways however to transform highly complicated scientific data into formats that are engaging to the general community. Taking inspiration from patterns observed in nature and from some of the principles of jazz bebop improvisation, we have generated Microbial Bebop, a method by which microbial environmental data are transformed into music. Microbial Bebop uses meter, pitch, duration, and harmony to highlight the relationships between multiple data types in complex biological datasets. We use a comprehensive microbial ecology, time course dataset collected at the L4 marine monitoring station in the Western English Channel as an example of microbial ecological data that can be transformed into music. Four compositions were generated (www.bio.anl.gov/MicrobialBebop.htm. from L4 Station data using Microbial Bebop. Each composition, though deriving from the same dataset, is created to highlight different relationships between environmental conditions and microbial community structure. The approach presented here can be applied to a wide variety of complex biological datasets.

  7. Microbial bebop: creating music from complex dynamics in microbial ecology.

    Science.gov (United States)

    Larsen, Peter; Gilbert, Jack

    2013-01-01

    In order for society to make effective policy decisions on complex and far-reaching subjects, such as appropriate responses to global climate change, scientists must effectively communicate complex results to the non-scientifically specialized public. However, there are few ways however to transform highly complicated scientific data into formats that are engaging to the general community. Taking inspiration from patterns observed in nature and from some of the principles of jazz bebop improvisation, we have generated Microbial Bebop, a method by which microbial environmental data are transformed into music. Microbial Bebop uses meter, pitch, duration, and harmony to highlight the relationships between multiple data types in complex biological datasets. We use a comprehensive microbial ecology, time course dataset collected at the L4 marine monitoring station in the Western English Channel as an example of microbial ecological data that can be transformed into music. Four compositions were generated (www.bio.anl.gov/MicrobialBebop.htm.) from L4 Station data using Microbial Bebop. Each composition, though deriving from the same dataset, is created to highlight different relationships between environmental conditions and microbial community structure. The approach presented here can be applied to a wide variety of complex biological datasets.

  8. Popcorn genotypes resistance to fall armyworm

    Directory of Open Access Journals (Sweden)

    Nádia Cristina de Oliveira

    2018-02-01

    Full Text Available ABSTRACT: The aim of this study was to evaluate popcorn genotypes for resistance to the fall armyworm, Spodoptera frugiperda. The experiment used a completely randomized design with 30 replicates. The popcorn genotypes Aelton, Arzm 05 083, Beija-Flor, Colombiana, Composto Chico, Composto Gaúcha, Márcia, Mateus, Ufvm Barão Viçosa, Vanin, and Viviane were evaluated,along with the common maize variety Zapalote Chico. Newly hatched fall armyworm larvae were individually assessed with regard to biological development and consumption of food. The data were subjected to multivariate analyses of variance and genetic divergence among genotypes was evaluated through the clustering methods of Tocher based on generalized Mahalanobis distances and canonical variable analyses. Seven popcorn genotypes, namely, Aelton, Arzm 05 083, Composto Chico, Composto Gaúcha, Márcia, Mateus, and Viviane,were shown to form a cluster (cluster I that had antibiosis as the mechanism of resistance to the pest. Cluster I genotypes and the Zapalote Chico genotype could be used for stacking genes for antibiosis and non-preference resistance.

  9. How can conceptual schemes change teaching?

    Science.gov (United States)

    Wickman, Per-Olof

    2012-03-01

    Lundqvist, Almqvist and Östman describe a teacher's manner of teaching and the possible consequences it may have for students' meaning making. In doing this the article examines a teacher's classroom practice by systematizing the teacher's transactions with the students in terms of certain conceptual schemes, namely the epistemological moves, educational philosophies and the selective traditions of this practice. In connection to their study one may ask how conceptual schemes could change teaching. This article examines how the relationship of the conceptual schemes produced by educational researchers to educational praxis has developed from the middle of the last century to today. The relationship is described as having been transformed in three steps: (1) teacher deficit and social engineering, where conceptual schemes are little acknowledged, (2) reflecting practitioners, where conceptual schemes are mangled through teacher practice to aid the choices of already knowledgeable teachers, and (3) the mangling of the conceptual schemes by researchers through practice with the purpose of revising theory.

  10. Resonance ionization scheme development for europium

    Energy Technology Data Exchange (ETDEWEB)

    Chrysalidis, K., E-mail: katerina.chrysalidis@cern.ch; Goodacre, T. Day; Fedosseev, V. N.; Marsh, B. A. [CERN (Switzerland); Naubereit, P. [Johannes Gutenberg-Universität, Institiut für Physik (Germany); Rothe, S.; Seiffert, C. [CERN (Switzerland); Kron, T.; Wendt, K. [Johannes Gutenberg-Universität, Institiut für Physik (Germany)

    2017-11-15

    Odd-parity autoionizing states of europium have been investigated by resonance ionization spectroscopy via two-step, two-resonance excitations. The aim of this work was to establish ionization schemes specifically suited for europium ion beam production using the ISOLDE Resonance Ionization Laser Ion Source (RILIS). 13 new RILIS-compatible ionization schemes are proposed. The scheme development was the first application of the Photo Ionization Spectroscopy Apparatus (PISA) which has recently been integrated into the RILIS setup.

  11. Secure RAID Schemes for Distributed Storage

    OpenAIRE

    Huang, Wentao; Bruck, Jehoshua

    2016-01-01

    We propose secure RAID, i.e., low-complexity schemes to store information in a distributed manner that is resilient to node failures and resistant to node eavesdropping. We generalize the concept of systematic encoding to secure RAID and show that systematic schemes have significant advantages in the efficiencies of encoding, decoding and random access. For the practical high rate regime, we construct three XOR-based systematic secure RAID schemes with optimal or almost optimal encoding and ...

  12. Analyzing the genomic variation of microbial cell factories in the era of “New Biotechnology”

    DEFF Research Database (Denmark)

    Herrgard, Markus; Panagiotou, Gianni

    2012-01-01

    The application of genome-scale technologies, both experimental and in silico, to industrial biotechnology has allowed improving the conversion of biomass-derived feedstocks to chemicals, materials and fuels through microbial fermentation. In particular, due to rapidly decreasing costs and its...... technologies for finding the underlying molecular mechanisms for (a) improved carbon source utilization, (b) increased product formation, and (c) stress tolerance. We also discuss the strengths and weaknesses of different strategies for mapping industrially relevant genotype-to-phenotype links including...

  13. A new access scheme in OFDMA systems

    Institute of Scientific and Technical Information of China (English)

    GU Xue-lin; YAN Wei; TIAN Hui; ZHANG Ping

    2006-01-01

    This article presents a dynamic random access scheme for orthogonal frequency division multiple access (OFDMA) systems. The key features of the proposed scheme are:it is a combination of both the distributed and the centralized schemes, it can accommodate several delay sensitivity classes,and it can adjust the number of random access channels in a media access control (MAC) frame and the access probability according to the outcome of Mobile Terminals access attempts in previous MAC frames. For floating populated packet-based networks, the proposed scheme possibly leads to high average user satisfaction.

  14. A Spatial Domain Quantum Watermarking Scheme

    International Nuclear Information System (INIS)

    Wei Zhan-Hong; Chen Xiu-Bo; Niu Xin-Xin; Yang Yi-Xian; Xu Shu-Jiang

    2016-01-01

    This paper presents a spatial domain quantum watermarking scheme. For a quantum watermarking scheme, a feasible quantum circuit is a key to achieve it. This paper gives a feasible quantum circuit for the presented scheme. In order to give the quantum circuit, a new quantum multi-control rotation gate, which can be achieved with quantum basic gates, is designed. With this quantum circuit, our scheme can arbitrarily control the embedding position of watermark images on carrier images with the aid of auxiliary qubits. Besides reversely acting the given quantum circuit, the paper gives another watermark extracting algorithm based on quantum measurements. Moreover, this paper also gives a new quantum image scrambling method and its quantum circuit. Differ from other quantum watermarking schemes, all given quantum circuits can be implemented with basic quantum gates. Moreover, the scheme is a spatial domain watermarking scheme, and is not based on any transform algorithm on quantum images. Meanwhile, it can make sure the watermark be secure even though the watermark has been found. With the given quantum circuit, this paper implements simulation experiments for the presented scheme. The experimental result shows that the scheme does well in the visual quality and the embedding capacity. (paper)

  15. Quantum signature scheme for known quantum messages

    International Nuclear Information System (INIS)

    Kim, Taewan; Lee, Hyang-Sook

    2015-01-01

    When we want to sign a quantum message that we create, we can use arbitrated quantum signature schemes which are possible to sign for not only known quantum messages but also unknown quantum messages. However, since the arbitrated quantum signature schemes need the help of a trusted arbitrator in each verification of the signature, it is known that the schemes are not convenient in practical use. If we consider only known quantum messages such as the above situation, there can exist a quantum signature scheme with more efficient structure. In this paper, we present a new quantum signature scheme for known quantum messages without the help of an arbitrator. Differing from arbitrated quantum signature schemes based on the quantum one-time pad with the symmetric key, since our scheme is based on quantum public-key cryptosystems, the validity of the signature can be verified by a receiver without the help of an arbitrator. Moreover, we show that our scheme provides the functions of quantum message integrity, user authentication and non-repudiation of the origin as in digital signature schemes. (paper)

  16. Microbial ecology of phototrophic biofilms

    NARCIS (Netherlands)

    Roeselers, G.

    2007-01-01

    Biofilms are layered structures of microbial cells and an extracellular matrix of polymeric substances, associated with surfaces and interfaces. Biofilms trap nutrients for growth of the enclosed microbial community and help prevent detachment of cells from surfaces in flowing systems. Phototrophic

  17. Hydrodynamics of microbial filter feeding

    DEFF Research Database (Denmark)

    Nielsen, Lasse Tor; Asadzadeh, Seyed Saeed; Dölger, Julia

    2017-01-01

    Microbial filter feeders are an important group of grazers, significant to the microbial loop, aquatic food webs, and biogeochemical cycling. Our understanding of microbial filter feeding is poor, and, importantly, it is unknown what force microbial filter feeders must generate to process adequate......-feeding choanoflagellate Diaphanoeca grandis using particle tracking, and demonstrate that the current understanding of microbial filter feeding is inconsistent with computational fluid dynamics (CFD) and analytical estimates. Both approaches underestimate observed filtration rates by more than an order of magnitude......; the beating flagellum is simply unable to draw enough water through the fine filter. We find similar discrepancies for other choanoflagellate species, highlighting an apparent paradox. Our observations motivate us to suggest a radically different filtration mechanism that requires a flagellar vane (sheet...

  18. Cotton genotypes selection through artificial neural networks.

    Science.gov (United States)

    Júnior, E G Silva; Cardoso, D B O; Reis, M C; Nascimento, A F O; Bortolin, D I; Martins, M R; Sousa, L B

    2017-09-27

    Breeding programs currently use statistical analysis to assist in the identification of superior genotypes at various stages of a cultivar's development. Differently from these analyses, the computational intelligence approach has been little explored in genetic improvement of cotton. Thus, this study was carried out with the objective of presenting the use of artificial neural networks as auxiliary tools in the improvement of the cotton to improve fiber quality. To demonstrate the applicability of this approach, this research was carried out using the evaluation data of 40 genotypes. In order to classify the genotypes for fiber quality, the artificial neural networks were trained with replicate data of 20 genotypes of cotton evaluated in the harvests of 2013/14 and 2014/15, regarding fiber length, uniformity of length, fiber strength, micronaire index, elongation, short fiber index, maturity index, reflectance degree, and fiber quality index. This quality index was estimated by means of a weighted average on the determined score (1 to 5) of each characteristic of the HVI evaluated, according to its industry standards. The artificial neural networks presented a high capacity of correct classification of the 20 selected genotypes based on the fiber quality index, so that when using fiber length associated with the short fiber index, fiber maturation, and micronaire index, the artificial neural networks presented better results than using only fiber length and previous associations. It was also observed that to submit data of means of new genotypes to the neural networks trained with data of repetition, provides better results of classification of the genotypes. When observing the results obtained in the present study, it was verified that the artificial neural networks present great potential to be used in the different stages of a genetic improvement program of the cotton, aiming at the improvement of the fiber quality of the future cultivars.

  19. Molecular characterization of varicella-zoster virus clinical isolates from 2006 to 2008 in a tertiary care hospital, Dublin, Ireland, using different genotyping methods.

    LENUS (Irish Health Repository)

    Roycroft, Emma

    2012-10-01

    Varicella-zoster virus (VZV), a herpesvirus, is a ubiquitous organism that causes considerable morbidity worldwide and can cause severe complications on reactivation. Phylogenetic analysis was performed on 19 clinical VZV isolates (16 zoster and 3 varicella) found in Ireland, between December 2006 and November 2008, in order to determine whether previously reported viral heterogeneity was still present and whether viral recombination was evident. Open reading-frames (ORFs) from genes 1, 21, 50, and 54, were sequenced. Clades 1, 2, 3, and 5 were identified. Four putative recombinant isolates were detected (three clade 3\\/1 and one clade 5\\/3\\/1). Further sequencing and examination of ORF 22 and 21\\/50, did not elucidate the putative recombinant genotypes further. These two previously published genotyping schemes were examined in light of the new consensus genotyping scheme proposed in 2010. Remarkable VZV heterogeneity remains prevalent in Ireland. This is the first evidence of putative VZV recombination found in Ireland.

  20. Biomek®-3000 and GenPlex SNP Genotyping in Forensic Genetics

    DEFF Research Database (Denmark)

    Stangegaard, Michael; Tomas, Carmen; Hansen, Anders J.

    2008-01-01

    Single nucleotide polymorphism genotyping provides a supplement for conventional short tandem repeats-based kits currently used for human identification. GenPlex (Applied Biosystems (AB), Foster City, CA) is an SNP-genotyping kit based on a multiplex of 48 informative, autosomal SNPs from...... the SNPforID Consortium. Our objective was to setup, implement, and validate a small and affordable automated liquid-handling robot for forensic casework samples (buccal swaps on FTA-paper and Qiagen purified blood). The reaction scheme consisted of numerous steps and was cumbersome to perform consistently...... manually. Automation was accomplished with a Biomek-3000 (Beckmann Coulter) laboratory-automated workstation using five in-house-developed methods. All methods allowed the user to select the number of subsequent injections to the capillary electrophoresis instrument (ABI 3130xl, AB) enabling processing...

  1. NS3 protease polymorphisms and genetic barrier to drug resistance of distinct hepatitis C virus genotypes from worldwide treatment-naïve subjects.

    Science.gov (United States)

    Vidal, L L; Soares, M A; Santos, A F

    2016-11-01

    Hepatitis C virus (HCV) NS3 protease inhibitors have been primarily designed against genotype 1, the one with the lowest response to dual therapy. However, less evidence of their efficacy on non-1 genotypes is available, and any such information is mostly concentrated on genotypes 2-4. This study evaluated HCV protease resistance profiles in the major six HCV genotypes and identified genetic barrier (GB) profiles to each available protease inhibitor across HCV strains from different locations worldwide. We obtained 15 099 HCV sequences from treatment-naïve subjects retrieved at the Los Alamos HCV Sequence Database. The wild-type codons of different HCV genotypes were used to analyse the smallest number of nucleotide substitution steps required for changing that codon to the closest one associated with drug resistance. The 36L and 175L RAVs were found as genetic signatures of genotypes 2-5, while the 80K RAV was found in all genotype 5 sequences. Genotypes 4 and 6 showed a higher GB to RAV mutations conferring resistance to telaprevir, while genotypes 2-5 presented baseline resistance to that drug, carrying the 36L mutation. Genotype 4 had a higher GB to simeprevir resistance, requiring three substitutions to acquire the 155K mutation. Subtype 1b showed a higher GB than subtype 1a to resistance for most PIs, with RAVs at codons 36 and 155. Geographic disparities were also found in frequencies of certain RAVs in genotypes 2 and 3. Under a scenario of unprecedented evolution of anti-HCV direct-acting agents, the genetic composition of the circulating HCV sequences should be evaluated worldwide to choose the most appropriate/feasible therapeutic schemes with the highest genetic barriers to resistance. © 2016 John Wiley & Sons Ltd.

  2. Molecular musings in microbial ecology and evolution.

    Science.gov (United States)

    Case, Rebecca J; Boucher, Yan

    2011-11-10

    A few major discoveries have influenced how ecologists and evolutionists study microbes. Here, in the format of an interview, we answer questions that directly relate to how these discoveries are perceived in these two branches of microbiology, and how they have impacted on both scientific thinking and methodology.The first question is "What has been the influence of the 'Universal Tree of Life' based on molecular markers?" For evolutionists, the tree was a tool to understand the past of known (cultured) organisms, mapping the invention of various physiologies on the evolutionary history of microbes. For ecologists the tree was a guide to discover the current diversity of unknown (uncultured) organisms, without much knowledge of their physiology.The second question we ask is "What was the impact of discovering frequent lateral gene transfer among microbes?" In evolutionary microbiology, frequent lateral gene transfer (LGT) made a simple description of relationships between organisms impossible, and for microbial ecologists, functions could not be easily linked to specific genotypes. Both fields initially resisted LGT, but methods or topics of inquiry were eventually changed in one to incorporate LGT in its theoretical models (evolution) and in the other to achieve its goals despite that phenomenon (ecology).The third and last question we ask is "What are the implications of the unexpected extent of diversity?" The variation in the extent of diversity between organisms invalidated the universality of species definitions based on molecular criteria, a major obstacle to the adaptation of models developed for the study of macroscopic eukaryotes to evolutionary microbiology. This issue has not overtly affected microbial ecology, as it had already abandoned species in favor of the more flexible operational taxonomic units. This field is nonetheless moving away from traditional methods to measure diversity, as they do not provide enough resolution to uncover what lies

  3. Hepatitis C virus genotypes in Bahawalpur

    International Nuclear Information System (INIS)

    Qazi, M.A.; Fayyaz, M.; Chaudhry, G.M.D.; Jamil, A.

    2006-01-01

    This study was conducted at Medical Unit-II Bahawal Victoria Hospital / Quaid-e-Azam Medical College Bahawalpur from May 1st , 2005 to December 31st 2005. The objective of this study was to determine hepatitis C virus (HCV) genotypes in Bahawalpur, Pakistan. In consecutive 105 anti-HCV (ELISA-3) positive patients, complete history and physical examination was performed. Liver function tests, complete blood counts and platelet count, blood sugar fasting and 2 hours after breakfast, prothrombin time, serum albumin, serum globulin and abdominal ultrasound were carried out in all the patients. Tru cut biopsy was performed on 17 patients. We studied HCV RNA in all these patients by Nested PCR method. HCV RNA was detected in 98 patients and geno typing assay was done by genotype specific PCR. Among total of 105 anti-HCV positive patients, HCV-RNA was detected in 98 patients. Out of these 98 patients there were 57 (58.2%) males and 41 (42.8%) females. Their age range was 18-75 years. The age 18-29 years 26 (26.5%), 30-39 years 35 (35.7%) and 40-75 37 (37.8%), while 10 (10.2%) patients were diabetics and 34 (34.7%) patients were obese. Liver cirrhosis was present in 10 (10.2%) patients. Forty two (43.9%) patients were symptomatic while 56 (57.1%) were asymptomatic. Out of 98 patients 11 (11.2%) were un type-able and 87 (88.8%) were type able. 70/98 (71.4%) were genotype 3; 10/98 (10.2%) were genotype 1; 03/98 (3.1%) were genotype 2; 03/98 (3.1%) were mixed genotype 2 and 3; 01/98 (1%) were mixed genotype 3a and 3b. Genotype 3 is the most common HCV virus in our area which shows that both virological and biochemical response will be better. Because HCV genotype 3 is more frequent among the drug users which points towards unsafe injection practices in our area. (author)

  4. Soil microbial community responses to antibiotic-contaminated manure under different soil moisture regimes.

    Science.gov (United States)

    Reichel, Rüdiger; Radl, Viviane; Rosendahl, Ingrid; Albert, Andreas; Amelung, Wulf; Schloter, Michael; Thiele-Bruhn, Sören

    2014-01-01

    Sulfadiazine (SDZ) is an antibiotic frequently administered to livestock, and it alters microbial communities when entering soils with animal manure, but understanding the interactions of these effects to the prevailing climatic regime has eluded researchers. A climatic factor that strongly controls microbial activity is soil moisture. Here, we hypothesized that the effects of SDZ on soil microbial communities will be modulated depending on the soil moisture conditions. To test this hypothesis, we performed a 49-day fully controlled climate chamber pot experiments with soil grown with Dactylis glomerata (L.). Manure-amended pots without or with SDZ contamination were incubated under a dynamic moisture regime (DMR) with repeated drying and rewetting changes of >20 % maximum water holding capacity (WHCmax) in comparison to a control moisture regime (CMR) at an average soil moisture of 38 % WHCmax. We then monitored changes in SDZ concentration as well as in the phenotypic phospholipid fatty acid and genotypic 16S rRNA gene fragment patterns of the microbial community after 7, 20, 27, 34, and 49 days of incubation. The results showed that strongly changing water supply made SDZ accessible to mild extraction in the short term. As a result, and despite rather small SDZ effects on community structures, the PLFA-derived microbial biomass was suppressed in the SDZ-contaminated DMR soils relative to the CMR ones, indicating that dynamic moisture changes accelerate the susceptibility of the soil microbial community to antibiotics.

  5. Phenotypic and genotypic variation in Iranian Pistachios

    Directory of Open Access Journals (Sweden)

    Somayeh Tayefeh Aliakbarkhani

    2015-12-01

    Full Text Available As Iran is one of the richest pistachio germplasms a few studies have been conducted on different sexes of pistachio trees, in areas where this crop emerged. To this end, 40 male and female Iranian pistachio genotypes from Feizabad region, Khorasan, Iran; were evaluated using morphological characters and randomly amplified polymorphic DNA (RAPD markers. For morphological assessments, 54 variables were considered to investigate similarities between and among the studied genotypes. Morphological data indicated relative superiority in some female genotypes (such as Sefid 1, Sefid Sabuni 2, Garmesiah, and Ghermezdorosht Z regarding characters such as halfcrackedness, the percentages of protein and fat content. 115 polymorphic bands were recorded with 92.83% average polymorphism among all primers. The total resolving power (Rp of the primers was 74.54. The range of genetic similarity varied from about 0.31 to about 0.70. Genotypes were segregated into eight groups at the similarity limit of 0.41. Results of present investigation could be helpful for strategic decisions for maintaining Iranian pistachio genotypes.

  6. Precise genotyping and recombination detection of Enterovirus

    Science.gov (United States)

    2015-01-01

    Enteroviruses (EV) with different genotypes cause diverse infectious diseases in humans and mammals. A correct EV typing result is crucial for effective medical treatment and disease control; however, the emergence of novel viral strains has impaired the performance of available diagnostic tools. Here, we present a web-based tool, named EVIDENCE (EnteroVirus In DEep conception, http://symbiont.iis.sinica.edu.tw/evidence), for EV genotyping and recombination detection. We introduce the idea of using mixed-ranking scores to evaluate the fitness of prototypes based on relatedness and on the genome regions of interest. Using phylogenetic methods, the most possible genotype is determined based on the closest neighbor among the selected references. To detect possible recombination events, EVIDENCE calculates the sequence distance and phylogenetic relationship among sequences of all sliding windows scanning over the whole genome. Detected recombination events are plotted in an interactive figure for viewing of fine details. In addition, all EV sequences available in GenBank were collected and revised using the latest classification and nomenclature of EV in EVIDENCE. These sequences are built into the database and are retrieved in an indexed catalog, or can be searched for by keywords or by sequence similarity. EVIDENCE is the first web-based tool containing pipelines for genotyping and recombination detection, with updated, built-in, and complete reference sequences to improve sensitivity and specificity. The use of EVIDENCE can accelerate genotype identification, aiding clinical diagnosis and enhancing our understanding of EV evolution. PMID:26678286

  7. Brazilian kefir: structure, microbial communities and chemical composition

    Science.gov (United States)

    Magalhães, Karina Teixeira; de Melo Pereira, Gilberto Vinícius; Campos, Cássia Roberta; Dragone, Giuliano; Schwan, Rosane Freitas

    2011-01-01

    Microbial ecology and chemical composition of Brazilian kefir beverage was performed. The microorganisms associated with Brazilian kefir were investigated using a combination of phenotypic and genotypic methods. A total of 359 microbial isolates were identified. Lactic acid bacteria (60.5%) were the major isolated group identified, followed by yeasts (30.6%) and acetic acid bacteria (8.9%). Lactobacillus paracasei (89 isolates), Lactobacillus parabuchneri (41 isolates), Lactobacillus casei (32 isolates), Lactobacillus kefiri (31 isolates), Lactococcus lactis (24 isolates), Acetobacter lovaniensis (32 isolates), Kluyveromyces lactis (31 isolates), Kazachstania aerobia (23 isolates), Saccharomyces cerevisiae (41 isolates) and Lachancea meyersii (15 isolates) were the microbial species isolated. Scanning electron microscopy showed that the microbiota was dominated by bacilli (short and curved long) cells growing in close association with lemon-shaped yeasts cells. During the 24 h of fermentation, the protein content increased, while lactose and fat content decreased. The concentration of lactic acid ranged from 1.4 to 17.4 mg/ml, and that of acetic acid increased from 2.1 to 2.73 mg/ml. The production of ethanol was limited, reaching a final mean value of 0.5 mg/ml. PMID:24031681

  8. Brazilian kefir: structure, microbial communities and chemical composition

    Directory of Open Access Journals (Sweden)

    Karina Teixeira Magalhães

    2011-06-01

    Full Text Available Microbial ecology and chemical composition of Brazilian kefir beverage was performed. The microorganisms associated with Brazilian kefir were investigated using a combination of phenotypic and genotypic methods. A total of 359 microbial isolates were identified. Lactic acid bacteria (60.5% were the major isolated group identified, followed by yeasts (30.6% and acetic acid bacteria (8.9%. Lactobacillus paracasei (89 isolates, Lactobacillus parabuchneri (41 isolates, Lactobacillus casei (32 isolates, Lactobacillus kefiri (31 isolates, Lactococcus lactis (24 isolates, Acetobacter lovaniensis (32 isolates, Kluyveromyces lactis (31 isolates, Kazachstania aerobia (23 isolates, Saccharomyces cerevisiae (41 isolates and Lachancea meyersii (15 isolates were the microbial species isolated. Scanning electron microscopy showed that the microbiota was dominated by bacilli (short and curved long cells growing in close association with lemon-shaped yeasts cells. During the 24 h of fermentation, the protein content increased, while lactose and fat content decreased. The concentration of lactic acid ranged from 1.4 to 17.4 mg/ml, and that of acetic acid increased from 2.1 to 2.73 mg/ml. The production of ethanol was limited, reaching a final mean value of 0.5 mg/ml.

  9. Microbial brokers of insect-plant interactions revisited.

    Science.gov (United States)

    Douglas, Angela E

    2013-07-01

    Recent advances in sequencing methods have transformed the field of microbial ecology, making it possible to determine the composition and functional capabilities of uncultured microorganisms. These technologies have been instrumental in the recognition that resident microorganisms can have profound effects on the phenotype and fitness of their animal hosts by modulating the animal signaling networks that regulate growth, development, behavior, etc. Against this backdrop, this review assesses the impact of microorganisms on insect-plant interactions, in the context of the hypothesis that microorganisms are biochemical brokers of plant utilization by insects. There is now overwhelming evidence for a microbial role in insect utilization of certain plant diets with an extremely low or unbalanced nutrient content. Specifically, microorganisms enable insect utilization of plant sap by synthesizing essential amino acids. They also can broker insect utilization of plant products of extremely high lignocellulose content, by enzymatic breakdown of complex plant polysaccharides, nitrogen fixation, and sterol synthesis. However, the experimental evidence for microbial-mediated detoxification of plant allelochemicals is limited. The significance of microorganisms as brokers of plant utilization by insects is predicted to vary, possibly widely, as a result of potentially complex interactions between the composition of the microbiota and the diet and insect developmental age or genotype. For every insect species feeding on plant material, the role of resident microbiota as biochemical brokers of plant utilization is a testable hypothesis.

  10. Monitoring Microbially Influenced Corrosion

    DEFF Research Database (Denmark)

    Hilbert, Lisbeth Rischel

    and diffusional effects and unreliable corrosion rates, when biofilm and ferrous sulphide corrosion products cover the steel surface. Corrosion rates can be overestimated by a factor of 10 to 100 by electrochemical techniques. Weight loss coupons and ER are recommended as necessary basic monitoring techniques......Abstract Microbially influenced corrosion (MIC) of carbon steel may occur in media with microbiological activity of especially sulphate-reducing bacteria (SRB). The applicability and reliability of a number of corrosion monitoring techniques for monitoring MIC has been evaluated in experiments....... EIS might be used for detection of MIC as the appearance of very large capacitances can be attributed to the combined ferrous sulphide and biofilm formation. Capacitance correlates directly with sulphide concentration in sterile sulphide media. Keywords: Corrosion monitoring, carbon steel, MIC, SRB...

  11. New microbial growth factor

    Science.gov (United States)

    Bok, S. H.; Casida, L. E., Jr.

    1977-01-01

    A screening procedure was used to isolate from soil a Penicillium sp., two bacterial isolates, and a Streptomyces sp. that produced a previously unknown microbial growth factor. This factor was an absolute growth requirement for three soil bacteria. The Penicillium sp. and one of the bacteria requiring the factor, an Arthrobacter sp., were selected for more extensive study concerning the production and characteristics of the growth factor. It did not seem to be related to the siderochromes. It was not present in soil extract, rumen fluid, or any other medium component tested. It appears to be a glycoprotein of high molecular weight and has high specific activity. When added to the diets for a meadow-vole mammalian test system, it caused an increased consumption of diet without a concurrent increase in rate of weight gain.

  12. Anonymous Credential Schemes with Encrypted Attributes

    NARCIS (Netherlands)

    Guajardo Merchan, J.; Mennink, B.; Schoenmakers, B.

    2011-01-01

    In anonymous credential schemes, users obtain credentials on certain attributes from an issuer, and later show these credentials to a relying party anonymously and without fully disclosing the attributes. In this paper, we introduce the notion of (anonymous) credential schemes with encrypted

  13. Community healthcare financing scheme: findings among residents ...

    African Journals Online (AJOL)

    ... none were active participants as 2(0.6%) were indifferent. There was a statistically significant relationship, Fischers <0.0001 between sex and the scheme's knowledge. Conclusion: Knowledge of the scheme was poor among majority of the respondents and none were active participants. Bribery and corruption was the ...

  14. Improved Load Shedding Scheme considering Distributed Generation

    DEFF Research Database (Denmark)

    Das, Kaushik; Nitsas, Antonios; Altin, Müfit

    2017-01-01

    With high penetration of distributed generation (DG), the conventional under-frequency load shedding (UFLS) face many challenges and may not perform as expected. This article proposes new UFLS schemes, which are designed to overcome the shortcomings of traditional load shedding scheme...

  15. A generalized scheme for designing multistable continuous ...

    Indian Academy of Sciences (India)

    In this paper, a generalized scheme is proposed for designing multistable continuous dynamical systems. The scheme is based on the concept of partial synchronization of states and the concept of constants of motion. The most important observation is that by coupling two mdimensional dynamical systems, multistable ...

  16. Consolidation of the health insurance scheme

    CERN Document Server

    Association du personnel

    2009-01-01

    In the last issue of Echo, we highlighted CERN’s obligation to guarantee a social security scheme for all employees, pensioners and their families. In that issue we talked about the first component: pensions. This time we shall discuss the other component: the CERN Health Insurance Scheme (CHIS).

  17. A hierarchical classification scheme of psoriasis images

    DEFF Research Database (Denmark)

    Maletti, Gabriela Mariel; Ersbøll, Bjarne Kjær

    2003-01-01

    A two-stage hierarchical classification scheme of psoriasis lesion images is proposed. These images are basically composed of three classes: normal skin, lesion and background. The scheme combines conventional tools to separate the skin from the background in the first stage, and the lesion from...

  18. Privacy Preserving Mapping Schemes Supporting Comparison

    NARCIS (Netherlands)

    Tang, Qiang

    2010-01-01

    To cater to the privacy requirements in cloud computing, we introduce a new primitive, namely Privacy Preserving Mapping (PPM) schemes supporting comparison. An PPM scheme enables a user to map data items into images in such a way that, with a set of images, any entity can determine the <, =, >

  19. Mixed ultrasoft/norm-conserved pseudopotential scheme

    DEFF Research Database (Denmark)

    Stokbro, Kurt

    1996-01-01

    A variant of the Vanderbilt ultrasoft pseudopotential scheme, where the norm conservation is released for only one or a few angular channels, is presented. Within this scheme some difficulties of the truly ultrasoft pseudopotentials are overcome without sacrificing the pseudopotential softness. (...

  20. Identification of Characteristic Macromolecules of Escherichia coli Genotypes by Atomic Force Microscope Nanoscale Mechanical Mapping

    Science.gov (United States)

    Chang, Alice Chinghsuan; Liu, Bernard Haochih

    2018-02-01

    The categorization of microbial strains is conventionally based on the molecular method, and seldom are the morphological characteristics in the bacterial strains studied. In this research, we revealed the macromolecular structures of the bacterial surface via AFM mechanical mapping, whose resolution was not only determined by the nanoscale tip size but also the mechanical properties of the specimen. This technique enabled the nanoscale study of membranous structures of microbial strains with simple specimen preparation and flexible working environments, which overcame the multiple restrictions in electron microscopy and label-enable biochemical analytical methods. The characteristic macromolecules located among cellular surface were considered as surface layer proteins and were found to be specific to the Escherichia coli genotypes, from which the averaged molecular sizes were characterized with diameters ranging from 38 to 66 nm, and the molecular shapes were kidney-like or round. In conclusion, the surface macromolecular structures have unique characteristics that link to the E. coli genotype, which suggests that the genomic effects on cellular morphologies can be rapidly identified using AFM mechanical mapping. [Figure not available: see fulltext.

  1. A Single Multilocus Sequence Typing (MLST) Scheme for Seven Pathogenic Leptospira Species

    Science.gov (United States)

    Amornchai, Premjit; Wuthiekanun, Vanaporn; Bailey, Mark S.; Holden, Matthew T. G.; Zhang, Cuicai; Jiang, Xiugao; Koizumi, Nobuo; Taylor, Kyle; Galloway, Renee; Hoffmaster, Alex R.; Craig, Scott; Smythe, Lee D.; Hartskeerl, Rudy A.; Day, Nicholas P.; Chantratita, Narisara; Feil, Edward J.; Aanensen, David M.; Spratt, Brian G.; Peacock, Sharon J.

    2013-01-01

    Background The available Leptospira multilocus sequence typing (MLST) scheme supported by a MLST website is limited to L. interrogans and L. kirschneri. Our aim was to broaden the utility of this scheme to incorporate a total of seven pathogenic species. Methodology and Findings We modified the existing scheme by replacing one of the seven MLST loci (fadD was changed to caiB), as the former gene did not appear to be present in some pathogenic species. Comparison of the original and modified schemes using data for L. interrogans and L. kirschneri demonstrated that the discriminatory power of the two schemes was not significantly different. The modified scheme was used to further characterize 325 isolates (L. alexanderi [n = 5], L. borgpetersenii [n = 34], L. interrogans [n = 222], L. kirschneri [n = 29], L. noguchii [n = 9], L. santarosai [n = 10], and L. weilii [n = 16]). Phylogenetic analysis using concatenated sequences of the 7 loci demonstrated that each species corresponded to a discrete clade, and that no strains were misclassified at the species level. Comparison between genotype and serovar was possible for 254 isolates. Of the 31 sequence types (STs) represented by at least two isolates, 18 STs included isolates assigned to two or three different serovars. Conversely, 14 serovars were identified that contained between 2 to 10 different STs. New observations were made on the global phylogeography of Leptospira spp., and the utility of MLST in making associations between human disease and specific maintenance hosts was demonstrated. Conclusion The new MLST scheme, supported by an updated MLST website, allows the characterization and species assignment of isolates of the seven major pathogenic species associated with leptospirosis. PMID:23359622

  2. Cell Line Controls for the Genotyping of a Spectrum of Human Single Nucleotide Polymorphisms in the Clinical Laboratory.

    Science.gov (United States)

    Kimbacher, Christine; Paar, Christian; Freystetter, Andrea; Berg, Joerg

    2018-05-01

    Genotyping for clinically important single nucleotide polymorphisms (SNPs) is performed by many clinical routine laboratories. To support testing, quality controls and reference materials are needed. Those may be derived from residual patient samples, left over samples of external quality assurance schemes, plasmid DNA or DNA from cell lines. DNAs from cell lines are commutable and available in large amounts. DNA from 38 cell lines were examined for suitability as controls in 11 SNP assays that are frequently used in a clinical routine laboratory: FV (1691G>A), FII (20210G>A), PAI-1 4G/5G polymorphism, MTHFR (677C>T, 1298A>C), HFE (H63D, S65C, C282Y), APOE (E2, E3, E4), LPH (-13910C>T), UGT1A1 (*28, *36, *37), TPMT (*2, *3A, *3B, *3C), VKORC1 (-1639G>A, 1173C>T), CYP2C9 (*2, *3, *5). Genotyping was performed by real-time PCR with melting curve analysis and confirmed by bi-directional sequencing. We find an almost complete spectrum of genotypic constellations within these 38 cell lines. About 12 cell lines appear sufficient as genotypic controls for the 11 SNP assays by covering almost all of the genotypes. However, hetero- and homozygous genotypes for FII and the alleles TPMT*2, UGT1A1*37 and CYP2C9*5 were not detected in any of the cell lines. DNA from most of the examined cell lines appear suitable as quality controls for these SNP assays in the laboratory routine, as to the implementation of those assays or to prepare samples for quality assurance schemes. Our study may serve as a pilot to further characterize these cell lines to arrive at the status of reference materials.

  3. Evaluation of customised lineage-specific sets of MIRU-VNTR loci for genotyping Mycobacterium tuberculosis complex isolates in Ghana.

    Science.gov (United States)

    Asante-Poku, Adwoa; Nyaho, Michael Selasi; Borrell, Sonia; Comas, Iñaki; Gagneux, Sebastien; Yeboah-Manu, Dorothy

    2014-01-01

    Different combinations of variable number of tandem repeat (VNTR) loci have been proposed for genotyping Mycobacterium tuberculosis complex (MTBC). Existing VNTR schemes show different discriminatory capacity among the six human MTBC lineages. Here, we evaluated the discriminatory power of a "customized MIRU12" loci format proposed previously by Comas et al. based on the standard 24 loci defined by Supply et al. for VNTR-typing of MTBC in Ghana. One hundred and fifty-eight MTBC isolates classified into Lineage 4 and Lineage 5 were used to compare a customized lineage-specific panel of 12 MIRU-VNTR loci ("customized MIRU-12") to the standard MIRU-15 genotyping scheme. The resolution power of each typing method was determined based on the Hunter-Gaston- Discriminatory Index (HGDI). A minimal set of customized MIRU-VNTR loci for typing Lineages 4 (Euro-American) and 5 (M. africanum West African 1) strains from Ghana was defined based on the cumulative HGDI. Among the 106 Lineage 4 strains, the customized MIRU-12 identified a total of 104 distinct genotypes consisting of 2 clusters of 2 isolates each (clustering rate 1.8%), and 102 unique strains while standard MIRU-15 yielded a total of 105 different genotypes, including 1 cluster of 2 isolates (clustering rate: 0.9%) and 104 singletons. Among, 52 Lineage 5 isolates, customized MIRU-12 genotyping defined 51 patterns with 1 cluster of 2 isolates (clustering rate: 0.9%) and 50 unique strains whereas MIRU-15 classified all 52 strains as unique. Cumulative HGDI values for customized MIRU-12 for Lineages 4 and 5 were 0.98 respectively whilst that of standard MIRU-15 was 0.99. A union of loci from the customised MIRU-12 and standard MIRU-15 revealed a set of customized eight highly discriminatory loci: 4052, 2163B, 40, 4165, 2165, 10,16 and 26 with a cumulative HGDI of 0.99 for genotyping Lineage 4 and 5 strains from Ghana.

  4. Labelling schemes: From a consumer perspective

    DEFF Research Database (Denmark)

    Juhl, Hans Jørn; Stacey, Julia

    2000-01-01

    Labelling of food products attracts a lot of political attention these days. As a result of a number of food scandals, most European countries have acknowledged the need for more information and better protection of consumers. Labelling schemes are one way of informing and guiding consumers....... However, initiatives in relation to labelling schemes seldom take their point of departure in consumers' needs and expectations; and in many cases, the schemes are defined by the institutions guaranteeing the label. It is therefore interesting to study how consumers actually value labelling schemes....... A recent MAPP study has investigated the value consumers attach the Government-controlled labels 'Ø-mærket' and 'Den Blå Lup' and the private supermarket label 'Mesterhakket' when they purchase minced meat. The results reveal four consumer segments that use labelling schemes for food products very...

  5. Birkhoffian Symplectic Scheme for a Quantum System

    International Nuclear Information System (INIS)

    Su Hongling

    2010-01-01

    In this paper, a classical system of ordinary differential equations is built to describe a kind of n-dimensional quantum systems. The absorption spectrum and the density of the states for the system are defined from the points of quantum view and classical view. From the Birkhoffian form of the equations, a Birkhoffian symplectic scheme is derived for solving n-dimensional equations by using the generating function method. Besides the Birkhoffian structure-preserving, the new scheme is proven to preserve the discrete local energy conservation law of the system with zero vector f. Some numerical experiments for a 3-dimensional example show that the new scheme can simulate the general Birkhoffian system better than the implicit midpoint scheme, which is well known to be symplectic scheme for Hamiltonian system. (general)

  6. Autonomous droop scheme with reduced generation cost

    DEFF Research Database (Denmark)

    Nutkani, Inam Ullah; Loh, Poh Chiang; Blaabjerg, Frede

    2013-01-01

    Droop scheme has been widely applied to the control of Distributed Generators (DGs) in microgrids for proportional power sharing based on their ratings. For standalone microgrid, where centralized management system is not viable, the proportional power sharing based droop might not suit well since...... DGs are usually of different types unlike synchronous generators. This paper presents an autonomous droop scheme that takes into consideration the operating cost, efficiency and emission penalty of each DG since all these factors directly or indirectly contributes to the Total Generation Cost (TGC......) of the overall microgrid. Comparing it with the traditional scheme, the proposed scheme has retained its simplicity, which certainly is a feature preferred by the industry. The overall performance of the proposed scheme has been verified through simulation and experiment....

  7. The maturing of microbial ecology.

    Science.gov (United States)

    Schmidt, Thomas M

    2006-09-01

    A.J. Kluyver and C.B. van Niel introduced many scientists to the exceptional metabolic capacity of microbes and their remarkable ability to adapt to changing environments in The Microbe's Contribution to Biology. Beyond providing an overview of the physiology and adaptability of microbes, the book outlined many of the basic principles for the emerging discipline of microbial ecology. While the study of pure cultures was highlighted, provided a unifying framework for understanding the vast metabolic potential of microbes and their roles in the global cycling of elements, extrapolation from pure cultures to natural environments has often been overshadowed by microbiologists inability to culture many of the microbes seen in natural environments. A combination of genomic approaches is now providing a culture-independent view of the microbial world, revealing a more diverse and dynamic community of microbes than originally anticipated. As methods for determining the diversity of microbial communities become increasingly accessible, a major challenge to microbial ecologists is to link the structure of natural microbial communities with their functions. This article presents several examples from studies of aquatic and terrestrial microbial communities in which culture and culture-independent methods are providing an enhanced appreciation for the microbe's contribution to the evolution and maintenance of life on Earth, and offers some thoughts about the graduate-level educational programs needed to enhance the maturing field of microbial ecology.

  8. Global microbialization of coral reefs.

    Science.gov (United States)

    Haas, Andreas F; Fairoz, Mohamed F M; Kelly, Linda W; Nelson, Craig E; Dinsdale, Elizabeth A; Edwards, Robert A; Giles, Steve; Hatay, Mark; Hisakawa, Nao; Knowles, Ben; Lim, Yan Wei; Maughan, Heather; Pantos, Olga; Roach, Ty N F; Sanchez, Savannah E; Silveira, Cynthia B; Sandin, Stuart; Smith, Jennifer E; Rohwer, Forest

    2016-04-25

    Microbialization refers to the observed shift in ecosystem trophic structure towards higher microbial biomass and energy use. On coral reefs, the proximal causes of microbialization are overfishing and eutrophication, both of which facilitate enhanced growth of fleshy algae, conferring a competitive advantage over calcifying corals and coralline algae. The proposed mechanism for this competitive advantage is the DDAM positive feedback loop (dissolved organic carbon (DOC), disease, algae, microorganism), where DOC released by ungrazed fleshy algae supports copiotrophic, potentially pathogenic bacterial communities, ultimately harming corals and maintaining algal competitive dominance. Using an unprecedented data set of >400 samples from 60 coral reef sites, we show that the central DDAM predictions are consistent across three ocean basins. Reef algal cover is positively correlated with lower concentrations of DOC and higher microbial abundances. On turf and fleshy macroalgal-rich reefs, higher relative abundances of copiotrophic microbial taxa were identified. These microbial communities shift their metabolic potential for carbohydrate degradation from the more energy efficient Embden-Meyerhof-Parnas pathway on coral-dominated reefs to the less efficient Entner-Doudoroff and pentose phosphate pathways on algal-dominated reefs. This 'yield-to-power' switch by microorganism directly threatens reefs via increased hypoxia and greater CO2 release from the microbial respiration of DOC.

  9. Microbial biosensors for environmental monitoring

    Directory of Open Access Journals (Sweden)

    David VOGRINC

    2015-12-01

    Full Text Available Microbial biosensors are analytical devices capable of sensing substances in the environment due to the specific biological reaction of the microorganism or its parts. Construction of a microbial biosensor requires knowledge of microbial response to the specific analyte. Linking this response with the quantitative data, using a transducer, is the crucial step in the construction of a biosensor. Regarding the transducer type, biosensors are divided into electrochemical, optical biosensors and microbial fuel cells. The use of the proper configuration depends on the selection of the biosensing element. With the use of transgenic E. coli strains, bioluminescence or fluorescence based biosensors were developed. Microbial fuel cells enable the use of the heterogeneous microbial populations, isolated from wastewater. Different microorganisms are used for different pollutants – pesticides, heavy metals, phenolic compounds, organic waste, etc. Biosensing enables measurement of their concentration and their toxic or genotoxic effects on the microbes. Increasing environmental awareness has contributed to the increase of interest for biomonitoring. Although technologies, such as bioinformatics and genetic engineering, allow us to design complex and efficient microbial biosensors for environmental pollutants, the transfer of the laboratory work to the field still remains a problem to solve.

  10. Microbial electrode sensor for alcohols

    Energy Technology Data Exchange (ETDEWEB)

    Hikuma, M [Ajinomoto Co., Inc., Kawasaki, Japan; Kubo, T; Yasuda, T; Karube, I; Suzuki, S

    1979-10-01

    A microbial electrode consisting of immobilized microorganisms, a gas permeable Teflon membrane, and an oxygen electrode was prepared for the continuous determination of methyl and ethyl alcohols. Immobilized Trichosporon brassicae was employed for a microbial electrode sensor for ethyl alcohol. When a sample solution containing ethyl alcohol was injected into a microbial electrode system, the current of the electrode decreased markedly with time until a steady state was reached. The response time was within 10 min by the steady state method and within 6 min by the pulse method. A linear relationship was observed between the current decrease and the concentration of ethyl alcohol below 22.5 mg/liter. The current was reproducible within +- 6% of the relative error when a sample solution containing 16.5 mg/liter ethyl alcohol. The standard deviation was 0.5 mg/liter in 40 experiments. The selectivity of the microbial electrode sensor for ethyl alcohol was satisfactory. The microbial electrode sensor was applied to a fermentation broth of yeasts and satisfactory comparative results were obtained (correlation coefficient 0.98). The current output of the microbial electrode sensor was almost constant for more than three weeks and 2100 assays. A microbial electrode sensor using immobilized bacteria for methyl alcohol was also described.

  11. Exact analysis of Packet Reversed Packet Combining Scheme and Modified Packet Combining Scheme; and a combined scheme

    International Nuclear Information System (INIS)

    Bhunia, C.T.

    2007-07-01

    Packet combining scheme is a well defined simple error correction scheme for the detection and correction of errors at the receiver. Although it permits a higher throughput when compared to other basic ARQ protocols, packet combining (PC) scheme fails to correct errors when errors occur in the same bit locations of copies. In a previous work, a scheme known as Packet Reversed Packet Combining (PRPC) Scheme that will correct errors which occur at the same bit location of erroneous copies, was studied however PRPC does not handle a situation where a packet has more than 1 error bit. The Modified Packet Combining (MPC) Scheme that can correct double or higher bit errors was studied elsewhere. Both PRPC and MPC schemes are believed to offer higher throughput in previous studies, however neither adequate investigation nor exact analysis was done to substantiate this claim of higher throughput. In this work, an exact analysis of both PRPC and MPC is carried out and the results reported. A combined protocol (PRPC and MPC) is proposed and the analysis shows that it is capable of offering even higher throughput and better error correction capability at high bit error rate (BER) and larger packet size. (author)

  12. Analysis of central and upwind compact schemes

    International Nuclear Information System (INIS)

    Sengupta, T.K.; Ganeriwal, G.; De, S.

    2003-01-01

    Central and upwind compact schemes for spatial discretization have been analyzed with respect to accuracy in spectral space, numerical stability and dispersion relation preservation. A von Neumann matrix spectral analysis is developed here to analyze spatial discretization schemes for any explicit and implicit schemes to investigate the full domain simultaneously. This allows one to evaluate various boundary closures and their effects on the domain interior. The same method can be used for stability analysis performed for the semi-discrete initial boundary value problems (IBVP). This analysis tells one about the stability for every resolved length scale. Some well-known compact schemes that were found to be G-K-S and time stable are shown here to be unstable for selective length scales by this analysis. This is attributed to boundary closure and we suggest special boundary treatment to remove this shortcoming. To demonstrate the asymptotic stability of the resultant schemes, numerical solution of the wave equation is compared with analytical solution. Furthermore, some of these schemes are used to solve two-dimensional Navier-Stokes equation and a computational acoustic problem to check their ability to solve problems for long time. It is found that those schemes, that were found unstable for the wave equation, are unsuitable for solving incompressible Navier-Stokes equation. In contrast, the proposed compact schemes with improved boundary closure and an explicit higher-order upwind scheme produced correct results. The numerical solution for the acoustic problem is compared with the exact solution and the quality of the match shows that the used compact scheme has the requisite DRP property

  13. ALIS-FLP: Amplified ligation selected fragment-length polymorphism method for microbial genotyping

    DEFF Research Database (Denmark)

    Brillowska-Dabrowska, A.; Wianecka, M.; Dabrowski, Slawomir

    2008-01-01

    A DNA fingerprinting method known as ALIS-FLP (amplified ligation selected fragment-length polymorphism) has been developed for selective and specific amplification of restriction fragments from TspRI restriction endonuclease digested genomic DNA. The method is similar to AFLP, but differs...

  14. Saponin profile of green asparagus genotypes.

    Science.gov (United States)

    Vázquez-Castilla, Sara; Jaramillo-Carmona, Sara; Fuentes-Alventosa, Jose María; Jiménez-Araujo, Ana; Rodríguez-Arcos, Rocío; Cermeño-Sacristán, Pedro; Espejo-Calvo, Juan Antonio; Guillén-Bejarano, Rafael

    2013-11-20

    The main goal of this study was to determine the saponin profiles of different "triguero" asparagus genotypes and to compare them to green asparagus commercial hybrids. The samples consisted of 31 commercial hybrids and 58 genotypes from the Huétor-Tájar (HT) population variety ("triguero"). The saponin analysis by high-performance liquid chromatography-mass spectrometry allowed for the determination of 12 saponins derived from a furostan-type steroidal genin, 4 of which had never been described in the edible part of asparagus. The saponin profile of "triguero" asparagus was a combination of these new saponins and protodioscin. Although protodioscin was the major saponin found in commercial hybrids, some of these 12 saponins were detected as major components in some of the commercial hybrids. The total contents of saponins described in some of these HT genotypes reach values as high as 10-100 times higher than those found in commercial hybrids.

  15. Carcass traits of four rabbit genotypes

    Directory of Open Access Journals (Sweden)

    Ajda Kermauner

    2010-01-01

    Full Text Available Seventy-three rabbits of four genotypes (A - SIKA maternal line; C - SIKA sire line; AxC - hybrids between line A and C; AxCal - crossbreds between line A and the Californian breed were used to evaluate the effect of genotype on carcass traits. Rabbits were weaned at 35 days and slaughtered at 93 days of age. Rabbits were fed standard feed mixture ad libitum. The highest live weight at slaughter and dressing percentage was achieved by line C, and the lowest in line A. Hybrids between line A and C exhibited slightly worse carcass traits than rabbits in line C, but the differences were not statistically significant. The Californian breed gave worse results than crossbreeding with line C, though in most cases the differences between AxC and AxCal were not significant. The differences between genotypes in hind leg tissue composition, pH and meat colour were not statistically significant.

  16. The microbial ecology of permafrost

    DEFF Research Database (Denmark)

    Jansson, Janet; Tas, Neslihan

    2014-01-01

    Permafrost constitutes a major portion of the terrestrial cryosphere of the Earth and is a unique ecological niche for cold-adapted microorganisms. There is a relatively high microbial diversity in permafrost, although there is some variation in community composition across different permafrost......-gas emissions. This Review describes new data on the microbial ecology of permafrost and provides a platform for understanding microbial life strategies in frozen soil as well as the impact of climate change on permafrost microorganisms and their functional roles....

  17. Defining Disturbance for Microbial Ecology.

    Science.gov (United States)

    Plante, Craig J

    2017-08-01

    Disturbance can profoundly modify the structure of natural communities. However, microbial ecologists' concept of "disturbance" has often deviated from conventional practice. Definitions (or implicit usage) have frequently included climate change and other forms of chronic environmental stress, which contradict the macrobiologist's notion of disturbance as a discrete event that removes biomass. Physical constraints and disparate biological characteristics were compared to ask whether disturbances fundamentally differ in microbial and macroorganismal communities. A definition of "disturbance" for microbial ecologists is proposed that distinguishes from "stress" and other competing terms, and that is in accord with definitions accepted by plant and animal ecologists.

  18. Genotype x environment interaction for grain yield of wheat genotypes tested under water stress conditions

    International Nuclear Information System (INIS)

    Sail, M.A.; Dahot, M.U.; Mangrio, S.M.; Memon, S.

    2007-01-01

    Effect of water stress on grain yield in different wheat genotypes was studied under field conditions at various locations. Grain yield is a complex polygenic trait influenced by genotype, environment and genotype x environment (GxE) interaction. To understand the stability among genotypes for grain yield, twenty-one wheat genotypes developed Through hybridization and radiation-induced mutations at Nuclear Institute of Agriculture (NIA) TandoJam were evaluated with four local check varieties (Sarsabz, Thori, Margalla-99 and Chakwal-86) in multi-environmental trails (MET/sub s/). The experiments were conducted over 5 different water stress environments in Sindh. Data on grain yield were recorded from each site and statistically analyzed. Combined analysis of variance for all the environments indicated that the genotype, environment and genotype x environment (GxE) interaction were highly significant (P greater then 0.01) for grain yield. Genotypes differed in their response to various locations. The overall highest site mean yield (4031 kg/ha) recorded at Moro and the lowest (2326 kg/ha) at Thatta. Six genotypes produced significantly (P=0.01) the highest grain yield overall the environments. Stability analysis was applied to estimate stability parameters viz., regression coefficient (b), standard error of regression coefficient and variance due to deviation from regression (S/sub 2/d) genotypes 10/8, BWS-78 produced the highest mean yield over all the environments with low regression coefficient (b=0.68, 0.67 and 0.63 respectively and higher S/sup 2/ d value, showing specific adaptation to poor (un favorable) environments. Genotype 8/7 produced overall higher grain yield (3647 kg/ha) and ranked as third high yielding genotype had regression value close to unity (b=0.9) and low S/sup d/ value, indicating more stability and wide adaptation over the all environments. The knowledge of the presence and magnitude of genotype x environment (GE) interaction is important to

  19. Oilseed rape genotypes response to boron toxicity

    Directory of Open Access Journals (Sweden)

    Savić Jasna

    2013-01-01

    Full Text Available Response of 16 oilseed rape genotypes to B (boron toxicity was analyzed by comparing the results of two experiments conducted in a glasshouse. In Experiment 1 plants were grown in standard nutrient solutions with 10 µMB (control and 1000 µM B. Relative root and shoot growth varied from 20-120% and 31-117%, respectively. Variation in B concentration in shoots was also wide (206.5-441.7 µg B g-1 DW as well as total B uptake by plant (62.3-281.2 µg B g1. Four selected genotypes were grown in Experiment 2 in pots filled with high B soil (8 kg ha-1 B; B8. Shoot growth was not affected by B8 treatment, while root and shoot B concentration was significantly increased compared to control. Genotypes Panther and Pronto which performed low relative root and shoot growth and high B accumulation in plants in Experiment 1, had good growth in B8 treatment. In Experiment 2 genotype NS-L-7 had significantly lower B concentration in shots under treatment B8, but also very high B accumulation in Experiment 1. In addition, cluster analyses classified genotypes in three groups according to traits contrasting in their significance for analyzing response to B toxicity. The first group included four varieties based on their shared characteristics that have small value for the relative growth of roots and shoots and large values of B concentration in shoot. In the second largest group were connected ten genotypes that are heterogeneous in traits and do not stand out on any characteristic. Genotypes NS-L-7 and Navajo were separated in the third group because they had big relative growth of root and shoot, but also a high concentration of B in the shoot, and high total B uptake. Results showed that none of tested genotypes could not be recommended for breeding process to tolerance for B toxicity. [Projekat Ministarstva nauke Republike Srbije, br. OI 173028

  20. Microbial ecology-based engineering of Microbial Electrochemical Technologies.

    Science.gov (United States)

    Koch, Christin; Korth, Benjamin; Harnisch, Falk

    2018-01-01

    Microbial ecology is devoted to the understanding of dynamics, activity and interaction of microorganisms in natural and technical ecosystems. Bioelectrochemical systems represent important technical ecosystems, where microbial ecology is of highest importance for their function. However, whereas aspects of, for example, materials and reactor engineering are commonly perceived as highly relevant, the study and engineering of microbial ecology are significantly underrepresented in bioelectrochemical systems. This shortfall may be assigned to a deficit on knowledge and power of these methods as well as the prerequisites for their thorough application. This article discusses not only the importance of microbial ecology for microbial electrochemical technologies but also shows which information can be derived for a knowledge-driven engineering. Instead of providing a comprehensive list of techniques from which it is hard to judge the applicability and value of information for a respective one, this review illustrates the suitability of selected techniques on a case study. Thereby, best practice for different research questions is provided and a set of key questions for experimental design, data acquisition and analysis is suggested. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  1. Symmetric weak ternary quantum homomorphic encryption schemes

    Science.gov (United States)

    Wang, Yuqi; She, Kun; Luo, Qingbin; Yang, Fan; Zhao, Chao

    2016-03-01

    Based on a ternary quantum logic circuit, four symmetric weak ternary quantum homomorphic encryption (QHE) schemes were proposed. First, for a one-qutrit rotation gate, a QHE scheme was constructed. Second, in view of the synthesis of a general 3 × 3 unitary transformation, another one-qutrit QHE scheme was proposed. Third, according to the one-qutrit scheme, the two-qutrit QHE scheme about generalized controlled X (GCX(m,n)) gate was constructed and further generalized to the n-qutrit unitary matrix case. Finally, the security of these schemes was analyzed in two respects. It can be concluded that the attacker can correctly guess the encryption key with a maximum probability pk = 1/33n, thus it can better protect the privacy of users’ data. Moreover, these schemes can be well integrated into the future quantum remote server architecture, and thus the computational security of the users’ private quantum information can be well protected in a distributed computing environment.

  2. Ponzi scheme diffusion in complex networks

    Science.gov (United States)

    Zhu, Anding; Fu, Peihua; Zhang, Qinghe; Chen, Zhenyue

    2017-08-01

    Ponzi schemes taking the form of Internet-based financial schemes have been negatively affecting China's economy for the last two years. Because there is currently a lack of modeling research on Ponzi scheme diffusion within social networks yet, we develop a potential-investor-divestor (PID) model to investigate the diffusion dynamics of Ponzi scheme in both homogeneous and inhomogeneous networks. Our simulation study of artificial and real Facebook social networks shows that the structure of investor networks does indeed affect the characteristics of dynamics. Both the average degree of distribution and the power-law degree of distribution will reduce the spreading critical threshold and will speed up the rate of diffusion. A high speed of diffusion is the key to alleviating the interest burden and improving the financial outcomes for the Ponzi scheme operator. The zero-crossing point of fund flux function we introduce proves to be a feasible index for reflecting the fast-worsening situation of fiscal instability and predicting the forthcoming collapse. The faster the scheme diffuses, the higher a peak it will reach and the sooner it will collapse. We should keep a vigilant eye on the harm of Ponzi scheme diffusion through modern social networks.

  3. Optimal Face-Iris Multimodal Fusion Scheme

    Directory of Open Access Journals (Sweden)

    Omid Sharifi

    2016-06-01

    Full Text Available Multimodal biometric systems are considered a way to minimize the limitations raised by single traits. This paper proposes new schemes based on score level, feature level and decision level fusion to efficiently fuse face and iris modalities. Log-Gabor transformation is applied as the feature extraction method on face and iris modalities. At each level of fusion, different schemes are proposed to improve the recognition performance and, finally, a combination of schemes at different fusion levels constructs an optimized and robust scheme. In this study, CASIA Iris Distance database is used to examine the robustness of all unimodal and multimodal schemes. In addition, Backtracking Search Algorithm (BSA, a novel population-based iterative evolutionary algorithm, is applied to improve the recognition accuracy of schemes by reducing the number of features and selecting the optimized weights for feature level and score level fusion, respectively. Experimental results on verification rates demonstrate a significant improvement of proposed fusion schemes over unimodal and multimodal fusion methods.

  4. Microbial Cell Imaging

    Energy Technology Data Exchange (ETDEWEB)

    Doktycz, Mitchel John [ORNL; Sullivan, Claretta [Eastern Virginia Medical School; Mortensen, Ninell P [ORNL; Allison, David P [ORNL

    2011-01-01

    limitation on the maximum scan size (roughly 100 x 100 {mu}m) and the restricted movement of the cantilever in the Z (or height) direction. In most commercial AFMs, the Z range is restricted to roughly 10 {mu}m such that the height of cells to be imaged must be seriously considered. Nevertheless, AFM can provide structural-functional information at nanometer resolution and do so in physiologically relevant environments. Further, instrumentation for scanning probe microscopy continues to advance. Systems for high-speed imaging are becoming available, and techniques for looking inside the cells are being demonstrated. The ability to combine AFM with other imaging modalities is likely to have an even greater impact on microbiological studies. AFM studies of intact microbial cells started to appear in the literature in the 1990s. For example, AFM studies of Saccharomyces cerevisiae examined buddings cars after cell division and detailed changes related to cell growth processes. Also, the first AFM studies of bacterial biofilms appeared. In the late 1990s, AFM studies of intact fungal spores described clear changes in spore surfaces upon germination, and studies of individual bacterial cells were also described. These early bacterial imaging studies examined changes in bacterial morphology due to antimicrobial peptides exposure and bacterial adhesion properties. The majority of these early studies were carried out on dried samples and took advantage of the resolving power of AFM. The lack of cell mounting procedures presented an impediment for cell imaging studies. Subsequently, several approaches to mounting microbial cells have been developed, and these techniques are described later. Also highlighted are general considerations for microbial imaging and a description of some of the various applications of AFM to microbiology.

  5. MICROBIAL MATS - A JOINT VENTURE

    NARCIS (Netherlands)

    VANGEMERDEN, H

    Microbial mats characteristically are dominated by a few functional groups of microbes: cyanobacteria, colorless sulfur bacteria, purple sulfur bacteria, and sulfate-reducing bacteria. Their combined metabolic activities result in steep environmental microgradients, particularly of oxygen and

  6. Microbial production of gaseous hydrocarbons

    Energy Technology Data Exchange (ETDEWEB)

    Fukuda, Hideo

    1987-10-20

    Microbial production of ethylene, isobutane and a saturated gaseous hydrocarbon mixture was described. Microbial ethylene production was studied with Penicillium digitatum IFO 9372 and a novel pathway of the ethylene biosynthesis through alpha-ketoglutarate was proposed. Rhodotorula minuta IFO 1102 was selected for the microbial production of isobutane and the interesting actions of L-leucine and L-phenylalanine for the isobutane production were found. It was finally presented about the microbial production of a saturated gaseous hydrocarbon mixture with Rhizopus japonicus IFO 4758 was described. A gas mixture was produced through a chemical reaction of SH compounds and some cellular component such as squalene under aerobic conditions. (4 figs, 7 tabs, 41 refs)

  7. Seasonality in ocean microbial communities.

    Science.gov (United States)

    Giovannoni, Stephen J; Vergin, Kevin L

    2012-02-10

    Ocean warming occurs every year in seasonal cycles that can help us to understand long-term responses of plankton to climate change. Rhythmic seasonal patterns of microbial community turnover are revealed when high-resolution measurements of microbial plankton diversity are applied to samples collected in lengthy time series. Seasonal cycles in microbial plankton are complex, but the expansion of fixed ocean stations monitoring long-term change and the development of automated instrumentation are providing the time-series data needed to understand how these cycles vary across broad geographical scales. By accumulating data and using predictive modeling, we gain insights into changes that will occur as the ocean surface continues to warm and as the extent and duration of ocean stratification increase. These developments will enable marine scientists to predict changes in geochemical cycles mediated by microbial communities and to gauge their broader impacts.

  8. Microbial safety of foods

    International Nuclear Information System (INIS)

    Bandekar, J.R.

    2013-01-01

    Despite advances in hygiene, consumer knowledge and food treatment and processing, food-borne diseases have become one of the most widespread public health problems in the world to-day. About two thirds of all outbreaks are traced to microbial contaminated food - one of the most hazardous being Clostridium botulinum, E. coli 0157: H7 and Salmonella. The pathogens can be introduced in the food products anywhere in the food chain and hence it is of prime important to have microbial vigilance in the entire food chain. WHO estimates that food-borne and water-borne diarrhoeal diseases taken together kill about 2.2 million people annually. The infants, children, elderly and immune-compromised people are particularly susceptible to food-borne diseases. Unsafe food causes many acute and life-long diseases, ranging from diarrhoeal diseases to various forms of cancer. A number of factors such as emergence of new food-borne pathogens, development of drug resistance in the pathogens, changing life style, global trade of food etc. are responsible for the continued persistence of food-borne diseases. Due to consumer demand, a number of Ready-To-Eat (RTE) minimally processed foods are increasingly marketed. However, there is increased risk of food-borne diseases with these products. The food-borne disease outbreaks due to E. coli O157:H7, Listeria monocytogenes, Salmonella and Campylobacter are responsible for recall of many foods resulting in heavy losses to food industry. The development of multi drug resistant pathogens due to indiscriminate use of antibiotics is also a major problem. Food Technology Division of Bhabha Atomic Research Centre has been working on food-borne bacterial pathogens particularly Salmonella, Campylobacter, Vibrio and Aeromonas species, their prevalence in export quality seafood as well in foods sold in retail market such as poultry, fish, sprouts and salads. These pathogens from Indian foods have been characterized for the presence of virulence genes

  9. Microbially mediated mineral carbonation

    Science.gov (United States)

    Power, I. M.; Wilson, S. A.; Dipple, G. M.; Southam, G.

    2010-12-01

    Mineral carbonation involves silicate dissolution and carbonate precipitation, which are both natural processes that microorganisms are able to mediate in near surface environments (Ferris et al., 1994; Eq. 1). (Ca,Mg)SiO3 + 2H2CO3 + H2O → (Ca,Mg)CO3 + H2O + H4SiO4 + O2 (1) Cyanobacteria are photoautotrophs with cell surface characteristics and metabolic processes involving inorganic carbon that can induce carbonate precipitation. This occurs partly by concentrating cations within their net-negative cell envelope and through the alkalinization of their microenvironment (Thompson & Ferris, 1990). Regions with mafic and ultramafic bedrock, such as near Atlin, British Columbia, Canada, represent the best potential sources of feedstocks for mineral carbonation. The hydromagnesite playas near Atlin are a natural biogeochemical model for the carbonation of magnesium silicate minerals (Power et al., 2009). Field-based studies at Atlin and corroborating laboratory experiments demonstrate the ability of a microbial consortium dominated by filamentous cyanobacteria to induce the precipitation of carbonate minerals. Phototrophic microbes, such as cyanobacteria, have been proposed as a means for producing biodiesel and other value added products because of their efficiency as solar collectors and low requirement for valuable, cultivable land in comparison to crops (Dismukes et al., 2008). Carbonate precipitation and biomass production could be facilitated using specifically designed ponds to collect waters rich in dissolved cations (e.g., Mg2+ and Ca2+), which would allow for evapoconcentration and provide an appropriate environment for growth of cyanobacteria. Microbially mediated carbonate precipitation does not require large quantities of energy or chemicals needed for industrial systems that have been proposed for rapid carbon capture and storage via mineral carbonation (e.g., Lackner et al., 1995). Therefore, this biogeochemical approach may represent a readily

  10. The effectiveness of different antiviral treatment regimens in patients with chronic hepatitis C infected with genotype 3 virus

    Directory of Open Access Journals (Sweden)

    E.V. Riabokon

    2018-02-01

    Full Text Available Background. Chronic hepatitis C (CHC remains one of the most urgent problems of modern infectology. In recent years, the principles of antiviral therapy have substantially changed due to the emergence of new drugs with a direct mechanism of action and the development of non-interferon treatment regimens. Two regimens included HCV NS5B polymerase inhibitors were available in Ukraine for treating CHC patients infected with genotype 3 virus. Objective: to analyze the effectiveness of different schemes of antiviral treatment in patients with chronic hepatitis C infected with genotype 3 virus. Materials and methods. The study included 66 patients with CHC infected with genotype 3 virus. All patients underwent study of liver fibrosis degree by the method of fibrotest; in the dynamics, we have tested viral load, liver tests, indicators of complete blood count, functional kidney tests. Antiviral treatment and analysis of its effectiveness were carried out in accordance with the Unified Protocol of the Ministry of Health of Ukraine. Results. According to the results of treating CHC patients infected with genotype 3 virus, high efficacy of both applied schemes of antiviral therapy in clinical practice is shown. A rapid virologic response occurred in 93.5 % of CHC patients treated with peginterferon (peg-IFN α2a + sofosbuvir (SOF + ribavirin (RBV regimen, and in 82.9 % of patients receiving non-interferon therapy with SOF + RBV. The immediate response to treatment was achieved according to treatment regimens in 90.3 and 94.3 % of patients. Sustained virological response at week 24 after antiviral treatment was noted in 87.5 and 91.4 % of patients, respectively. The frequency of virological response to antiviral treatment in CHC patients infected with genotype 3 virus did not depend on the stage of liver fibrosis, either in the use of non-interferon treatment by SOF + RBV scheme, or in the treatment with interferon-containing scheme included the drug with

  11. Multidimensional flux-limited advection schemes

    International Nuclear Information System (INIS)

    Thuburn, J.

    1996-01-01

    A general method for building multidimensional shape preserving advection schemes using flux limiters is presented. The method works for advected passive scalars in either compressible or incompressible flow and on arbitrary grids. With a minor modification it can be applied to the equation for fluid density. Schemes using the simplest form of the flux limiter can cause distortion of the advected profile, particularly sideways spreading, depending on the orientation of the flow relative to the grid. This is partly because the simple limiter is too restrictive. However, some straightforward refinements lead to a shape-preserving scheme that gives satisfactory results, with negligible grid-flow angle-dependent distortion

  12. Finite-volume scheme for anisotropic diffusion

    Energy Technology Data Exchange (ETDEWEB)

    Es, Bram van, E-mail: bramiozo@gmail.com [Centrum Wiskunde & Informatica, P.O. Box 94079, 1090GB Amsterdam (Netherlands); FOM Institute DIFFER, Dutch Institute for Fundamental Energy Research, The Netherlands" 1 (Netherlands); Koren, Barry [Eindhoven University of Technology (Netherlands); Blank, Hugo J. de [FOM Institute DIFFER, Dutch Institute for Fundamental Energy Research, The Netherlands" 1 (Netherlands)

    2016-02-01

    In this paper, we apply a special finite-volume scheme, limited to smooth temperature distributions and Cartesian grids, to test the importance of connectivity of the finite volumes. The area of application is nuclear fusion plasma with field line aligned temperature gradients and extreme anisotropy. We apply the scheme to the anisotropic heat-conduction equation, and compare its results with those of existing finite-volume schemes for anisotropic diffusion. Also, we introduce a general model adaptation of the steady diffusion equation for extremely anisotropic diffusion problems with closed field lines.

  13. Vector domain decomposition schemes for parabolic equations

    Science.gov (United States)

    Vabishchevich, P. N.

    2017-09-01

    A new class of domain decomposition schemes for finding approximate solutions of timedependent problems for partial differential equations is proposed and studied. A boundary value problem for a second-order parabolic equation is used as a model problem. The general approach to the construction of domain decomposition schemes is based on partition of unity. Specifically, a vector problem is set up for solving problems in individual subdomains. Stability conditions for vector regionally additive schemes of first- and second-order accuracy are obtained.

  14. The new WAGR data acquisition scheme

    International Nuclear Information System (INIS)

    Ellis, W.E.; Leng, J.H.; Smith, I.C.; Smith, M.R.

    1976-06-01

    The existing WAGR data acquisition equipment was inadequate to meet the requirements introduced by the installation of two additional experimental loops and was in any case due for replacement. A completely new scheme was planned and implemented based on mini-computers, which while preserving all the useful features of the old scheme provided additional flexibility and improved data display. Both the initial objectives of the design and the final implementation are discussed without introducing detailed descriptions of hardware or the programming techniques employed. Although the scheme solves a specific problem the general principles are more widely applicable and could readily be adapted to other data checking and display problems. (author)

  15. Kinematic reversal schemes for the geomagnetic dipole.

    Science.gov (United States)

    Levy, E. H.

    1972-01-01

    Fluctuations in the distribution of cyclonic convective cells, in the earth's core, can reverse the sign of the geomagnetic field. Two kinematic reversal schemes are discussed. In the first scheme, a field maintained by cyclones concentrated at low latitude is reversed by a burst of cyclones at high latitude. Conversely, in the second scheme, a field maintained predominantly by cyclones in high latitudes is reversed by a fluctuation consisting of a burst of cyclonic convection at low latitude. The precise fluid motions which produce the geomagnetic field are not known. However, it appears that, whatever the details are, a fluctuation in the distribution of cyclonic cells over latitude can cause a geomagnetic reversal.

  16. Autonomous Droop Scheme With Reduced Generation Cost

    DEFF Research Database (Denmark)

    Nutkani, Inam Ullah; Loh, Poh Chiang; Wang, Peng

    2014-01-01

    ) of the microgrid. To reduce this TGC without relying on fast communication links, an autonomous droop scheme is proposed here, whose resulting power sharing is decided by the individual DG generation costs. Comparing it with the traditional scheme, the proposed scheme retains its simplicity and it is hence more....... This objective might, however, not suit microgrids well since DGs are usually of different types, unlike synchronous generators. Other factors like cost, efficiency, and emission penalty of each DG at different loading must be considered since they contribute directly to the total generation cost (TGC...

  17. Cognitive radio networks dynamic resource allocation schemes

    CERN Document Server

    Wang, Shaowei

    2014-01-01

    This SpringerBrief presents a survey of dynamic resource allocation schemes in Cognitive Radio (CR) Systems, focusing on the spectral-efficiency and energy-efficiency in wireless networks. It also introduces a variety of dynamic resource allocation schemes for CR networks and provides a concise introduction of the landscape of CR technology. The author covers in detail the dynamic resource allocation problem for the motivations and challenges in CR systems. The Spectral- and Energy-Efficient resource allocation schemes are comprehensively investigated, including new insights into the trade-off

  18. Algebraic K-theory of generalized schemes

    DEFF Research Database (Denmark)

    Anevski, Stella Victoria Desiree

    and geometry over the field with one element. It also permits the construction of important Arakelov theoretical objects, such as the completion \\Spec Z of Spec Z. In this thesis, we prove a projective bundle theorem for the eld with one element and compute the Chow rings of the generalized schemes Sp\\ec ZN......Nikolai Durov has developed a generalization of conventional scheme theory in which commutative algebraic monads replace commutative unital rings as the basic algebraic objects. The resulting geometry is expressive enough to encompass conventional scheme theory, tropical algebraic geometry......, appearing in the construction of \\Spec Z....

  19. Contaminant immobilization via microbial activity

    International Nuclear Information System (INIS)

    1991-11-01

    The aim of this study was to search the literature to identify biological techniques that could be applied to the restoration of contaminated groundwaters near uranium milling sites. Through bioremediation it was hypothesized that the hazardous heavy metals could be immobilized in a stable, low-solubility form, thereby halting their progress in the migrating groundwater. Three basic mechanisms were examined: reduction of heavy metals by microbially produced hydrogen sulfide; direct microbial mediated reduction; and biosorption

  20. Microbial genomes: Blueprints for life

    Energy Technology Data Exchange (ETDEWEB)

    Relman, David A.; Strauss, Evelyn

    2000-12-31

    Complete microbial genome sequences hold the promise of profound new insights into microbial pathogenesis, evolution, diagnostics, and therapeutics. From these insights will come a new foundation for understanding the evolution of single-celled life, as well as the evolution of more complex life forms. This report is an in-depth analysis of scientific issues that provides recommendations and will be widely disseminated to the scientific community, federal agencies, industry and the public.

  1. Chronic alcoholism and microbial keratitis.

    OpenAIRE

    Ormerod, L. D.; Gomez, D. S.; Schanzlin, D. J.; Smith, R. E.

    1988-01-01

    In a series of 227 consecutive, non-referred patients with microbial keratitis an analysis of the accumulated hospital records showed that one-third were associated with chronic alcoholism. The diagnosis of alcoholism was usually unsuspected on admission to hospital. The microbial pathogenesis in these patients was distinctive; coagulase-negative staphylococci, alpha- and beta-streptococci, moraxellae, enteric Gram-negative bacilli, and polymicrobial infections were unusually prominent. Pseud...

  2. Specificity of the Linear Array HPV Genotyping Test for detecting human papillomavirus genotype 52 (HPV-52)

    OpenAIRE

    Kocjan, Boštjan; Poljak, Mario; Oštrbenk, Anja

    2015-01-01

    Introduction: HPV-52 is one of the most frequent human papillomavirus (HPV) genotypes causing significant cervical pathology. The most widely used HPV genotyping assay, the Roche Linear Array HPV Genotyping Test (Linear Array), is unable to identify HPV- 52 status in samples containing HPV-33, HPV-35, and/or HPV-58. Methods: Linear Array HPV-52 analytical specificity was established by testing 100 specimens reactive with the Linear Array HPV- 33/35/52/58 cross-reactive probe, but not with the...

  3. In-Drift Microbial Communities

    Energy Technology Data Exchange (ETDEWEB)

    D. Jolley

    2000-11-09

    As directed by written work direction (CRWMS M and O 1999f), Performance Assessment (PA) developed a model for microbial communities in the engineered barrier system (EBS) as documented here. The purpose of this model is to assist Performance Assessment and its Engineered Barrier Performance Section in modeling the geochemical environment within a potential repository drift for TSPA-SR/LA, thus allowing PA to provide a more detailed and complete near-field geochemical model and to answer the key technical issues (KTI) raised in the NRC Issue Resolution Status Report (IRSR) for the Evolution of the Near Field Environment (NFE) Revision 2 (NRC 1999). This model and its predecessor (the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document, CRWMS M and O 1998a) was developed to respond to the applicable KTIs. Additionally, because of the previous development of the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document (CRWMS M and O 1998a), the M and O was effectively able to resolve a previous KTI concern regarding the effects of microbial processes on seepage and flow (NRC 1998). This document supercedes the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document (CRWMS M and O 1998a). This document provides the conceptual framework of the revised in-drift microbial communities model to be used in subsequent performance assessment (PA) analyses.

  4. In-Drift Microbial Communities

    International Nuclear Information System (INIS)

    Jolley, D.

    2000-01-01

    As directed by written work direction (CRWMS M and O 1999f), Performance Assessment (PA) developed a model for microbial communities in the engineered barrier system (EBS) as documented here. The purpose of this model is to assist Performance Assessment and its Engineered Barrier Performance Section in modeling the geochemical environment within a potential repository drift for TSPA-SR/LA, thus allowing PA to provide a more detailed and complete near-field geochemical model and to answer the key technical issues (KTI) raised in the NRC Issue Resolution Status Report (IRSR) for the Evolution of the Near Field Environment (NFE) Revision 2 (NRC 1999). This model and its predecessor (the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document, CRWMS M and O 1998a) was developed to respond to the applicable KTIs. Additionally, because of the previous development of the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document (CRWMS M and O 1998a), the M and O was effectively able to resolve a previous KTI concern regarding the effects of microbial processes on seepage and flow (NRC 1998). This document supercedes the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document (CRWMS M and O 1998a). This document provides the conceptual framework of the revised in-drift microbial communities model to be used in subsequent performance assessment (PA) analyses

  5. Human papillomavirus genotyping by multiplex pyrosequencing in ...

    Indian Academy of Sciences (India)

    PRAKASH KUMAR G

    malignant cervical samples ... low- and high-risk HPV genotypes without identifying ... Since these samples were not from “healthy .... major capsid protein, any variation in its coding sequence is .... worldwide: a meta-analysis; Br. J. Cancer 88 63–73.

  6. Physicochemical and sensorial quality of banana genotypes

    Directory of Open Access Journals (Sweden)

    Ronielli Cardoso Reis

    2016-03-01

    Full Text Available Despite the diversity of banana varieties in Brazil, only a few cultivars have the proper agronomic traits and fruit quality for commercial exploitation. This study aimed at evaluating the physicochemical traits and sensorial acceptance of banana genotypes, in order to identify those with potential for commercial growing. Six improved banana genotypes were assessed (BRS Maravilha, PC 0101, FHIA 18, TM 2803, YB 4203 and BRS Caipira, as well as three commercial cultivars (Grand Naine, Pacovan and Prata Anã. Analyses of peel and pulp color, peel thickness, pulp yield, moisture, pH, soluble solids, titratable acidity, total carotenoids and sensorial acceptance were performed. The BRS Maravilha, FHIA 18, YB 4203 and BRS Caipira genotypes presented physicochemical traits similar to the Grand Naine, Pacovan and Prata Anã commercial cultivars. The BRS Maravilha and TM 2803 genotypes had sensorial acceptance similar to the Prata Anã and Grand Naine cultivars, and are therefore promising for commercial growing, with the advantage of being resistant to the black Sigatoka and Panama disease.

  7. Genotyping of human pappilomavirus in cervical precancerous ...

    African Journals Online (AJOL)

    Background: Cervical cancer caused by human papilloma virus (HPV), is the second most common cancer for women. This cancer is distributed worldwide, with ~80% of cases are found in the developing countries. In Indonesia, data of HPV genotypes are still limited and do not represent all regions of the country. Thus ...

  8. Cryptosporidium Pig Genotype II in Immunocompetent Man

    Czech Academy of Sciences Publication Activity Database

    Kváč, Martin; Květoňová, Dana; Sak, Bohumil; Ditrich, Oleg

    2009-01-01

    Roč. 15, č. 6 (2009), s. 982-983 ISSN 1080-6040 R&D Projects: GA ČR GP523/07/P117 Institutional research plan: CEZ:AV0Z60220518 Keywords : immunocompetent patients * cryptosporidiosis * Cryptosporidium pig genotype II Subject RIV: GJ - Animal Vermins ; Diseases , Veterinary Medicine Impact factor: 6.794, year: 2009

  9. Morphometric characteristics of Lotus corniculatus L. genotypes ...

    African Journals Online (AJOL)

    The aim of this study was to examine the degree of variability in morphological and agronomic characteristics of 20 Lotus corniculatus L. local genotypes, and also to set aside germplasm that will be used as a source of genetic basis for improvement of the studied properties. In poor quality soils, L. corniculatus L. plays an ...

  10. Genotype X Fertility Interactions in Seedling Sweetgum

    Science.gov (United States)

    Scott X. Chang; Daniel J. Robison

    2002-01-01

    Genotype x fertility interactions may affect the suitability of sweetgum (Liquidambar styraciflua L.) for specific sites or the efficiency of nutrient use. To gain a better understanding of these interactions, 2-year-old sweetgum seedlings from two half-sib families were tested for growth response to N (0 and 100 kg/ha equivalent) and P (0 and 50 kg...

  11. (AMMI) and genotype by environment interaction

    African Journals Online (AJOL)

    SARAH

    2014-04-30

    Apr 30, 2014 ... Background and justification: Lack of stable high yielding cultivars is one ... of advanced finger millet genotypes evaluated in multiple environments, and (ii) identify stable high yielding .... for interaction principal component axis (IPCA) n, γgn ..... Table 2: Analysis of variance for grain yield using AMMI model.

  12. Microbial production of biovanillin

    Directory of Open Access Journals (Sweden)

    A. Converti

    2010-10-01

    Full Text Available This review aims at providing an overview on the microbial production of vanillin, a new alternative method for the production of this important flavor of the food industry, which has the potential to become economically competitive in the next future. After a brief description of the applications of vanillin in different industrial sectors and of its physicochemical properties, we described the traditional ways of providing vanillin, specifically extraction and chemical synthesis (mainly oxidation and compared them with the new biotechnological options, i.e., biotransformations of caffeic acid, veratraldehyde and mainly ferulic acid. In the second part of the review, emphasis has been addressed to the factors most influencing the bioproduction of vanillin, specifically the age of inoculum, pH, temperature, type of co-substrate, as well as the inhibitory effects exerted either by excess substrate or product. The final part of the work summarized the downstream processes and the related unit operations involved in the recovery of vanillin from the bioconversion medium.

  13. Microbial production of biovanillin.

    Science.gov (United States)

    Converti, A; Aliakbarian, B; Domínguez, J M; Bustos Vázquez, G; Perego, P

    2010-07-01

    This review aims at providing an overview on the microbial production of vanillin, a new alternative method for the production of this important flavor of the food industry, which has the potential to become economically competitive in the next future. After a brief description of the applications of vanillin in different industrial sectors and of its physicochemical properties, we described the traditional ways of providing vanillin, specifically extraction and chemical synthesis (mainly oxidation) and compared them with the new biotechnological options, i.e., biotransformations of caffeic acid, veratraldehyde and mainly ferulic acid. In the second part of the review, emphasis has been addressed to the factors most influencing the bioproduction of vanillin, specifically the age of inoculum, pH, temperature, type of co-substrate, as well as the inhibitory effects exerted either by excess substrate or product. The final part of the work summarized the downstream processes and the related unit operations involved in the recovery of vanillin from the bioconversion medium.

  14. Microbial Propionic Acid Production

    Directory of Open Access Journals (Sweden)

    R. Axayacatl Gonzalez-Garcia

    2017-05-01

    Full Text Available Propionic acid (propionate is a commercially valuable carboxylic acid produced through microbial fermentation. Propionic acid is mainly used in the food industry but has recently found applications in the cosmetic, plastics and pharmaceutical industries. Propionate can be produced via various metabolic pathways, which can be classified into three major groups: fermentative pathways, biosynthetic pathways, and amino acid catabolic pathways. The current review provides an in-depth description of the major metabolic routes for propionate production from an energy optimization perspective. Biological propionate production is limited by high downstream purification costs which can be addressed if the target yield, productivity and titre can be achieved. Genome shuffling combined with high throughput omics and metabolic engineering is providing new opportunities, and biological propionate production is likely to enter the market in the not so distant future. In order to realise the full potential of metabolic engineering and heterologous expression, however, a greater understanding of metabolic capabilities of the native producers, the fittest producers, is required.

  15. Impact of inter-genotypic recombination and probe cross-reactivity on the performance of the Abbott RealTime HCV Genotype II assay for hepatitis C genotyping.

    Science.gov (United States)

    Sridhar, Siddharth; Yip, Cyril C Y; Chan, Jasper F W; To, Kelvin K W; Cheng, Vincent C C; Yuen, Kwok-Yung

    2018-05-01

    The Abbott RealTime HCV Genotype II assay (Abbott-RT-HCV assay) is a real-time PCR based genotyping method for hepatitis C virus (HCV). This study measured the impact of inter-genotypic recombination and probe cross-reactivity on the performance of the Abbott-RT-HCV assay. 517 samples were genotyped using the Abbott-RT-HCV assay over a one-year period, 34 (6.6%) were identified as HCV genotype 1 without further subtype designation raising the possibility of inaccurate genotyping. These samples were subjected to confirmatory sequencing. 27 of these 34 (79%) samples were genotype 1b while five (15%) were genotype 6. One HCV isolate was an inter-genotypic 1a/4o recombinant. This is a novel natural HCV recombinant that has never been reported. Inter-genotypic recombination and probe cross-reactivity can affect the accuracy of the Abbott-RT-HCV assay, both of which have significant implications on antiviral regimen choice. Confirmatory sequencing of ambiguous results is crucial for accurate genotyping. Copyright © 2018 Elsevier Inc. All rights reserved.

  16. A comprehensive review on two-stage integrative schemes for the valorization of dark fermentative effluents.

    Science.gov (United States)

    Sivagurunathan, Periyasamy; Kuppam, Chandrasekhar; Mudhoo, Ackmez; Saratale, Ganesh D; Kadier, Abudukeremu; Zhen, Guangyin; Chatellard, Lucile; Trably, Eric; Kumar, Gopalakrishnan

    2017-12-21

    This review provides the alternative routes towards the valorization of dark H 2 fermentation effluents that are mainly rich in volatile fatty acids such as acetate and butyrate. Various enhancement and alternative routes such as photo fermentation, anaerobic digestion, utilization of microbial electrochemical systems, and algal system towards the generation of bioenergy and electricity and also for efficient organic matter utilization are highlighted. What is more, various integration schemes and two-stage fermentation for the possible scale up are reviewed. Moreover, recent progress for enhanced performance towards waste stabilization and overall utilization of useful and higher COD present in the organic source into value-added products are extensively discussed.

  17. A survey of Strong Convergent Schemes for the Simulation of ...

    African Journals Online (AJOL)

    We considered strong convergent stochastic schemes for the simulation of stochastic differential equations. The stochastic Taylor's expansion, which is the main tool used for the derivation of strong convergent schemes; the Euler Maruyama, Milstein scheme, stochastic multistep schemes, Implicit and Explicit schemes were ...

  18. Setting aside transactions from pyramid schemes as impeachable ...

    African Journals Online (AJOL)

    These schemes, which are often referred to as pyramid or Ponzi schemes, are unsustainable operations and give rise to problems in the law of insolvency. Investors in these schemes are often left empty-handed upon the scheme's eventual collapse and insolvency. Investors who received pay-outs from the scheme find ...

  19. Betatron tune correction schemes in nuclotron

    International Nuclear Information System (INIS)

    Shchepunov, V.A.

    1992-01-01

    Algorithms of the betatron tune corrections in Nuclotron with sextupolar and octupolar magnets are considered. Second order effects caused by chromaticity correctors are taken into account and sextupolar compensation schemes are proposed to suppress them. 6 refs.; 1 tab

  20. A Directed Signature Scheme and its Applications

    OpenAIRE

    Lal, Sunder; Kumar, Manoj

    2004-01-01

    This paper presents a directed signature scheme with the property that the signature can be verified only with the help of signer or signature receiver. We also propose its applications to share verification of signatures and to threshold cryptosystems.

  1. ONU Power Saving Scheme for EPON System

    Science.gov (United States)

    Mukai, Hiroaki; Tano, Fumihiko; Tanaka, Masaki; Kozaki, Seiji; Yamanaka, Hideaki

    PON (Passive Optical Network) achieves FTTH (Fiber To The Home) economically, by sharing an optical fiber among plural subscribers. Recently, global climate change has been recognized as a serious near term problem. Power saving techniques for electronic devices are important. In PON system, the ONU (Optical Network Unit) power saving scheme has been studied and defined in XG-PON. In this paper, we propose an ONU power saving scheme for EPON. Then, we present an analysis of the power reduction effect and the data transmission delay caused by the ONU power saving scheme. According to the analysis, we propose an efficient provisioning method for the ONU power saving scheme which is applicable to both of XG-PON and EPON.

  2. Nigeria's first national social protection scheme | IDRC ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    2017-06-14

    Jun 14, 2017 ... Women and children at an IDP Camp in DRC ... The cash transfer was provided through the Nigerian Ekiti State Social Security Scheme, ... national policy conference to discuss the findings with media and policy stakeholders.

  3. Verifiable Secret Redistribution for Threshold Sharing Schemes

    National Research Council Canada - National Science Library

    Wong, Theodore M; Wang, Chenxi; Wing, Jeannette M

    2002-01-01

    .... Our protocol guards against dynamic adversaries. We observe that existing protocols either cannot be readily extended to allow redistribution between different threshold schemes, or have vulnerabilities that allow faulty old shareholders...

  4. Boson expansion theory in the seniority scheme

    International Nuclear Information System (INIS)

    Tamura, T.; Li, C.; Pedrocchi, V.G.

    1985-01-01

    A boson expansion formalism in the seniority scheme is presented and its relation with number-conserving quasiparticle calculations is elucidated. Accuracy and convergence are demonstrated numerically. A comparative discussion with other related approaches is given

  5. Designing optimal sampling schemes for field visits

    CSIR Research Space (South Africa)

    Debba, Pravesh

    2008-10-01

    Full Text Available This is a presentation of a statistical method for deriving optimal spatial sampling schemes. The research focuses on ground verification of minerals derived from hyperspectral data. Spectral angle mapper (SAM) and spectral feature fitting (SFF...

  6. Secret Sharing Schemes and Advanced Encryption Standard

    Science.gov (United States)

    2015-09-01

    25 4.7 Computational Example . . . . . . . . . . . . . . . . . . . . . 26 5 Side-Channel Effect on Advanced Encryption Standard ( AES ) 31...improvements, and to build upon them to discuss the side-channel effects on the Advanced Encryption Standard ( AES ). The following questions are asked...secret sharing scheme? • Can the improvements to the current secret sharing scheme prove to be beneficial in strengthening/weakening AES encryption

  7. Cost Comparison Among Provable Data Possession Schemes

    Science.gov (United States)

    2016-03-01

    of Acronyms and Abbreviations AE authenticated encryption AWS Amazon Web Services CIO Chief Information Officer DISA Defense Information Systems Agency...the number of possible challenges, H be a cryptographic hash function, AE be an authenticated encryption scheme, f be a keyed pseudo-random function...key kenc R←− Kenc for symmetric encryption scheme Enc, and a random HMAC key kmac R←− Kmac. The secret key is sk = 〈kenc, kmac〉 and public key is pk

  8. A Classification Scheme for Production System Processes

    DEFF Research Database (Denmark)

    Sørensen, Daniel Grud Hellerup; Brunø, Thomas Ditlev; Nielsen, Kjeld

    2018-01-01

    Manufacturing companies often have difficulties developing production platforms, partly due to the complexity of many production systems and difficulty determining which processes constitute a platform. Understanding production processes is an important step to identifying candidate processes...... for a production platform based on existing production systems. Reviewing a number of existing classifications and taxonomies, a consolidated classification scheme for processes in production of discrete products has been outlined. The classification scheme helps ensure consistency during mapping of existing...

  9. A scheme for the hadron spectrum

    International Nuclear Information System (INIS)

    Hoyer, P.

    1978-03-01

    A theoretically self-consistent dual scheme is proposed for the hadron spectrum, which follows naturally from basic requirements and phenomenology. All resonance properties and couplings are calculable in terms of a limited number of input parameters. A first application to ππ→ππ explains the linear trajectory and small daughter couplings. The Zweig rule and the decoupling of baryonium from mesons are expected to be consequences of the scheme. (Auth.)

  10. A Practical Voter-Verifiable Election Scheme.

    OpenAIRE

    Chaum, D; Ryan, PYA; Schneider, SA

    2005-01-01

    We present an election scheme designed to allow voters to verify that their vote is accurately included in the count. The scheme provides a high degree of transparency whilst ensuring the secrecy of votes. Assurance is derived from close auditing of all the steps of the vote recording and counting process with minimal dependence on the system components. Thus, assurance arises from verification of the election rather than having to place trust in the correct behaviour of components of the vot...

  11. Sellafield site (including Drigg) emergency scheme manual

    International Nuclear Information System (INIS)

    1987-02-01

    This Emergency Scheme defines the organisation and procedures available should there be an accident at the Sellafield Site which results in, or may result in, the release of radioactive material, or the generation of a high radiation field, which might present a hazard to employees and/or the general public. This manual covers the general principles of the total emergency scheme and those detailed procedures which are not specific to any single department. (U.K.)

  12. Signature scheme based on bilinear pairs

    Science.gov (United States)

    Tong, Rui Y.; Geng, Yong J.

    2013-03-01

    An identity-based signature scheme is proposed by using bilinear pairs technology. The scheme uses user's identity information as public key such as email address, IP address, telephone number so that it erases the cost of forming and managing public key infrastructure and avoids the problem of user private generating center generating forgery signature by using CL-PKC framework to generate user's private key.

  13. An Optimization Scheme for ProdMod

    International Nuclear Information System (INIS)

    Gregory, M.V.

    1999-01-01

    A general purpose dynamic optimization scheme has been devised in conjunction with the ProdMod simulator. The optimization scheme is suitable for the Savannah River Site (SRS) High Level Waste (HLW) complex operations, and able to handle different types of optimizations such as linear, nonlinear, etc. The optimization is performed in the stand-alone FORTRAN based optimization deliver, while the optimizer is interfaced with the ProdMod simulator for flow of information between the two

  14. Employee-referral schemes and discrimination law

    OpenAIRE

    Connolly, M.

    2015-01-01

    Employee-referral schemes (‘introduce a friend’) are in common usage in recruitment. They carry a potential to discriminate by perpetuating an already unbalanced workforce (say, by gender and ethnicity). With this, or course, comes the risk of litigation and bad publicity as well as any inherent inefficiencies associated with discrimination. This article is threefold. First, it examines the present state of the law. Second, it is based on a survey of employers who use these schemes. Third, it...

  15. Basis scheme of personnel training system

    International Nuclear Information System (INIS)

    Rerucha, F.; Odehnal, J.

    1998-01-01

    Basic scheme of the training system for NPP personnel of CEZ-EDU personnel training system is described in detail. This includes: specific training both basic and periodic, and professional training meaning specialized and continuous training. The following schemes are shown: licence acquisition and authorisation for PWR-440 Control Room Personnel; upgrade training for job positions of Control Room personnel; maintaining and refresh training; module training for certificate acquisition of servicing shift and operating personnel

  16. Navigators’ Behavior in Traffic Separation Schemes

    Directory of Open Access Journals (Sweden)

    Zbigniew Pietrzykowski

    2015-03-01

    Full Text Available One of the areas of decision support in the navigational ship conduct process is a Traffic Separation Scheme. TSSs are established in areas with high traffic density, often near the shore and in port approaches. The main purpose of these schemes is to improve maritime safety by channeling vessel traffic into streams. Traffic regulations as well as ships behavior in real conditions in chosen TSSs have been analyzed in order to develop decision support algorithms.

  17. The potential of plant viruses to promote genotypic diversity via genotype x environment interactions

    DEFF Research Database (Denmark)

    van Mölken, Tamara; Stuefer, Josef F.

    2011-01-01

    † Background and Aims Genotype by environment (G × E) interactions are important for the long-term persistence of plant species in heterogeneous environments. It has often been suggested that disease is a key factor for the maintenance of genotypic diversity in plant populations. However, empirical...... and the G × E interactions were examined with respect to genotypespecific plant responses to WClMV infection. Thus, the environment is defined as the presence or absence of the virus. † Key Results WClMV had a negative effect on plant performance as shown by a decrease in biomass and number of ramets...... evidence for this contention is scarce. Here virus infection is proposed as a possible candidate for maintaining genotypic diversity in their host plants. † Methods The effects of White clover mosaic virus (WClMV) on the performance and development of different Trifolium repens genotypes were analysed...

  18. Genotypic Variation of Early Maturing Soybean Genotypes for Phosphorus Utilization Efficiency under Field Grown Conditions

    Energy Technology Data Exchange (ETDEWEB)

    Abaidoo, R. C. [Kwame Nkrumah University of Technology, Kumasi (Ghana); International Institute of Tropical Agriculture, Ibadan (Nigeria); Opoku, A.; Boahen, S. [Kwame Nkrumah University of Technology, Kumasi (Ghana); Dare, M. O. [Federal University of Agriculture, Abeokuta (Nigeria)

    2013-11-15

    Variability in the utilization of phosphorus (P) by 64 early-maturing soybean (Glycine max L. Merr.) genotypes under low-P soil conditions were evaluated in 2009 and 2010 at Shika, Nigeria. Fifteen phenotypic variables; number of nodules, nodule dry weight, grain yield, plant biomass, total biomass, biomass N and P content, Phosphorus Utilization Index (PUI), shoot P Utilization efficiency (PUIS), grain P Utilization efficiency (PUIG), Harvest Index (HI), Biological N fixed (BNF), total N fixed and N and P uptake were measured. The four clusters revealed by cluster analysis were basically divided along (1) plant biomass and uptake, (2) nutrient acquisition and utilization and (3) nodulation components. Three early maturing genotypes, TGx1842-14E, TGx1912-11F and TGx1913-5F, were identified as having high P utilization index and low P uptake. These genotypes could be a potential source for breeding for P use efficiency in early maturing soybean genotypes. (author)

  19. Effect of ecosystems substitutions and CO2 increase of the atmosphere on the microbial ecosystems of forests

    International Nuclear Information System (INIS)

    Martin, F.

    2007-01-01

    Biological diversity is often exclusively considered at the level of plants and animals, whereas the bulk of global biodiversity is in fact at the microbial level. Although it is clear that the ecology of our planet is driven by microbial ecosystems, we are severely hampered by our limited understanding of the diversity and function of such microbial ecosystems. In the present project, teams in the disciplines of geochemistry, soil microbiology, genomics and ecosystem processes are assembled to study the relationship between environmental change, land use changes, biodiversity, and functioning of forest ecosystems. The network has a strong focus on developing and applying biochemical and genotyping methodologies to address key scientific issues in soil microbial ecology. These include assessing the impact of environmental- and land use changes on microbial diversity and function and exploring the evolutionary and mechanistic links between biological diversity and ecosystem function. In the present study, we have shown that: (1) The native mixed forest showed the highest microbial diversity (2) The mono specific plantations of tree species (e.g., oak, beech, pine, spruce) strikingly alter genetic and functional diversities of soil bacterial and fungal species. (3) Bacterial denitrification rates were dramatically modified by the planted species. Only by taking into account the impact of forest management on below-ground microbial diversity can one hope to get a full ecosystem-based understanding, and this must be addressed via modelling in order to provide relevant and useful information for conservation and policy making. (author)

  20. [Characterization and microbial community shifts of rice strawdegrading microbial consortia].

    Science.gov (United States)

    Wang, Chunfang; Ma, Shichun; Huang, Yan; Liu, Laiyan; Fan, Hui; Deng, Yu

    2016-12-04

    To study the relationship between microbial community and degradation rate of rice straw, we compared and analyzed cellulose-decomposing ability, microbial community structures and shifts of microbial consortia F1 and F2. We determined exoglucanase activity by 3, 5-dinitrosalicylic acid colorimetry. We determined content of cellulose, hemicellulose and lignin in rice straw by Van Soest method, and calculated degradation rates of rice straw by the weight changes before and after a 10-day incubation. We analyzed and compared the microbial communities and functional microbiology shifts by clone libraries, Miseq analysis and real time-PCR based on the 16S rRNA gene and cel48 genes. Total degradation rate, cellulose, and hemicellulose degradation rate of microbial consortia F1 were significantly higher than that of F2. The variation trend of exoglucanase activity in both microbial consortia F1 and F2 was consistent with that of cel48 gene copies. Microbial diversity of F1 was complex with aerobic bacteria as dominant species, whereas that of F2 was simple with a high proportion of anaerobic cellulose decomposing bacteria in the later stage of incubation. In the first 4 days, unclassified Bacillales and Bacillus were dominant in both F1 and F2. The dominant species and abundance became different after 4-day incubation, Bacteroidetes and Firmicutes were dominant phyla of F1 and F2, respectively. Although Petrimonas and Pusillimonas were common dominant species in F1 and F2, abundance of Petrimonas in F2 (38.30%) was significantly higher than that in F1 (9.47%), and the abundance of Clostridiales OPB54 in F2 increased to 14.85% after 8-day incubation. The abundance of cel48 gene related with cellulose degradation rate and exoglucanase activity, and cel48 gene has the potential as a molecular marker to monitor the process of cellulose degradation. Microbial community structure has a remarkable impact on the degradation efficiency of straw cellulose, and Petrimonas

  1. A Classification Scheme for Literary Characters

    Directory of Open Access Journals (Sweden)

    Matthew Berry

    2017-10-01

    Full Text Available There is no established classification scheme for literary characters in narrative theory short of generic categories like protagonist vs. antagonist or round vs. flat. This is so despite the ubiquity of stock characters that recur across media, cultures, and historical time periods. We present here a proposal of a systematic psychological scheme for classifying characters from the literary and dramatic fields based on a modification of the Thomas-Kilmann (TK Conflict Mode Instrument used in applied studies of personality. The TK scheme classifies personality along the two orthogonal dimensions of assertiveness and cooperativeness. To examine the validity of a modified version of this scheme, we had 142 participants provide personality ratings for 40 characters using two of the Big Five personality traits as well as assertiveness and cooperativeness from the TK scheme. The results showed that assertiveness and cooperativeness were orthogonal dimensions, thereby supporting the validity of using a modified version of TK’s two-dimensional scheme for classifying characters.

  2. Canonical, stable, general mapping using context schemes.

    Science.gov (United States)

    Novak, Adam M; Rosen, Yohei; Haussler, David; Paten, Benedict

    2015-11-15

    Sequence mapping is the cornerstone of modern genomics. However, most existing sequence mapping algorithms are insufficiently general. We introduce context schemes: a method that allows the unambiguous recognition of a reference base in a query sequence by testing the query for substrings from an algorithmically defined set. Context schemes only map when there is a unique best mapping, and define this criterion uniformly for all reference bases. Mappings under context schemes can also be made stable, so that extension of the query string (e.g. by increasing read length) will not alter the mapping of previously mapped positions. Context schemes are general in several senses. They natively support the detection of arbitrary complex, novel rearrangements relative to the reference. They can scale over orders of magnitude in query sequence length. Finally, they are trivially extensible to more complex reference structures, such as graphs, that incorporate additional variation. We demonstrate empirically the existence of high-performance context schemes, and present efficient context scheme mapping algorithms. The software test framework created for this study is available from https://registry.hub.docker.com/u/adamnovak/sequence-graphs/. anovak@soe.ucsc.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  3. Cancelable remote quantum fingerprint templates protection scheme

    International Nuclear Information System (INIS)

    Liao Qin; Guo Ying; Huang Duan

    2017-01-01

    With the increasing popularity of fingerprint identification technology, its security and privacy have been paid much attention. Only the security and privacy of biological information are insured, the biological technology can be better accepted and used by the public. In this paper, we propose a novel quantum bit (qbit)-based scheme to solve the security and privacy problem existing in the traditional fingerprint identification system. By exploiting the properties of quantm mechanics, our proposed scheme, cancelable remote quantum fingerprint templates protection scheme, can achieve the unconditional security guaranteed in an information-theoretical sense. Moreover, this novel quantum scheme can invalidate most of the attacks aimed at the fingerprint identification system. In addition, the proposed scheme is applicable to the requirement of remote communication with no need to worry about its security and privacy during the transmission. This is an absolute advantage when comparing with other traditional methods. Security analysis shows that the proposed scheme can effectively ensure the communication security and the privacy of users’ information for the fingerprint identification. (paper)

  4. Efficient multiparty quantum-secret-sharing schemes

    International Nuclear Information System (INIS)

    Xiao Li; Deng Fuguo; Long Guilu; Pan Jianwei

    2004-01-01

    In this work, we generalize the quantum-secret-sharing scheme of Hillery, Buzek, and Berthiaume [Phys. Rev. A 59, 1829 (1999)] into arbitrary multiparties. Explicit expressions for the shared secret bit is given. It is shown that in the Hillery-Buzek-Berthiaume quantum-secret-sharing scheme the secret information is shared in the parity of binary strings formed by the measured outcomes of the participants. In addition, we have increased the efficiency of the quantum-secret-sharing scheme by generalizing two techniques from quantum key distribution. The favored-measuring-basis quantum-secret-sharing scheme is developed from the Lo-Chau-Ardehali technique [H. K. Lo, H. F. Chau, and M. Ardehali, e-print quant-ph/0011056] where all the participants choose their measuring-basis asymmetrically, and the measuring-basis-encrypted quantum-secret-sharing scheme is developed from the Hwang-Koh-Han technique [W. Y. Hwang, I. G. Koh, and Y. D. Han, Phys. Lett. A 244, 489 (1998)] where all participants choose their measuring basis according to a control key. Both schemes are asymptotically 100% in efficiency, hence nearly all the Greenberger-Horne-Zeilinger states in a quantum-secret-sharing process are used to generate shared secret information

  5. Responses of Soil Microbial Community Structure and Diversity to Agricultural Deintensification

    Institute of Scientific and Technical Information of China (English)

    ZHANG Wei-Jian; S.HU; RUI Wen-Yi; C.TU; H.G.DIAB; F.J.LOUWS; J.P.MUELLER; N.CREAMER; M.BELL; M.G.WAGGER

    2005-01-01

    Using a scheme of agricultural fields with progressively less intensive management (deintensification), different management practices in six agroecosystems located near Goldsboro, NC, USA were tested in a large-scale experiment, including two cash-grain cropping systems employing either tillage (CT) or no-tillage (NT), an organic farming system (OR), an integrated cropping system with animals (IN), a successional field (SU), and a plantation woodlot (WO). Microbial phospholipid fatty acid (PLFA) profiles and substrate utilization patterns (BIOLOG ECO plates) were measured to examine the effects of deintensification on the structure and diversity of soil microbial communities. Principle component analyses of PLFA and BIOLOG data showed that the microbial community structure diverged among the soils of the six systems.Lower microbial diversity was found in lowly managed ecosystem than that in intensive and moderately managed agroecosystems, and both fungal contribution to the total identified PLFAs and the ratio of microbial biomass C/N increased along with agricultural deintensification. Significantly higher ratios of C/N (P < 0.05) were found in the WO and SU systems, and for fungal/bacterial PLFAs in the WO system (P < 0.05). There were also significant decreases (P < 0.05)along with agricultural deintensification for contributions of total bacterial and gram positive (G+) bacterial PLFAs.Agricultural deintensification could facilitate the development of microbial communities that favor soil fungi over bacteria.

  6. Biotechnological Aspects of Microbial Extracellular Electron Transfer

    Science.gov (United States)

    Kato, Souichiro

    2015-01-01

    Extracellular electron transfer (EET) is a type of microbial respiration that enables electron transfer between microbial cells and extracellular solid materials, including naturally-occurring metal compounds and artificial electrodes. Microorganisms harboring EET abilities have received considerable attention for their various biotechnological applications, in addition to their contribution to global energy and material cycles. In this review, current knowledge on microbial EET and its application to diverse biotechnologies, including the bioremediation of toxic metals, recovery of useful metals, biocorrosion, and microbial electrochemical systems (microbial fuel cells and microbial electrosynthesis), were introduced. Two potential biotechnologies based on microbial EET, namely the electrochemical control of microbial metabolism and electrochemical stimulation of microbial symbiotic reactions (electric syntrophy), were also discussed. PMID:26004795

  7. Distribution of genotype network sizes in sequence-to-structure genotype-phenotype maps.

    Science.gov (United States)

    Manrubia, Susanna; Cuesta, José A

    2017-04-01

    An essential quantity to ensure evolvability of populations is the navigability of the genotype space. Navigability, understood as the ease with which alternative phenotypes are reached, relies on the existence of sufficiently large and mutually attainable genotype networks. The size of genotype networks (e.g. the number of RNA sequences folding into a particular secondary structure or the number of DNA sequences coding for the same protein structure) is astronomically large in all functional molecules investigated: an exhaustive experimental or computational study of all RNA folds or all protein structures becomes impossible even for moderately long sequences. Here, we analytically derive the distribution of genotype network sizes for a hierarchy of models which successively incorporate features of increasingly realistic sequence-to-structure genotype-phenotype maps. The main feature of these models relies on the characterization of each phenotype through a prototypical sequence whose sites admit a variable fraction of letters of the alphabet. Our models interpolate between two limit distributions: a power-law distribution, when the ordering of sites in the prototypical sequence is strongly constrained, and a lognormal distribution, as suggested for RNA, when different orderings of the same set of sites yield different phenotypes. Our main result is the qualitative and quantitative identification of those features of sequence-to-structure maps that lead to different distributions of genotype network sizes. © 2017 The Author(s).

  8. Hydrodynamics of microbial filter feeding.

    Science.gov (United States)

    Nielsen, Lasse Tor; Asadzadeh, Seyed Saeed; Dölger, Julia; Walther, Jens H; Kiørboe, Thomas; Andersen, Anders

    2017-08-29

    Microbial filter feeders are an important group of grazers, significant to the microbial loop, aquatic food webs, and biogeochemical cycling. Our understanding of microbial filter feeding is poor, and, importantly, it is unknown what force microbial filter feeders must generate to process adequate amounts of water. Also, the trade-off in the filter spacing remains unexplored, despite its simple formulation: A filter too coarse will allow suitably sized prey to pass unintercepted, whereas a filter too fine will cause strong flow resistance. We quantify the feeding flow of the filter-feeding choanoflagellate Diaphanoeca grandis using particle tracking, and demonstrate that the current understanding of microbial filter feeding is inconsistent with computational fluid dynamics (CFD) and analytical estimates. Both approaches underestimate observed filtration rates by more than an order of magnitude; the beating flagellum is simply unable to draw enough water through the fine filter. We find similar discrepancies for other choanoflagellate species, highlighting an apparent paradox. Our observations motivate us to suggest a radically different filtration mechanism that requires a flagellar vane (sheet), something notoriously difficult to visualize but sporadically observed in the related choanocytes (sponges). A CFD model with a flagellar vane correctly predicts the filtration rate of D. grandis , and using a simple model we can account for the filtration rates of other microbial filter feeders. We finally predict how optimum filter mesh size increases with cell size in microbial filter feeders, a prediction that accords very well with observations. We expect our results to be of significance for small-scale biophysics and trait-based ecological modeling.

  9. Pollen diversity, viability and floral structure of some Musa genotypes

    African Journals Online (AJOL)

    Pollen diversity, viability and floral structure of some Musa genotypes. ... This experiment was designed to study the floral structure, pollen morphology and the potential pollen viability of five Musa genotypes obtained ... HOW TO USE AJOL.

  10. Behavior of durum wheat genotypes under normal irrigation and ...

    African Journals Online (AJOL)

    Behavior of durum wheat genotypes under normal irrigation and drought stress conditions in the greenhouse. ... African Journal of Biotechnology ... Genotypes were grouped in cluster analysis (using Ward's method) based on Yp, Ys and ...

  11. Genetic variability in cowpea (Vigna unguiculata (L.) Walp.) genotypes

    African Journals Online (AJOL)

    sive protein in human diets with grains containing about. 23–25% protein ... Keywords: heritability, phenotype, principal component analysis, variance. Introduction .... be due to genotype, environment, and the interaction of genotype and ...

  12. magnitude of genotype x environment interaction for bacterial leaf

    African Journals Online (AJOL)

    ACSS

    African Crop Science Journal, Vol. ... effects of treatments into genotype, environment, and genotype x environment (G x E) interactions. Results .... method is economically effective (Niño-Liu et al., ..... This phenomenon indicated differences in.

  13. Genotype 3 is the predominant hepatitis C genotype in a multi-ethnic Asian population in Malaysia.

    Science.gov (United States)

    Ho, Shiaw-Hooi; Ng, Kee-Peng; Kaur, Harvinder; Goh, Khean-Lee

    2015-06-01

    Genotypes of hepatitis C virus (HCV) are distributed differently across the world. There is a paucity of such data in a multi-ethnic Asian population like Malaysia. The objectives of this study were to determine the distribution of HCV genotypes between major ethnic groups and to ascertain their association with basic demographic variables like age and gender. This was a cross-sectional prospective study conducted from September 2007 to September 2013. Consecutive patients who were detected to have anti-HCV antibodies in the University of Malaya Medical Centre were included and tested for the presence of HCV RNA using Roche Cobas Amplicor Analyzer and HCV genotype using Roche single Linear Array HCV Genotyping strip. Five hundred and ninety-six subjects were found to have positive anti-HCV antibodies during this period of time. However, only 396 (66.4%) were HCV RNA positive and included in the final analysis. Our results showed that HCV genotype 3 was the predominant genotype with overall frequency of 61.9% followed by genotypes 1 (35.9%), 2 (1.8%) and 6 (0.5%). There was a slightly higher prevalence of HCV genotype 3 among the Malays when compared to the Chinese (P=0.043). No other statistical significant differences were observed in the distribution of HCV genotypes among the major ethnic groups. There was also no association between the predominant genotypes and basic demographic variables. In a multi-ethnic Asian society in Malaysia, genotype 3 is the predominant genotype among all the major ethnic groups with genotype 1 as the second commonest genotype. Both genotypes 2 and 6 are uncommon. Neither genotype 4 nor 5 was detected. There is no identification of HCV genotype according to ethnic origin, age and gender.

  14. First step in using molecular data for microbial food safety risk assessment; hazard identification of Escherichia coli O157:H7 by coupling genomic data with in vitro adherence to human epithelial cells.

    Science.gov (United States)

    Pielaat, Annemarie; Boer, Martin P; Wijnands, Lucas M; van Hoek, Angela H A M; Bouw, El; Barker, Gary C; Teunis, Peter F M; Aarts, Henk J M; Franz, Eelco

    2015-11-20

    The potential for using whole genome sequencing (WGS) data in microbiological risk assessment (MRA) has been discussed on several occasions since the beginning of this century. Still, the proposed heuristic approaches have never been applied in a practical framework. This is due to the non-trivial problem of mapping microbial information consisting of thousands of loci onto a probabilistic scale for risks. The paradigm change for MRA involves translation of multidimensional microbial genotypic information to much reduced (integrated) phenotypic information and onwards to a single measure of human risk (i.e. probability of illness). In this paper a first approach in methodology development is described for the application of WGS data in MRA; this is supported by a practical example. That is, combining genetic data (single nucleotide polymorphisms; SNPs) for Shiga toxin-producing Escherichia coli (STEC) O157 with phenotypic data (in vitro adherence to epithelial cells as a proxy for virulence) leads to hazard identification in a Genome Wide Association Study (GWAS). This application revealed practical implications when using SNP data for MRA. These can be summarized by considering the following main issues: optimum sample size for valid inference on population level, correction for population structure, quantification and calibration of results, reproducibility of the analysis, links with epidemiological data, anchoring and integration of results into a systems biology approach for the translation of molecular studies to human health risk. Future developments in genetic data analysis for MRA should aim at resolving the mapping problem of processing genetic sequences to come to a quantitative description of risk. The development of a clustering scheme focusing on biologically relevant information of the microbe involved would be a useful approach in molecular data reduction for risk assessment. Copyright © 2015. Published by Elsevier B.V.

  15. Genotypic and phenotypic diversity in populations of plant-probiotic Pseudomonas spp. colonizing roots

    Science.gov (United States)

    Picard, Christine; Bosco, Marco

    2008-01-01

    Several soil microorganisms colonizing roots are known to naturally promote the health of plants by controlling a range of plant pathogens, including bacteria, fungi, and nematodes. The use of theses antagonistic microorganisms, recently named plant-probiotics, to control plant-pathogenic fungi is receiving increasing attention, as they may represent a sustainable alternative to chemical pesticides. Many years of research on plant-probiotic microorganisms (PPM) have indicated that fluorescent pseudomonads producing antimicrobial compounds are largely involved in the suppression of the most widespread soilborne pathogens. Phenotype and genotype analysis of plant-probiotic fluorescent pseudomonads (PFP) have shown considerable genetic variation among these types of strains. Such variability plays an important role in the rhizosphere competence and the biocontrol ability of PFP strains. Understanding the mechanisms by which genotypic and phenotypic diversity occurs in natural populations of PFP could be exploited to choose those agricultural practices which best exploit the indigenous PFP populations, or to isolate new plant-probiotic strains for using them as inoculants. A number of different methods have been used to study diversity within PFP populations. Because different resolutions of the existing microbial diversity can be revealed depending on the approach used, this review first describes the most important methods used for the assessment of fluorescent Pseudomonas diversity. Then, we focus on recent data relating how differences in genotypic and phenotypic diversity within PFP communities can be attributed to geographic location, climate, soil type, soil management regime, and interactions with other soil microorganisms and host plants. It becomes evident that plant-related parameters exert the strongest influence on the genotypic and phenotypic variations in PFP populations.

  16. HPV genotypes in invasive cervical cancer in Danish women

    DEFF Research Database (Denmark)

    Kirschner, Benny; Junge, Jette; Holl, Katsiaryna

    2013-01-01

    Human papillomavirus (HPV) genotype distribution in invasive cervical cancers may differ by geographic region. The primary objective of this study was to estimate HPV-genotype distribution in Danish women with a diagnosis of invasive cervical cancer.......Human papillomavirus (HPV) genotype distribution in invasive cervical cancers may differ by geographic region. The primary objective of this study was to estimate HPV-genotype distribution in Danish women with a diagnosis of invasive cervical cancer....

  17. Identification / characterisation and authentication of microbial strains by MALDI-TOF ICMS

    OpenAIRE

    Santos, C.; Lima, Nelson

    2011-01-01

    The identification of species is an important goal in microbial taxonomy. Information about each microorganism (e.g. morphological description, physiological and biochemical properties, molecular biology sequencings, ecological roles, and societal risks or benefits) is key element in this process. Identifications can been a long and seemingly never-ended process with frequent revisions of the taxonomic schemes. The application of sound tolls to smooth the progress of identifica...

  18. Identifying a few foot-and-mouth disease virus signature nucleotide strings for computational genotyping

    Directory of Open Access Journals (Sweden)

    Xu Lizhe

    2008-06-01

    Full Text Available Abstract Background Serotypes of the Foot-and-Mouth disease viruses (FMDVs were generally determined by biological experiments. The computational genotyping is not well studied even with the availability of whole viral genomes, due to uneven evolution among genes as well as frequent genetic recombination. Naively using sequence comparison for genotyping is only able to achieve a limited extent of success. Results We used 129 FMDV strains with known serotype as training strains to select as many as 140 most serotype-specific nucleotide strings. We then constructed a linear-kernel Support Vector Machine classifier using these 140 strings. Under the leave-one-out cross validation scheme, this classifier was able to assign correct serotype to 127 of these 129 strains, achieving 98.45% accuracy. It also assigned serotype correctly to an independent test set of 83 other FMDV strains downloaded separately from NCBI GenBank. Conclusion Computational genotyping is much faster and much cheaper than the wet-lab based biological experiments, upon the availability of the detailed molecular sequences. The high accuracy of our proposed method suggests the potential of utilizing a few signature nucleotide strings instead of whole genomes to determine the serotypes of novel FMDV strains.

  19. Evaluation of promising sweetpotato genotypes for high altitude ...

    African Journals Online (AJOL)

    The trials were set up to identify sweetpotato genotypes with adaptation to highland agroecologies with special reference to resistance to Ahemaria blight ... growth and at harvest, four genotypes and the local check, Magabari, bad high levels of resistance toA/Jemaria blight. Eight genotypes had total storage root yield ...

  20. Hepatitis B virus Genotypes in West Azarbayjan Province, Northwest Iran

    Directory of Open Access Journals (Sweden)

    Mohammad Hasan Khadem Ansari

    2017-12-01

    CONCLUSIONS: The results reveal that D genotype is the main genotype of HBV in West Azarbayjan province. Presence of this genotype conformed with the low rate of acute liver diseases caused by hepatitis B chronic infection, cirrhosis of the liver and hepatocellular carcinoma.

  1. Genotype-based personalised nutrition for obesity prevention and ...

    African Journals Online (AJOL)

    Typically, genotype-based personalised nutrition involves genotyping for a number of susceptibility SNPs associated with the prevention, or management, of a particular disease. Dietary advice is then personalised to the individual's genotype to ensure optimal prevention or treatment outcomes. To ensure evidence-based ...

  2. Introduction to a special issue on genotype by environment interaction

    Science.gov (United States)

    Expression of a phenotype is a function of the genotype, the environment, and the differential sensitivity of certain genotypes to different environments, also known as genotype by environment (G × E) interaction. This special issue of Crop Science includes a collection of manuscripts that reviews t...

  3. Core Gene Expression and Association of Genotypes with Viral ...

    African Journals Online (AJOL)

    Purpose: To determine genotypic distribution, ribonucleic acid (RNA) RNA viral load and express core gene from Hepatitis C Virus (HCV) infected patients in Punjab, Pakistan. Methods: A total of 1690 HCV RNA positive patients were included in the study. HCV genotyping was tested by type-specific genotyping assay, viral ...

  4. Effect of Genotype and Age on Some Morphometric, Body Linear ...

    African Journals Online (AJOL)

    A population of 231 roosters of the Nigerian indigenous chickens of normal feathered frizzle feathered and naked neck genotypes was evaluated for the effect of genotype and age on some morphometric body linear measurements and semen characteristics of three Nigerian chicken genotypes. 20 roosters from each ...

  5. 21 CFR 862.3360 - Drug metabolizing enzyme genotyping system.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Drug metabolizing enzyme genotyping system. 862... Test Systems § 862.3360 Drug metabolizing enzyme genotyping system. (a) Identification. A drug metabolizing enzyme genotyping system is a device intended for use in testing deoxyribonucleic acid (DNA...

  6. Relationship of status of polymorphic rapd bands with genotypic ...

    African Journals Online (AJOL)

    Relationship of status of polymorphic rapd bands with genotypic adaptation in early finger millet genotypes. S Das, RC Misra, GR Rout, MC Pattanaik, S Aparajita. Abstract. Molecular characterisation of the 15 early duration finger millet (Eleusine coracana G) genotypes was done through RAPD markers. Twenty-five ...

  7. Genotype x Environment Interaction for Tuber Yield, Dry Matter ...

    African Journals Online (AJOL)

    A study was conducted to determine stability of tuber yield, dry matter content and specific gravity, and the nature and magnitude of genotype x environment (G x E) interaction in elite tetraploid potato genotypes. Eleven potato genotypes including two standard checks were evaluated in the eastern part of Ethiopia at ...

  8. [Evaluation of hepatitis B virus genotyping EIA kit].

    Science.gov (United States)

    Tanaka, Yasuhito; Sugauchi, Fuminaka; Matsuuraa, Kentaro; Naganuma, Hatsue; Tatematsu, Kanako; Takagi, Kazumi; Hiramatsu, Kumiko; Kani, Satomi; Gotoh, Takaaki; Wakimoto, Yukio; Mizokami, Masashi

    2009-01-01

    Clinical significance of Hepatitis B virus(HBV) genotyping is increasingly recognized. The aim of this study was to evaluate reproducibility, accuracy, and sensitivity of an enzyme immunoassay (EIA) based HBV genotyping kit, which designed to discriminate between genotypes to A, B, C, or D by detecting genotype-specific epitopes in PreS2 region. Using the four genotypes panels, the EIA demonstrated complete inter and intra-assay genotyping reproducibility. Serum specimens had stable results after 8 days at 4 degrees C, or 10 cycles of freezing-thawing. In 91 samples that have been genotyped by DNA sequencing, 87(95.6%) were in complete accordance with EIA genotyping. Of examined 344 HBsAg-positive serum specimens, genotypes A, B, C and D were determined in 26 (7.6%), 62 (18.0%), 228 (66.3%), and 9 (2.6%) cases, respectively. Of 19 (5.5%) specimens unclassified by the EIA, 13 were found to have low titer of HBsAg concentration (< 3 IU/ml), and the other 5 had amino acid mutations or deletions within targeted PreS2 epitopes. The EIA allowed genotyping even in HBV DNA negative samples (96.2%). In conclusion, HBV genotype EIA is reliable, sensitive and easy assay for HBV genotyping. The assay would be useful for clinical use.

  9. Genotype by environment interactions and yield stability of stem ...

    African Journals Online (AJOL)

    In a maize breeding program, potential genotypes are usually evaluated in different environments before desirable ones are selected. Genotype x environment (G x E) interaction is associated with the differential performance of genotypes tested at different locations and in different years, and influences selection and ...

  10. Genotype x environment interaction and stability analysis for yield ...

    African Journals Online (AJOL)

    Chickpea is the major pulse crop cultivated in Ethiopia. However, its production is constrained due to genotype instability and environmental variability. This research was carried out to examine the magnitude of environmental effect on yield of chickpea genotypes and to investigate the stability and adaptability of genotypes ...

  11. Reactions of some potato genotypes to late blight in Cameroon ...

    African Journals Online (AJOL)

    Reactions of some potato genotypes to late blight in Cameroon. D. K. Njualem, P. Demo, H. A. Mendoza, J. T. Koi, S. F. Nana. Abstract. Field experiments were conducted in Cameroon in 1995 and 1996 to evaluate reactions of different potato genotypes to late blight. There were significant differences among genotypes for ...

  12. Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias

    Directory of Open Access Journals (Sweden)

    Didion John P

    2012-01-01

    Full Text Available Abstract Background High-density genotyping arrays that measure hybridization of genomic DNA fragments to allele-specific oligonucleotide probes are widely used to genotype single nucleotide polymorphisms (SNPs in genetic studies, including human genome-wide association studies. Hybridization intensities are converted to genotype calls by clustering algorithms that assign each sample to a genotype class at each SNP. Data for SNP probes that do not conform to the expected pattern of clustering are often discarded, contributing to ascertainment bias and resulting in lost information - as much as 50% in a recent genome-wide association study in dogs. Results We identified atypical patterns of hybridization intensities that were highly reproducible and demonstrated that these patterns represent genetic variants that were not accounted for in the design of the array platform. We characterized variable intensity oligonucleotide (VINO probes that display such patterns and are found in all hybridization-based genotyping platforms, including those developed for human, dog, cattle, and mouse. When recognized and properly interpreted, VINOs recovered a substantial fraction of discarded probes and counteracted SNP ascertainment bias. We developed software (MouseDivGeno that identifies VINOs and improves the accuracy of genotype calling. MouseDivGeno produced highly concordant genotype calls when compared with other methods but it uniquely identified more than 786000 VINOs in 351 mouse samples. We used whole-genome sequence from 14 mouse strains to confirm the presence of novel variants explaining 28000 VINOs in those strains. We also identified VINOs in human HapMap 3 samples, many of which were specific to an African population. Incorporating VINOs in phylogenetic analyses substantially improved the accuracy of a Mus species tree and local haplotype assignment in laboratory mouse strains. Conclusion The problems of ascertainment bias and missing

  13. MICROBIAL SURFACTANTS IN ENVIRONMENTAL TECHNOLOGIES

    Directory of Open Access Journals (Sweden)

    T. P. Pirog

    2015-08-01

    Full Text Available It was shown literature and own experimental data concerning the use of microbial surface active glycolipids (rhamno-, sophoro- and trehalose lipids and lipopeptides for water and soil purification from oil and other hydrocarbons, removing toxic heavy metals (Cu2+, Cd2+, Ni2+, Pb2+, degradation of complex pollution (oil and other hydrocarbons with heavy metals, and the role of microbial surfactants in phytoremediation processes. The factors that limit the use of microbial surfactants in environmental technologies are discussed. Thus, at certain concentrations biosurfactant can exhibit antimicrobial properties and inhibit microorganisms destructing xenobiotics. Microbial biodegradability of surfactants may also reduce the effectiveness of bioremediation. Development of effective technologies using microbial surfactants should include the following steps: monitoring of contaminated sites to determine the nature of pollution and analysis of the autochthonous microbiota; determining the mode of surfactant introduction (exogenous addition of stimulation of surfactant synthesis by autochthonous microbiota; establishing an optimal concentration of surfactant to prevent exhibition of antimicrobial properties and rapid biodegradation; research both in laboratory and field conditions.

  14. A molecular scheme for Yersinia enterocolitica patho-serotyping derived from genome-wide analysis.

    Science.gov (United States)

    Garzetti, Debora; Susen, Rosa; Fruth, Angelika; Tietze, Erhard; Heesemann, Jürgen; Rakin, Alexander

    2014-05-01

    Yersinia enterocolitica is a food-borne, gastro-intestinal pathogen with world-wide distribution. Only 11 serotypes have been isolated from patients, with O:3, O:9, O:8 and O:5,27 being the serotypes most commonly associated with human yersiniosis. Serotype is an important characteristic of Y. enterocolitica strains, allowing differentiation for epidemiology, diagnosis and phylogeny studies. Conventional serotyping, performed by slide agglutination, is a tedious and laborious procedure whose interpretation tends to be subjective, leading to poor reproducibility. Here we present a PCR-based typing scheme for molecular identification and patho-serotyping of Y. enterocolitica. Genome-wide comparison of Y. enterocolitica sequences allowed analysis of the O-antigen gene clusters of different serotypes, uncovering their formerly unknown genomic locations, and selection of targets for serotype-specific amplification. Two multiplex PCRs and one additional PCR were designed and tested on various reference strains and isolates from different origins. Our genotypic assay proved to be highly specific for identification of Y. enterocolitica species, discrimination between virulent and non-virulent strains, distinguishing the main human-related serotypes, and typing of conventionally untypeable strains. This genotyping scheme could be applied in microbiology laboratories as an alternative or complementary method to the traditional phenotypic assays, providing data for epidemiological studies. Copyright © 2013 Elsevier GmbH. All rights reserved.

  15. Phenotypic and Genotypic Eligible Methods for Salmonella Typhimurium Source Tracking.

    Science.gov (United States)

    Ferrari, Rafaela G; Panzenhagen, Pedro H N; Conte-Junior, Carlos A

    2017-01-01

    Salmonellosis is one of the most common causes of foodborne infection and a leading cause of human gastroenteritis. Throughout the last decade, Salmonella enterica serotype Typhimurium (ST) has shown an increase report with the simultaneous emergence of multidrug-resistant isolates, as phage type DT104. Therefore, to successfully control this microorganism, it is important to attribute salmonellosis to the exact source. Studies of Salmonella source attribution have been performed to determine the main food/food-production animals involved, toward which, control efforts should be correctly directed. Hence, the election of a ST subtyping method depends on the particular problem that efforts must be directed, the resources and the data available. Generally, before choosing a molecular subtyping, phenotyping approaches such as serotyping, phage typing, and antimicrobial resistance profiling are implemented as a screening of an investigation, and the results are computed using frequency-matching models (i.e., Dutch, Hald and Asymmetric Island models). Actually, due to the advancement of molecular tools as PFGE, MLVA, MLST, CRISPR, and WGS more precise results have been obtained, but even with these technologies, there are still gaps to be elucidated. To address this issue, an important question needs to be answered: what are the currently suitable subtyping methods to source attribute ST. This review presents the most frequently applied subtyping methods used to characterize ST, analyses the major available microbial subtyping attribution models and ponders the use of conventional phenotyping methods, as well as, the most applied genotypic tools in the context of their potential applicability to investigates ST source tracking.

  16. Phenotypic and Genotypic Eligible Methods for Salmonella Typhimurium Source Tracking

    Directory of Open Access Journals (Sweden)

    Rafaela G. Ferrari

    2017-12-01

    Full Text Available Salmonellosis is one of the most common causes of foodborne infection and a leading cause of human gastroenteritis. Throughout the last decade, Salmonella enterica serotype Typhimurium (ST has shown an increase report with the simultaneous emergence of multidrug-resistant isolates, as phage type DT104. Therefore, to successfully control this microorganism, it is important to attribute salmonellosis to the exact source. Studies of Salmonella source attribution have been performed to determine the main food/food-production animals involved, toward which, control efforts should be correctly directed. Hence, the election of a ST subtyping method depends on the particular problem that efforts must be directed, the resources and the data available. Generally, before choosing a molecular subtyping, phenotyping approaches such as serotyping, phage typing, and antimicrobial resistance profiling are implemented as a screening of an investigation, and the results are computed using frequency-matching models (i.e., Dutch, Hald and Asymmetric Island models. Actually, due to the advancement of molecular tools as PFGE, MLVA, MLST, CRISPR, and WGS more precise results have been obtained, but even with these technologies, there are still gaps to be elucidated. To address this issue, an important question needs to be answered: what are the currently suitable subtyping methods to source attribute ST. This review presents the most frequently applied subtyping methods used to characterize ST, analyses the major available microbial subtyping attribution models and ponders the use of conventional phenotyping methods, as well as, the most applied genotypic tools in the context of their potential applicability to investigates ST source tracking.

  17. COMT genotype, gambling activity, and cognition

    DEFF Research Database (Denmark)

    Grant, Jon E; Leppink, Eric W; Redden, Sarah A

    2015-01-01

    adjustment and delay aversion) and the Spatial Working Memory task (total errors). This study adds to the growing literature on the role of COMT in impulsive behaviors by showing that the Val/Val genotype was associated with specific clinical and cognitive elements among young adults who gamble......Neuropsychological studies of adults with problem gambling indicate impairments across multiple cognitive domains. Catechol-O-methyltransferase (COMT) plays a unique role in the regulation of dopamine in the prefrontal cortex, and has been implicated in the cognitive dysfunction evident in problem...... gambling. This study examined adults with varying levels of gambling behavior to determine whether COMT genotype was associated with differences in gambling symptoms and cognitive functioning. 260 non-treatment-seeking adults aged 18-29 years with varying degrees of gambling behavior provided saliva...

  18. FRUIT QUALITY CHARACTERISTICS OF SOME BLUEBERRY GENOTYPES

    Directory of Open Access Journals (Sweden)

    Irina Ancu

    2013-12-01

    Full Text Available In Romania the blueberry breeding program started in 1982 and till now was conducted by dr. Paulina Mladin. For inducing the variability, different genetic resources of American blueberry cultivars (V. corymbosum, V. angustifolium were involved in a high number of crosses. For identify the genotype with the best fruit quality, some biometric quality indicators (average fruit weight, size index and basically chemical compounds of fruits including ascorbic acid, dry matter, ash, soluble solids, total sugar, titratable acidity, tanoid substances, pectic substances, protein crude, phosphorus and potassium were determined. Of the eleven chemical studied properties who reflected the fruits quality, for five of them were found no statistically significant differences. The purpose of this paper work was to evaluate fruit quality and to identify the valuable genotypes resulted from Romanian blueberry breeding program.

  19. BCL2 genotypes and prostate cancer survival

    Energy Technology Data Exchange (ETDEWEB)

    Renner, Wilfried [Medical University of Graz, Clinical Institute of Medical and Chemical Laboratory Diagnostics, Graz (Austria); Langsenlehner, Uwe [GKK Outpatient Department, Division of Internal Medicine, Graz (Austria); Krenn-Pilko, Sabine; Langsenlehner, Tanja [Medical University of Graz, Department of Therapeutic Radiology and Oncology, Graz (Austria); Eder, Petra [University Hospital Wuerzburg, Department of Internal Medicine I, Wuerzburg (Germany)

    2017-06-15

    The antiapoptotic B-cell lymphoma 2 (BCL2) gene is a key player in cancer development and progression. A functional single-nucleotide polymorphism (c.-938C>A, rs2279115) in the inhibitory P2 BCL2 gene promoter has been associated with clinical outcomes in various types of cancer. Aim of the present study was to analyze the role of BCL2-938C>A genotypes in prostate cancer mortality. The association between BCL2-938C>A (rs2279115) genotypes and prostate cancer outcome was studied within the prospective PROCAGENE study comprising 702 prostate cancer patients. During a median follow-up time of 92 months, 120 (17.1%) patients died. A univariate Cox regression model showed a significant association of the CC genotype with reduced cancer-specific survival (CSS; hazard ratio, HR, 2.13, 95% confidence interval, CI, 1.10-4.12; p = 0.024) and overall survival (OS; HR 2.34, 95% CI 1.58-3.47; p < 0.001). In a multivariate Cox regression model including age at diagnosis, risk group, and androgen deprivation therapy, the CC genotype remained a significant predictor of poor CSS (HR 2.05, 95% CI 1.05-3.99; p = 0.034) and OS (HR 2.25, 95% CI 1.51-3.36; p < 0.001). This study provides evidence that the homozygous BCL2-938 CC genotype is associated with OS and C in prostate cancer patients. (orig.) [German] Das antiapoptotische Gen B cell lymphoma 2 (BCL2) spielt eine Schluesselrolle in der Entstehung und Progression von Krebserkrankungen. Ein funktioneller Einzelnukleotid-Polymorphismus (c.-938C>A, rs2279115) im inhibitorischen P2-BCL2-Promotor wurde mit dem klinischen Outcome verschiedener Krebserkrankungen verknuepft. Ziel der vorliegenden Studie war die Untersuchung der Rolle von BCL2-938C>A-Genotypen fuer die Mortalitaet bei Patienten mit Prostatakarzinom. Der Zusammenhang zwischen BCL2-938C>A-Genotypen (rs2279115) und dem Outcome bei Prostatakrebs wurde in der prospektiven PROCAGENE-Studie, die 702 Patienten mit Prostatakarzinom umfasste, untersucht. Waehrend der medianen

  20. Measuring microbial fitness in a field reciprocal transplant experiment.

    Science.gov (United States)

    Boynton, Primrose J; Stelkens, Rike; Kowallik, Vienna; Greig, Duncan

    2017-05-01

    Microbial fitness is easy to measure in the laboratory, but difficult to measure in the field. Laboratory fitness assays make use of controlled conditions and genetically modified organisms, neither of which are available in the field. Among other applications, fitness assays can help researchers detect adaptation to different habitats or locations. We designed a competitive fitness assay to detect adaptation of Saccharomyces paradoxus isolates to the habitat they were isolated from (oak or larch leaf litter). The assay accurately measures relative fitness by tracking genotype frequency changes in the field using digital droplet PCR (DDPCR). We expected locally adapted S. paradoxus strains to increase in frequency over time when growing on the leaf litter type from which they were isolated. The DDPCR assay successfully detected fitness differences among S. paradoxus strains, but did not find a tendency for strains to be adapted to the habitat they were isolated from. Instead, we found that the natural alleles of the hexose transport gene we used to distinguish S. paradoxus strains had significant effects on fitness. The origin of a strain also affected its fitness: strains isolated from oak litter were generally fitter than strains from larch litter. Our results suggest that dispersal limitation and genetic drift shape S. paradoxus populations in the forest more than local selection does, although further research is needed to confirm this. Tracking genotype frequency changes using DDPCR is a practical and accurate microbial fitness assay for natural environments. © 2016 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd.

  1. Novel approach for CES1 genotyping

    DEFF Research Database (Denmark)

    Bjerre, Ditte; Berg Rasmussen, Henrik

    2018-01-01

    AIM: Development of a specific procedure for genotyping of CES1A1 (CES1) and CES1A2, a hybrid of CES1A1 and the pseudogene CES1P1. MATERIALS & METHODS: The number of CES1A1 and CES1A2 copies and that of CES1P1 were determined using real-time PCR. Long range PCRs followed by secondary PCRs allowed...

  2. What is microbial community ecology?

    Science.gov (United States)

    Konopka, Allan

    2009-11-01

    The activities of complex communities of microbes affect biogeochemical transformations in natural, managed and engineered ecosystems. Meaningfully defining what constitutes a community of interacting microbial populations is not trivial, but is important for rigorous progress in the field. Important elements of research in microbial community ecology include the analysis of functional pathways for nutrient resource and energy flows, mechanistic understanding of interactions between microbial populations and their environment, and the emergent properties of the complex community. Some emergent properties mirror those analyzed by community ecologists who study plants and animals: biological diversity, functional redundancy and system stability. However, because microbes possess mechanisms for the horizontal transfer of genetic information, the metagenome may also be considered as a community property.

  3. Microbial processes in coastal pollution

    International Nuclear Information System (INIS)

    Capone, D.G.; Bauer, J.E.

    1992-01-01

    In this chapter, the authors describe the nature and range of some of the interactions that can occur between the microbiota and environmental contaminants in coastal areas. The implications of such interactions are also discussed. Pollutant types include inorganic nutrients, heavy metals, bulk organics, organic contaminants, pathogenic microorganisms and microbial pollutants. Both the effects of pollutants such as petroleum hydrocarbons on natural microbial populations and the mitigation of contaminant effects by complexation and biodegradation are considered. Finally, several areas of emerging concerns are presented that involve a confluence of biogeochemistry, microbial ecology and applied and public health microbiology. These concerns range in relevance from local/regional to oceanic/global scales. 308 ref

  4. Financial incentive schemes in primary care

    Directory of Open Access Journals (Sweden)

    Gillam S

    2015-09-01

    Full Text Available Stephen Gillam Department of Public Health and Primary Care, Institute of Public Health, University of Cambridge, Cambridge, UK Abstract: Pay-for-performance (P4P schemes have become increasingly common in primary care, and this article reviews their impact. It is based primarily on existing systematic reviews. The evidence suggests that P4P schemes can change health professionals' behavior and improve recorded disease management of those clinical processes that are incentivized. P4P may narrow inequalities in performance comparing deprived with nondeprived areas. However, such schemes have unintended consequences. Whether P4P improves the patient experience, the outcomes of care or population health is less clear. These practical uncertainties mirror the ethical concerns of many clinicians that a reductionist approach to managing markers of chronic disease runs counter to the humanitarian values of family practice. The variation in P4P schemes between countries reflects different historical and organizational contexts. With so much uncertainty regarding the effects of P4P, policy makers are well advised to proceed carefully with the implementation of such schemes until and unless clearer evidence for their cost–benefit emerges. Keywords: financial incentives, pay for performance, quality improvement, primary care

  5. Short-Term Saved Leave Scheme

    CERN Multimedia

    2007-01-01

    As announced at the meeting of the Standing Concertation Committee (SCC) on 26 June 2007 and in http://Bulletin No. 28/2007, the existing Saved Leave Scheme will be discontinued as of 31 December 2007. Staff participating in the Scheme will shortly receive a contract amendment stipulating the end of financial contributions compensated by save leave. Leave already accumulated on saved leave accounts can continue to be taken in accordance with the rules applicable to the current scheme. A new system of saved leave will enter into force on 1 January 2008 and will be the subject of a new implementation procedure entitled "Short-term saved leave scheme" dated 1 January 2008. At its meeting on 4 December 2007, the SCC agreed to recommend the Director-General to approve this procedure, which can be consulted on the HR Department’s website at the following address: https://cern.ch/hr-services/services-Ben/sls_shortterm.asp All staff wishing to participate in the new scheme a...

  6. Short-Term Saved Leave Scheme

    CERN Multimedia

    HR Department

    2007-01-01

    As announced at the meeting of the Standing Concertation Committee (SCC) on 26 June 2007 and in http://Bulletin No. 28/2007, the existing Saved Leave Scheme will be discontinued as of 31 December 2007. Staff participating in the Scheme will shortly receive a contract amendment stipulating the end of financial contributions compensated by save leave. Leave already accumulated on saved leave accounts can continue to be taken in accordance with the rules applicable to the current scheme. A new system of saved leave will enter into force on 1 January 2008 and will be the subject of a new im-plementation procedure entitled "Short-term saved leave scheme" dated 1 January 2008. At its meeting on 4 December 2007, the SCC agreed to recommend the Director-General to approve this procedure, which can be consulted on the HR Department’s website at the following address: https://cern.ch/hr-services/services-Ben/sls_shortterm.asp All staff wishing to participate in the new scheme ...

  7. Screening cotton genotypes for seedling drought tolerance

    Directory of Open Access Journals (Sweden)

    Penna Julio C. Viglioni

    1998-01-01

    Full Text Available The objectives of this study were to adapt a screening method previously used to assess seedling drought tolerance in cereals for use in cotton (Gossypium hirsutum L. and to identify tolerant accessions among a wide range of genotypes. Ninety genotypes were screened in seven growth chamber experiments. Fifteen-day-old seedlings were subjected to four 4-day drought cycles, and plant survival was evaluated after each cycle. Three cycles are probably the minimum required in cotton work. Significant differences (at the 0.05 level or lower among entries were obtained in four of the seven experiments. A "confirmation test" with entries previously evaluated as "tolerant" (high survival and "susceptible" (low survival was run. A number of entries duplicated their earlier performance, but others did not, which indicates the need to reevaluate selections. Germplasms considered tolerant included: `IAC-13-1', `IAC-RM4-SM5', `Minas Sertaneja', `Acala 1517E-1' and `4521'. In general, the technique is simple, though time-consuming, with practical value for screening a large number of genotypes. Results from the screening tests generally agreed with field information. The screening procedure is suitable to select tolerant accessions from among a large number of entries in germplasm collections as a preliminary step in breeding for drought tolerance. This research also demonstrated the need to characterize the internal lack of uniformity in growth chambers to allow for adequate designs of experiments.

  8. Soil microbial activities and its relationship with soil chemical ...

    African Journals Online (AJOL)

    The fields assessed are organically managed Soils (OMS), Inorganically Managed Soils (IMS) and an Uncultivated Land having grass coverage (ULS). Soil Microbial Respiration (SMR), Microbial Biomass Carbon (MBC), Microbial Biomass Nitrogen (MBN) and Microbial Biomass Phosphorus (MBP) were analyzed.

  9. A fast resonance interference treatment scheme with subgroup method

    International Nuclear Information System (INIS)

    Cao, L.; He, Q.; Wu, H.; Zu, T.; Shen, W.

    2015-01-01

    A fast Resonance Interference Factor (RIF) scheme is proposed to treat the resonance interference effects between different resonance nuclides. This scheme utilizes the conventional subgroup method to evaluate the self-shielded cross sections of the dominant resonance nuclide in the heterogeneous system and the hyper-fine energy group method to represent the resonance interference effects in a simplified homogeneous model. In this paper, the newly implemented scheme is compared to the background iteration scheme, the Resonance Nuclide Group (RNG) scheme and the conventional RIF scheme. The numerical results show that the errors of the effective self-shielded cross sections are significantly reduced by the fast RIF scheme compared with the background iteration scheme and the RNG scheme. Besides, the fast RIF scheme consumes less computation time than the conventional RIF schemes. The speed-up ratio is ~4.5 for MOX pin cell problems. (author)

  10. Advanced Microscopy of Microbial Cells

    DEFF Research Database (Denmark)

    Haagensen, Janus Anders Juul; Regenberg, Birgitte; Sternberg, Claus

    2011-01-01

    Growing awareness of heterogeneity in cells of microbial populations has emphasized the importance of advanced microscopy for visualization and understanding of the molecular mechanisms underlying cell-to-cell variation. In this review, we highlight some of the recent advances in confocal...... microscopy, super-resolution optical microscopy (STED, SIM, PALM) as well as atomic force microscopy and Raman spectroscopy. Using examples of bistability in microbial populations as well as biofilm development and differentiation in bacterial and yeast consortia, we demonstrate the importance of microscopy...

  11. Systems biology of Microbial Communities

    Energy Technology Data Exchange (ETDEWEB)

    Navid, A; Ghim, C; Fenley, A; Yoon, S; Lee, S; Almaas, E

    2008-04-11

    Microbes exist naturally in a wide range of environments, spanning the extremes of high acidity and high temperature to soil and the ocean, in communities where their interactions are significant. We present a practical discussion of three different approaches for modeling microbial communities: rate equations, individual-based modeling, and population dynamics. We illustrate the approaches with detailed examples. Each approach is best fit to different levels of system representation, and they have different needs for detailed biological input. Thus, this set of approaches is able to address the operation and function of microbial communities on a wide range of organizational levels.

  12. Identification of polymorphic inversions from genotypes

    Directory of Open Access Journals (Sweden)

    Cáceres Alejandro

    2012-02-01

    Full Text Available Abstract Background Polymorphic inversions are a source of genetic variability with a direct impact on recombination frequencies. Given the difficulty of their experimental study, computational methods have been developed to infer their existence in a large number of individuals using genome-wide data of nucleotide variation. Methods based on haplotype tagging of known inversions attempt to classify individuals as having a normal or inverted allele. Other methods that measure differences between linkage disequilibrium attempt to identify regions with inversions but unable to classify subjects accurately, an essential requirement for association studies. Results We present a novel method to both identify polymorphic inversions from genome-wide genotype data and classify individuals as containing a normal or inverted allele. Our method, a generalization of a published method for haplotype data 1, utilizes linkage between groups of SNPs to partition a set of individuals into normal and inverted subpopulations. We employ a sliding window scan to identify regions likely to have an inversion, and accumulation of evidence from neighboring SNPs is used to accurately determine the inversion status of each subject. Further, our approach detects inversions directly from genotype data, thus increasing its usability to current genome-wide association studies (GWAS. Conclusions We demonstrate the accuracy of our method to detect inversions and classify individuals on principled-simulated genotypes, produced by the evolution of an inversion event within a coalescent model 2. We applied our method to real genotype data from HapMap Phase III to characterize the inversion status of two known inversions within the regions 17q21 and 8p23 across 1184 individuals. Finally, we scan the full genomes of the European Origin (CEU and Yoruba (YRI HapMap samples. We find population-based evidence for 9 out of 15 well-established autosomic inversions, and for 52 regions

  13. Microbial Heat Recovery Cell (MHRC) System Concept

    Energy Technology Data Exchange (ETDEWEB)

    None

    2017-09-01

    This factsheet describes a project that aimed to develop a microbial heat recovery cell (MHRC) system that combines a microbial reverse electrodialysis technology with waste heat recovery to convert industrial effluents into electricity and hydrogen.

  14. Microbial quality of a marine tidal pool

    CSIR Research Space (South Africa)

    Genthe, Bettina

    1995-01-01

    Full Text Available In this study the source of microbial pollution to a tidal pool was investigated. Both adjacent seawater which could contribute to possible faecal pollution and potential direct bather pollution were studied. The microbial quality of the marine...

  15. How update schemes influence crowd simulations

    International Nuclear Information System (INIS)

    Seitz, Michael J; Köster, Gerta

    2014-01-01

    Time discretization is a key modeling aspect of dynamic computer simulations. In current pedestrian motion models based on discrete events, e.g. cellular automata and the Optimal Steps Model, fixed-order sequential updates and shuffle updates are prevalent. We propose to use event-driven updates that process events in the order they occur, and thus better match natural movement. In addition, we present a parallel update with collision detection and resolution for situations where computational speed is crucial. Two simulation studies serve to demonstrate the practical impact of the choice of update scheme. Not only do density-speed relations differ, but there is a statistically significant effect on evacuation times. Fixed-order sequential and random shuffle updates with a short update period come close to event-driven updates. The parallel update scheme overestimates evacuation times. All schemes can be employed for arbitrary simulation models with discrete events, such as car traffic or animal behavior. (paper)

  16. Asynchronous discrete event schemes for PDEs

    Science.gov (United States)

    Stone, D.; Geiger, S.; Lord, G. J.

    2017-08-01

    A new class of asynchronous discrete-event simulation schemes for advection-diffusion-reaction equations is introduced, based on the principle of allowing quanta of mass to pass through faces of a (regular, structured) Cartesian finite volume grid. The timescales of these events are linked to the flux on the face. The resulting schemes are self-adaptive, and local in both time and space. Experiments are performed on realistic physical systems related to porous media flow applications, including a large 3D advection diffusion equation and advection diffusion reaction systems. The results are compared to highly accurate reference solutions where the temporal evolution is computed with exponential integrator schemes using the same finite volume discretisation. This allows a reliable estimation of the solution error. Our results indicate a first order convergence of the error as a control parameter is decreased, and we outline a framework for analysis.

  17. An adaptive Cartesian control scheme for manipulators

    Science.gov (United States)

    Seraji, H.

    1987-01-01

    A adaptive control scheme for direct control of manipulator end-effectors to achieve trajectory tracking in Cartesian space is developed. The control structure is obtained from linear multivariable theory and is composed of simple feedforward and feedback controllers and an auxiliary input. The direct adaptation laws are derived from model reference adaptive control theory and are not based on parameter estimation of the robot model. The utilization of feedforward control and the inclusion of auxiliary input are novel features of the present scheme and result in improved dynamic performance over existing adaptive control schemes. The adaptive controller does not require the complex mathematical model of the robot dynamics or any knowledge of the robot parameters or the payload, and is computationally fast for online implementation with high sampling rates.

  18. A Traffic Restriction Scheme for Enhancing Carpooling

    Directory of Open Access Journals (Sweden)

    Dong Ding

    2017-01-01

    Full Text Available For the purpose of alleviating traffic congestion, this paper proposes a scheme to encourage travelers to carpool by traffic restriction. By a variational inequity we describe travelers’ mode (solo driving and carpooling and route choice under user equilibrium principle in the context of fixed demand and detect the performance of a simple network with various restriction links, restriction proportions, and carpooling costs. Then the optimal traffic restriction scheme aiming at minimal total travel cost is designed through a bilevel program and applied to a Sioux Fall network example with genetic algorithm. According to various requirements, optimal restriction regions and proportions for restricted automobiles are captured. From the results it is found that traffic restriction scheme is possible to enhance carpooling and alleviate congestion. However, higher carpooling demand is not always helpful to the whole network. The topology of network, OD demand, and carpooling cost are included in the factors influencing the performance of the traffic system.

  19. Quantum Watermarking Scheme Based on INEQR

    Science.gov (United States)

    Zhou, Ri-Gui; Zhou, Yang; Zhu, Changming; Wei, Lai; Zhang, Xiafen; Ian, Hou

    2018-04-01

    Quantum watermarking technology protects copyright by embedding invisible quantum signal in quantum multimedia data. In this paper, a watermarking scheme based on INEQR was presented. Firstly, the watermark image is extended to achieve the requirement of embedding carrier image. Secondly, the swap and XOR operation is used on the processed pixels. Since there is only one bit per pixel, XOR operation can achieve the effect of simple encryption. Thirdly, both the watermark image extraction and embedding operations are described, where the key image, swap operation and LSB algorithm are used. When the embedding is made, the binary image key is changed. It means that the watermark has been embedded. Of course, if the watermark image is extracted, the key's state need detected. When key's state is |1>, this extraction operation is carried out. Finally, for validation of the proposed scheme, both the Signal-to-noise ratio (PSNR) and the security of the scheme are analyzed.

  20. Improvement of One Quantum Encryption Scheme

    Science.gov (United States)

    Cao, Zhengjun; Liu, Lihua

    2012-01-01

    Zhou et al. proposed a quantum encryption scheme based on quantum computation in 2006 [N. Zhou et al., Physica A362 (2006) 305]. Each qubit of the ciphertext is constrained to two pairs of conjugate states. So, its implementation is feasible with the existing technology. But it is inefficient since it entails six key bits to encrypt one message bit, and the resulting ciphertext for one message bit consists of three qubits. In addition, its security cannot be directly reduced to the well-known BB84 protocol. In this paper, we improve it using the technique developed in BB84 protocol. The new scheme entails only two key bits to encrypt one message bit. The resulting ciphertext is just composed of two qubits. It saves about a half cost without the loss of security. Moreover, the new scheme is probabilistic instead of deterministic.

  1. Marine Microbial Systems Ecology: Microbial Networks in the Sea

    NARCIS (Netherlands)

    Muijzer, G.; Stal, L.J.; Cretoiu, M.S.

    2016-01-01

    Next-generation sequencing of DNA has revolutionized microbial ecology. Using this technology, it became for the first time possible to analyze hundreds of samples simultaneously and in great detail. 16S rRNA amplicon sequencing, metagenomics and metatranscriptomics became available to determine the

  2. Microbial stratification and microbially catalyzed processes along a hypersaline chemocline

    Science.gov (United States)

    Hyde, A.; Joye, S. B.; Teske, A.

    2017-12-01

    Orca Basin is the largest deep hypersaline anoxic basin in the world, covering over 400 km2. Located at the bottom of the Gulf of Mexico, this body of water reaches depths of 200 meters and is 8 times denser (and more saline) than the overlying seawater. The sharp pycnocline prevents any significant vertical mixing and serves as a particle trap for sinking organic matter. These rapid changes in salinity, oxygen, organic matter, and other geochemical parameters present unique conditions for the microbial communities present. We collected samples in 10m intervals throughout the chemocline. After filtering the water, we used high-throughput bacterial and archaeal 16S rRNA gene sequencing to characterize the changing microbial community along the Orca Basin chemocline. The results reveal a dominance of microbial taxa whose biogeochemical function is entirely unknown. We then used metagenomic sequencing and reconstructed genomes for select samples, revealing the potential dominant metabolic processes in the Orca Basin chemocline. Understanding how these unique geochemical conditions shape microbial communities and metabolic capabilities will have implications for the ocean's biogeochemical cycles and the consequences of expanding oxygen minimum zones.

  3. A universal encoding scheme for MIMO transmission using a single active element for PSK modulation schemes

    DEFF Research Database (Denmark)

    Alrabadi, Osama; Papadias, C.B.; Kalis, A.

    2009-01-01

    A universal scheme for encoding multiple symbol streams using a single driven element (and consequently a single radio frequency (RF) frontend) surrounded by parasitic elements (PE) loaded with variable reactive loads, is proposed in this paper. The proposed scheme is based on creating a MIMO sys...

  4. A simple angular transmit diversity scheme using a single RF frontend for PSK modulation schemes

    DEFF Research Database (Denmark)

    Alrabadi, Osama Nafeth Saleem; Papadias, Constantinos B.; Kalis, Antonis

    2009-01-01

    array (SPA) with a single transceiver, and an array area of 0.0625 square wavelengths. The scheme which requires no channel state information (CSI) at the transmitter, provides mainly a diversity gain to combat against multipath fading. The performance/capacity of the proposed diversity scheme...

  5. Genotypic diversity of root and shoot characteristics of

    Directory of Open Access Journals (Sweden)

    ali ganjali

    2009-06-01

    Full Text Available Root and shoot characteristics of chickpea (Cicer arietinum L. genotypes are believed to be important in drought tolerance. There is a little information about the response of genotypes root growth in hydroponics and greenhouse culture, also the relationships between root size and drought tolerance. This study was conducted to observe whether genotypes differ in root size, and to see that root size is associated with drought tolerance during early vegetative growth. We found significant differences (p0.01 in root dry weight, total root length, tap root length, root area, leaf dry weight, leaf area and shoot biomass per plant among 30 genotypes of chickpea grown in hydroponics culture for three weeks. Each of these parameters correlated with all others, positively. Among 30 genotypes, 10 genotypes with different root sizes were selected and were grown in a greenhouse in sand culture experiment under drought stress (FC %30 for three weeks. There were not linear or non-linear significant correlations between root characters in hydroponics and greenhouse environments. It seems that environmental factors are dominant on genetic factors in seedling stage and so, the expression of genotypics potential for root growth characteristics of genotypes are different in hydroponic and greenhouse conditions. In this study, the selection of genotypes with vigorous roots system in hydroponic condition did not lead to genotypes with the same root characters in greenhouse environment. The genotype×drought interactions for root characters of chickpea seedlings in 30 days were not significant (p

  6. Carbon trading: Current schemes and future developments

    International Nuclear Information System (INIS)

    Perdan, Slobodan; Azapagic, Adisa

    2011-01-01

    This paper looks at the greenhouse gas (GHG) emissions trading schemes and examines the prospects of carbon trading. The first part of the paper gives an overview of several mandatory GHG trading schemes around the world. The second part focuses on the future trends in carbon trading. It argues that the emergence of new schemes, a gradual enlargement of the current ones, and willingness to link existing and planned schemes seem to point towards geographical, temporal and sectoral expansion of emissions trading. However, such expansion would need to overcome some considerable technical and non-technical obstacles. Linking of the current and emerging trading schemes requires not only considerable technical fixes and harmonisation of different trading systems, but also necessitates clear regulatory and policy signals, continuing political support and a more stable economic environment. Currently, the latter factors are missing. The global economic turmoil and its repercussions for the carbon market, a lack of the international deal on climate change defining the Post-Kyoto commitments, and unfavourable policy shifts in some countries, cast serious doubts on the expansion of emissions trading and indicate that carbon trading enters an uncertain period. - Highlights: → The paper provides an extensive overview of mandatory emissions trading schemes around the world. → Geographical, temporal and sectoral expansion of emissions trading are identified as future trends. → The expansion requires considerable technical fixes and harmonisation of different trading systems. → Clear policy signals, political support and a stable economic environment are needed for the expansion. → A lack of the post-Kyoto commitments and unfavourable policy shifts indicate an uncertain future for carbon trading.

  7. Pressure correction schemes for compressible flows

    International Nuclear Information System (INIS)

    Kheriji, W.

    2011-01-01

    This thesis is concerned with the development of semi-implicit fractional step schemes, for the compressible Navier-Stokes equations; these schemes are part of the class of the pressure correction methods. The chosen spatial discretization is staggered: non conforming mixed finite elements (Crouzeix-Raviart or Rannacher-Turek) or the classic MA C scheme. An upwind finite volume discretization of the mass balance guarantees the positivity of the density. The positivity of the internal energy is obtained by discretizing the internal energy balance by an upwind finite volume scheme and b y coupling the discrete internal energy balance with the pressure correction step. A special finite volume discretization on dual cells is performed for the convection term in the momentum balance equation, and a renormalisation step for the pressure is added to the algorithm; this ensures the control in time of the integral of the total energy over the domain. All these a priori estimates imply the existence of a discrete solution by a topological degree argument. The application of this scheme to Euler equations raises an additional difficulty. Indeed, obtaining correct shocks requires the scheme to be consistent with the total energy balance, property which we obtain as follows. First of all, a local discrete kinetic energy balance is established; it contains source terms winch we somehow compensate in the internal energy balance. The kinetic and internal energy equations are associated with the dual and primal meshes respectively, and thus cannot be added to obtain a total energy balance; its continuous counterpart is however recovered at the limit: if we suppose that a sequence of discrete solutions converges when the space and time steps tend to 0, we indeed show, in 1D at least, that the limit satisfies a weak form of the equation. These theoretical results are comforted by numerical tests. Similar results are obtained for the baro-tropic Navier-Stokes equations. (author)

  8. Microbial community structure elucidates performance of Glyceria maxima plant microbial fuel cell

    NARCIS (Netherlands)

    Timmers, R.A.; Rothballer, M.; Strik, D.P.B.T.B.; Engel, M.; Schulz, M.; Hartmann, A.; Hamelers, H.V.M.; Buisman, C.J.N.

    2012-01-01

    The plant microbial fuel cell (PMFC) is a technology in which living plant roots provide electron donor, via rhizodeposition, to a mixed microbial community to generate electricity in a microbial fuel cell. Analysis and localisation of the microbial community is necessary for gaining insight into

  9. Performance of chickpea genotypes under Swat valley conditions

    International Nuclear Information System (INIS)

    Khan, A.; Rahim, M.; Ahmad, F.; Ali, A.

    2004-01-01

    Twenty-two genetically diverse chickpeas genotypes were studied for their physiological efficiency to select the most desirable genotype/genotypes for breeding program on chickpea. Genotype 'CM7-1' was found physiologically efficient stain with maximum harvest index (37.33%) followed by genotype 'CM1571-1-A' with harvest index of 35.73%. Genotype '90206' produced maximum biological yield (7463 kg ha/sup -1/) followed by genotypes 'CM31-1' and 'E-2034' with biological yield of 7352 and 7167 kg ha/sup -1/, respectively. Harvest index and economic yield showed significant positive correlation value of (r=+0.595), while negative correlation value of (r = -0.435) was observed between harvest index and biological yield. (author)

  10. EPU correction scheme study at the CLS

    Energy Technology Data Exchange (ETDEWEB)

    Bertwistle, Drew, E-mail: drew.bertwistle@lightsource.ca; Baribeau, C.; Dallin, L.; Chen, S.; Vogt, J.; Wurtz, W. [Canadian Light Source Inc. 44 Innovation Boulevard, Saskatoon, SK S7N 2V3 (Canada)

    2016-07-27

    The Canadian Light Source (CLS) Quantum Materials Spectroscopy Center (QMSC) beamline will employ a novel double period (55 mm, 180 mm) elliptically polarizing undulator (EPU) to produce photons of arbitrary polarization in the soft X-ray regime. The long period and high field of the 180 mm period EPU will have a strong dynamic focusing effect on the storage ring electron beam. We have considered two partial correction schemes, a 4 m long planar array of BESSY-II style current strips, and soft iron L-shims. In this paper we briefly consider the implementation of these correction schemes.

  11. Verification of an objective analysis scheme

    International Nuclear Information System (INIS)

    Cats, G.J.; Haan, B.J. de; Hafkenscheid, L.M.

    1987-01-01

    An intermittent data assimilation scheme has been used to produce wind and precipitation fields during the 10 days after the explosion at the Chernobyl nuclear power plant on 25 April 1986. The wind fields are analyses, the precipitation fields have been generated by the forecast model part of the scheme. The precipitation fields are of fair quality. The quality of the wind fields has been monitored by the ensuing trajectories. These were found to describe the arrival times of radioactive air in good agreement with most observational data, taken all over Europe. The wind analyses are therefore considered to be reliable. 25 refs.; 13 figs

  12. Optimal powering schemes for legged robotics

    Science.gov (United States)

    Muench, Paul; Bednarz, David; Czerniak, Gregory P.; Cheok, Ka C.

    2010-04-01

    Legged Robots have tremendous mobility, but they can also be very inefficient. These inefficiencies can be due to suboptimal control schemes, among other things. If your goal is to get from point A to point B in the least amount of time, your control scheme will be different from if your goal is to get there using the least amount of energy. In this paper, we seek a balance between these extremes by looking at both efficiency and speed. We model a walking robot as a rimless wheel, and, using Pontryagin's Maximum Principle (PMP), we find an "on-off" control for the model, and describe the switching curve between these control extremes.

  13. System Protection Schemes in Eastern Denmark

    DEFF Research Database (Denmark)

    Rasmussen, Joana

    outages in the southern part of the 132-kV system introduce further stress in the power system, eventually leading to a voltage collapse. The local System Protection Scheme against voltage collapse is designed as a response-based scheme, which is dependent on local indication of reactive and active power...... effective measures, because they are associated with large reactive power losses in the transmission system. Ordered reduction of wind generation is considered an effective measure to maintain voltage stability in the system. Reactive power in the system is released due to tripping of a significant amount...... system. In that way, the power system capability could be extended beyond normal limits....

  14. Group Buying Schemes : A Sustainable Business Model?

    OpenAIRE

    Köpp, Sebastian; Mukhachou, Aliaksei; Schwaninger, Markus

    2013-01-01

    Die Autoren gehen der Frage nach, ob "Group Buying Schemes" wie beispielsweise von den Unternehmen Groupon und Dein Deal angeboten, ein nachhaltiges Geschäftsmodell sind. Anhand der Fallstudie Groupon wird mit einem System Dynamics Modell festgestellt, dass das Geschäftsmodell geändert werden muss, wenn die Unternehmung auf Dauer lebensfähig sein soll. The authors examine if group buying schemes are a sustainable business model. By means of the Groupon case study and using a System Dynami...

  15. New Imaging Operation Scheme at VLTI

    Science.gov (United States)

    Haubois, Xavier

    2018-04-01

    After PIONIER and GRAVITY, MATISSE will soon complete the set of 4 telescope beam combiners at VLTI. Together with recent developments in the image reconstruction algorithms, the VLTI aims to develop its operation scheme to allow optimized and adaptive UV plane coverage. The combination of spectro-imaging instruments, optimized operation framework and image reconstruction algorithms should lead to an increase of the reliability and quantity of the interferometric images. In this contribution, I will present the status of this new scheme as well as possible synergies with other instruments.

  16. Hilbert schemes of points and Heisenberg algebras

    International Nuclear Information System (INIS)

    Ellingsrud, G.; Goettsche, L.

    2000-01-01

    Let X [n] be the Hilbert scheme of n points on a smooth projective surface X over the complex numbers. In these lectures we describe the action of the Heisenberg algebra on the direct sum of the cohomologies of all the X [n] , which has been constructed by Nakajima. In the second half of the lectures we study the relation of the Heisenberg algebra action and the ring structures of the cohomologies of the X [n] , following recent work of Lehn. In particular we study the Chern and Segre classes of tautological vector bundles on the Hilbert schemes X [n] . (author)

  17. Security problem on arbitrated quantum signature schemes

    International Nuclear Information System (INIS)

    Choi, Jeong Woon; Chang, Ku-Young; Hong, Dowon

    2011-01-01

    Many arbitrated quantum signature schemes implemented with the help of a trusted third party have been developed up to now. In order to guarantee unconditional security, most of them take advantage of the optimal quantum one-time encryption based on Pauli operators. However, in this paper we point out that the previous schemes provide security only against a total break attack and show in fact that there exists an existential forgery attack that can validly modify the transmitted pair of message and signature. In addition, we also provide a simple method to recover security against the proposed attack.

  18. Optimal sampling schemes applied in geology

    CSIR Research Space (South Africa)

    Debba, Pravesh

    2010-05-01

    Full Text Available Methodology 6 Results 7 Background and Research Question for Study 2 8 Study Area and Data 9 Methodology 10 Results 11 Conclusions Debba (CSIR) Optimal Sampling Schemes applied in Geology UP 2010 2 / 47 Outline 1 Introduction to hyperspectral remote... sensing 2 Objective of Study 1 3 Study Area 4 Data used 5 Methodology 6 Results 7 Background and Research Question for Study 2 8 Study Area and Data 9 Methodology 10 Results 11 Conclusions Debba (CSIR) Optimal Sampling Schemes applied in Geology...

  19. Quadratically convergent MCSCF scheme using Fock operators

    International Nuclear Information System (INIS)

    Das, G.

    1981-01-01

    A quadratically convergent formulation of the MCSCF method using Fock operators is presented. Among its advantages the present formulation is quadratically convergent unlike the earlier ones based on Fock operators. In contrast to other quadratically convergent schemes as well as the one based on generalized Brillouin's theorem, this method leads easily to a hybrid scheme where the weakly coupled orbitals (such as the core) are handled purely by Fock equations, while the rest of the orbitals are treated by a quadratically convergent approach with a truncated virtual space obtained by the use of the corresponding Fock equations

  20. Security problem on arbitrated quantum signature schemes

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Jeong Woon [Emerging Technology R and D Center, SK Telecom, Kyunggi 463-784 (Korea, Republic of); Chang, Ku-Young; Hong, Dowon [Cryptography Research Team, Electronics and Telecommunications Research Institute, Daejeon 305-700 (Korea, Republic of)

    2011-12-15

    Many arbitrated quantum signature schemes implemented with the help of a trusted third party have been developed up to now. In order to guarantee unconditional security, most of them take advantage of the optimal quantum one-time encryption based on Pauli operators. However, in this paper we point out that the previous schemes provide security only against a total break attack and show in fact that there exists an existential forgery attack that can validly modify the transmitted pair of message and signature. In addition, we also provide a simple method to recover security against the proposed attack.

  1. Clocking Scheme for Switched-Capacitor Circuits

    DEFF Research Database (Denmark)

    Steensgaard-Madsen, Jesper

    1998-01-01

    A novel clocking scheme for switched-capacitor (SC) circuits is presented. It can enhance the understanding of SC circuits and the errors caused by MOSFET (MOS) switches. Charge errors, and techniques to make SC circuits less sensitive to them are discussed.......A novel clocking scheme for switched-capacitor (SC) circuits is presented. It can enhance the understanding of SC circuits and the errors caused by MOSFET (MOS) switches. Charge errors, and techniques to make SC circuits less sensitive to them are discussed....

  2. Microbial incorporation of nitrogen in stream detritus

    Science.gov (United States)

    Diane M. Sanzone; Jennifer L. Tank; Judy L. Meyer; Patrick J. Mulholland; Stuart E.G. Findlay

    2001-01-01

    We adapted the chloroform fumigation method to determine microbial nitrogen (N) and microbial incorporation of 15N on three common substrates [leaves, wood and fine benthic organic matter (FBOM)] in three forest streams. We compared microbial N and 15 content of samples collected during a 6-week15N-NH...

  3. Microbially produced phytotoxins and plant disease management ...

    African Journals Online (AJOL)

    Nowadays, these evaluation techniques are becoming an important complement to classical breeding methods. The knowledge of the inactivation of microbial toxins has led to the use of microbial enzymes to inactivate phytotoxins thereby reducing incidence and severity of disease induced by microbial toxins. Considering ...

  4. Microbial communities in blueberry soils

    Science.gov (United States)

    Microbial communities thrive in the soil of the plant root zone and it is clear that these communities play a role in plant health. Although blueberry fields can be productive for decades, yields are sometimes below expectations and fields that are replanted sometimes underperform and/or take too lo...

  5. Advanced Microscopy of Microbial Cells

    DEFF Research Database (Denmark)

    Haagensen, Janus Anders Juul; Regenberg, Birgitte; Sternberg, Claus

    2011-01-01

    microscopy, super-resolution optical microscopy (STED, SIM, PALM) as well as atomic force microscopy and Raman spectroscopy. Using examples of bistability in microbial populations as well as biofilm development and differentiation in bacterial and yeast consortia, we demonstrate the importance of microscopy...

  6. Analysis of Program Obfuscation Schemes with Variable Encoding Technique

    Science.gov (United States)

    Fukushima, Kazuhide; Kiyomoto, Shinsaku; Tanaka, Toshiaki; Sakurai, Kouichi

    Program analysis techniques have improved steadily over the past several decades, and software obfuscation schemes have come to be used in many commercial programs. A software obfuscation scheme transforms an original program or a binary file into an obfuscated program that is more complicated and difficult to analyze, while preserving its functionality. However, the security of obfuscation schemes has not been properly evaluated. In this paper, we analyze obfuscation schemes in order to clarify the advantages of our scheme, the XOR-encoding scheme. First, we more clearly define five types of attack models that we defined previously, and define quantitative resistance to these attacks. Then, we compare the security, functionality and efficiency of three obfuscation schemes with encoding variables: (1) Sato et al.'s scheme with linear transformation, (2) our previous scheme with affine transformation, and (3) the XOR-encoding scheme. We show that the XOR-encoding scheme is superior with regard to the following two points: (1) the XOR-encoding scheme is more secure against a data-dependency attack and a brute force attack than our previous scheme, and is as secure against an information-collecting attack and an inverse transformation attack as our previous scheme, (2) the XOR-encoding scheme does not restrict the calculable ranges of programs and the loss of efficiency is less than in our previous scheme.

  7. Investigation of schemes for incorporating generator Q limits in the ...

    Indian Academy of Sciences (India)

    Handling generator Q limits is one such important feature needed in any practical load flow method. This paper presents a comprehensive investigation of two classes of schemes intended to handle this aspect i.e. the bus type switching scheme and the sensitivity scheme. We propose two new sensitivity based schemes ...

  8. Laboratory Information Management Software for genotyping workflows: applications in high throughput crop genotyping

    Directory of Open Access Journals (Sweden)

    Prasanth VP

    2006-08-01

    Full Text Available Abstract Background With the advances in DNA sequencer-based technologies, it has become possible to automate several steps of the genotyping process leading to increased throughput. To efficiently handle the large amounts of genotypic data generated and help with quality control, there is a strong need for a software system that can help with the tracking of samples and capture and management of data at different steps of the process. Such systems, while serving to manage the workflow precisely, also encourage good laboratory practice by standardizing protocols, recording and annotating data from every step of the workflow. Results A laboratory information management system (LIMS has been designed and implemented at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT that meets the requirements of a moderately high throughput molecular genotyping facility. The application is designed as modules and is simple to learn and use. The application leads the user through each step of the process from starting an experiment to the storing of output data from the genotype detection step with auto-binning of alleles; thus ensuring that every DNA sample is handled in an identical manner and all the necessary data are captured. The application keeps track of DNA samples and generated data. Data entry into the system is through the use of forms for file uploads. The LIMS provides functions to trace back to the electrophoresis gel files or sample source for any genotypic data and for repeating experiments. The LIMS is being presently used for the capture of high throughput SSR (simple-sequence repeat genotyping data from the legume (chickpea, groundnut and pigeonpea and cereal (sorghum and millets crops of importance in the semi-arid tropics. Conclusion A laboratory information management system is available that has been found useful in the management of microsatellite genotype data in a moderately high throughput genotyping

  9. Sources of funding for community schemes

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1999-11-01

    There is an increasing level of interest amongst community groups in the UK to become involved in the development of renewable energy schemes. Often however these community groups have only limited funds of their own, so any additional funds that can be identified to help fund their renewable energy scheme can be very useful. There are a range of funding sources available that provide grants or loans for which community groups are eligible to apply. Few of these funding sources are targeted towards renewable energy specifically, nevertheless the funds may be applicable to renewable energy schemes under appropriate circumstances. To date, however, few of these funds have been accessed by community groups for renewable energy initiatives. One of the reasons for this low take-up of funds on offer could be that the funding sources may be difficult and time-consuming to identify, especially where the energy component of the fund is not readily apparent. This directory draws together details about many of the principal funding sources available in the UK that may consider providing funds to community groups wanting to develop a renewable energy scheme. (author)

  10. The QKD network: model and routing scheme

    Science.gov (United States)

    Yang, Chao; Zhang, Hongqi; Su, Jinhai

    2017-11-01

    Quantum key distribution (QKD) technology can establish unconditional secure keys between two communicating parties. Although this technology has some inherent constraints, such as the distance and point-to-point mode limits, building a QKD network with multiple point-to-point QKD devices can overcome these constraints. Considering the development level of current technology, the trust relaying QKD network is the first choice to build a practical QKD network. However, the previous research didn't address a routing method on the trust relaying QKD network in detail. This paper focuses on the routing issues, builds a model of the trust relaying QKD network for easily analysing and understanding this network, and proposes a dynamical routing scheme for this network. From the viewpoint of designing a dynamical routing scheme in classical network, the proposed scheme consists of three components: a Hello protocol helping share the network topology information, a routing algorithm to select a set of suitable paths and establish the routing table and a link state update mechanism helping keep the routing table newly. Experiments and evaluation demonstrates the validity and effectiveness of the proposed routing scheme.

  11. SYNTHESIS OF VISCOELASTIC MATERIAL MODELS (SCHEMES

    Directory of Open Access Journals (Sweden)

    V. Bogomolov

    2014-10-01

    Full Text Available The principles of structural viscoelastic schemes construction for materials with linear viscoelastic properties in accordance with the given experimental data on creep tests are analyzed. It is shown that there can be only four types of materials with linear visco-elastic properties.

  12. BPHZL-subtraction scheme and axial gauges

    Energy Technology Data Exchange (ETDEWEB)

    Kreuzer, M.; Rebhan, A.; Schweda, M.; Piguet, O.

    1986-03-27

    The application of the BPHZL subtraction scheme to Yang-Mills theories in axial gauges is presented. In the auxillary mass formulation we show the validity of the convergence theorems for subtracted momentum space integrals, and we give the integral formulae necessary for one-loop calculations. (orig.).

  13. The data cyclotron query processing scheme

    NARCIS (Netherlands)

    R.A. Goncalves (Romulo); M.L. Kersten (Martin)

    2010-01-01

    htmlabstractDistributed database systems exploit static workload characteristics to steer data fragmentation and data allocation schemes. However, the grand challenge of distributed query processing is to come up with a self-organizing architecture, which exploits all resources to manage the hot

  14. THE DEVELOPMENT OF FREE PRIMARY EDUCATION SCHEME ...

    African Journals Online (AJOL)

    user

    Education scheme in Western Region and marked a radical departure from the hitherto ... academic symposia, lectures, debates, reputable journals and standard .... Enrolment in Primary Schools in the Western Region by Sex, 1953 – 1960. Year Boys .... “Possibly no single decision of the decade prior to independence had.

  15. High Order Semi-Lagrangian Advection Scheme

    Science.gov (United States)

    Malaga, Carlos; Mandujano, Francisco; Becerra, Julian

    2014-11-01

    In most fluid phenomena, advection plays an important roll. A numerical scheme capable of making quantitative predictions and simulations must compute correctly the advection terms appearing in the equations governing fluid flow. Here we present a high order forward semi-Lagrangian numerical scheme specifically tailored to compute material derivatives. The scheme relies on the geometrical interpretation of material derivatives to compute the time evolution of fields on grids that deform with the material fluid domain, an interpolating procedure of arbitrary order that preserves the moments of the interpolated distributions, and a nonlinear mapping strategy to perform interpolations between undeformed and deformed grids. Additionally, a discontinuity criterion was implemented to deal with discontinuous fields and shocks. Tests of pure advection, shock formation and nonlinear phenomena are presented to show performance and convergence of the scheme. The high computational cost is considerably reduced when implemented on massively parallel architectures found in graphic cards. The authors acknowledge funding from Fondo Sectorial CONACYT-SENER Grant Number 42536 (DGAJ-SPI-34-170412-217).

  16. An HFB scheme in natural orbitals

    International Nuclear Information System (INIS)

    Reinhard, P.G.; Rutz, K.; Maruhn, J.A.

    1997-01-01

    We present a formulation of the Hartree-Fock-Bogoliubov (HFB) equations which solves the problem directly in the basis of natural orbitals. This provides a very efficient scheme which is particularly suited for large scale calculations on coordinate-space grids. (orig.)

  17. A classification scheme for LWR fuel assemblies

    Energy Technology Data Exchange (ETDEWEB)

    Moore, R.S.; Williamson, D.A.; Notz, K.J.

    1988-11-01

    With over 100 light water nuclear reactors operating nationwide, representing designs by four primary vendors, and with reload fuel manufactured by these vendors and additional suppliers, a wide variety of fuel assembly types are in existence. At Oak Ridge National Laboratory, both the Systems Integration Program and the Characteristics Data Base project required a classification scheme for these fuels. This scheme can be applied to other areas and is expected to be of value to many Office of Civilian Radioactive Waste Management programs. To develop the classification scheme, extensive information on the fuel assemblies that have been and are being manufactured by the various nuclear fuel vendors was compiled, reviewed, and evaluated. It was determined that it is possible to characterize assemblies in a systematic manner, using a combination of physical factors. A two-stage scheme was developed consisting of 79 assembly types, which are grouped into 22 assembly classes. The assembly classes are determined by the general design of the reactor cores in which the assemblies are, or were, used. The general BWR and PWR classes are divided differently but both are based on reactor core configuration. 2 refs., 15 tabs.

  18. The EU Greenhouse Gas Emissions Trading Scheme

    NARCIS (Netherlands)

    Woerdman, Edwin; Woerdman, Edwin; Roggenkamp, Martha; Holwerda, Marijn

    2015-01-01

    This chapter explains how greenhouse gas emissions trading works, provides the essentials of the Directive on the European Union Emissions Trading Scheme (EU ETS) and summarizes the main implementation problems of the EU ETS. In addition, a law and economics approach is used to discuss the dilemmas

  19. Study of 228Ac decay scheme

    International Nuclear Information System (INIS)

    Pinto, H.V.

    1976-02-01

    Calibration in energy and efficiency of the system used. Obtainement of singles gamma ray spectra of low and high energy. Reduction of the data obtained in the spectrometer by means of computer: localization and determination of the areas of the peaks, also the analysis of the shape of the peaks for identification of doublets. Checking of the decay scheme [pt

  20. Parallel knock-out schemes in networks

    NARCIS (Netherlands)

    Broersma, H.J.; Fomin, F.V.; Woeginger, G.J.

    2004-01-01

    We consider parallel knock-out schemes, a procedure on graphs introduced by Lampert and Slater in 1997 in which each vertex eliminates exactly one of its neighbors in each round. We are considering cases in which after a finite number of rounds, where the minimimum number is called the parallel

  1. Nonclassical lightstates in optical communication schemes

    International Nuclear Information System (INIS)

    Mattle, K. U.

    1997-11-01

    The present thesis is a result in theoretical and experimental work on quant information and quant communication. The first part describes a new high intense source for polarization entangled photon pairs. The high quality of the source is clearly demonstrated by violating a Bell-inequality in less than 5 minutes with 100 standard deviations. This new source is a genius tool for new experiments in the field of fundamental physics as well as applied physics. The next chapter shows an experimental implementation of an optical dense quantum coding scheme. The combination of Bell-state generation and analysis of this entangled states leads to a new nonclassical communication scheme, where the channel capacity is enhanced. A single two state photon can be used for coding and decoding 1.58 bit instead of 1 bit for classical two state systems. The following chapter discusses two photon interference effects for two independent light sources. In an experiment two independent fluorescence pulses show this kind of interference effects. The fifth chapter describes 3-photon interference effects. This nonclassical interference effect is the elementary process for the quantum teleportation scheme. In this scheme an unknown particle state is transmitted from A to B without sending the particle itself. (author)

  2. The complete flux scheme in cylindrical coordinates

    NARCIS (Netherlands)

    Anthonissen, M.J.H.; Thije Boonkkamp, ten J.H.M.

    2014-01-01

    We consider the complete ¿ux (CF) scheme, a ¿nite volume method (FVM) presented in [1]. CF is based on an integral representation for the ¿uxes, found by solving a local boundary value problem that includes the source term. It performs well (second order accuracy) for both diffusion and advection

  3. Traffic calming schemes : opportunities and implementation strategies.

    NARCIS (Netherlands)

    Schagen, I.N.L.G. van (ed.)

    2003-01-01

    Commissioned by the Swedish National Road Authority, this report aims to provide a concise overview of knowledge of and experiences with traffic calming schemes in urban areas, both on a technical level and on a policy level. Traffic calming refers to a combination of network planning and

  4. Harmonic generation with multiple wiggler schemes

    Energy Technology Data Exchange (ETDEWEB)

    Bonifacio, R.; De Salvo, L.; Pierini, P. [Universita degli Studi, Milano (Italy)

    1995-02-01

    In this paper the authors give a simple theoretical description of the basic physics of the single pass high gain free electron laser (FEL), describing in some detail the FEL bunching properties and the harmonic generation technique with a multiple-wiggler scheme or a high gain optical klystron configuration.

  5. Zero leakage quantization scheme for biometric verification

    NARCIS (Netherlands)

    Groot, de J.A.; Linnartz, J.P.M.G.

    2011-01-01

    Biometrics gain increasing interest as a solution for many security issues, but privacy risks exist in case we do not protect the stored templates well. This paper presents a new verification scheme, which protects the secrets of the enrolled users. We will show that zero leakage is achieved if

  6. A classification scheme for LWR fuel assemblies

    International Nuclear Information System (INIS)

    Moore, R.S.; Williamson, D.A.; Notz, K.J.

    1988-11-01

    With over 100 light water nuclear reactors operating nationwide, representing designs by four primary vendors, and with reload fuel manufactured by these vendors and additional suppliers, a wide variety of fuel assembly types are in existence. At Oak Ridge National Laboratory, both the Systems Integration Program and the Characteristics Data Base project required a classification scheme for these fuels. This scheme can be applied to other areas and is expected to be of value to many Office of Civilian Radioactive Waste Management programs. To develop the classification scheme, extensive information on the fuel assemblies that have been and are being manufactured by the various nuclear fuel vendors was compiled, reviewed, and evaluated. It was determined that it is possible to characterize assemblies in a systematic manner, using a combination of physical factors. A two-stage scheme was developed consisting of 79 assembly types, which are grouped into 22 assembly classes. The assembly classes are determined by the general design of the reactor cores in which the assemblies are, or were, used. The general BWR and PWR classes are divided differently but both are based on reactor core configuration. 2 refs., 15 tabs

  7. Asynchronous schemes for CFD at extreme scales

    Science.gov (United States)

    Konduri, Aditya; Donzis, Diego

    2013-11-01

    Recent advances in computing hardware and software have made simulations an indispensable research tool in understanding fluid flow phenomena in complex conditions at great detail. Due to the nonlinear nature of the governing NS equations, simulations of high Re turbulent flows are computationally very expensive and demand for extreme levels of parallelism. Current large simulations are being done on hundreds of thousands of processing elements (PEs). Benchmarks from these simulations show that communication between PEs take a substantial amount of time, overwhelming the compute time, resulting in substantial waste in compute cycles as PEs remain idle. We investigate a novel approach based on widely used finite-difference schemes in which computations are carried out asynchronously, i.e. synchronization of data among PEs is not enforced and computations proceed regardless of the status of messages. This drastically reduces PE idle time and results in much larger computation rates. We show that while these schemes remain stable, their accuracy is significantly affected. We present new schemes that maintain accuracy under asynchronous conditions and provide a viable path towards exascale computing. Performance of these schemes will be shown for simple models like Burgers' equation.

  8. Generalization of binary tensor product schemes depends upon four parameters

    International Nuclear Information System (INIS)

    Bashir, R.; Bari, M.; Mustafa, G.

    2018-01-01

    This article deals with general formulae of parametric and non parametric bivariate subdivision scheme with four parameters. By assigning specific values to those parameters we get some special cases of existing tensor product schemes as well as a new proposed scheme. The behavior of schemes produced by the general formulae is interpolating, approximating and relaxed. Approximating bivariate subdivision schemes produce some other surfaces as compared to interpolating bivariate subdivision schemes. Polynomial reproduction and polynomial generation are desirable properties of subdivision schemes. Capability of polynomial reproduction and polynomial generation is strongly connected with smoothness, sum rules, convergence and approximation order. We also calculate the polynomial generation and polynomial reproduction of 9-point bivariate approximating subdivision scheme. Comparison of polynomial reproduction, polynomial generation and continuity of existing and proposed schemes has also been established. Some numerical examples are also presented to show the behavior of bivariate schemes. (author)

  9. Genotyping of Coxiella burnetii from domestic ruminants in northern Spain

    Directory of Open Access Journals (Sweden)

    Astobiza Ianire

    2012-12-01

    Full Text Available Abstract Background Information on the genotypic diversity of Coxiella burnetii isolates from infected domestic ruminants in Spain is limited. The aim of this study was to identify the C. burnetii genotypes infecting livestock in Northern Spain and compare them to other European genotypes. A commercial real-time PCR targeting the IS1111a insertion element was used to detect the presence of C. burnetii DNA in domestic ruminants from Spain. Genotypes were determined by a 6-loci Multiple Locus Variable number tandem repeat analysis (MLVA panel and Multispacer Sequence Typing (MST. Results A total of 45 samples from 4 goat herds (placentas, N = 4, 12 dairy cattle herds (vaginal mucus, individual milk, bulk tank milk, aerosols, N = 20 and 5 sheep flocks (placenta, vaginal swabs, faeces, air samples, dust, N = 21 were included in the study. Samples from goats and sheep were obtained from herds which had suffered abortions suspected to be caused by C. burnetii, whereas cattle samples were obtained from animals with reproductive problems compatible with C. burnetii infection, or consisted of bulk tank milk (BTM samples from a Q fever surveillance programme. C. burnetii genotypes identified in ruminants from Spain were compared to those detected in other countries. Three MLVA genotypes were found in 4 goat farms, 7 MLVA genotypes were identified in 12 cattle herds and 4 MLVA genotypes were identified in 5 sheep flocks. Clustering of the MLVA genotypes using the minimum spanning tree method showed a high degree of genetic similarity between most MLVA genotypes. Overall 11 different MLVA genotypes were obtained corresponding to 4 different MST genotypes: MST genotype 13, identified in goat, sheep and cattle from Spain; MST genotype 18, only identified in goats; and, MST genotypes 8 and 20, identified in small ruminants and cattle, respectively. All these genotypes had been previously identified in animal and human clinical samples from several

  10. Audioprofiles and antioxidant enzyme genotypes in presbycusis.

    Science.gov (United States)

    Angeli, Simon I; Bared, Anthony; Ouyang, Xiaomei; Du, Li Lin; Yan, Denise; Zhong Liu, Xue

    2012-11-01

    Audiometric patterns have been shown to indirectly provide information regarding the pathophysiology of presbycusis and be useful in the phenotyping of hereditary deafness. Hospital-based cohort study of adults with presbycusis, comparing the association of audiometric patterns and polymorphisms of antioxidant enzymes that have been linked to presbycusis: GSTT1, GSTM1 and NAT2. All subjects underwent a clinical evaluation and completed questionnaires regarding ototoxicity and noise exposure. Pure-tone threshold audiometry was obtained and subjects' audiograms were classified into specific patterns. DNA was extracted from blood and the polymorphisms of GSTT1, GSTM1, and the NAT2 variants (NAT2* 5A; NAT2* 6A,B) were analyzed by PCR. The audiometric patterns that were more prevalent in our cohort were "High-Frequency Steeply Sloping" or HFSS (33%), "High-Frequency Gently Sloping" or HFGS (31%), and "Flat" (27%), with other patterns being rare. We did not find a statistical significant effect of gender, age, hearing level, and ear side on the audiometric pattern. Subjects with mutant alleles for GSTT1 were more likely to have a HFSS audiogram than subjects with the wild type genotype. In this cohort, there was a similar prevalence for the three audiometric configurations HFSS, HFGS, and Flat, with other configurations being rare. Subjects with mutant alleles for GSTT1 were more likely to have a HFSS audiogram than subjects with the wild type genotype, suggesting that the basal turn of the cochlea is susceptible to GSTT1 regulated oxidative stress. However, further studies of audioprofiles with larger sample sizes may be needed to establish phenotype-genotype correlations in presbycusis. Copyright © 2012 The American Laryngological, Rhinological, and Otological Society, Inc.

  11. LevelScheme: A level scheme drawing and scientific figure preparation system for Mathematica

    Science.gov (United States)

    Caprio, M. A.

    2005-09-01

    LevelScheme is a scientific figure preparation system for Mathematica. The main emphasis is upon the construction of level schemes, or level energy diagrams, as used in nuclear, atomic, molecular, and hadronic physics. LevelScheme also provides a general infrastructure for the preparation of publication-quality figures, including support for multipanel and inset plotting, customizable tick mark generation, and various drawing and labeling tasks. Coupled with Mathematica's plotting functions and powerful programming language, LevelScheme provides a flexible system for the creation of figures combining diagrams, mathematical plots, and data plots. Program summaryTitle of program:LevelScheme Catalogue identifier:ADVZ Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADVZ Operating systems:Any which supports Mathematica; tested under Microsoft Windows XP, Macintosh OS X, and Linux Programming language used:Mathematica 4 Number of bytes in distributed program, including test and documentation:3 051 807 Distribution format:tar.gz Nature of problem:Creation of level scheme diagrams. Creation of publication-quality multipart figures incorporating diagrams and plots. Method of solution:A set of Mathematica packages has been developed, providing a library of level scheme drawing objects, tools for figure construction and labeling, and control code for producing the graphics.

  12. Plant genotypic diversity reduces the rate of consumer resource utilization.

    Science.gov (United States)

    McArt, Scott H; Thaler, Jennifer S

    2013-07-07

    While plant species diversity can reduce herbivore densities and herbivory, little is known regarding how plant genotypic diversity alters resource utilization by herbivores. Here, we show that an invasive folivore--the Japanese beetle (Popillia japonica)--increases 28 per cent in abundance, but consumes 24 per cent less foliage in genotypic polycultures compared with monocultures of the common evening primrose (Oenothera biennis). We found strong complementarity for reduced herbivore damage among plant genotypes growing in polycultures and a weak dominance effect of particularly resistant genotypes. Sequential feeding by P. japonica on different genotypes from polycultures resulted in reduced consumption compared with feeding on different plants of the same genotype from monocultures. Thus, diet mixing among plant genotypes reduced herbivore consumption efficiency. Despite positive complementarity driving an increase in fruit production in polycultures, we observed a trade-off between complementarity for increased plant productivity and resistance to herbivory, suggesting costs in the complementary use of resources by plant genotypes may manifest across trophic levels. These results elucidate mechanisms for how plant genotypic diversity simultaneously alters resource utilization by both producers and consumers, and show that population genotypic diversity can increase the resistance of a native plant to an invasive herbivore.

  13. Relationship of some upland rice genotype after gamma irradiation

    Science.gov (United States)

    Suliartini, N. W. S.; Wijayanto, T.; Madiki, A.; Boer, D.; Muhidin; Juniawan

    2018-02-01

    The objective of the research was to group local upland rice genotypes after being treated with gamma irradiation. The research materials were upland rice genotypes resulted from mutation of the second generation and two parents: Pae Loilo (K3D0) and Pae Pongasi (K2D0) Cultivars. The research was conducted at the Indonesian Sweetener and Fiber Crops Research Institute, Malang Regency, and used the augmented design method. Research data were analyzed with R Program. Eight hundred and seventy one genotypes were selected with the selection criteria were based on yields on the average parents added 1.5 standard deviation. Based on the selection, eighty genotypes were analyzed with cluster analyses. Nine observation variables were used to develop cluster dendrogram using average linked method. Genetic distance was measured by euclidean distance. The results of cluster dendrogram showed that tested genotypes were divided into eight groups. Group 1, 2, 7, and 8 each had one genotype, group 3 and 6 each had two genotypes, group 4 had 25 genotypes, and group 5 had 51 genotypes. Check genotypes formed a separate group. Group 6 had the highest yield per plant of 126.11 gram, followed by groups 5 and 4 of 97.63 and 94.08 gram, respectively.

  14. A novel secret image sharing scheme based on chaotic system

    Science.gov (United States)

    Li, Li; Abd El-Latif, Ahmed A.; Wang, Chuanjun; Li, Qiong; Niu, Xiamu

    2012-04-01

    In this paper, we propose a new secret image sharing scheme based on chaotic system and Shamir's method. The new scheme protects the shadow images with confidentiality and loss-tolerance simultaneously. In the new scheme, we generate the key sequence based on chaotic system and then encrypt the original image during the sharing phase. Experimental results and analysis of the proposed scheme demonstrate a better performance than other schemes and confirm a high probability to resist brute force attack.

  15. Simple Numerical Schemes for the Korteweg-deVries Equation

    International Nuclear Information System (INIS)

    McKinstrie, C. J.; Kozlov, M.V.

    2000-01-01

    Two numerical schemes, which simulate the propagation of dispersive non-linear waves, are described. The first is a split-step Fourier scheme for the Korteweg-de Vries (KdV) equation. The second is a finite-difference scheme for the modified KdV equation. The stability and accuracy of both schemes are discussed. These simple schemes can be used to study a wide variety of physical processes that involve dispersive nonlinear waves

  16. Simple Numerical Schemes for the Korteweg-deVries Equation

    Energy Technology Data Exchange (ETDEWEB)

    C. J. McKinstrie; M. V. Kozlov

    2000-12-01

    Two numerical schemes, which simulate the propagation of dispersive non-linear waves, are described. The first is a split-step Fourier scheme for the Korteweg-de Vries (KdV) equation. The second is a finite-difference scheme for the modified KdV equation. The stability and accuracy of both schemes are discussed. These simple schemes can be used to study a wide variety of physical processes that involve dispersive nonlinear waves.

  17. Electricity storage using a thermal storage scheme

    Energy Technology Data Exchange (ETDEWEB)

    White, Alexander, E-mail: ajw36@cam.ac.uk [Hopkinson Laboratory, Cambridge University Engineering Department, Trumpington Street, Cambridge. CB2 1PZ (United Kingdom)

    2015-01-22

    The increasing use of renewable energy technologies for electricity generation, many of which have an unpredictably intermittent nature, will inevitably lead to a greater demand for large-scale electricity storage schemes. For example, the expanding fraction of electricity produced by wind turbines will require either backup or storage capacity to cover extended periods of wind lull. This paper describes a recently proposed storage scheme, referred to here as Pumped Thermal Storage (PTS), and which is based on “sensible heat” storage in large thermal reservoirs. During the charging phase, the system effectively operates as a high temperature-ratio heat pump, extracting heat from a cold reservoir and delivering heat to a hot one. In the discharge phase the processes are reversed and it operates as a heat engine. The round-trip efficiency is limited only by process irreversibilities (as opposed to Second Law limitations on the coefficient of performance and the thermal efficiency of the heat pump and heat engine respectively). PTS is currently being developed in both France and England. In both cases, the schemes operate on the Joule-Brayton (gas turbine) cycle, using argon as the working fluid. However, the French scheme proposes the use of turbomachinery for compression and expansion, whereas for that being developed in England reciprocating devices are proposed. The current paper focuses on the impact of the various process irreversibilities on the thermodynamic round-trip efficiency of the scheme. Consideration is given to compression and expansion losses and pressure losses (in pipe-work, valves and thermal reservoirs); heat transfer related irreversibility in the thermal reservoirs is discussed but not included in the analysis. Results are presented demonstrating how the various loss parameters and operating conditions influence the overall performance.

  18. Analysis of adaptive walks on NK fitness landscapes with different interaction schemes

    International Nuclear Information System (INIS)

    Nowak, Stefan; Krug, Joachim

    2015-01-01

    Fitness landscapes are genotype to fitness mappings commonly used in evolutionary biology and computer science which are closely related to spin glass models. In this paper, we study the NK model for fitness landscapes where the interaction scheme between genes can be explicitly defined. The focus is on how this scheme influences the overall shape of the landscape. Our main tool for the analysis are adaptive walks, an idealized dynamics by which the population moves uphill in fitness and terminates at a local fitness maximum. We use three different types of walks and investigate how their length (the number of steps required to reach a local peak) and height (the fitness at the endpoint of the walk) depend on the dimensionality and structure of the landscape. We find that the distribution of local maxima over the landscape is particularly sensitive to the choice of interaction pattern. Most quantities that we measure are simply correlated to the rank of the scheme, which is equal to the number of nonzero coefficients in the expansion of the fitness landscape in terms of Walsh functions

  19. Toward Understanding, Managing, and Protecting Microbial Ecosystems

    Science.gov (United States)

    Bodelier, Paul L. E.

    2011-01-01

    Microbial communities are at the very basis of life on earth, catalyzing biogeochemical reactions driving global nutrient cycles. However, unlike for plants and animals, microbial diversity is not on the biodiversity–conservation agenda. The latter, however, would imply that microbial diversity is not under any threat by anthropogenic disturbance or climate change. This maybe a misconception caused by the rudimentary knowledge we have concerning microbial diversity and its role in ecosystem functioning. This perspective paper identifies major areas with knowledge gaps within the field of environmental microbiology that preclude a comprehension of microbial ecosystems on the level we have for plants and animals. Opportunities and challenges are pointed out to open the microbial black box and to go from descriptive to predictive microbial ecology. PMID:21747797

  20. Towards understanding, managing and protecting microbial ecosystems

    Directory of Open Access Journals (Sweden)

    Paul eBodelier

    2011-04-01

    Full Text Available Microbial communities are at the very basis of life on earth, catalysing biogeochemical reactions driving global nutrient cycles. However, unlike for plants and animals, microbial diversity is not on the biodiversity conservation agenda. The latter, however, would imply that microbial diversity is not under any threat by anthropogenic disturbance or climate change. This maybe a misconception caused by the rudimentary knowledge we have concerning microbial diversity and its role in ecosystem functioning. This perspective paper indentifies major areas with knowledge gaps within the field of environmental microbiology that preclude a comprehension of microbial ecosystems on the level we have for plants and animals. Opportunities and challenges are pointed out to open the microbial black box and to go from descriptive to predictive microbial ecology.

  1. Toward understanding, managing, and protecting microbial ecosystems.

    Science.gov (United States)

    Bodelier, Paul L E

    2011-01-01

    Microbial communities are at the very basis of life on earth, catalyzing biogeochemical reactions driving global nutrient cycles. However, unlike for plants and animals, microbial diversity is not on the biodiversity-conservation agenda. The latter, however, would imply that microbial diversity is not under any threat by anthropogenic disturbance or climate change. This maybe a misconception caused by the rudimentary knowledge we have concerning microbial diversity and its role in ecosystem functioning. This perspective paper identifies major areas with knowledge gaps within the field of environmental microbiology that preclude a comprehension of microbial ecosystems on the level we have for plants and animals. Opportunities and challenges are pointed out to open the microbial black box and to go from descriptive to predictive microbial ecology.

  2. A classification scheme for risk assessment methods.

    Energy Technology Data Exchange (ETDEWEB)

    Stamp, Jason Edwin; Campbell, Philip LaRoche

    2004-08-01

    This report presents a classification scheme for risk assessment methods. This scheme, like all classification schemes, provides meaning by imposing a structure that identifies relationships. Our scheme is based on two orthogonal aspects--level of detail, and approach. The resulting structure is shown in Table 1 and is explained in the body of the report. Each cell in the Table represent a different arrangement of strengths and weaknesses. Those arrangements shift gradually as one moves through the table, each cell optimal for a particular situation. The intention of this report is to enable informed use of the methods so that a method chosen is optimal for a situation given. This report imposes structure on the set of risk assessment methods in order to reveal their relationships and thus optimize their usage.We present a two-dimensional structure in the form of a matrix, using three abstraction levels for the rows and three approaches for the columns. For each of the nine cells in the matrix we identify the method type by name and example. The matrix helps the user understand: (1) what to expect from a given method, (2) how it relates to other methods, and (3) how best to use it. Each cell in the matrix represent a different arrangement of strengths and weaknesses. Those arrangements shift gradually as one moves through the table, each cell optimal for a particular situation. The intention of this report is to enable informed use of the methods so that a method chosen is optimal for a situation given. The matrix, with type names in the cells, is introduced in Table 2 on page 13 below. Unless otherwise stated we use the word 'method' in this report to refer to a 'risk assessment method', though often times we use the full phrase. The use of the terms 'risk assessment' and 'risk management' are close enough that we do not attempt to distinguish them in this report. The remainder of this report is organized as follows. In

  3. New advection schemes for free surface flows

    International Nuclear Information System (INIS)

    Pavan, Sara

    2016-01-01

    The purpose of this thesis is to build higher order and less diffusive schemes for pollutant transport in shallow water flows or 3D free surface flows. We want robust schemes which respect the main mathematical properties of the advection equation with relatively low numerical diffusion and apply them to environmental industrial applications. Two techniques are tested in this work: a classical finite volume method and a residual distribution technique combined with a finite element method. For both methods we propose a decoupled approach since it is the most advantageous in terms of accuracy and CPU time. Concerning the first technique, a vertex-centred finite volume method is used to solve the augmented shallow water system where the numerical flux is computed through an Harten-Lax-Van Leer-Contact Riemann solver. Starting from this solution, a decoupled approach is formulated and is preferred since it allows to compute with a larger time step the advection of a tracer. This idea was inspired by Audusse, E. and Bristeau, M.O. [13]. The Monotonic Upwind Scheme for Conservation Law, combined with the decoupled approach, is then used for the second order extension in space. The wetting and drying problem is also analysed and a possible solution is presented. In the second case, the shallow water system is entirely solved using the finite element technique and the residual distribution method is applied to the solution of the tracer equation, focusing on the case of time-dependent problems. However, for consistency reasons the resolution of the continuity equation must be considered in the numerical discretization of the tracer. In order to get second order schemes for unsteady cases a predictor-corrector scheme is used in this work. A first order but less diffusive version of the predictor-corrector scheme is also introduced. Moreover, we also present a new locally semi-implicit version of the residual distribution method which, in addition to good properties in

  4. Linking genotypes database with locus-specific database and genotype-phenotype correlation in phenylketonuria.

    Science.gov (United States)

    Wettstein, Sarah; Underhaug, Jarl; Perez, Belen; Marsden, Brian D; Yue, Wyatt W; Martinez, Aurora; Blau, Nenad

    2015-03-01

    The wide range of metabolic phenotypes in phenylketonuria is due to a large number of variants causing variable impairment in phenylalanine hydroxylase function. A total of 834 phenylalanine hydroxylase gene variants from the locus-specific database PAHvdb and genotypes of 4181 phenylketonuria patients from the BIOPKU database were characterized using FoldX, SIFT Blink, Polyphen-2 and SNPs3D algorithms. Obtained data was correlated with residual enzyme activity, patients' phenotype and tetrahydrobiopterin responsiveness. A descriptive analysis of both databases was compiled and an interactive viewer in PAHvdb database was implemented for structure visualization of missense variants. We found a quantitative relationship between phenylalanine hydroxylase protein stability and enzyme activity (r(s) = 0.479), between protein stability and allelic phenotype (r(s) = -0.458), as well as between enzyme activity and allelic phenotype (r(s) = 0.799). Enzyme stability algorithms (FoldX and SNPs3D), allelic phenotype and enzyme activity were most powerful to predict patients' phenotype and tetrahydrobiopterin response. Phenotype prediction was most accurate in deleterious genotypes (≈ 100%), followed by homozygous (92.9%), hemizygous (94.8%), and compound heterozygous genotypes (77.9%), while tetrahydrobiopterin response was correctly predicted in 71.0% of all cases. To our knowledge this is the largest study using algorithms for the prediction of patients' phenotype and tetrahydrobiopterin responsiveness in phenylketonuria patients, using data from the locus-specific and genotypes database.

  5. Genome-wide association study of Arabidopsis thaliana leaf microbial community.

    Science.gov (United States)

    Horton, Matthew W; Bodenhausen, Natacha; Beilsmith, Kathleen; Meng, Dazhe; Muegge, Brian D; Subramanian, Sathish; Vetter, M Madlen; Vilhjálmsson, Bjarni J; Nordborg, Magnus; Gordon, Jeffrey I; Bergelson, Joy

    2014-11-10

    Identifying the factors that influence the outcome of host-microbial interactions is critical to protecting biodiversity, minimizing agricultural losses and improving human health. A few genes that determine symbiosis or resistance to infectious disease have been identified in model species, but a comprehensive examination of how a host genotype influences the structure of its microbial community is lacking. Here we report the results of a field experiment with the model plant Arabidopsis thaliana to identify the fungi and bacteria that colonize its leaves and the host loci that influence the microbe numbers. The composition of this community differs among accessions of A. thaliana. Genome-wide association studies (GWAS) suggest that plant loci responsible for defense and cell wall integrity affect variation in this community. Furthermore, species richness in the bacterial community is shaped by host genetic variation, notably at loci that also influence the reproduction of viruses, trichome branching and morphogenesis.

  6. Pyroprinting: a rapid and flexible genotypic fingerprinting method for typing bacterial strains.

    Science.gov (United States)

    Black, Michael W; VanderKelen, Jennifer; Montana, Aldrin; Dekhtyar, Alexander; Neal, Emily; Goodman, Anya; Kitts, Christopher L

    2014-10-01

    Bacterial strain typing is commonly employed in studies involving epidemiology, population ecology, and microbial source tracking to identify sources of fecal contamination. Methods for differentiating strains generally use either a collection of phenotypic traits or rely on some interrogation of the bacterial genotype. This report introduces pyroprinting, a novel genotypic strain typing method that is rapid, inexpensive, and discriminating compared to the most sensitive methods already in use. Pyroprinting relies on the simultaneous pyrosequencing of polymorphic multicopy loci, such as the intergenic transcribed spacer regions of rRNA operons in bacterial genomes. Data generated by sequencing combinations of variable templates are reproducible and intrinsically digitized. The theory and development of pyroprinting in Escherichia coli, including the selection of similarity thresholds to define matches between isolates, are presented. The pyroprint-based strain differentiation limits and phylogenetic relevance compared to other typing methods are also explored. Pyroprinting is unique in its simplicity and, paradoxically, in its intrinsic complexity. This new approach serves as an excellent alternative to more cumbersome or less phylogenetically relevant strain typing methods. Copyright © 2014 Elsevier B.V. All rights reserved.

  7. Microbial Metabolism in Serpentinite Fluids

    Science.gov (United States)

    Crespo-Medina, M.; Brazelton, W. J.; Twing, K. I.; Kubo, M.; Hoehler, T. M.; Schrenk, M. O.

    2013-12-01

    Serpentinization is the process in which ultramafic rocks, characteristic of the upper mantle, react with water liberating mantle carbon and reducing power to potenially support chemosynthetic microbial communities. These communities may be important mediators of carbon and energy exchange between the deep Earth and the surface biosphere. Our work focuses on the Coast Range Ophiolite Microbial Observatory (CROMO) in Northern California where subsurface fluids are accessible through a series of wells. Preliminary analyses indicate that the highly basic fluids (pH 9-12) have low microbial diversity, but there is limited knowledge about the metabolic capabilities of these communties. Metagenomic data from similar serpentine environments [1] have identified Betaproteobacteria belonging to the order Burkholderiales and Gram-positive bacteria from the order Clostridiales as key components of the serpentine microbiome. In an effort to better characterize the microbial community, metabolism, and geochemistry at CROMO, fluids from two representative wells (N08B and CSWold) were sampled during recent field campaigns. Geochemical characterization of the fluids includes measurements of dissolved gases (H2, CO, CH4), dissolved inorganic and organic carbon, volatile fatty acids, and nutrients. The wells selected can be differentiated in that N08B had higher pH (10-11), lower dissolved oxygen, and cell counts ranging from 105-106 cells mL-1 of fluid, with an abundance of the betaproteobacterium Hydrogenophaga. In contrast, fluids from CSWold have slightly lower pH (9-9.5), DO, and conductivity, as well as higher TDN and TDP. CSWold fluid is also characterized for having lower cell counts (~103 cells mL-1) and an abundance of Dethiobacter, a taxon within the phylum Clostridiales. Microcosm experiments were conducted with the purpose of monitoring carbon fixation, methanotrophy and metabolism of small organic compounds, such as acetate and formate, while tracing changes in fluid

  8. Key Concepts in Microbial Oceanography

    Science.gov (United States)

    Bruno, B. C.; Achilles, K.; Walker, G.; Weersing, K.; Team, A

    2008-12-01

    The Center for Microbial Oceanography: Research and Education (C-MORE) is a multi-institution Science and Technology Center, established by the National Science Foundation in 2006. C-MORE's research mission is to facilitate a more comprehensive understanding of the diverse assemblages of microorganisms in the sea, ranging from the genetic basis of marine microbial biogeochemistry including the metabolic regulation and environmental controls of gene expression, to the processes that underpin the fluxes of carbon, related bioelements, and energy in the marine environment. The C-MORE education and outreach program is focused on increasing scientific literacy in microbial oceanography among students, educators, and the general public. A first step toward this goal is defining the key concepts that constitute microbial oceanography. After lengthy discussions with scientists and educators, both within and outside C-MORE, we have arrived at six key concepts: 1) Marine microbes are very small and have been around for a long time; 2) Life on Earth could not exist without microbes; 3) Most marine microbes are beneficial; 4) Microbes are everywhere: they are extremely abundant and diverse; 5) Microbes significantly impact our global climate; and 6) There are new discoveries every day in the field of microbial oceanography. A C-MORE-produced brochure on these six key concepts will be distributed at the meeting. Advanced copies may be requested by email or downloaded from the C-MORE web site(http://cmore.soest.hawaii.edu/downloads/MO_key_concepts_hi-res.pdf). This brochure also includes information on career pathways in microbial oceanography, with the aim of broadening participation in the field. C-MORE is eager to work in partnership to incorporate these key concepts into other science literacy publications, particularly those involving ocean and climate literacy. We thank the following contributors and reviewers: P Chisholm, A Dolberry, and A Thompson (MIT); N Lawrence

  9. The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes

    Science.gov (United States)

    van Overbeek, Leonard S.; Berg, Gabriele; Pirttilä, Anna Maria; Compant, Stéphane; Campisano, Andrea; Döring, Matthias; Sessitsch, Angela

    2015-01-01

    SUMMARY All plants are inhabited internally by diverse microbial communities comprising bacterial, archaeal, fungal, and protistic taxa. These microorganisms showing endophytic lifestyles play crucial roles in plant development, growth, fitness, and diversification. The increasing awareness of and information on endophytes provide insight into the complexity of the plant microbiome. The nature of plant-endophyte interactions ranges from mutualism to pathogenicity. This depends on a set of abiotic and biotic factors, including the genotypes of plants and microbes, environmental conditions, and the dynamic network of interactions within the plant biome. In this review, we address the concept of endophytism, considering the latest insights into evolution, plant ecosystem functioning, and multipartite interactions. PMID:26136581

  10. Enhancing microbial production of biofuels by expanding microbial metabolic pathways.

    Science.gov (United States)

    Yu, Ping; Chen, Xingge; Li, Peng

    2017-09-01

    Fatty acid, isoprenoid, and alcohol pathways have been successfully engineered to produce biofuels. By introducing three genes, atfA, adhE, and pdc, into Escherichia coli to expand fatty acid pathway, up to 1.28 g/L of fatty acid ethyl esters can be achieved. The isoprenoid pathway can be expanded to produce bisabolene with a high titer of 900 mg/L in Saccharomyces cerevisiae. Short- and long-chain alcohols can also be effectively biosynthesized by extending the carbon chain of ketoacids with an engineered "+1" alcohol pathway. Thus, it can be concluded that expanding microbial metabolic pathways has enormous potential for enhancing microbial production of biofuels for future industrial applications. However, some major challenges for microbial production of biofuels should be overcome to compete with traditional fossil fuels: lowering production costs, reducing the time required to construct genetic elements and to increase their predictability and reliability, and creating reusable parts with useful and predictable behavior. To address these challenges, several aspects should be further considered in future: mining and transformation of genetic elements related to metabolic pathways, assembling biofuel elements and coordinating their functions, enhancing the tolerance of host cells to biofuels, and creating modular subpathways that can be easily interconnected. © 2016 International Union of Biochemistry and Molecular Biology, Inc.

  11. Antioxidant capacity of anthocyanins from acerola genotypes

    Directory of Open Access Journals (Sweden)

    Vera Lúcia Arroxelas Galvão De Lima

    2011-03-01

    Full Text Available Anthocyanins from 12 acerola genotypes cultivated at the Active Germplasm Bank at Federal Rural University of Pernambuco were isolated for antioxidant potential evaluation. The antioxidant activity and radical scavenging capacity of the anthocyanin isolates were measured according to the β-carotene bleaching method and 1,1-diphenyl-2-picrylhydrazyl (DPPH free radical scavenging assay, respectively. The antioxidant activity varied from 25.58 to 47.04% at 0.2 mg.mL-1, and it was measured using the β-carotene bleaching method. The free radical scavenging capacity increased according to the increase in concentration and reaction time by the DPPH assay. At 16.7 μg.mL-1 concentration and after 5 minutes and 2 hours reaction time, the percentage of scavenged radicals varied from 36.97 to 63.92% and 73.27 to 94.54%, respectively. Therefore, the antioxidant capacity of acerola anthocyanins varied amongst acerola genotypes and methods used. The anthocyanins present in this fruit may supply substantial dietary source of antioxidant which may promote health and produce disease prevention effects.

  12. [Mexican phenotype and genotype Vibrio cholerae 01].

    Science.gov (United States)

    Giono, S; Gutiérrez Cogno, L; Rodríguez Angeles, G; del Rio Zolezzi, A; Valdespino González, J L; Sepúlveda Amor, J

    1995-01-01

    This paper presents the phenotypical and genotypical characterization of 26922 Vibrio cholerae 01 strains isolated in Mexico from 1991 to 1993. All strains isolated were El Tor biovar. Strains were sensitive to antibiotics excluding furazolidone, streptomycin and sulfisoxasole to which we found resistance in 97% and we are using this characteristic as epidemiological markers. We detected a marked change in frequency of Inaba serotype from 1991, when it was dominant, with 99.5%, until 1992 when Ogawa serotype turned to be dominant with 95% of isolates. All Vibrio cholerae 01 strains, except one Ogawa strain, were to igenic, and V. choleraeno 01 were not toxigenic by ELISA, PCR and cell culture tests. Dominant ribotype was 5, but we found some strains with 6a pattern and two with ribotype 12. We are searching for ribotype 2 among hemolytic strains in order to learn if there is any relation to Gulf Coast strains prevalent in the USA, but until now we have not found any V. cholerae ribotype 2 in our isolates. Even if rapid tests are recommended for immediate diagnosis of cholera, it is necessary to continue bacterial isolation in order to have strains for phenotyping and genotyping studies that may support epidemiological analysis.

  13. HFE genotype affects exosome phenotype in cancer.

    Science.gov (United States)

    Mrowczynski, Oliver D; Madhankumar, A B; Slagle-Webb, Becky; Lee, Sang Y; Zacharia, Brad E; Connor, James R

    2017-08-01

    Neuroblastoma is the third most common childhood cancer, and timely diagnosis and sensitive therapeutic monitoring remain major challenges. Tumor progression and recurrence is common with little understanding of mechanisms. A major recent focus in cancer biology is the impact of exosomes on metastatic behavior and the tumor microenvironment. Exosomes have been demonstrated to contribute to the oncogenic effect on the surrounding tumor environment and also mediate resistance to therapy. The effect of genotype on exosomal phenotype has not yet been explored. We interrogated exosomes from human neuroblastoma cells that express wild-type or mutant forms of the HFE gene. HFE, one of the most common autosomal recessive polymorphisms in the Caucasian population, originally associated with hemochromatosis, has also been associated with increased tumor burden, therapeutic resistance boost, and negative impact on patient survival. Herein, we demonstrate that changes in genotype cause major differences in the molecular and functional properties of exosomes; specifically, HFE mutant derived exosomes have increased expression of proteins relating to invasion, angiogenesis, and cancer therapeutic resistance. HFE mutant derived exosomes were also shown to transfer this cargo to recipient cells and cause an increased oncogenic functionality in those recipient cells. Copyright © 2017. Published by Elsevier B.V.

  14. Haplotype-Based Genotyping in Polyploids

    Directory of Open Access Journals (Sweden)

    Josh P. Clevenger

    2018-04-01

    Full Text Available Accurate identification of polymorphisms from sequence data is crucial to unlocking the potential of high throughput sequencing for genomics. Single nucleotide polymorphisms (SNPs are difficult to accurately identify in polyploid crops due to the duplicative nature of polyploid genomes leading to low confidence in the true alignment of short reads. Implementing a haplotype-based method in contrasting subgenome-specific sequences leads to higher accuracy of SNP identification in polyploids. To test this method, a large-scale 48K SNP array (Axiom Arachis2 was developed for Arachis hypogaea (peanut, an allotetraploid, in which 1,674 haplotype-based SNPs were included. Results of the array show that 74% of the haplotype-based SNP markers could be validated, which is considerably higher than previous methods used for peanut. The haplotype method has been implemented in a standalone program, HAPLOSWEEP, which takes as input bam files and a vcf file and identifies haplotype-based markers. Haplotype discovery can be made within single reads or span paired reads, and can leverage long read technology by targeting any length of haplotype. Haplotype-based genotyping is applicable in all allopolyploid genomes and provides confidence in marker identification and in silico-based genotyping for polyploid genomics.

  15. Hearing impairment in genotyped Wolfram syndrome patients.

    Science.gov (United States)

    Plantinga, Rutger F; Pennings, Ronald J E; Huygen, Patrick L M; Bruno, Rocco; Eller, Philipp; Barrett, Timothy G; Vialettes, Bernard; Paquis-Fluklinger, Veronique; Lombardo, Fortunato; Cremers, Cor W R J

    2008-07-01

    Wolfram syndrome is a progressive neurodegenerative syndrome characterized by the features "DIDMOAD" (diabetes insipidus, diabetes mellitus, optic atrophy, and deafness). We sought to study the audiometric data of genotyped Wolfram syndrome patients with sensorineural hearing impairment. Pure tone threshold data of 23 Wolfram syndrome patients were used for cross-sectional analysis in subgroups (age less than 16 years or between 19 and 25 years, gender, and origin). All subgroups, with 1 exception, showed a fairly similar type of hearing impairment with, on average, thresholds of about 25 dB (range, 0 to 65 dB) at 0.25 to 1 kHz, gently sloping downward to about 60 dB (range, 25 to 95 dB) at 8 kHz. The subgroup of Dutch women, which was excluded from the calculations of the average hearing thresholds, showed a higher degree of hearing impairment. Only the latter subgroup showed progression; however, contrary to the previous longitudinal analysis, progression was not significant in the present cross-sectional analysis, presumably because of the high degree of cross-subject variability. This unique collection of audiometric data from genotyped Wolfram syndrome patients shows no substantial progression in sensorineural hearing impairment with advancing age, no relation to the types of WFS1 mutations identified, and, with exclusion of the subgroup of Dutch female patients, no significant sex-related differences.

  16. Microbial Safety of Fishery Products

    Digital Repository Service at National Institute of Oceanography (India)

    Karunasagar, Indrani; Karunasagar, Iddya; Parvathi, A.

    taxonomic group (Lees, 2000). A number of genotypes linked to geographical regions can be differentiated (Tsarevo et al., 1999). The virus causes an acute, self- limiting liver disease, but in contrast to hepatitis A, there could be high mortality rate...; Jaykus et al., 1996). Epidemiological studies have suggested the diversity of Norovirus strains, though recent reports have suggested existence of two broad genogroups (Lees, 2000). Nevertheless, genomic regions with sufficient commonality to permit...

  17. An Efficient Explicit Finite-Difference Scheme for Simulating Coupled Biomass Growth on Nutritive Substrates

    Directory of Open Access Journals (Sweden)

    G. F. Sun

    2015-01-01

    Full Text Available A novel explicit finite-difference (FD method is presented to simulate the positive and bounded development process of a microbial colony subjected to a substrate of nutrients, which is governed by a nonlinear parabolic partial differential equations (PDE system. Our explicit FD scheme is uniquely designed in such a way that it transfers the nonlinear terms in the original PDE into discrete sets of linear ones in the algebraic equation system that can be solved very efficiently, while ensuring the stability and the boundedness of the solution. This is achieved through (1 a proper design of intertwined FD approximations for the diffusion function term in both time and spatial variations and (2 the control of the time-step through establishing theoretical stability criteria. A detailed theoretical stability analysis is conducted to reveal that our FD method is indeed stable. Our examples verified the fact that the numerical solution can be ensured nonnegative and bounded to simulate the actual physics. Numerical examples have also been presented to demonstrate the efficiency of the proposed scheme. The present scheme is applicable for solving similar systems of PDEs in the investigation of the dynamics of biological films.

  18. Scheme for Quantum Computing Immune to Decoherence

    Science.gov (United States)

    Williams, Colin; Vatan, Farrokh

    2008-01-01

    A constructive scheme has been devised to enable mapping of any quantum computation into a spintronic circuit in which the computation is encoded in a basis that is, in principle, immune to quantum decoherence. The scheme is implemented by an algorithm that utilizes multiple physical spins to encode each logical bit in such a way that collective errors affecting all the physical spins do not disturb the logical bit. The scheme is expected to be of use to experimenters working on spintronic implementations of quantum logic. Spintronic computing devices use quantum-mechanical spins (typically, electron spins) to encode logical bits. Bits thus encoded (denoted qubits) are potentially susceptible to errors caused by noise and decoherence. The traditional model of quantum computation is based partly on the assumption that each qubit is implemented by use of a single two-state quantum system, such as an electron or other spin-1.2 particle. It can be surprisingly difficult to achieve certain gate operations . most notably, those of arbitrary 1-qubit gates . in spintronic hardware according to this model. However, ironically, certain 2-qubit interactions (in particular, spin-spin exchange interactions) can be achieved relatively easily in spintronic hardware. Therefore, it would be fortunate if it were possible to implement any 1-qubit gate by use of a spin-spin exchange interaction. While such a direct representation is not possible, it is possible to achieve an arbitrary 1-qubit gate indirectly by means of a sequence of four spin-spin exchange interactions, which could be implemented by use of four exchange gates. Accordingly, the present scheme provides for mapping any 1-qubit gate in the logical basis into an equivalent sequence of at most four spin-spin exchange interactions in the physical (encoded) basis. The complexity of the mathematical derivation of the scheme from basic quantum principles precludes a description within this article; it must suffice to report

  19. Microbial Nitrogen-Cycle Gene Abundance in Soil of Cropland Abandoned for Different Periods.

    Directory of Open Access Journals (Sweden)

    Huhe

    Full Text Available In Inner Mongolia, steppe grasslands face desertification or degradation because of human overuse and abandonment after inappropriate agricultural management. The soils in these abandoned croplands exist in heterogeneous environments characterized by widely fluctuating microbial growth. Quantitative polymerase chain reaction analysis of microbial genes encoding proteins involved in the nitrogen cycle was used to study Azotobacter species, nitrifiers, and denitrifiers in the soils from steppe grasslands and croplands abandoned for 2, 6, and 26 years. Except for nitrifying archaea and nitrous oxide-reducing bacteria, the relative genotypic abundance of microbial communities involved in nitrogen metabolism differed by approximately 2- to 10-fold between abandoned cropland and steppe grassland soils. Although nitrogen-cycle gene abundances varied with abandonment time, the abundance patterns of nitrogen-cycle genes separated distinctly into abandoned cropland versus light-grazing steppe grassland, despite the lack of any cultivation for over a quarter-century. Plant biomass and plant diversity exerted a significant effect on the abundance of microbial communities that mediate the nitrogen cycle (P < 0.002 and P < 0.03, respectively. The present study elucidates the ecology of bacteria that mediate the nitrogen cycle in recently abandoned croplands.

  20. Microbial Nitrogen-Cycle Gene Abundance in Soil of Cropland Abandoned for Different Periods.

    Science.gov (United States)

    Huhe; Borjigin, Shinchilelt; Buhebaoyin; Wu, Yanpei; Li, Minquan; Cheng, Yunxiang

    2016-01-01

    In Inner Mongolia, steppe grasslands face desertification or degradation because of human overuse and abandonment after inappropriate agricultural management. The soils in these abandoned croplands exist in heterogeneous environments characterized by widely fluctuating microbial growth. Quantitative polymerase chain reaction analysis of microbial genes encoding proteins involved in the nitrogen cycle was used to study Azotobacter species, nitrifiers, and denitrifiers in the soils from steppe grasslands and croplands abandoned for 2, 6, and 26 years. Except for nitrifying archaea and nitrous oxide-reducing bacteria, the relative genotypic abundance of microbial communities involved in nitrogen metabolism differed by approximately 2- to 10-fold between abandoned cropland and steppe grassland soils. Although nitrogen-cycle gene abundances varied with abandonment time, the abundance patterns of nitrogen-cycle genes separated distinctly into abandoned cropland versus light-grazing steppe grassland, despite the lack of any cultivation for over a quarter-century. Plant biomass and plant diversity exerted a significant effect on the abundance of microbial communities that mediate the nitrogen cycle (P nitrogen cycle in recently abandoned croplands.

  1. Experimentally simulated global warming and nitrogen enrichment effects on microbial litter decomposers in a marsh.

    Science.gov (United States)

    Flury, Sabine; Gessner, Mark O

    2011-02-01

    Atmospheric warming and increased nitrogen deposition can lead to changes of microbial communities with possible consequences for biogeochemical processes. We used an enclosure facility in a freshwater marsh to assess the effects on microbes associated with decomposing plant litter under conditions of simulated climate warming and pulsed nitrogen supply. Standard batches of litter were placed in coarse-mesh and fine-mesh bags and submerged in a series of heated, nitrogen-enriched, and control enclosures. They were retrieved later and analyzed for a range of microbial parameters. Fingerprinting profiles obtained by denaturing gradient gel electrophoresis (DGGE) indicated that simulated global warming induced a shift in bacterial community structure. In addition, warming reduced fungal biomass, whereas bacterial biomass was unaffected. The mesh size of the litter bags and sampling date also had an influence on bacterial community structure, with the apparent number of dominant genotypes increasing from spring to summer. Microbial respiration was unaffected by any treatment, and nitrogen enrichment had no clear effect on any of the microbial parameters considered. Overall, these results suggest that microbes associated with decomposing plant litter in nutrient-rich freshwater marshes are resistant to extra nitrogen supplies but are likely to respond to temperature increases projected for this century.

  2. Deep sequencing analysis of HBV genotype shift and correlation with antiviral efficiency during adefovir dipivoxil therapy.

    Directory of Open Access Journals (Sweden)

    Yuwei Wang

    Full Text Available Viral genotype shift in chronic hepatitis B (CHB patients during antiviral therapy has been reported, but the underlying mechanism remains elusive.38 CHB patients treated with ADV for one year were selected for studying genotype shift by both deep sequencing and Sanger sequencing method.Sanger sequencing method found that 7.9% patients showed mixed genotype before ADV therapy. In contrast, all 38 patients showed mixed genotype before ADV treatment by deep sequencing. 95.5% mixed genotype rate was also obtained from additional 200 treatment-naïve CHB patients. Of the 13 patients with genotype shift, the fraction of the minor genotype in 5 patients (38% increased gradually during the course of ADV treatment. Furthermore, responses to ADV and HBeAg seroconversion were associated with the high rate of genotype shift, suggesting drug and immune pressure may be key factors to induce genotype shift. Interestingly, patients with genotype C had a significantly higher rate of genotype shift than genotype B. In genotype shift group, ADV treatment induced a marked enhancement of genotype B ratio accompanied by a reduction of genotype C ratio, suggesting genotype C may be more sensitive to ADV than genotype B. Moreover, patients with dominant genotype C may have a better therapeutic effect. Finally, genotype shifts was correlated with clinical improvement in terms of ALT.Our findings provided a rational explanation for genotype shift among ADV-treated CHB patients. The genotype and genotype shift might be associated with antiviral efficiency.

  3. The genotype-phenotype map of an evolving digital organism

    OpenAIRE

    Fortuna, Miguel A.; Zaman, Luis; Ofria, Charles; Wagner, Andreas

    2017-01-01

    To understand how evolving systems bring forth novel and useful phenotypes, it is essential to understand the relationship between genotypic and phenotypic change. Artificial evolving systems can help us understand whether the genotype-phenotype maps of natural evolving systems are highly unusual, and it may help create evolvable artificial systems. Here we characterize the genotype-phenotype map of digital organisms in Avida, a platform for digital evolution. We consider digital organisms fr...

  4. Molecular genotyping of HCV infection in seropositive blood donor

    Science.gov (United States)

    Zarin, Siti Noraziah Abu; Ibrahim, Nazlina

    2013-11-01

    This study is to investigate the prevalence of hepatitis C virus infection in seropositive blood donor. RNA was extracted from 32 positive samples in National Blood Centre and Melaka Hospital. The core and NS5B sequences were obtained from 23 samples. Genotype 3a is most prevalent in this study followed by genotype 1a. Evidence of mixed-genotypes (3a and 1b) infections was found in 5 subjects.

  5. An authentication scheme for secure access to healthcare services.

    Science.gov (United States)

    Khan, Muhammad Khurram; Kumari, Saru

    2013-08-01

    Last few decades have witnessed boom in the development of information and communication technologies. Health-sector has also been benefitted with this advancement. To ensure secure access to healthcare services some user authentication mechanisms have been proposed. In 2012, Wei et al. proposed a user authentication scheme for telecare medical information system (TMIS). Recently, Zhu pointed out offline password guessing attack on Wei et al.'s scheme and proposed an improved scheme. In this article, we analyze both of these schemes for their effectiveness in TMIS. We show that Wei et al.'s scheme and its improvement proposed by Zhu fail to achieve some important characteristics necessary for secure user authentication. We find that security problems of Wei et al.'s scheme stick with Zhu's scheme; like undetectable online password guessing attack, inefficacy of password change phase, traceability of user's stolen/lost smart card and denial-of-service threat. We also identify that Wei et al.'s scheme lacks forward secrecy and Zhu's scheme lacks session key between user and healthcare server. We therefore propose an authentication scheme for TMIS with forward secrecy which preserves the confidentiality of air messages even if master secret key of healthcare server is compromised. Our scheme retains advantages of Wei et al.'s scheme and Zhu's scheme, and offers additional security. The security analysis and comparison results show the enhanced suitability of our scheme for TMIS.

  6. Microbial Flocculant for Nature Soda

    Energy Technology Data Exchange (ETDEWEB)

    Qin, Peiyong; Zhang, Tong; Chen, Cuixian

    2004-03-31

    Microbial flocculant for nature soda has been studied. Lactobacillus TRJ21, which was able to produce an excellent biopolymer flocculant for nature soda, was obtained in our lab. The microbial flocculant was mainly produced when the bacteria laid in stationary growth phase. Fructose or glucose, as carbon sources, were more favorable for the bacterial growth and flocculant production. The bacteria was able to use ammonium sulfate or Urea as nitrogen to produce flocculant, but was not able to use peptone effectively. High C/N ratio was more favorable to Lactobacillus TRJ21 growth and flocculant production than low C/N ratio. The biopolymer flocculant was mainly composed of polysaccharide and protein with a molecular weight 1.38x106 by gel permeation chromatography. It was able to be easily purified from the culture medium by acetone. Protein in the flocculant was tested for the flocculating activity ingredient by heating the flocculant.

  7. Subsurface microbial habitats on Mars

    Science.gov (United States)

    Boston, P. J.; Mckay, C. P.

    1991-01-01

    We developed scenarios for shallow and deep subsurface cryptic niches for microbial life on Mars. Such habitats could have considerably prolonged the persistence of life on Mars as surface conditions became increasingly inhospitable. The scenarios rely on geothermal hot spots existing below the near or deep subsurface of Mars. Recent advances in the comparatively new field of deep subsurface microbiology have revealed previously unsuspected rich aerobic and anaerobic microbal communities far below the surface of the Earth. Such habitats, protected from the grim surface conditions on Mars, could receive warmth from below and maintain water in its liquid state. In addition, geothermally or volcanically reduced gases percolating from below through a microbiologically active zone could provide the reducing power needed for a closed or semi-closed microbial ecosystem to thrive.

  8. Microbial activity at Yucca Mountain

    International Nuclear Information System (INIS)

    Horn, J.M.; Meike, A.

    1995-01-01

    The U.S. Department of Energy is engaged in a suitability study for a potential geological repository at Yucca Mountain, Nevada, for the containment and storage of commercially generated spent fuel and defense high-level nuclear waste. There is growing recognition of the role that biotic factors could play in this repository, either directly through microbially induced corrosion (MIC), or indirectly by altering the chemical environment or contributing to the transport of radionuclides. As a first step toward describing and predicting these processes, a workshop was held on April 10-12, 1995, in Lafayette, California. The immediate aims of the workshop were: (1) To identify microbially related processes relevant to the design of a radioactive waste repository under conditions similar to those at Yucca Mountain. (2) To determine parameters that are critical to the evaluation of a disturbed subterranean environment. (3) To define the most effective means of investigating the factors thus identified

  9. Microbial activity at Yucca Mountain

    Energy Technology Data Exchange (ETDEWEB)

    Horn, J.M.; Meike, A.

    1995-09-25

    The U.S. Department of Energy is engaged in a suitability study for a potential geological repository at Yucca Mountain, Nevada, for the containment and storage of commercially generated spent fuel and defense high-level nuclear waste. There is growing recognition of the role that biotic factors could play in this repository, either directly through microbially induced corrosion (MIC), or indirectly by altering the chemical environment or contributing to the transport of radionuclides. As a first step toward describing and predicting these processes, a workshop was held on April 10-12, 1995, in Lafayette, California. The immediate aims of the workshop were: (1) To identify microbially related processes relevant to the design of a radioactive waste repository under conditions similar to those at Yucca Mountain. (2) To determine parameters that are critical to the evaluation of a disturbed subterranean environment. (3) To define the most effective means of investigating the factors thus identified.

  10. Laser engineering of microbial systems

    Science.gov (United States)

    Yusupov, V. I.; Gorlenko, M. V.; Cheptsov, V. S.; Minaev, N. V.; Churbanova, E. S.; Zhigarkov, V. S.; Chutko, E. A.; Evlashin, S. A.; Chichkov, B. N.; Bagratashvili, V. N.

    2018-06-01

    A technology of laser engineering of microbial systems (LEMS) based on the method of laser-induced transfer of heterogeneous mixtures containing microorganisms (laser bioprinting) is described. This technology involves laser printing of soil microparticles by focusing near-infrared laser pulses on a specially prepared gel/soil mixture spread onto a gold-coated glass plate. The optimal range of laser energies from the point of view of the formation of stable jets and droplets with minimal negative impact on living systems of giant accelerations, laser pulse irradiation, and Au nanoparticles was found. Microsamples of soil were printed on glucose-peptone-yeast agar plates to estimate the LEMS process influence on structural and morphological microbial diversity. The obtained results were compared with traditionally treated soil samples. It was shown that LEMS technology allows significantly increasing the biodiversity of printed organisms and is effective for isolating rare or unculturable microorganisms.

  11. Low-cost ultra-wide genotyping using Roche/454 pyrosequencing for surveillance of HIV drug resistance.

    Directory of Open Access Journals (Sweden)

    Dawn M Dudley

    Full Text Available Great efforts have been made to increase accessibility of HIV antiretroviral therapy (ART in low and middle-income countries. The threat of wide-scale emergence of drug resistance could severely hamper ART scale-up efforts. Population-based surveillance of transmitted HIV drug resistance ensures the use of appropriate first-line regimens to maximize efficacy of ART programs where drug options are limited. However, traditional HIV genotyping is extremely expensive, providing a cost barrier to wide-scale and frequent HIV drug resistance surveillance.We have developed a low-cost laboratory-scale next-generation sequencing-based genotyping method to monitor drug resistance. We designed primers specifically to amplify protease and reverse transcriptase from Brazilian HIV subtypes and developed a multiplexing scheme using multiplex identifier tags to minimize cost while providing more robust data than traditional genotyping techniques. Using this approach, we characterized drug resistance from plasma in 81 HIV infected individuals collected in São Paulo, Brazil. We describe the complexities of analyzing next-generation sequencing data and present a simplified open-source workflow to analyze drug resistance data. From this data, we identified drug resistance mutations in 20% of treatment naïve individuals in our cohort, which is similar to frequencies identified using traditional genotyping in Brazilian patient samples.The developed ultra-wide sequencing approach described here allows multiplexing of at least 48 patient samples per sequencing run, 4 times more than the current genotyping method. This method is also 4-fold more sensitive (5% minimal detection frequency vs. 20% at a cost 3-5× less than the traditional Sanger-based genotyping method. Lastly, by using a benchtop next-generation sequencer (Roche/454 GS Junior, this approach can be more easily implemented in low-resource settings. This data provides proof-of-concept that next

  12. A hybrid Lagrangian Voronoi-SPH scheme

    Science.gov (United States)

    Fernandez-Gutierrez, D.; Souto-Iglesias, A.; Zohdi, T. I.

    2017-11-01

    A hybrid Lagrangian Voronoi-SPH scheme, with an explicit weakly compressible formulation for both the Voronoi and SPH sub-domains, has been developed. The SPH discretization is substituted by Voronoi elements close to solid boundaries, where SPH consistency and boundary conditions implementation become problematic. A buffer zone to couple the dynamics of both sub-domains is used. This zone is formed by a set of particles where fields are interpolated taking into account SPH particles and Voronoi elements. A particle may move in or out of the buffer zone depending on its proximity to a solid boundary. The accuracy of the coupled scheme is discussed by means of a set of well-known verification benchmarks.

  13. Exclusion from the Health Insurance Scheme

    CERN Multimedia

    2003-01-01

    A CERN pensioner, member of the Organization's Health Insurance Scheme (CHIS), recently provided fake documents in support of claims for medical expenses, in order to receive unjustified reimbursement from the CHIS. The Administrator of the CHIS, UNIQA, suspected a case of fraud: Accordingly, an investigation and interview of the person concerned was carried out and brought the Organization to the conclusion that fraud had actually taken place. Consequently and in accordance with Article VIII 3.12 of the CHIS Rules, it was decided to exclude this member permanently from the CHIS. The Organization takes the opportunity to remind Scheme members that any fraud or attempt to fraud established within the framework of the CHIS exposes them to: - disciplinary action, according to the Staff Rules and Regulations, for CERN members of the personnel; - definitive exclusion from the CHIS for members affiliated on a voluntary basis. Human Resources Division Tel. 73635

  14. A numerical relativity scheme for cosmological simulations

    Science.gov (United States)

    Daverio, David; Dirian, Yves; Mitsou, Ermis

    2017-12-01

    Cosmological simulations involving the fully covariant gravitational dynamics may prove relevant in understanding relativistic/non-linear features and, therefore, in taking better advantage of the upcoming large scale structure survey data. We propose a new 3  +  1 integration scheme for general relativity in the case where the matter sector contains a minimally-coupled perfect fluid field. The original feature is that we completely eliminate the fluid components through the constraint equations, thus remaining with a set of unconstrained evolution equations for the rest of the fields. This procedure does not constrain the lapse function and shift vector, so it holds in arbitrary gauge and also works for arbitrary equation of state. An important advantage of this scheme is that it allows one to define and pass an adaptation of the robustness test to the cosmological context, at least in the case of pressureless perfect fluid matter, which is the relevant one for late-time cosmology.

  15. Genomic Variants Revealed by Invariably Missing Genotypes in Nelore Cattle.

    Directory of Open Access Journals (Sweden)

    Joaquim Manoel da Silva

    Full Text Available High density genotyping panels have been used in a wide range of applications. From population genetics to genome-wide association studies, this technology still offers the lowest cost and the most consistent solution for generating SNP data. However, in spite of the application, part of the generated data is always discarded from final datasets based on quality control criteria used to remove unreliable markers. Some discarded data consists of markers that failed to generate genotypes, labeled as missing genotypes. A subset of missing genotypes that occur in the whole population under study may be caused by technical issues but can also be explained by the presence of genomic variations that are in the vicinity of the assayed SNP and that prevent genotyping probes from annealing. The latter case may contain relevant information because these missing genotypes might be used to identify population-specific genomic variants. In order to assess which case is more prevalent, we used Illumina HD Bovine chip genotypes from 1,709 Nelore (Bos indicus samples. We found 3,200 missing genotypes among the whole population. NGS re-sequencing data from 8 sires were used to verify the presence of genomic variations within their flanking regions in 81.56% of these missing genotypes. Furthermore, we discovered 3,300 novel SNPs/Indels, 31% of which are located in genes that may affect traits of importance for the genetic improvement of cattle production.

  16. Phosphorus use efficiency in pima cotton (Gossypium barbadense L. genotypes

    Directory of Open Access Journals (Sweden)

    Elcio Santos

    2015-06-01

    Full Text Available In the Brazilian Cerrado, P deficiency restricts cotton production, which requires large amounts of phosphate fertilizer. To improve the yield of cotton crops, genotypes with high P use efficiency must be identified and used. The present study evaluated P uptake and use efficiency of different Gossypium barbadense L. genotypes grown in the Cerrado. The experiment was carried out in a greenhouse with a completely randomized design, 15 x 2 factorial treatment structure (15 genotypes x 2 P levels, and four replicates. The genotypes were MT 69, MT 70, MT 87, MT 91, MT 92, MT 94, MT 101, MT 102, MT 103, MT 105, MT 106, MT 110, MT 112, MT 124, and MT 125; P levels were sufficient (1000 mg pot-1, PS treatment or deficient (PD treatment. Dry matter (DM and P levels were determined in cotton plant parts and used to calculate plant P content and use efficiency. In general, DM and P content were higher in the PS than in the PD treatment, with the exception of root DM and total DM in some genotypes. Genotypes also differed in terms of P uptake and use capacity. In the PS treatment, genotypes MT 92 and MT 102 had the highest response to phosphate fertilization. Genotype MT 69 exhibited the most efficient P uptake in the PD treatment. Genotype MT 124 showed the best shoot physiological efficiency, apparent recovery efficiency, and utilization efficiency, whereas MT 110 exhibited the highest root physiological efficiency.

  17. Theory of microbial genome evolution

    Science.gov (United States)

    Koonin, Eugene

    Bacteria and archaea have small genomes tightly packed with protein-coding genes. This compactness is commonly perceived as evidence of adaptive genome streamlining caused by strong purifying selection in large microbial populations. In such populations, even the small cost incurred by nonfunctional DNA because of extra energy and time expenditure is thought to be sufficient for this extra genetic material to be eliminated by selection. However, contrary to the predictions of this model, there exists a consistent, positive correlation between the strength of selection at the protein sequence level, measured as the ratio of nonsynonymous to synonymous substitution rates, and microbial genome size. By fitting the genome size distributions in multiple groups of prokaryotes to predictions of mathematical models of population evolution, we show that only models in which acquisition of additional genes is, on average, slightly beneficial yield a good fit to genomic data. Thus, the number of genes in prokaryotic genomes seems to reflect the equilibrium between the benefit of additional genes that diminishes as the genome grows and deletion bias. New genes acquired by microbial genomes, on average, appear to be adaptive. Evolution of bacterial and archaeal genomes involves extensive horizontal gene transfer and gene loss. Many microbes have open pangenomes, where each newly sequenced genome contains more than 10% `ORFans', genes without detectable homologues in other species. A simple, steady-state evolutionary model reveals two sharply distinct classes of microbial genes, one of which (ORFans) is characterized by effectively instantaneous gene replacement, whereas the other consists of genes with finite, distributed replacement rates. These findings imply a conservative estimate of at least a billion distinct genes in the prokaryotic genomic universe.

  18. A new chaotic secure communication scheme

    International Nuclear Information System (INIS)

    Hua Changchun; Yang Bo; Ouyang Gaoxiang; Guan Xinping

    2005-01-01

    A new chaotic secure communication scheme is constructed. Unified chaotic system is used to encrypt the emitted signal. Different from the existing chaotic secure communication methods, the useful information is embodied in the parameter of chaotic systems in this Letter. The receiver is designed which can succeed in recovering the former signal. Finally computer simulations are done to verify the proposed methods, and the results show that the obtained theoretic results are feasible and efficient

  19. On Some Incompatible Properties of Voting Schemes

    OpenAIRE

    Chevallier-Mames , Benoît; Fouque , Pierre-Alain; Pointcheval , David; Stern , Julien; Traoré , Jacques

    2010-01-01

    In this paper, we study the problem of simultaneously achieving several security properties, for voting schemes, without non-standard assumptions. More specifically, we focus on the universal veriability of the computation of the tally, on the unconditional privacy/anonymity of the votes, and on the receipt-freeness properties, for the most classical election processes. Under usual assumptions and efficiency requirements, we show that a voting system that wants to publish the final list of th...

  20. Conservative Semidiscrete Difference Schemes for Timoshenko Systems

    OpenAIRE

    Júnior, D. S. Almeida

    2014-01-01

    We present a parameterized family of finite-difference schemes to analyze the energy properties for linearly elastic constant-coefficient Timoshenko systems considering shear deformation and rotatory inertia. We derive numerical energies showing the positivity, and the energy conservation property and we show how to avoid a numerical anomaly known as locking phenomenon on shear force. Our method of proof relies on discrete multiplier techniques.

  1. Droop Scheme With Consideration of Operating Costs

    DEFF Research Database (Denmark)

    Nutkani, I. U.; Loh, Poh Chiang; Blaabjerg, Frede

    2014-01-01

    considered even though they are different for different types of DGs. This letter thus proposes an alternative droop scheme, which can better distinguish the different operating characteristics and objectives of the DGs grouped together in a weighted droop expression. The power sharing arrived in the steady...... state will meet the intended objectives, as demonstrated in the experiment with a defined objective of minimizing the total microgrid operating cost....

  2. A Scheme of Controlled Quantum State Swapping

    International Nuclear Information System (INIS)

    Zha Xinwei; Zou Zhichun; Qi Jianxia; Song Haiyang

    2012-01-01

    A scheme for controlled quantum state swapping is presented using maximally entangled five-qubit state, i.e., Alice wants to transmit an entangled state of particle a to Bob and at the same time Bob wants to transmit an entangled state of particle b to Alice via the control of the supervisor Charlie. The operations used in this swapping process including C-not operation and a series of single-qubit measurements performed by Alice, Bob, and Charlie.

  3. Efficient Scheme for Chemical Flooding Simulation

    Directory of Open Access Journals (Sweden)

    Braconnier Benjamin

    2014-07-01

    Full Text Available In this paper, we investigate an efficient implicit scheme for the numerical simulation of chemical enhanced oil recovery technique for oil fields. For the sake of brevity, we only focus on flows with polymer to describe the physical and numerical models. In this framework, we consider a black oil model upgraded with the polymer modeling. We assume the polymer only transported in the water phase or adsorbed on the rock following a Langmuir isotherm. The polymer reduces the water phase mobility which can change drastically the behavior of water oil interfaces. Then, we propose a fractional step technique to resolve implicitly the system. The first step is devoted to the resolution of the black oil subsystem and the second to the polymer mass conservation. In such a way, jacobian matrices coming from the implicit formulation have a moderate size and preserve solvers efficiency. Nevertheless, the coupling between the black-oil subsystem and the polymer is not fully resolved. For efficiency and accuracy comparison, we propose an explicit scheme for the polymer for which large time step is prohibited due to its CFL (Courant-Friedrichs-Levy criterion and consequently approximates accurately the coupling. Numerical experiments with polymer are simulated : a core flood, a 5-spot reservoir with surfactant and ions and a 3D real case. Comparisons are performed between the polymer explicit and implicit scheme. They prove that our polymer implicit scheme is efficient, robust and resolves accurately the coupling physics. The development and the simulations have been performed with the software PumaFlow [PumaFlow (2013 Reference manual, release V600, Beicip Franlab].

  4. The Emergent Universe scheme and tunneling

    Energy Technology Data Exchange (ETDEWEB)

    Labraña, Pedro [Departamento de Física, Universidad del Bío-Bío, Avenida Collao 1202, Casilla 5-C, Concepción, Chile and Departament d' Estructura i Constituents de la Matèria and Institut de Ciències del Cosmos, Universitat (Spain)

    2014-07-23

    We present an alternative scheme for an Emergent Universe scenario, developed previously in Phys. Rev. D 86, 083524 (2012), where the universe is initially in a static state supported by a scalar field located in a false vacuum. The universe begins to evolve when, by quantum tunneling, the scalar field decays into a state of true vacuum. The Emergent Universe models are interesting since they provide specific examples of non-singular inflationary universes.

  5. Evolutionary Algorithm for Optimal Vaccination Scheme

    International Nuclear Information System (INIS)

    Parousis-Orthodoxou, K J; Vlachos, D S

    2014-01-01

    The following work uses the dynamic capabilities of an evolutionary algorithm in order to obtain an optimal immunization strategy in a user specified network. The produced algorithm uses a basic genetic algorithm with crossover and mutation techniques, in order to locate certain nodes in the inputted network. These nodes will be immunized in an SIR epidemic spreading process, and the performance of each immunization scheme, will be evaluated by the level of containment that provides for the spreading of the disease

  6. Welcome to the neighbourhood: interspecific genotype by genotype interactions in Solidago influence above- and belowground biomass and associated communities.

    Science.gov (United States)

    Genung, Mark A; Bailey, Joseph K; Schweitzer, Jennifer A

    2012-01-01

    Intra- and interspecific plant-plant interactions are fundamental to patterns of community assembly and to the mixture effects observed in biodiversity studies. Although much research has been conducted at the species level, very little is understood about how genetic variation within and among interacting species may drive these processes. Using clones of both Solidago altissima and Solidago gigantea, we found that genotypic variation in a plant's neighbours affected both above- and belowground plant traits, and that genotype by genotype interactions between neighbouring plants impacted associated pollinator communities. The traits for which focal plant genotypic variation explained the most variation varied by plant species, whereas neighbour genotypic variation explained the most variation in coarse root biomass. Our results provide new insight into genotypic and species diversity effects in plant-neighbour interactions, the extended consequences of diversity effects, and the potential for evolution in response to competitive or to facilitative plant-neighbour interactions. © 2011 Blackwell Publishing Ltd/CNRS.

  7. Microbial terroir for wine grapes

    Energy Technology Data Exchange (ETDEWEB)

    Gilbert, J. A.; van der Lelie, D.; Zarraonaindia, I.

    2013-12-05

    The viticulture industry has been selectively growing vine cultivars with different traits (grape size, shape, color, flavor, yield of fruit, and so forth) for millennia, and small variations in soil composition, water management, climate, and the aspect of vineyards have long been associated with shifts in these traits. As such, many different clonal varieties of vines exist, even within given grape varieties, such as merlot, pinot noir, and chardonnay. The commensal microbial flora that coexists with the plant may be one of the key factors that influence these traits. To date, the role of microbes has been largely ignored, outside of microbial pathogens, mainly because the technologies did not exist to allow us to look in any real depth or breadth at the community structure of the multitudes of bacterial and fungal species associated with each plant. In PNAS, Bokulich et al. (1) used next-generation sequencing of 16S rRNA and internal transcribed spacer ribosomal sequence to determine the relative abundances of bacteria and fungi, respectively, from grape must (freshly pressed grape juice, containing the skins and seeds) from plants in eight vineyards representing four of the major wine growing regions in California. The authors show that the microbiomes (bacterial and fungal taxonomic structure) associated with this early fermentation stage show defined biogeography, illustrating that different wine-growing regions maintain different microbial communities, with some influences from the grape variety and the year of production.

  8. INFORMATION FROM THE CERN HEALTH INSURANCE SCHEME

    CERN Document Server

    Tel : 7-3635

    2002-01-01

    Please note that, from 1 July 2002, the tariff agreement between CERN and the Hôpital de la Tour will no longer be in force. As a result the members of the CERN Health Insurance Scheme will no longer obtain a 5% discount for quick payment of bills. More information on the termination of the agreement and the implications for our Health Insurance Scheme will be provided in the next issue of the CHIS Bull', due for publication in the first half of July. It will be sent to your home address, so, if you have moved recently, please check that your divisional secretariat has your current address. Tel.: 73635 The Organization's Health Insurance Scheme (CHIS) has launched its own Web pages, located on the Website of the Social & Statutory Conditions Group of HR Division (HR-SOC). The address is short and easy-to-remember www.cern.ch/chis The pages currently available concentrate on providing basic information. Over the coming months it is planned to fill out the details and introduce new topics. Please give us ...

  9. Doppler Shift Compensation Schemes in VANETs

    Directory of Open Access Journals (Sweden)

    F. Nyongesa

    2015-01-01

    Full Text Available Over the last decade vehicle-to-vehicle (V2V communication has received a lot of attention as it is a crucial issue in intravehicle communication as well as in Intelligent Transportation System (ITS. In ITS the focus is placed on integration of communication between mobile and fixed infrastructure to execute road safety as well as nonsafety information dissemination. The safety application such as emergence alerts lays emphasis on low-latency packet delivery rate (PDR, whereas multimedia and infotainment call for high data rates at low bit error rate (BER. The nonsafety information includes multimedia streaming for traffic information and infotainment applications such as playing audio content, utilizing navigation for driving, and accessing Internet. A lot of vehicular ad hoc network (VANET research has focused on specific areas including channel multiplexing, antenna diversity, and Doppler shift compensation schemes in an attempt to optimize BER performance. Despite this effort few surveys have been conducted to highlight the state-of-the-art collection on Doppler shift compensation schemes. Driven by this cause we survey some of the recent research activities in Doppler shift compensation schemes and highlight challenges and solutions as a stock-taking exercise. Moreover, we present open issues to be further investigated in order to address the challenges of Doppler shift in VANETs.

  10. Boudot's Range-Bounded Commitment Scheme Revisited

    Science.gov (United States)

    Cao, Zhengjun; Liu, Lihua

    Checking whether a committed integer lies in a specific interval has many cryptographic applications. In Eurocrypt'98, Chan et al. proposed an instantiation (CFT Proof). Based on CFT, Boudot presented a popular range-bounded commitment scheme in Eurocrypt'2000. Both CFT Proof and Boudot Proof are based on the encryption E(x, r)=g^xh^r mod n, where n is an RSA modulus whose factorization is unknown by the prover. They did not use a single base as usual. Thus an increase in cost occurs. In this paper, we show that it suffices to adopt a single base. The cost of the modified Boudot Proof is about half of that of the original scheme. Moreover, the key restriction in the original scheme, i.e., both the discrete logarithm of g in base h and the discrete logarithm of h in base g are unknown by the prover, which is a potential menace to the Boudot Proof, is definitely removed.

  11. An evaluation scheme for nanotechnology policies

    International Nuclear Information System (INIS)

    Soltani, Ali M.; Tabatabaeian, Seyed H.; Hanafizadeh, Payam; Bamdad Soofi, Jahanyar

    2011-01-01

    Dozens of countries are executing national nanotechnology plans. No rigorous evaluation scheme for these plans exists, although stakeholders—especially policy makers, top-level agencies and councils, as well as the society at large—are eager to learn the outcome of these policies. In this article, we recommend an evaluation scheme for national nanotechnology policies that would be used to review the whole or any component part of a national nanotechnology plan. In this scheme, a component at any level of aggregation is evaluated. The component may be part of the plan’s overarching policy goal, which for most countries is to create wealth and improve the quality of life of their nation with nanotechnology. Alternatively, the component may be a programme or an activity related to a programme. The evaluation could be executed at different times in the policy’s life cycle, i.e., before the policy is formulated, during its execution or after its completion. The three criteria for policy evaluation are appropriateness, efficiency and effectiveness. The evaluator should select the appropriate qualitative or quantitative methods to evaluate the various components of national nanotechnology plans.

  12. Parallel S/sub n/ iteration schemes

    International Nuclear Information System (INIS)

    Wienke, B.R.; Hiromoto, R.E.

    1986-01-01

    The iterative, multigroup, discrete ordinates (S/sub n/) technique for solving the linear transport equation enjoys widespread usage and appeal. Serial iteration schemes and numerical algorithms developed over the years provide a timely framework for parallel extension. On the Denelcor HEP, the authors investigate three parallel iteration schemes for solving the one-dimensional S/sub n/ transport equation. The multigroup representation and serial iteration methods are also reviewed. This analysis represents a first attempt to extend serial S/sub n/ algorithms to parallel environments and provides good baseline estimates on ease of parallel implementation, relative algorithm efficiency, comparative speedup, and some future directions. The authors examine ordered and chaotic versions of these strategies, with and without concurrent rebalance and diffusion acceleration. Two strategies efficiently support high degrees of parallelization and appear to be robust parallel iteration techniques. The third strategy is a weaker parallel algorithm. Chaotic iteration, difficult to simulate on serial machines, holds promise and converges faster than ordered versions of the schemes. Actual parallel speedup and efficiency are high and payoff appears substantial

  13. Optimization of a middle atmosphere diagnostic scheme

    Science.gov (United States)

    Akmaev, Rashid A.

    1997-06-01

    A new assimilative diagnostic scheme based on the use of a spectral model was recently tested on the CIRA-86 empirical model. It reproduced the observed climatology with an annual global rms temperature deviation of 3.2 K in the 15-110 km layer. The most important new component of the scheme is that the zonal forcing necessary to maintain the observed climatology is diagnosed from empirical data and subsequently substituted into the simulation model at the prognostic stage of the calculation in an annual cycle mode. The simulation results are then quantitatively compared with the empirical model, and the above mentioned rms temperature deviation provides an objective measure of the `distance' between the two climatologies. This quantitative criterion makes it possible to apply standard optimization procedures to the whole diagnostic scheme and/or the model itself. The estimates of the zonal drag have been improved in this study by introducing a nudging (Newtonian-cooling) term into the thermodynamic equation at the diagnostic stage. A proper optimal adjustment of the strength of this term makes it possible to further reduce the rms temperature deviation of simulations down to approximately 2.7 K. These results suggest that direct optimization can successfully be applied to atmospheric model parameter identification problems of moderate dimensionality.

  14. Evaluation of customised lineage-specific sets of MIRU-VNTR loci for genotyping Mycobacterium tuberculosis complex isolates in Ghana.

    Directory of Open Access Journals (Sweden)

    Adwoa Asante-Poku

    Full Text Available BACKGROUND: Different combinations of variable number of tandem repeat (VNTR loci have been proposed for genotyping Mycobacterium tuberculosis complex (MTBC. Existing VNTR schemes show different discriminatory capacity among the six human MTBC lineages. Here, we evaluated the discriminatory power of a "customized MIRU12" loci format proposed previously by Comas et al. based on the standard 24 loci defined by Supply et al. for VNTR-typing of MTBC in Ghana. METHOD: One hundred and fifty-eight MTBC isolates classified into Lineage 4 and Lineage 5 were used to compare a customized lineage-specific panel of 12 MIRU-VNTR loci ("customized MIRU-12" to the standard MIRU-15 genotyping scheme. The resolution power of each typing method was determined based on the Hunter-Gaston- Discriminatory Index (HGDI. A minimal set of customized MIRU-VNTR loci for typing Lineages 4 (Euro-American and 5 (M. africanum West African 1 strains from Ghana was defined based on the cumulative HGDI. RESULTS AND CONCLUSION: Among the 106 Lineage 4 strains, the customized MIRU-12 identified a total of 104 distinct genotypes consisting of 2 clusters of 2 isolates each (clustering rate 1.8%, and 102 unique strains while standard MIRU-15 yielded a total of 105 different genotypes, including 1 cluster of 2 isolates (clustering rate: 0.9% and 104 singletons. Among, 52 Lineage 5 isolates, customized MIRU-12 genotyping defined 51 patterns with 1 cluster of 2 isolates (clustering rate: 0.9% and 50 unique strains whereas MIRU-15 classified all 52 strains as unique. Cumulative HGDI values for customized MIRU-12 for Lineages 4 and 5 were 0.98 respectively whilst that of standard MIRU-15 was 0.99. A union of loci from the customised MIRU-12 and standard MIRU-15 revealed a set of customized eight highly discriminatory loci: 4052, 2163B, 40, 4165, 2165, 10,16 and 26 with a cumulative HGDI of 0.99 for genotyping Lineage 4 and 5 strains from Ghana.

  15. Computing with high-resolution upwind schemes for hyperbolic equations

    International Nuclear Information System (INIS)

    Chakravarthy, S.R.; Osher, S.; California Univ., Los Angeles)

    1985-01-01

    Computational aspects of modern high-resolution upwind finite-difference schemes for hyperbolic systems of conservation laws are examined. An operational unification is demonstrated for constructing a wide class of flux-difference-split and flux-split schemes based on the design principles underlying total variation diminishing (TVD) schemes. Consideration is also given to TVD scheme design by preprocessing, the extension of preprocessing and postprocessing approaches to general control volumes, the removal of expansion shocks and glitches, relaxation methods for implicit TVD schemes, and a new family of high-accuracy TVD schemes. 21 references

  16. Error forecasting schemes of error correction at receiver

    International Nuclear Information System (INIS)

    Bhunia, C.T.

    2007-08-01

    To combat error in computer communication networks, ARQ (Automatic Repeat Request) techniques are used. Recently Chakraborty has proposed a simple technique called the packet combining scheme in which error is corrected at the receiver from the erroneous copies. Packet Combining (PC) scheme fails: (i) when bit error locations in erroneous copies are the same and (ii) when multiple bit errors occur. Both these have been addressed recently by two schemes known as Packet Reversed Packet Combining (PRPC) Scheme, and Modified Packet Combining (MPC) Scheme respectively. In the letter, two error forecasting correction schemes are reported, which in combination with PRPC offer higher throughput. (author)

  17. Cryptanalytic Performance Appraisal of Improved CCH2 Proxy Multisignature Scheme

    Directory of Open Access Journals (Sweden)

    Raman Kumar

    2014-01-01

    Full Text Available Many of the signature schemes are proposed in which the t out of n threshold schemes are deployed, but they still lack the property of security. In this paper, we have discussed implementation of improved CCH1 and improved CCH2 proxy multisignature scheme based on elliptic curve cryptosystem. We have represented time complexity, space complexity, and computational overhead of improved CCH1 and CCH2 proxy multisignature schemes. We have presented cryptanalysis of improved CCH2 proxy multisignature scheme and showed that improved CCH2 scheme suffered from various attacks, that is, forgery attack and framing attack.

  18. A rational function based scheme for solving advection equation

    International Nuclear Information System (INIS)

    Xiao, Feng; Yabe, Takashi.

    1995-07-01

    A numerical scheme for solving advection equations is presented. The scheme is derived from a rational interpolation function. Some properties of the scheme with respect to convex-concave preserving and monotone preserving are discussed. We find that the scheme is attractive in surpressinging overshoots and undershoots even in the vicinities of discontinuity. The scheme can also be easily swicthed as the CIP (Cubic interpolated Pseudo-Particle) method to get a third-order accuracy in smooth region. Numbers of numerical tests are carried out to show the non-oscillatory and less diffusive nature of the scheme. (author)

  19. Sources of Wilhelm Johannsen's genotype theory.

    Science.gov (United States)

    Roll-Hansen, Nils

    2009-01-01

    This paper describes the historical background and early formation of Wilhelm Johannsen's distinction between genotype and phenotype. It is argued that contrary to a widely accepted interpretation (For instance, W. Provine, 1971. The Origins of Theoretical Population Genetics. Chicago: The University of Chicago Press; Mayr, 1973; F. B. Churchill, 1974. Journal of the History of Biology 7: 5-30; E. Mayr, 1982. The Growth of Biological Thought, Cambridge: Harvard University Press; J. Sapp, 2003. Genesis. The Evolution of Biology. New York: Oxford University Press) his concepts referred primarily to properties of individual organisms and not to statistical averages. Johannsen's concept of genotype was derived from the idea of species in the tradition of biological systematics from Linnaeus to de Vries: An individual belonged to a group - species, subspecies, elementary species - by representing a certain underlying type (S. Müller-Wille and V. Orel, 2007. Annals of Science 64: 171-215). Johannsen sharpened this idea theoretically in the light of recent biological discoveries, not least those of cytology. He tested and confirmed it experimentally combining the methods of biometry, as developed by Francis Galton, with the individual selection method and pedigree analysis, as developed for instance by Louis Vilmorin. The term "genotype" was introduced in W. Johannsen's 1909 (Elemente der Exakten Erblichkeitslehre. Jena: Gustav Fischer) treatise, but the idea of a stable underlying biological "type" distinct from observable properties was the core idea of his classical bean selection experiment published 6 years earlier (W. Johannsen, 1903. Ueber Erblichkeit in Populationen und reinen Linien. Eine Beitrag zur Beleuchtung schwebender Selektionsfragen, Jena: Gustav Fischer, pp. 58-59). The individual ontological foundation of population analysis was a self-evident presupposition in Johannsen's studies of heredity in populations from their start in the early 1890s till his

  20. Identification of Zoonotic Genotypes of Giardia duodenalis

    DEFF Research Database (Denmark)

    Sprong, H.; Cacciò, S.M.; van der Giessen, J.W.B

    2009-01-01

    Giardia duodenalis, originally regarded as a commensal organism, is the etiologic agent of giardiasis, a gastrointestinal disease of humans and animals. Giardiasis causes major public and veterinary health concerns worldwide. Transmission is either direct, through the faecal-oral route, or indirect......, through ingestion of contaminated water or food. Genetic characterization of G. duodenalis isolates has revealed the existence of seven groups (assemblages A to G) which differ in their host distribution. Assemblages A and B are found in humans and in many other mammals, but the role of animals......, mixtures of genotypes in individual isolates were repeatedly observed. Possible explanations are the uptake of genetically different Giardia cysts by a host, or subsequent infection of an already infected host, likely without overt symptoms, with a different Giardia species, which may cause disease. Other...