Complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera, and comparative analyses with other grass genomes

Science.gov (United States)

Saski, Christopher; Lee, Seung-Bum; Fjellheim, Siri; Guda, Chittibabu; Jansen, Robert K.; Luo, Hong; Tomkins, Jeffrey; Rognli, Odd Arne; Clarke, Jihong Liu

2009-01-01

Comparisons of complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera to six published grass chloroplast genomes reveal that gene content and order are similar but two microstructural changes have occurred. First, the expansion of the IR at the SSC/IRa boundary that duplicates a portion of the 5′ end of ndhH is restricted to the three genera of the subfamily Pooideae (Agrostis, Hordeum and Triticum). Second, a 6 bp deletion in ndhK is shared by Agrostis, Hordeum, Oryza and Triticum, and this event supports the sister relationship between the subfamilies Erhartoideae and Pooideae. Repeat analysis identified 19–37 direct and inverted repeats 30 bp or longer with a sequence identity of at least 90%. Seventeen of the 26 shared repeats are found in all the grass chloroplast genomes examined and are located in the same genes or intergenic spacer (IGS) regions. Examination of simple sequence repeats (SSRs) identified 16–21 potential polymorphic SSRs. Five IGS regions have 100% sequence identity among Zea mays, Saccharum officinarum and Sorghum bicolor, whereas no spacer regions were identical among Oryza sativa, Triticum aestivum, H. vulgare and A. stolonifera despite their close phylogenetic relationship. Alignment of EST sequences and DNA coding sequences identified six C–U conversions in both Sorghum bicolor and H. vulgare but only one in A. stolonifera. Phylogenetic trees based on DNA sequences of 61 protein-coding genes of 38 taxa using both maximum parsimony and likelihood methods provide moderate support for a sister relationship between the subfamilies Erhartoideae and Pooideae. PMID:17534593

De novo Sequencing and Analysis of Lemongrass Transcriptome Provides First Insights into the Essential Oil Biosynthesis of Aromatic Grasses

Directory of Open Access Journals (Sweden)

Seema Meena

2016-07-01

Full Text Available Aromatic grasses of the genus Cymbopogon (Poaceae family represent unique group of plants that produce diverse composition of monoterpene rich essential oils, which have great value in flavour, fragrance, cosmetic and aromatherapy industries. Despite the commercial importance of these natural aromatic oils, their biosynthesis at the molecular level remains unexplored. As the first step towards understanding the essential oil biosynthesis, we performed de novo transcriptome assembly and analysis of C. flexuosus (lemongrass by employing Illumina sequencing. Mining of transcriptome data and subsequent phylogenetic analysis led to identification of terpene synthases (TPS, pyrophosphatases (PPase, alcohol dehydrogenases (ADH, aldo-keto reductases (AKR, carotenoid cleavage dioxygenases (CCD, alcohol acetyltransferases (AAT and aldehyde dehydrogenases (ALDH, which are potentially involved in essential oil biosynthesis. Comparative essential oil profiling and mRNA expression analysis in three Cymbopogon species (C. flexuosus, aldehyde type; C. martinii, alcohol type; and C. winterianus, intermediate type with varying essential oil composition indicated the involvement of identified candidate genes in the formation of alcohols, aldehydes and acetates. Molecular modeling and docking further supported the role of identified enzymes in aroma formation in Cymbopogon. Also, simple sequence repeats (SSRs were found in the transcriptome with many linked to terpene pathway genes including the genes potentially involved in aroma biosynthesis. This work provides the first insights into the essential oil biosynthesis of aromatic grasses, and the identified candidate genes and markers can be a great resource for biotechnological and molecular breeding approaches to modulate the essential oil composition.

Bacterial endophyte communities of three agricultural important grass species differ in their response towards management regimes

Science.gov (United States)

Wemheuer, Franziska; Kaiser, Kristin; Karlovsky, Petr; Daniel, Rolf; Vidal, Stefan; Wemheuer, Bernd

2017-01-01

Endophytic bacteria are critical for plant growth and health. However, compositional and functional responses of bacterial endophyte communities towards agricultural practices are still poorly understood. Hence, we analyzed the influence of fertilizer application and mowing frequency on bacterial endophytes in three agriculturally important grass species. For this purpose, we examined bacterial endophytic communities in aerial plant parts of Dactylis glomerata L., Festuca rubra L., and Lolium perenne L. by pyrotag sequencing of bacterial 16S rRNA genes over two consecutive years. Although management regimes influenced endophyte communities, observed responses were grass species-specific. This might be attributed to several bacteria specifically associated with a single grass species. We further predicted functional profiles from obtained 16S rRNA data. These profiles revealed that predicted abundances of genes involved in plant growth promotion or nitrogen metabolism differed between grass species and between management regimes. Moreover, structural and functional community patterns showed no correlation to each other indicating that plant species-specific selection of endophytes is driven by functional rather than phylogenetic traits. The unique combination of 16S rRNA data and functional profiles provided a holistic picture of compositional and functional responses of bacterial endophytes in agricultural relevant grass species towards management practices.

Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential

DEFF Research Database (Denmark)

Zhang, Gengyun; Liu, Xin; Quan, Zhiwu

2012-01-01

Foxtail millet (Setaria italica), a member of the Poaceae grass family, is an important food and fodder crop in arid regions and has potential for use as a C(4) biofuel. It is a model system for other biofuel grasses, including switchgrass and pearl millet. We produced a draft genome (∼423 Mb) an...

Current Models for Transcriptional Regulation of Secondary Cell Wall Biosynthesis in Grasses

Directory of Open Access Journals (Sweden)

Xiaolan Rao

2018-04-01

Full Text Available Secondary cell walls mediate many crucial biological processes in plants including mechanical support, water and nutrient transport and stress management. They also provide an abundant resource of renewable feed, fiber, and fuel. The grass family contains the most important food, forage, and biofuel crops. Understanding the regulatory mechanism of secondary wall formation in grasses is necessary for exploiting these plants for agriculture and industry. Previous research has established a detailed model of the secondary wall regulatory network in the dicot model species Arabidopsis thaliana. Grasses, branching off from the dicot ancestor 140–150 million years ago, display distinct cell wall morphology and composition, suggesting potential for a different secondary wall regulation program from that established for dicots. Recently, combined application of molecular, genetic and bioinformatics approaches have revealed more transcription factors involved in secondary cell wall biosynthesis in grasses. Compared with the dicots, grasses exhibit a relatively conserved but nevertheless divergent transcriptional regulatory program to activate their secondary cell wall development and to coordinate secondary wall biosynthesis with other physiological processes.

A model for backscattering characteristics of tall prairie grass canopies at microwave frequencies

International Nuclear Information System (INIS)

Bakhtiari, S.; Zoughi, R.

1991-01-01

We have developed a discrete microwave scattering model, describing the radar backscattering coefficient from two treatments (burned and unburned) of tall prairie grass canopies at VV (electric field vector of the transmitted and received signals are vertically oriented) and HH (electric field vector of the transmitted and received signals and horizontally oriented) polarizations, based on the physical, biophysical, and geometrical characteristics of such canopies. Grass blades are modeled as thin and finite dielectric ellipsoids with arbitrary orientations. Scattering by an individual grass blade is formulated using a generalization of the Rayleigh—Gans approximation with a quasistatic solution for the expansion of the interior field. By associating, with each grass blade, various appropriate distribution functions, the relative orientation, location, height, cross section, and permittivity of each grass blade is taken into account. This makes for a more realistic overall description of the canopy. Kirchhoff's surface scattering is used to model the backscatter from the soil surface. An incoherent summation of the effect of grass blades and soil surface is adopted to obtain the total canopy backscattering coefficient, taking into account the attenuation experienced by the signal as it travels through the canopy. The results of this model are given for 1.5, 5, and 10 GHz (L-, C-, and X-band). Although for the shorter wavelengths (X-band) the Rayleigh—Gans criteria is not totally satisfied, nevertheless, the limited available measured X-band data compare relatively well with the results of this model both quantitatively and qualitatively. (author)

Dynamic model for the transfer of CS-137 through the soil-grass-lamb foodchain

DEFF Research Database (Denmark)

Nielsen, S.P.

1994-01-01

A dynamic radioecological model for the transfer of radiocaesium through the soil-grass-lamb foodchain was constructed on the basis of field data collected in 1990–1993 from the Nordic countries: Denmark, Faroe Islands, Finland, Iceland, Norway and Sweden. The model assumes an initial soil...... contamination of one kilobecquerel of 137Cs per square metre and simulates the transfer to grass through root uptake in addition to direct contamination from resuspended activity. The model covers two different soil types: clay-loam and organic, with significantly different transfers of radiocaesium to grass...

The Perennial Ryegrass GenomeZipper – Targeted Use of Genome Resources for Comparative Grass Genomics

DEFF Research Database (Denmark)

Pfeiffer, Matthias; Martis, Mihaela; Asp, Torben

2013-01-01

(Lolium perenne) genome on the basis of conserved synteny to barley (Hordeum vulgare) and the model grass genome Brachypodium (Brachypodium distachyon) as well as rice (Oryza sativa) and sorghum (Sorghum bicolor). A transcriptome-based genetic linkage map of perennial ryegrass served as a scaffold......Whole-genome sequences established for model and major crop species constitute a key resource for advanced genomic research. For outbreeding forage and turf grass species like ryegrasses (Lolium spp.), such resources have yet to be developed. Here, we present a model of the perennial ryegrass...... to establish the chromosomal arrangement of syntenic genes from model grass species. This scaffold revealed a high degree of synteny and macrocollinearity and was then utilized to anchor a collection of perennial ryegrass genes in silico to their predicted genome positions. This resulted in the unambiguous...

Cell wall composition throughout development for the model grass Brachypodium distanchyon

Directory of Open Access Journals (Sweden)

David eRancour

2012-12-01

Full Text Available Temperate perennial grasses are important worldwide as a livestock nutritive energy source and a potential feedstock for lignocellulosic biofuel production. The annual temperate grass Brachypodium distanchyon has been championed as a useful model system to facilitate biological research in agriculturally important temperate forage grasses based on phylogenetic relationships. To physically corroborate genetic predictions, we determined the chemical composition profiles of organ-specific cell walls throughout the development of two common diploid accessions of Brachypodium distanchyon, Bd21-3 and Bd21. Chemical analysis was performed on cell walls isolated from distinct organs (i.e. leaves, sheaths, stems and roots at three developmental stages of 1 12-day seedling, 2 vegetative-to-reproductive transition, and 3 mature seed-fill. In addition, we have included cell wall analysis of embryonic callus used for genetic transformations. Composition of cell walls based on components lignin, hydroxycinnamates, uronosyls, neutral sugars, and protein suggests that Brachypodium distanchyon is similar chemically to agriculturally important forage grasses. There were modest compositional differences in hydroxycinnamate profiles between accessions Bd21-3 and Bd21. In addition, when compared to agronomical important C3 grasses, more mature Brachypodium stem cell walls have a relative increase in glucose of 48% and a decrease in lignin of 36%. Though differences exists between Brachypodium and agronomical important C3 grasses, Brachypodium distanchyon should be still a useful model system for genetic manipulation of cell wall composition to determine the impact upon functional characteristics such as rumen digestibility or energy conversion efficiency for bioenergy production.

Cell wall composition throughout development for the model grass Brachypodium distachyon

Science.gov (United States)

Rancour, David M.; Marita, Jane M.; Hatfield, Ronald D.

2012-01-01

Temperate perennial grasses are important worldwide as a livestock nutritive energy source and a potential feedstock for lignocellulosic biofuel production. The annual temperate grass Brachypodium distachyon has been championed as a useful model system to facilitate biological research in agriculturally important temperate forage grasses based on phylogenetic relationships. To physically corroborate genetic predictions, we determined the chemical composition profiles of organ-specific cell walls throughout the development of two common diploid accessions of Brachypodium distachyon, Bd21-3 and Bd21. Chemical analysis was performed on cell walls isolated from distinct organs (i.e., leaves, sheaths, stems, and roots) at three developmental stages of (1) 12-day seedling, (2) vegetative-to-reproductive transition, and (3) mature seed fill. In addition, we have included cell wall analysis of embryonic callus used for genetic transformations. Composition of cell walls based on components lignin, hydroxycinnamates, uronosyls, neutral sugars, and protein suggests that Brachypodium distachyon is similar chemically to agriculturally important forage grasses. There were modest compositional differences in hydroxycinnamate profiles between accessions Bd21-3 and Bd21. In addition, when compared to agronomical important C3 grasses, more mature Brachypodium stem cell walls have a relative increase in glucose of 48% and a decrease in lignin of 36%. Though differences exist between Brachypodium and agronomical important C3 grasses, Brachypodium distachyon should be still a useful model system for genetic manipulation of cell wall composition to determine the impact upon functional characteristics such as rumen digestibility or energy conversion efficiency for bioenergy production. PMID:23227028

Genotypic and phenotypic evaluation of off-type grasses in hybrid Bermudagrass [Cynodon dactylon (L.) Pers. x C. transvaalensis Burtt-Davy] putting greens using genotyping-by-sequencing and morphological characterization.

Science.gov (United States)

Reasor, Eric H; Brosnan, James T; Staton, Margaret E; Lane, Thomas; Trigiano, Robert N; Wadl, Phillip A; Conner, Joann A; Schwartz, Brian M

2018-01-01

Interspecific hybrid bermudagrass [ Cynodon dactylon (L.) Pers. x C. transvaalensis Burtt-Davy] is one of the most widely used grasses on golf courses, with cultivars derived from 'Tifgreen' or 'Tifdwarf' particularly used for putting greens. Many bermudagrass cultivars established for putting greens can be genetically unstable and lead to the occurrence of undesirable off-type grasses that vary in phenotype. The objective of this research was to genetically and phenotypically differentiate off-type grasses and hybrid cultivars. Beginning in 2013, off-type and desirable hybrid bermudagrass samples were collected from golf course putting greens in the southeastern United States and genetically and phenotypically characterized using genotyping-by-sequencing and morphology. Genotyping-by-sequencing determined that 11% (5) of off-type and desirable samples from putting greens were genetically divergent from standard cultivars such as Champion, MiniVerde, Tifdwarf, TifEagle, and Tifgreen. In addition, genotyping-by-sequencing was unable to genetically distinguish all standard cultivars from one another due to their similar origin and clonal propagation; however, over 90,000 potentially informative nucleotide variants were identified among the triploid hybrid cultivars. Although few genetic differences were found in this research, samples harvested from golf course putting greens had variable morphology and were clustered into three distinct phenotypic groups. The majority of off-type grasses in hybrid bermudagrass putting greens were genetically similar with variable morphological traits. Off-type grasses within golf course putting greens have the potential to compromise putting surface functionality and aesthetics.

Segmentation of myocardial perfusion MR sequences with multi-band Active Appearance Models driven by spatial and temporal features

NARCIS (Netherlands)

Baka, N.; Milles, J.; Hendriks, E.A.; Suinesiaputra, A.; Jerosh Herold, M.; Reiber, J.H.C.; Lelieveldt, B.P.F.

2008-01-01

This work investigates knowledge driven segmentation of cardiac MR perfusion sequences. We build upon previous work on multi-band AAMs to integrate into the segmentation both spatial priors about myocardial shape as well as temporal priors about characteristic perfusion patterns. Different temporal

Thermodynamics-based models of transcriptional regulation with gene sequence.

Science.gov (United States)

Wang, Shuqiang; Shen, Yanyan; Hu, Jinxing

2015-12-01

Quantitative models of gene regulatory activity have the potential to improve our mechanistic understanding of transcriptional regulation. However, the few models available today have been based on simplistic assumptions about the sequences being modeled or heuristic approximations of the underlying regulatory mechanisms. In this work, we have developed a thermodynamics-based model to predict gene expression driven by any DNA sequence. The proposed model relies on a continuous time, differential equation description of transcriptional dynamics. The sequence features of the promoter are exploited to derive the binding affinity which is derived based on statistical molecular thermodynamics. Experimental results show that the proposed model can effectively identify the activity levels of transcription factors and the regulatory parameters. Comparing with the previous models, the proposed model can reveal more biological sense.

Molecular Physiology of Root System Architecture in Model Grasses

Science.gov (United States)

Hixson, K.; Ahkami, A. H.; Anderton, C.; Veličković, D.; Myers, G. L.; Chrisler, W.; Lindenmaier, R.; Fang, Y.; Yabusaki, S.; Rosnow, J. J.; Farris, Y.; Khan, N. E.; Bernstein, H. C.; Jansson, C.

2017-12-01

Unraveling the molecular and physiological mechanisms involved in responses of Root System Architecture (RSA) to abiotic stresses and shifts in microbiome structure is critical to understand and engineer plant-microbe-soil interactions in the rhizosphere. In this study, accessions of Brachypodium distachyon Bd21 (C3 model grass) and Setaria viridis A10.1 (C4 model grass) were grown in phytotron chambers under current and elevated CO2 levels. Detailed growth stage-based phenotypic analysis revealed different above- and below-ground morphological and physiological responses in C3 and C4 grasses to enhanced CO2 levels. Based on our preliminary results and by screening values of total biomass, water use efficiency, root to shoot ratio, RSA parameters and net assimilation rates, we postulated a three-phase physiological mechanism, i.e. RootPlus, BiomassPlus and YieldPlus phases, for grass growth under elevated CO2 conditions. Moreover, this comprehensive set of morphological and process-based observations are currently in use to develop, test, and calibrate biophysical whole-plant models and in particular to simulate leaf-level photosynthesis at various developmental stages of C3 and C4 using the model BioCro. To further link the observed phenotypic traits at the organismal level to tissue and molecular levels, and to spatially resolve the origin and fate of key metabolites involved in primary carbohydrate metabolism in different root sections, we complement root phenotypic observations with spatial metabolomics data using mass spectrometry imaging (MSI) methods. Focusing on plant-microbe interactions in the rhizosphere, six bacterial strains with plant growth promoting features are currently in use in both gel-based and soil systems to screen root growth and development in Brachypodium. Using confocal microscopy, GFP-tagged bacterial systems are utilized to study the initiation of different root types of RSA, including primary root (PR), coleoptile node axile root (CNR

Seasonal variation in diurnal atmospheric grass pollen concentration profiles

DEFF Research Database (Denmark)

Peel, Robert George; Ørby, Pia Viuf; Skjøth, Carsten Ambelas

2014-01-01

the time of day when peak concentrations are most likely to occur using seasonally averaged diurnal profiles. Atmospheric pollen loads are highly dependent upon emissions, and different species of grass are known to flower and emit pollen at different times of the day and during different periods......In this study, the diurnal atmospheric grass pollen concentration profile within the Danish city of Aarhus was shown to change in a systematic manner as the pollen season progressed. Although diurnal grass pollen profiles can differ greatly from day-to-day, it is common practice to establish...... of the pollen season. Pollen concentrations are also influenced by meteorological factors - directly through those parameters that govern pollen dispersion and transport, and indirectly through the weather-driven flowering process. We found that three different profiles dominated the grass pollen season...

Model Driven Engineering

Science.gov (United States)

Gaševic, Dragan; Djuric, Dragan; Devedžic, Vladan

A relevant initiative from the software engineering community called Model Driven Engineering (MDE) is being developed in parallel with the Semantic Web (Mellor et al. 2003a). The MDE approach to software development suggests that one should first develop a model of the system under study, which is then transformed into the real thing (i.e., an executable software entity). The most important research initiative in this area is the Model Driven Architecture (MDA), which is Model Driven Architecture being developed under the umbrella of the Object Management Group (OMG). This chapter describes the basic concepts of this software engineering effort.

Purification and characterization of parvalbumin isotypes from grass carp (Ctenopharyngodon idella).

Science.gov (United States)

Li, Zheng; You, Juan; Luo, Yongkang; Wu, Jianping

2014-07-02

The prevalence of fish allergy is rapidly increasing because of a growing fish consumption driven mainly by a positive image of the fish and health relationship. The purpose of this study was to characterize parvalbumin isotypes from grass carp (Ctenopharyngodon idella), one of the most frequently consumed freshwater fish in China. Three parvalbumin isotypes were purified using consecutive gel filtration and reverse-phase chromatography and denoted as PVI, PVII, and PVIII. The molecular weights of the isotypes were determined to be 11.968, 11.430, and 11.512 kDa, respectively. PVI showed 74% matched amino acids sequence with PV isotype 4a from Danio rerio, while PVII and PVIII showed 46% matched amino acids sequence with PV isotypes from Hypophthalmichthys molitrix. PVII is the dominant allergen, but it was liable to gastrointestinal enzymes as PVIII; however, PVI was resistant to pepsin digestion. A further study is to characterize the epitopes of PVII, the dominant allergen.

Grass genomes

OpenAIRE

Bennetzen, Jeffrey L.; SanMiguel, Phillip; Chen, Mingsheng; Tikhonov, Alexander; Francki, Michael; Avramova, Zoya

1998-01-01

For the most part, studies of grass genome structure have been limited to the generation of whole-genome genetic maps or the fine structure and sequence analysis of single genes or gene clusters. We have investigated large contiguous segments of the genomes of maize, sorghum, and rice, primarily focusing on intergenic spaces. Our data indicate that much (>50%) of the maize genome is composed of interspersed repetitive DNAs, primarily nested retrotransposons that in...

Mutational landscape of EGFR-, MYC-, and Kras-driven genetically engineered mouse models of lung adenocarcinoma.

Science.gov (United States)

McFadden, David G; Politi, Katerina; Bhutkar, Arjun; Chen, Frances K; Song, Xiaoling; Pirun, Mono; Santiago, Philip M; Kim-Kiselak, Caroline; Platt, James T; Lee, Emily; Hodges, Emily; Rosebrock, Adam P; Bronson, Roderick T; Socci, Nicholas D; Hannon, Gregory J; Jacks, Tyler; Varmus, Harold

2016-10-18

Genetically engineered mouse models (GEMMs) of cancer are increasingly being used to assess putative driver mutations identified by large-scale sequencing of human cancer genomes. To accurately interpret experiments that introduce additional mutations, an understanding of the somatic genetic profile and evolution of GEMM tumors is necessary. Here, we performed whole-exome sequencing of tumors from three GEMMs of lung adenocarcinoma driven by mutant epidermal growth factor receptor (EGFR), mutant Kirsten rat sarcoma viral oncogene homolog (Kras), or overexpression of MYC proto-oncogene. Tumors from EGFR- and Kras-driven models exhibited, respectively, 0.02 and 0.07 nonsynonymous mutations per megabase, a dramatically lower average mutational frequency than observed in human lung adenocarcinomas. Tumors from models driven by strong cancer drivers (mutant EGFR and Kras) harbored few mutations in known cancer genes, whereas tumors driven by MYC, a weaker initiating oncogene in the murine lung, acquired recurrent clonal oncogenic Kras mutations. In addition, although EGFR- and Kras-driven models both exhibited recurrent whole-chromosome DNA copy number alterations, the specific chromosomes altered by gain or loss were different in each model. These data demonstrate that GEMM tumors exhibit relatively simple somatic genotypes compared with human cancers of a similar type, making these autochthonous model systems useful for additive engineering approaches to assess the potential of novel mutations on tumorigenesis, cancer progression, and drug sensitivity.

Mutational landscape of EGFR-, MYC-, and Kras-driven genetically engineered mouse models of lung adenocarcinoma

Science.gov (United States)

McFadden, David G.; Politi, Katerina; Bhutkar, Arjun; Chen, Frances K.; Song, Xiaoling; Pirun, Mono; Santiago, Philip M.; Kim-Kiselak, Caroline; Platt, James T.; Lee, Emily; Hodges, Emily; Rosebrock, Adam P.; Bronson, Roderick T.; Socci, Nicholas D.; Hannon, Gregory J.; Jacks, Tyler; Varmus, Harold

2016-01-01

Genetically engineered mouse models (GEMMs) of cancer are increasingly being used to assess putative driver mutations identified by large-scale sequencing of human cancer genomes. To accurately interpret experiments that introduce additional mutations, an understanding of the somatic genetic profile and evolution of GEMM tumors is necessary. Here, we performed whole-exome sequencing of tumors from three GEMMs of lung adenocarcinoma driven by mutant epidermal growth factor receptor (EGFR), mutant Kirsten rat sarcoma viral oncogene homolog (Kras), or overexpression of MYC proto-oncogene. Tumors from EGFR- and Kras-driven models exhibited, respectively, 0.02 and 0.07 nonsynonymous mutations per megabase, a dramatically lower average mutational frequency than observed in human lung adenocarcinomas. Tumors from models driven by strong cancer drivers (mutant EGFR and Kras) harbored few mutations in known cancer genes, whereas tumors driven by MYC, a weaker initiating oncogene in the murine lung, acquired recurrent clonal oncogenic Kras mutations. In addition, although EGFR- and Kras-driven models both exhibited recurrent whole-chromosome DNA copy number alterations, the specific chromosomes altered by gain or loss were different in each model. These data demonstrate that GEMM tumors exhibit relatively simple somatic genotypes compared with human cancers of a similar type, making these autochthonous model systems useful for additive engineering approaches to assess the potential of novel mutations on tumorigenesis, cancer progression, and drug sensitivity. PMID:27702896

Study on the Method of Grass Yield Model in the Source Region of Three Rivers with Multivariate Data

International Nuclear Information System (INIS)

You, Haoyan; Luo, Chengfeng; Liu, Zhengjun; Wang, Jiao

2014-01-01

This paper uses remote sensing and GIS technology to analyse the Source Region of Three Rivers (SRTR) to establish a grass yield estimation model during 2010 with remote sensing data, meteorological data, grassland type data and ground measured data. Analysis of the correlation between ground measured data, vegetation index based HJ-1A/B satellite data, meteorological data and grassland type data were used to establish the grass yield model. The grass yield model was studied by several statistical methods, such as multiple linear regression and Geographically Weighted Regression (GWR). The model's precision was validated. Finally, the best model to estimate the grass yield of Maduo County in SRTR was contrasted with the TM degraded grassland interpretation image of Maduo County from 2009. The result shows that: (1) Comparing with the multiple linear regression model, the GWR model gave a much better fitting result with the quality of fit increasing significantly from less than 0.3 to more than 0.8; (2) The most sensitive factors affecting the grass yield in SRTR were precipitation from May to August and drought index from May to August. From calculation of the five vegetation indices, MSAVI fitted the best; (3) The Maduo County grass yield estimated by the optimal model was consistent with the TM degraded grassland interpretation image, the spatial distribution of grass yield in Maduo County for 2010 showed a ''high south and low north'' pattern

Molecular detection of genotype II grass carp reovirus based on nucleic acid sequence-based amplification combined with enzyme-linked immunosorbent assay (NASBA-ELISA).

Science.gov (United States)

Zeng, Weiwei; Yao, Wei; Wang, Yingying; Li, Yingying; Bermann, Sven M; Ren, Yan; Shi, Cunbin; Song, Xinjian; Huang, Qiwen; Zheng, Shuchen; Wang, Qing

2017-05-01

Grass carp reovirus (GCRV) is the causative agent of the grass carp hemorrhagic disease that has resulted in severe economic losses in the grass carp (Ctenopharyngodon idella) farming industry in China. Early diagnosis and vaccine administration are important priorities for GCRV control. In this study, a nucleic acid sequence-based amplification with enzyme-linked immunosorbent assay (NASBA-ELISA) was developed for to detect genotype II GCRV (GCRV- II). Primers specifically targeting viral RNA genome segment 6 were utilized for amplification in an isothermal digoxigenin-labeling NASBA process, resulting in DIG-labeled RNA amplicons. The amplicons were hybridized to specific biotinylated DNA probes and the products were detected colorimetrically using horseradish peroxidase and a microplate reader. The new method is able to detect GCRV at 14 copies/μL within 5h and had a diagnostic sensitivity and a specificity of 100% when GCRV-II and non-target virus were tested. This NASBA-ELISA was evaluated using a panel of clinical samples (n=103) to demonstrate that it is a rapid, effective and sensitive method for GCRV detection in grass carp aquaculture. Copyright © 2017 Elsevier B.V. All rights reserved.

Mapping and modeling the biogeochemical cycling of turf grasses in the United States.

Science.gov (United States)

Milesi, Cristina; Running, Steven W; Elvidge, Christopher D; Dietz, John B; Tuttle, Benjamin T; Nemani, Ramakrishna R

2005-09-01

Turf grasses are ubiquitous in the urban landscape of the United States and are often associated with various types of environmental impacts, especially on water resources, yet there have been limited efforts to quantify their total surface and ecosystem functioning, such as their total impact on the continental water budget and potential net ecosystem exchange (NEE). In this study, relating turf grass area to an estimate of fractional impervious surface area, it was calculated that potentially 163,800 km2 (+/- 35,850 km2) of land are cultivated with turf grasses in the continental United States, an area three times larger than that of any irrigated crop. Using the Biome-BGC ecosystem process model, the growth of warm-season and cool-season turf grasses was modeled at a number of sites across the 48 conterminous states under different management scenarios, simulating potential carbon and water fluxes as if the entire turf surface was to be managed like a well-maintained lawn. The results indicate that well-watered and fertilized turf grasses act as a carbon sink. The potential NEE that could derive from the total surface potentially under turf (up to 17 Tg C/yr with the simulated scenarios) would require up to 695 to 900 liters of water per person per day, depending on the modeled water irrigation practices, suggesting that outdoor water conservation practices such as xeriscaping and irrigation with recycled waste-water may need to be extended as many municipalities continue to face increasing pressures on freshwater.

Modelling the transfer of 14C from the atmosphere to grass: A case study in a grass field near AREVA-NC La Hague

International Nuclear Information System (INIS)

Aulagnier, C.; Le Dizès, S.; Maro, D.; Hébert, D.; Lardy, R.; Martin, R.; Gonze, M.-A.

2012-01-01

Radioactive 14 C is formed as a by-product of nuclear power generation and from operation of nuclear fuel reprocessing plants like AREVA-NC La Hague (North France), which releases about 15 TBq per year of 14 C into the atmosphere. Since the autumn of 2006, 14 C activity concentrations in samples from the terrestrial environment (air, grass and soil) have been monitored monthly on grassland 2 km downwind of the reprocessing plant. The monitoring data provides an opportunity to validate radioecology models used to assess 14 C transfer to grassland ecosystems. This article compares and discusses the ability of two different models to reproduce the observed temporal variability in grass 14 C activity in the vicinity of AREVA-NC La Hague. These two models are the TOCATTA model which is specifically designed for modelling transfer of 14 C and tritium in the terrestrial environment, and PaSim, a pasture model for simulating grassland carbon and nitrogen cycling. Both TOCATTA and PaSim tend to under-estimate the magnitude of observed peaks in grass 14 C activity, although they reproduce the general trends. PaSim simulates 14 C activities in substrate and structural pools of the plant. We define a mean turn-over time for 14 C within the plant, which is based on both experimental data and the frequency of cuts. An adapted PaSim result is presented using the 15 and 20 day moving average results for the 14 C activity in the substrate pool, which shows a good match to the observations. This model reduces the Root Mean Square Error (RMSE) by nearly 40% in comparison to TOCATTA. - Highlights: ► We model 14 C transfer from the atmosphere to grass near AREVA-NC reprocessing plant. ► Both models considered under-estimate the observed variability and highest peaks. ► A model based solely on the sap 14 C activity and mean turn-over time is considered. ► It performs well and could be applied to case studies around nuclear facilities.

Growing C4 perennial grass for bioenergy using a new Agro-BGC ecosystem model

Science.gov (United States)

di Vittorio, A. V.; Anderson, R. S.; Miller, N. L.; Running, S. W.

2009-12-01

Accurate, spatially gridded estimates of bioenergy crop yields require 1) biophysically accurate crop growth models and 2) careful parameterization of unavailable inputs to these models. To meet the first requirement we have added the capacity to simulate C4 perennial grass as a bioenergy crop to the Biome-BGC ecosystem model. This new model, hereafter referred to as Agro-BGC, includes enzyme driven C4 photosynthesis, individual live and dead leaf, stem, and root carbon/nitrogen pools, separate senescence and litter fall processes, fruit growth, optional annual seeding, flood irrigation, a growing degree day phenology with a killing frost option, and a disturbance handler that effectively simulates fertilization, harvest, fire, and incremental irrigation. There are four Agro-BGC vegetation parameters that are unavailable for Panicum virgatum (switchgrass), and to meet the second requirement we have optimized the model across multiple calibration sites to obtain representative values for these parameters. We have verified simulated switchgrass yields against observations at three non-calibration sites in IL. Agro-BGC simulates switchgrass growth and yield at harvest very well at a single site. Our results suggest that a multi-site optimization scheme would be adequate for producing regional-scale estimates of bioenergy crop yields on high spatial resolution grids.

Setaria viridis and Setaria italica, model genetic systems for the Panicoid grasses.

Science.gov (United States)

Li, Pinghua; Brutnell, Thomas P

2011-05-01

Setaria italica and its wild ancestor Setaria viridis are diploid C(4) grasses with small genomes of ∼515 Mb. Both species have attributes that make them attractive as model systems. Setaria italica is a grain crop widely grown in Northern China and India that is closely related to the major food and feed crops maize and sorghum. A large collection of S. italica accessions are available and thus opportunities exist for association mapping and allele mining for novel variants that will have direct application in agriculture. Setaria viridis is the weedy relative of S. italica with many attributes suitable for genetic analyses including a small stature, rapid life cycle, and prolific seed production. Setaria sp. are morphologically similar to most of the Panicoideae grasses, including major biofuel feedstocks, switchgrass (Panicum virgatum) and Miscanthus (Miscanthus giganteus). They are broadly distributed geographically and occupy diverse ecological niches. The cross-compatibility of S. italica and S. viridis also suggests that gene flow is likely between wild and domesticated accessions. In addition to serving as excellent models for C(4) photosynthesis, these grasses provide novel opportunities to study abiotic stress tolerance and as models for bioenergy feedstocks.

Estimating grass and grass silage degradation characteristics by in situ and in vitro gas production methods

Directory of Open Access Journals (Sweden)

Danijel Karolyi

2010-01-01

Full Text Available Fermentation characteristics of grass and grass silage at different maturities were studied using in situ and in vitro gas production methods. In situ data determined difference between grass and silage. Degradable fraction decreased as grass matured while the undegradable fraction increased. Rate of degradation (kd was slower for silage than fresh grass. Gas production method (GP data showed that fermentation of degradable fraction was different between stage of maturity in both grass and silage. Other data did not show any difference with the exception for the rate of GP of soluble and undegradable fraction. The in situ degradation characteristics were estimated from GP characteristics. The degradable and undegradable fractions could be estimated by multiple relationships. Using the three-phases model for gas production kd and fermentable organic matter could be estimated from the same parameters. The only in situ parameter that could not be estimated with GP parameters was the soluble fraction. The GP method and the three phases model provided to be an alternative to the in situ method for animal feed evaluations.

Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential.

Science.gov (United States)

Zhang, Gengyun; Liu, Xin; Quan, Zhiwu; Cheng, Shifeng; Xu, Xun; Pan, Shengkai; Xie, Min; Zeng, Peng; Yue, Zhen; Wang, Wenliang; Tao, Ye; Bian, Chao; Han, Changlei; Xia, Qiuju; Peng, Xiaohua; Cao, Rui; Yang, Xinhua; Zhan, Dongliang; Hu, Jingchu; Zhang, Yinxin; Li, Henan; Li, Hua; Li, Ning; Wang, Junyi; Wang, Chanchan; Wang, Renyi; Guo, Tao; Cai, Yanjie; Liu, Chengzhang; Xiang, Haitao; Shi, Qiuxiang; Huang, Ping; Chen, Qingchun; Li, Yingrui; Wang, Jun; Zhao, Zhihai; Wang, Jian

2012-05-13

Foxtail millet (Setaria italica), a member of the Poaceae grass family, is an important food and fodder crop in arid regions and has potential for use as a C(4) biofuel. It is a model system for other biofuel grasses, including switchgrass and pearl millet. We produced a draft genome (∼423 Mb) anchored onto nine chromosomes and annotated 38,801 genes. Key chromosome reshuffling events were detected through collinearity identification between foxtail millet, rice and sorghum including two reshuffling events fusing rice chromosomes 7 and 9, 3 and 10 to foxtail millet chromosomes 2 and 9, respectively, that occurred after the divergence of foxtail millet and rice, and a single reshuffling event fusing rice chromosome 5 and 12 to foxtail millet chromosome 3 that occurred after the divergence of millet and sorghum. Rearrangements in the C(4) photosynthesis pathway were also identified.

De novo transcriptome assembly for the tropical grass Panicum maximum Jacq.

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Guilherme Toledo-Silva

Full Text Available Guinea grass (Panicum maximum Jacq. is a tropical African grass often used to feed beef cattle, which is an important economic activity in Brazil. Brazil is the leader in global meat exportation because of its exclusively pasture-raised bovine herds. Guinea grass also has potential uses in bioenergy production due to its elevated biomass generation through the C4 photosynthesis pathway. We generated approximately 13 Gb of data from Illumina sequencing of P. maximum leaves. Four different genotypes were sequenced, and the combined reads were assembled de novo into 38,192 unigenes and annotated; approximately 63% of the unigenes had homology to other proteins in the NCBI non-redundant protein database. Functional classification through COG (Clusters of Orthologous Groups, GO (Gene Ontology and KEGG (Kyoto Encyclopedia of Genes and Genomes analyses showed that the unigenes from Guinea grass leaves are involved in a wide range of biological processes and metabolic pathways, including C4 photosynthesis and lignocellulose generation, which are important for cattle grazing and bioenergy production. The most abundant transcripts were involved in carbon fixation, photosynthesis, RNA translation and heavy metal cellular homeostasis. Finally, we identified a number of potential molecular markers, including 5,035 microsatellites (SSRs and 346,456 single nucleotide polymorphisms (SNPs. To the best of our knowledge, this is the first study to characterize the complete leaf transcriptome of P. maximum using high-throughput sequencing. The biological information provided here will aid in gene expression studies and marker-assisted selection-based breeding research in tropical grasses.

Data-driven modelling of protein synthesis : A sequence perspective

NARCIS (Netherlands)

Gritsenko, A.

2017-01-01

Recent advances in DNA sequencing, synthesis and genetic engineering have enabled the introduction of choice DNA sequences into living cells. This is an exciting prospect for the field of industrial biotechnology, which aims at using microorganisms to produce foods, beverages, pharmaceuticals and

Analysis of two heterologous flowering genes in ¤Brachypodium distachyon¤ demonstrates its potential as a grass model plant

DEFF Research Database (Denmark)

Olsen, P.; Lenk, I.; Jensen, Christian S.

2006-01-01

Despite the great contribution of model organisms, such as Arabidopsis and rice to understand biological processes in plants, these models are less valuable for functional studies of particular genes from temperate grass crop species. Therefore a new model plant is required, displaying features...... including close phylogenetic relationship to the temperate grasses, vernalisation requirement, high transformation efficiency, small genome size and a rapid life cycle. These requirements are all fulfilled by the small annual grass Brachypodium distachyon. As a first step towards implementing this plant...

Reference genome sequence of the model plant Setaria.

Science.gov (United States)

Bennetzen, Jeffrey L; Schmutz, Jeremy; Wang, Hao; Percifield, Ryan; Hawkins, Jennifer; Pontaroli, Ana C; Estep, Matt; Feng, Liang; Vaughn, Justin N; Grimwood, Jane; Jenkins, Jerry; Barry, Kerrie; Lindquist, Erika; Hellsten, Uffe; Deshpande, Shweta; Wang, Xuewen; Wu, Xiaomei; Mitros, Therese; Triplett, Jimmy; Yang, Xiaohan; Ye, Chu-Yu; Mauro-Herrera, Margarita; Wang, Lin; Li, Pinghua; Sharma, Manoj; Sharma, Rita; Ronald, Pamela C; Panaud, Olivier; Kellogg, Elizabeth A; Brutnell, Thomas P; Doust, Andrew N; Tuskan, Gerald A; Rokhsar, Daniel; Devos, Katrien M

2012-05-13

We generated a high-quality reference genome sequence for foxtail millet (Setaria italica). The ∼400-Mb assembly covers ∼80% of the genome and >95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with >1.3 million expressed sequence tag reads. We produced more than 580 million RNA-Seq reads to facilitate expression analyses. We also sequenced Setaria viridis, the ancestral wild relative of S. italica, and identified regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion. The genus Setaria includes natural and cultivated species that demonstrate a wide capacity for adaptation. The genetic basis of this adaptation was investigated by comparing five sequenced grass genomes. We also used the diploid Setaria genome to evaluate the ongoing genome assembly of a related polyploid, switchgrass (Panicum virgatum).

Reference genome sequence of the model plant Setaria

Energy Technology Data Exchange (ETDEWEB)

Bennetzen, Jeffrey L [ORNL; Schmutz, Jeremy [Hudson Alpha Institute of Biotechnology; Wang, Hao [University of Georgia, Athens, GA; Percifield, Ryan [University of Georgia, Athens, GA; Hawkins, Jennifer [University of Georgia, Athens, GA; Pontaroli, Ana C. [University of Georgia, Athens, GA; Estep, Matt [University of Georgia, Athens, GA; Feng, Liang [University of Georgia, Athens, GA; Vaughn, Justin N [ORNL; Grimwood, Jane [Hudson Alpha Institute of Biotechnology; Jenkins, Jerry [Hudson Alpha Institute of Biotechnology; Barry, Kerrie [U.S. Department of Energy, Joint Genome Institute; Lindquist, Erika [U.S. Department of Energy, Joint Genome Institute; Hellsten, Uffe [U.S. Department of Energy, Joint Genome Institute; Deshpande, Shweta [U.S. Department of Energy, Joint Genome Institute; Wang, Xuewen [University of Georgia, Athens, GA; Wu, Xiaomei [University of Georgia, Athens, GA; Mitros, Therese [University of California, Berkeley; Triplett, Jimmy [University of Missouri, St. Louis; Yang, Xiaohan [ORNL; Ye, Chuyu [ORNL; Mauro-Herrera, Margarita [Oklahoma State University; Wang, Lin [Cornell University; Li, Pinghua [Cornell University; Sharma, Manoj [University of California, Davis; Sharma, Rita [University of California, Davis; Ronald, Pamela [University of California, Davis; Panaud, Olivier [Universite de Perpignan, Perpignan, France; Kellogg, Elizabeth A. [University of Missouri, St. Louis; Brutnell, Thomas P. [Cornell University; Doust, Andrew N. [Oklahoma State University; Tuskan, Gerald A [ORNL; Rokhsar, Daniel [U.S. Department of Energy, Joint Genome Institute; Devos, Katrien M [ORNL

2012-01-01

We generated a high-quality reference genome sequence for foxtail millet (Setaria italica). The ~400-Mb assembly covers ~80% of the genome and >95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with >1.3 million expressed sequence tag reads. We produced more than 580 million RNA-Seq reads to facilitate expression analyses. We also sequenced Setaria viridis, the ancestral wild relative of S. italica, and identified regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion. The genus Setaria includes natural and cultivated species that demonstrate a wide capacity for adaptation. The genetic basis of this adaptation was investigated by comparing five sequenced grass genomes. We also used the diploid Setaria genome to evaluate the ongoing genome assembly of a related polyploid, switchgrass (Panicum virgatum).

Reference genome sequence of the model plant Setaria

Energy Technology Data Exchange (ETDEWEB)

Bennetzen, Jeffrey L [ORNL; Yang, Xiaohan [ORNL; Ye, Chuyu [ORNL; Tuskan, Gerald A [ORNL

2012-01-01

We generated a high-quality reference genome sequence for foxtail millet (Setaria italica). The {approx}400-Mb assembly covers {approx}80% of the genome and >95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with >1.3 million expressed sequence tag reads. We produced more than 580 million RNA-Seq reads to facilitate expression analyses. We also sequenced Setaria viridis, the ancestral wild relative of S. italica, and identified regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion. The genus Setaria includes natural and cultivated species that demonstrate a wide capacity for adaptation. The genetic basis of this adaptation was investigated by comparing five sequenced grass genomes. We also used the diploid Setaria genome to evaluate the ongoing genome assembly of a related polyploid, switchgrass (Panicum virgatum).

Comparing Transformation Possibilities of Topological Functioning Model and BPMN in the Context of Model Driven Architecture

Directory of Open Access Journals (Sweden)

Solomencevs Artūrs

2016-05-01

Full Text Available The approach called “Topological Functioning Model for Software Engineering” (TFM4SE applies the Topological Functioning Model (TFM for modelling the business system in the context of Model Driven Architecture. TFM is a mathematically formal computation independent model (CIM. TFM4SE is compared to an approach that uses BPMN as a CIM. The comparison focuses on CIM modelling and on transformation to UML Sequence diagram on the platform independent (PIM level. The results show the advantages and drawbacks the formalism of TFM brings into the development.

GeMprospector--online design of cross-species genetic marker candidates in legumes and grasses.

Science.gov (United States)

Fredslund, Jakob; Madsen, Lene H; Hougaard, Birgit K; Sandal, Niels; Stougaard, Jens; Bertioli, David; Schauser, Leif

2006-07-01

The web program GeMprospector (URL: http://cgi-www.daimi.au.dk/cgi-chili/GeMprospector/main) allows users to automatically design large sets of cross-species genetic marker candidates targeting either legumes or grasses. The user uploads a collection of ESTs from one or more legume or grass species, and they are compared with a database of clusters of homologous EST and genomic sequences from other legumes or grasses, respectively. Multiple sequence alignments between submitted ESTs and their homologues in the appropriate database form the basis of automated PCR primer design in conserved exons such that each primer set amplifies an intron. The only user input is a collection of ESTs, not necessarily from more than one species, and GeMprospector can boost the potential of such an EST collection by combining it with a large database to produce cross-species genetic marker candidates for legumes or grasses.

A consensus linkage map of the grass carp (Ctenopharyngodon idella based on microsatellites and SNPs

Directory of Open Access Journals (Sweden)

Li Jiale

2010-02-01

Full Text Available Abstract Background Grass carp (Ctenopharyngodon idella belongs to the family Cyprinidae which includes more than 2000 fish species. It is one of the most important freshwater food fish species in world aquaculture. A linkage map is an essential framework for mapping traits of interest and is often the first step towards understanding genome evolution. The aim of this study is to construct a first generation genetic map of grass carp using microsatellites and SNPs to generate a new resource for mapping QTL for economically important traits and to conduct a comparative mapping analysis to shed new insights into the evolution of fish genomes. Results We constructed a first generation linkage map of grass carp with a mapping panel containing two F1 families including 192 progenies. Sixteen SNPs in genes and 263 microsatellite markers were mapped to twenty-four linkage groups (LGs. The number of LGs was corresponding to the haploid chromosome number of grass carp. The sex-specific map was 1149.4 and 888.8 cM long in females and males respectively whereas the sex-averaged map spanned 1176.1 cM. The average resolution of the map was 4.2 cM/locus. BLAST searches of sequences of mapped markers of grass carp against the whole genome sequence of zebrafish revealed substantial macrosynteny relationship and extensive colinearity of markers between grass carp and zebrafish. Conclusions The linkage map of grass carp presented here is the first linkage map of a food fish species based on co-dominant markers in the family Cyprinidae. This map provides a valuable resource for mapping phenotypic variations and serves as a reference to approach comparative genomics and understand the evolution of fish genomes and could be complementary to grass carp genome sequencing project.

Foxtail millet: a model crop for genetic and genomic studies in bioenergy grasses.

Science.gov (United States)

Lata, Charu; Gupta, Sarika; Prasad, Manoj

2013-09-01

Foxtail millet is one of the oldest domesticated diploid C4 Panicoid crops having a comparatively small genome size of approximately 515 Mb, short life cycle, and inbreeding nature. Its two species, Setaria italica (domesticated) and Setaria viridis (wild progenitor), have characteristics that classify them as excellent model systems to examine several aspects of architectural, evolutionary, and physiological importance in Panicoid grasses especially the biofuel crops such as switchgrass and napiergrass. Foxtail millet is a staple crop used extensively for food and fodder in parts of Asia and Africa. In its long history of cultivation, it has been adapted to arid and semi-arid areas of Asia, North Africa, South and North America. Foxtail millet has one of the largest collections of cultivated as well as wild-type germplasm rich with phenotypic variations and hence provides prospects for association mapping and allele-mining of elite and novel variants to be incorporated in crop improvement programs. Most of the foxtail millet accessions can be primarily abiotic stress tolerant particularly to drought and salinity, and therefore exploiting these agronomic traits can enhance its efficacy in marker-aided breeding as well as in genetic engineering for abiotic stress tolerance. In addition, the release of draft genome sequence of foxtail millet would be useful to the researchers worldwide in not only discerning the molecular basis of biomass production in biofuel crops and the methods to improve it, but also for the introgression of beneficial agronomically important characteristics in foxtail millet as well as in related Panicoid bioenergy grasses.

Dynamic modeling of the cesium, strontium, and ruthenium transfer to grass and vegetables

International Nuclear Information System (INIS)

Renaud, P.; Real, J.; Maubert, H.; Roussel-Debet, S.

1999-01-01

From 1988 to 1993, the Nuclear Safety and Protection Institute (Institut de Protection et de Surete Nucleaire -- IPSN) conducted experimental programs focused on transfers to vegetation following accidental localized deposits of radioactive aerosols. In relation to vegetable crops (fruit, leaves, and root vegetables) and meadow grass these experiments have enabled a determination of the factors involved in the transfer of cesium, strontium, and ruthenium at successive harvests, or cuttings, in respect of various time lags after contamination. The dynamic modeling given by these results allows an evaluation of changes in the mass activity of vegetables and grass during the months following deposit. It constitutes part of the ASTRAL post-accident radioecology model

Dichotomy in the NRT gene families of dicots and grass species.

Directory of Open Access Journals (Sweden)

Darren Plett

Full Text Available A large proportion of the nitrate (NO(3(- acquired by plants from soil is actively transported via members of the NRT families of NO(3(- transporters. In Arabidopsis, the NRT1 family has eight functionally characterised members and predominantly comprises low-affinity transporters; the NRT2 family contains seven members which appear to be high-affinity transporters; and there are two NRT3 (NAR2 family members which are known to participate in high-affinity transport. A modified reciprocal best hit (RBH approach was used to identify putative orthologues of the Arabidopsis NRT genes in the four fully sequenced grass genomes (maize, rice, sorghum, Brachypodium. We also included the poplar genome in our analysis to establish whether differences between Arabidopsis and the grasses may be generally applicable to monocots and dicots. Our analysis reveals fundamental differences between Arabidopsis and the grass species in the gene number and family structure of all three families of NRT transporters. All grass species possessed additional NRT1.1 orthologues and appear to lack NRT1.6/NRT1.7 orthologues. There is significant separation in the NRT2 phylogenetic tree between NRT2 genes from dicots and grass species. This indicates that determination of function of NRT2 genes in grass species will not be possible in cereals based simply on sequence homology to functionally characterised Arabidopsis NRT2 genes and that proper functional analysis will be required. Arabidopsis has a unique NRT3.2 gene which may be a fusion of the NRT3.1 and NRT3.2 genes present in all other species examined here. This work provides a framework for future analysis of NO(3(- transporters and NO(3(- transport in grass crop species.

Complete amino acid sequence of a Lolium perenne (perennial rye grass) pollen allergen, Lol p II.

Science.gov (United States)

Ansari, A A; Shenbagamurthi, P; Marsh, D G

1989-07-05

The complete amino acid sequence of a Lolium perenne (rye grass) pollen allergen, Lol p II was determined by automated Edman degradation of the protein and selected fragments. Cleavage of the protein by enzymatic and chemical techniques established an unambiguous sequence for the protein. Lol p II contains 97 amino acid residues, with a calculated molecular weight of 10,882. The protein lacks cysteine and glutamine and shows no evidence of glycosylation. Theoretical predictions by Fraga's (Fraga, S. (1982) Can. J. Chem. 60, 2606-2610) and Hopp and Woods' (Hopp, T. P., and Woods, K. R. (1981) Proc. Natl. Acad. Sci. U.S.A. 78, 3824-3828) methods indicate the presence of four hydrophilic regions, which may contribute to sequential or parts of conformational B-cell epitopes. Analysis of amphipathic regions by Berzofsky's method indicates the presence of a highly amphipathic region, which may contain, or contribute to, an Ia/T-cell epitope. This latter segment of Lol p II was found to be highly homologous with an antibody-binding segment of the major rye allergen Lol p I and may explain why immune responsiveness to both the allergens is associated with HLA-DR3.

Data Driven Economic Model Predictive Control

Directory of Open Access Journals (Sweden)

Masoud Kheradmandi

2018-04-01

Full Text Available This manuscript addresses the problem of data driven model based economic model predictive control (MPC design. To this end, first, a data-driven Lyapunov-based MPC is designed, and shown to be capable of stabilizing a system at an unstable equilibrium point. The data driven Lyapunov-based MPC utilizes a linear time invariant (LTI model cognizant of the fact that the training data, owing to the unstable nature of the equilibrium point, has to be obtained from closed-loop operation or experiments. Simulation results are first presented demonstrating closed-loop stability under the proposed data-driven Lyapunov-based MPC. The underlying data-driven model is then utilized as the basis to design an economic MPC. The economic improvements yielded by the proposed method are illustrated through simulations on a nonlinear chemical process system example.

GRASS GIS: a peer-reviewed scientific platform and future research repository

Science.gov (United States)

Chemin, Yann; Petras, Vaclav; Petrasova, Anna; Landa, Martin; Gebbert, Sören; Zambelli, Pietro; Neteler, Markus; Löwe, Peter; Di Leo, Margherita

2015-04-01

, Y. H. , 2014. Remote Sensing Raster Programming, 3rd Ed., Lulu (Eds). [5] Di Leo, M., de Rigo, D., Rodriguez-Aseretto, D., Bosco, C., Petroliagkis, T., Camia, A., San-Miguel-Ayanz, J., 2013. Dynamic data driven ensemble for wildfire behaviour assessment: A case study. IFIP Advances in Information and Communication Technology, vol. 413, pp. 11-22, 2013, ISSN:1868-4238. Special issue: "Environmental Software Systems. Fostering sharing information". [6] García, M., Villagarcía, L., Contreras, S., Domingo, F. & Puigdefábregas, J. (2007). Comparison of three operative models for estimating the surface water deficit using aster reflective and thermal data, Sensors 7(6): 860-883. [7] Gao, Y. & Long, D. ,2008. Intercomparison of remote sensing-based models for estimation of evapotranspiration and accuracy assessment based on swat, Hydrological Processes 22: 4850-4869. [8] GRASS GIS Trac, changelog for v.surf.rst, 2015. http://trac.osgeo.org/grass/ [9] GRASS GIS Trac, changelog for r.li, 2015. http://trac.osgeo.org/grass/ [10] McGarigal, K., and B. J. Marks. 1995. FRAGSTATS: spatial pattern analysis program for quantifying landscape structure. USDA For. Serv. Gen. Tech. Rep. PNW-351 [11] Mitas, L., and Mitasova H., 1988, General variational approach to the approximation problem, Computers and Mathematics with Applications, v.16, p. 983-992. [12] Mitas, L., and Mitasova, H., 1998, Distributed soil erosion simulation for effective erosion prevention. Water Resources Research, 34(3), 505-516. [13] Mitasova, H. and Mitas, L., 1993: Interpolation by Regularized Spline with Tension: I. Theory and Implementation, Mathematical Geology, 25, 641-655. [14] North Carolina State University, Geospatial Modeling Course, GIS/MEA582, 2015. http://courses.ncsu.edu/ [15] Petras, V., Gebbert, S., 2014. Testing framework for GRASS GIS: ensuring reproducibility of scientific geospatial computing. Poster presented at: AGU Fall Meeting, December 15-19, 2014, San Francisco, USA. [16] Petrasova, A

resistance of napier grass clones to napier grass stunt disease

African Journals Online (AJOL)

ACSS

Napier grass (Pennisetum purpureum Schumach) is the major livestock fodder under intensive and semi-intensive systems in East Africa. However, the productivity of the grass is constrained by Napier grass Stunt Disease. (NSD). The purpose of this study was to identify Napier grass clones with resistance to NSD.

Resistance of Napier grass clones to Napier grass Stunt Disease ...

African Journals Online (AJOL)

Napier grass (Pennisetum purpureum Schumach) is the major livestock fodder under intensive and semi-intensive systems in East Africa. However, the productivity of the grass is constrained by Napier grass Stunt Disease (NSD). The purpose of this study was to identify Napier grass clones with resistance to NSD.

Enhancing GRASS data communication with videographic technology

Energy Technology Data Exchange (ETDEWEB)

Sullivan, R.G. [Argonne National Lab., IL (United States); Gerdes, D.; Youngs, D. [Army Construction Engineering Research Lab., Champaign, IL (United States)

1992-07-01

Research at Argonne National Laboratory and the US Army Construction Engineering Research Laboratory has shown that computer videographic technology can be used to assist visualization and communication of GIS-generated geographic information. Videographic tools can be used to make results of GRASS analyses clear to decision-makers and to public interest groups, as well as to help GRASS users visualize geographic data more easily. Useful videographic visualization tools include graphic overlay of GRASS layers onto panchromatic images, allowing landscape features to be associated with GIS classifications; draping of GIS layers onto terrain models to create shaded relief maps; and incorporation of photographic imagery into GIS graphics. Useful videographic communications capabilities include convenient, direct interface to video formats, allowing incorporation of live video into GRASS graphics and output of GRASS graphics to video; convenient output of high-quality slides and prints; and enhanced labeling and editing of GRASS images. Conversion of GRASS imagery to standard videographic file formats also facilitates incorporation of GRASS images into other software programs, such as database and work-processing packages.

Enhancing GRASS data communication with videographic technology

Energy Technology Data Exchange (ETDEWEB)

Sullivan, R.G. (Argonne National Lab., IL (United States)); Gerdes, D.; Youngs, D. (Army Construction Engineering Research Lab., Champaign, IL (United States))

1992-01-01

Research at Argonne National Laboratory and the US Army Construction Engineering Research Laboratory has shown that computer videographic technology can be used to assist visualization and communication of GIS-generated geographic information. Videographic tools can be used to make results of GRASS analyses clear to decision-makers and to public interest groups, as well as to help GRASS users visualize geographic data more easily. Useful videographic visualization tools include graphic overlay of GRASS layers onto panchromatic images, allowing landscape features to be associated with GIS classifications; draping of GIS layers onto terrain models to create shaded relief maps; and incorporation of photographic imagery into GIS graphics. Useful videographic communications capabilities include convenient, direct interface to video formats, allowing incorporation of live video into GRASS graphics and output of GRASS graphics to video; convenient output of high-quality slides and prints; and enhanced labeling and editing of GRASS images. Conversion of GRASS imagery to standard videographic file formats also facilitates incorporation of GRASS images into other software programs, such as database and work-processing packages.

A Remote Sensing Based Forage Biomass Yield Inversion Model of Alpine-cold Meadow during Grass-withering Period in Sanjiangyuan Area

International Nuclear Information System (INIS)

Song, Weize; Jia, Haifeng; Liang, Shidong; Wang, Zheng; Liu, Shujie; Hao, Lizhuang; Chai, Shatuo

2014-01-01

Estimating forage biomass yield remotely from space is still challenging nowadays. Field experiments were conducted and ground measurements correlated to remote sensing data to estimate the forage biomass yield of Alpine-cold meadow grassland during the grass and grass-withering period in Sanjiangyuan area in Yushu county. Both Shapiro-Wilk and Kolmogorov-Smirnov two-tailed tests showed that the field training samples are normally distributed, the Spearman coefficient indicated that the parametric correlation analysis had significant differences. The optimal regression models were developed based on the Landsat Thematic Mapper Normalized Difference Vegetation Index (TM-NDVI) and the forage biomass field data during the grass and the grass-withering periods, respectively. Then an integration model was used to predict forage biomass yield of alpine-cold meadow in the grass-withering period. The model showed good prediction accuracy and reliability. It was found that this approach can not only estimate forage yield in large scale efficiently but also overcome the seasonal limitation of remote sensing inversion. This technique can provides valuable guidance to animal husbandry to resource more efficiently in winter

Modelling of excess noise attnuation by grass and forest | Onuu ...

African Journals Online (AJOL)

, guinea grass (panicum maximum) and forest which comprises iroko (milicia ezcelea) and white afara (terminalia superba) trees in the ratio of 2:1 approximately. Excess noise attenuation spectra have been plotted for the grass and forest for ...

Test-driven modeling of embedded systems

DEFF Research Database (Denmark)

Munck, Allan; Madsen, Jan

2015-01-01

To benefit maximally from model-based systems engineering (MBSE) trustworthy high quality models are required. From the software disciplines it is known that test-driven development (TDD) can significantly increase the quality of the products. Using a test-driven approach with MBSE may have...... a similar positive effect on the quality of the system models and the resulting products and may therefore be desirable. To define a test-driven model-based systems engineering (TD-MBSE) approach, we must define this approach for numerous sub disciplines such as modeling of requirements, use cases...... suggest that our method provides a sound foundation for rapid development of high quality system models....

Nowcasting daily minimum air and grass temperature

Science.gov (United States)

Savage, M. J.

2016-02-01

Site-specific and accurate prediction of daily minimum air and grass temperatures, made available online several hours before their occurrence, would be of significant benefit to several economic sectors and for planning human activities. Site-specific and reasonably accurate nowcasts of daily minimum temperature several hours before its occurrence, using measured sub-hourly temperatures hours earlier in the morning as model inputs, was investigated. Various temperature models were tested for their ability to accurately nowcast daily minimum temperatures 2 or 4 h before sunrise. Temperature datasets used for the model nowcasts included sub-hourly grass and grass-surface (infrared) temperatures from one location in South Africa and air temperature from four subtropical sites varying in altitude (USA and South Africa) and from one site in central sub-Saharan Africa. Nowcast models used employed either exponential or square root functions to describe the rate of nighttime temperature decrease but inverted so as to determine the minimum temperature. The models were also applied in near real-time using an open web-based system to display the nowcasts. Extrapolation algorithms for the site-specific nowcasts were also implemented in a datalogger in an innovative and mathematically consistent manner. Comparison of model 1 (exponential) nowcasts vs measured daily minima air temperatures yielded root mean square errors (RMSEs) <1 °C for the 2-h ahead nowcasts. Model 2 (also exponential), for which a constant model coefficient ( b = 2.2) was used, was usually slightly less accurate but still with RMSEs <1 °C. Use of model 3 (square root) yielded increased RMSEs for the 2-h ahead comparisons between nowcasted and measured daily minima air temperature, increasing to 1.4 °C for some sites. For all sites for all models, the comparisons for the 4-h ahead air temperature nowcasts generally yielded increased RMSEs, <2.1 °C. Comparisons for all model nowcasts of the daily grass

Bottom-up driven involuntary auditory evoked field change: constant sound sequencing amplifies but does not sharpen neural activity.

Science.gov (United States)

Okamoto, Hidehiko; Stracke, Henning; Lagemann, Lothar; Pantev, Christo

2010-01-01

The capability of involuntarily tracking certain sound signals during the simultaneous presence of noise is essential in human daily life. Previous studies have demonstrated that top-down auditory focused attention can enhance excitatory and inhibitory neural activity, resulting in sharpening of frequency tuning of auditory neurons. In the present study, we investigated bottom-up driven involuntary neural processing of sound signals in noisy environments by means of magnetoencephalography. We contrasted two sound signal sequencing conditions: "constant sequencing" versus "random sequencing." Based on a pool of 16 different frequencies, either identical (constant sequencing) or pseudorandomly chosen (random sequencing) test frequencies were presented blockwise together with band-eliminated noises to nonattending subjects. The results demonstrated that the auditory evoked fields elicited in the constant sequencing condition were significantly enhanced compared with the random sequencing condition. However, the enhancement was not significantly different between different band-eliminated noise conditions. Thus the present study confirms that by constant sound signal sequencing under nonattentive listening the neural activity in human auditory cortex can be enhanced, but not sharpened. Our results indicate that bottom-up driven involuntary neural processing may mainly amplify excitatory neural networks, but may not effectively enhance inhibitory neural circuits.

Estimating the energy requirements and CO{sub 2} emissions from production of the perennial grasses miscanthus, switchgrass and reed canary grass

Energy Technology Data Exchange (ETDEWEB)

Bullard, M.; Metcalfe, P.

2001-07-01

The perennial grasses miscanthus, reed canary and swithchgrass have attractions as energy crops in the United Kingdom: all have low demand for fertilizer and pesticide, and are harvested annually. Research on energy ratios and carbon ratios of the grasses is reported. A Microsoft Excel-based model was developed (from an ADAS database) and the input calculations and assumptions are explained. The study demonstrated the attractions of theses grasses as a source of fuel. The results agreed with those from a model developed for the SRC.

Modeled Changes in Potential Grassland Productivity and in Grass-Fed Ruminant Livestock Density in Europe over 1961-2010.

Directory of Open Access Journals (Sweden)

Jinfeng Chang

3% per decade was found: 97% of this increase was attributed to the rise in CO2, -3% to climate trends and 15% to trends in nitrogen fertilization and deposition. When compared with statistical data, ORCHIDEE-GM captures well the observed phase of climate-driven interannual variability in grassland production well, whereas the magnitude of the interannual variability in modeled productivity is larger than the statistical data. Regional grass-fed livestock numbers can be reproduced by ORCHIDEE-GM based on its simple assumptions and parameterization about productivity being the only limiting factor to define the sustainable number of animals per unit area. Causes for regional model-data misfits are discussed, including uncertainties in farming practices (e.g., nitrogen fertilizer application, and mowing and grazing intensity and in ruminant diet composition, as well as uncertainties in the statistical data and in model parameter values.

Modeled Changes in Potential Grassland Productivity and in Grass-Fed Ruminant Livestock Density in Europe over 1961-2010.

Science.gov (United States)

Chang, Jinfeng; Viovy, Nicolas; Vuichard, Nicolas; Ciais, Philippe; Campioli, Matteo; Klumpp, Katja; Martin, Raphaël; Leip, Adrian; Soussana, Jean-François

2015-01-01

was found: 97% of this increase was attributed to the rise in CO2, -3% to climate trends and 15% to trends in nitrogen fertilization and deposition. When compared with statistical data, ORCHIDEE-GM captures well the observed phase of climate-driven interannual variability in grassland production well, whereas the magnitude of the interannual variability in modeled productivity is larger than the statistical data. Regional grass-fed livestock numbers can be reproduced by ORCHIDEE-GM based on its simple assumptions and parameterization about productivity being the only limiting factor to define the sustainable number of animals per unit area. Causes for regional model-data misfits are discussed, including uncertainties in farming practices (e.g., nitrogen fertilizer application, and mowing and grazing intensity) and in ruminant diet composition, as well as uncertainties in the statistical data and in model parameter values.

CONFOLD2: improved contact-driven ab initio protein structure modeling.

Science.gov (United States)

Adhikari, Badri; Cheng, Jianlin

2018-01-25

Contact-guided protein structure prediction methods are becoming more and more successful because of the latest advances in residue-residue contact prediction. To support contact-driven structure prediction, effective tools that can quickly build tertiary structural models of good quality from predicted contacts need to be developed. We develop an improved contact-driven protein modelling method, CONFOLD2, and study how it may be effectively used for ab initio protein structure prediction with predicted contacts as input. It builds models using various subsets of input contacts to explore the fold space under the guidance of a soft square energy function, and then clusters the models to obtain the top five models. CONFOLD2 obtains an average reconstruction accuracy of 0.57 TM-score for the 150 proteins in the PSICOV contact prediction dataset. When benchmarked on the CASP11 contacts predicted using CONSIP2 and CASP12 contacts predicted using Raptor-X, CONFOLD2 achieves a mean TM-score of 0.41 on both datasets. CONFOLD2 allows to quickly generate top five structural models for a protein sequence when its secondary structures and contacts predictions at hand. The source code of CONFOLD2 is publicly available at https://github.com/multicom-toolbox/CONFOLD2/ .

Model-Driven Theme/UML

Science.gov (United States)

Carton, Andrew; Driver, Cormac; Jackson, Andrew; Clarke, Siobhán

Theme/UML is an existing approach to aspect-oriented modelling that supports the modularisation and composition of concerns, including crosscutting ones, in design. To date, its lack of integration with model-driven engineering (MDE) techniques has limited its benefits across the development lifecycle. Here, we describe our work on facilitating the use of Theme/UML as part of an MDE process. We have developed a transformation tool that adopts model-driven architecture (MDA) standards. It defines a concern composition mechanism, implemented as a model transformation, to support the enhanced modularisation features of Theme/UML. We evaluate our approach by applying it to the development of mobile, context-aware applications-an application area characterised by many non-functional requirements that manifest themselves as crosscutting concerns.

Novel application of ALMANAC: Modelling a functional group, exotic warm-season perennial grasses

Science.gov (United States)

Introduced perennial C4 grasses such buffelgrass (Pennisetum ciliare [(L.) Link]) and old world bluestems (OWB), including genera such as Bothriochloa Kuntze, Capillipedium Stapf, and Dichanthium Willemet have the potential to dominate landscapes. A process-based model that realistically simulates ...

Comparative genomics analysis of rice and pineapple contributes to understand the chromosome number reduction and genomic changes in grasses

Directory of Open Access Journals (Sweden)

Jinpeng Wang

2016-10-01

Full Text Available Rice is one of the most researched model plant, and has a genome structure most resembling that of the grass common ancestor after a grass common tetraploidization ~100 million years ago. There has been a standing controversy whether there had been 5 or 7 basic chromosomes, before the tetraploidization, which were tackled but could not be well solved for the lacking of a sequenced and assembled outgroup plant to have a conservative genome structure. Recently, the availability of pineapple genome, which has not been subjected to the grass-common tetraploidization, provides a precious opportunity to solve the above controversy and to research into genome changes of rice and other grasses. Here, we performed a comparative genomics analysis of pineapple and rice, and found solid evidence that grass-common ancestor had 2n =2x =14 basic chromosomes before the tetraploidization and duplicated to 2n = 4x = 28 after the event. Moreover, we proposed that enormous gene missing from duplicated regions in rice should be explained by an allotetraploid produced by prominently divergent parental lines, rather than gene losses after their divergence. This means that genome fractionation might have occurred before the formation of the allotetraploid grass ancestor.

A next-generation sequencing method for overcoming the multiple gene copy problem in polyploid phylogenetics, applied to Poa grasses

Directory of Open Access Journals (Sweden)

Robin Charles

2011-03-01

Full Text Available Abstract Background Polyploidy is important from a phylogenetic perspective because of its immense past impact on evolution and its potential future impact on diversification, survival and adaptation, especially in plants. Molecular population genetics studies of polyploid organisms have been difficult because of problems in sequencing multiple-copy nuclear genes using Sanger sequencing. This paper describes a method for sequencing a barcoded mixture of targeted gene regions using next-generation sequencing methods to overcome these problems. Results Using 64 3-bp barcodes, we successfully sequenced three chloroplast and two nuclear gene regions (each of which contained two gene copies with up to two alleles per individual in a total of 60 individuals across 11 species of Australian Poa grasses. This method had high replicability, a low sequencing error rate (after appropriate quality control and a low rate of missing data. Eighty-eight percent of the 320 gene/individual combinations produced sequence reads, and >80% of individuals produced sufficient reads to detect all four possible nuclear alleles of the homeologous nuclear loci with 95% probability. We applied this method to a group of sympatric Australian alpine Poa species, which we discovered to share an allopolyploid ancestor with a group of American Poa species. All markers revealed extensive allele sharing among the Australian species and so we recommend that the current taxonomy be re-examined. We also detected hypermutation in the trnH-psbA marker, suggesting it should not be used as a land plant barcode region. Some markers indicated differentiation between Tasmanian and mainland samples. Significant positive spatial genetic structure was detected at Conclusions Our results demonstrate that 454 sequencing of barcoded amplicon mixtures can be used to reliably sample all alleles of homeologous loci in polyploid species and successfully investigate phylogenetic relationships among

Modelling nutrient concentration to determine the environmental factors influencing grass quality

CSIR Research Space (South Africa)

Dudeni-Tlhone, N

2010-10-01

Full Text Available This paper uses the spatial and the least squares (Analysis of Covariance-ANCOVA) regression methods to evaluate the important environmental factors in estimating quality grass for grazing (based on the nitrogen (N) content in grass...

cDNA cloning and immunological characterization of the rye grass allergen Lol p I.

Science.gov (United States)

Perez, M; Ishioka, G Y; Walker, L E; Chesnut, R W

1990-09-25

The complete amino acid sequence of two "isoallergenic" forms of Lol p I, the major rye grass (Lolium perenne) pollen allergen, was deduced from cDNA sequence analysis. cDNA clones isolated from a Lolium perenne pollen library contained an open reading frame coding for a 240-amino acid protein. Comparison of the nucleotide and deduced amino acid sequence of two of these clones revealed four changes at the amino acid level and numerous nucleotide differences. Both clones contained one possible asparagine-linked glycosylation site. Northern blot analysis shows one RNA species of 1.2 kilobases. Based on the complete amino acid sequence of Lol p I, overlapping peptides covering the entire molecule were synthesized. Utilizing these peptides we have identified a determinant within the Lol p I molecule that is recognized by human leukocyte antigen class II-restricted T cells obtained from persons allergic to rye grass pollen.

Sequencing quality assessment tools to enable data-driven informatics for high throughput genomics

Directory of Open Access Journals (Sweden)

Richard Mark Leggett

2013-12-01

Full Text Available The processes of quality assessment and control are an active area of research at The Genome Analysis Centre (TGAC. Unlike other sequencing centres that often concentrate on a certain species or technology, TGAC applies expertise in genomics and bioinformatics to a wide range of projects, often requiring bespoke wet lab and in silico workflows. TGAC is fortunate to have access to a diverse range of sequencing and analysis platforms, and we are at the forefront of investigations into library quality and sequence data assessment. We have developed and implemented a number of algorithms, tools, pipelines and packages to ascertain, store, and expose quality metrics across a number of next-generation sequencing platforms, allowing rapid and in-depth cross-platform QC bioinformatics. In this review, we describe these tools as a vehicle for data-driven informatics, offering the potential to provide richer context for downstream analysis and to inform experimental design.

Chemical and radiation mutagenesis: Induction and detection by whole genome sequencing

Science.gov (United States)

Brachypodium distachyon has emerged as an effective model system to address fundamental questions in grass biology. With its small sequenced genome, short generation time and rapidly expanding array of genetic tools B. distachyon is an ideal system to elucidate the molecular basis of important trai...

Gene Expression Profiling of Grass Carp (Ctenopharyngodon idellus and Crisp Grass Carp

Directory of Open Access Journals (Sweden)

Ermeng Yu

2014-01-01

Full Text Available Grass carp (Ctenopharyngodon idellus is one of the most important freshwater fish that is native to China, and crisp grass carp is a kind of high value-added fishes which have higher muscle firmness. To investigate biological functions and possible signal transduction pathways that address muscle firmness increase of crisp grass carp, microarray analysis of 14,900 transcripts was performed. Compared with grass carp, 127 genes were upregulated and 114 genes were downregulated in crisp grass carp. Gene ontology (GO analysis revealed 30 GOs of differentially expressed genes in crisp grass carp. And strong correlation with muscle firmness increase of crisp grass carp was found for these genes from differentiation of muscle fibers and deposition of ECM, and also glycolysis/gluconeogenesis pathway and calcium metabolism may contribute to muscle firmness increase. In addition, a number of genes with unknown functions may be related to muscle firmness, and these genes are still further explored. Overall, these results had been demonstrated to play important roles in clarifying the molecular mechanism of muscle firmness increase in crisp grass carp.

Tracking the evolution of a cold stress associated gene family in cold tolerant grasses

DEFF Research Database (Denmark)

Sandve, Simen R; Rudi, Heidi; Asp, Torben

2008-01-01

to the repeat motifs of the IRI-domain in cold tolerant grasses. Finally we show that the LRR-domain of carrot and grass IRI proteins both share homology to an Arabidopsis thaliana LRR-trans membrane protein kinase (LRR-TPK). Conclusion The diverse IRI-like genes identified in this study tell a tale...... of a complex evolutionary history including birth of an ice binding domain, a burst of gene duplication events after cold tolerant grasses radiated from rice, protein domain structure differentiation between paralogs, and sub- and/or neofunctionalisation of IRI-like proteins. From our sequence analysis we...

Mutants of the major ryegrass pollen allergen, Lol p 5, with reduced IgE-binding capacity: candidates for grass pollen-specific immunotherapy.

Science.gov (United States)

Swoboda, Ines; De Weerd, Nicole; Bhalla, Prem L; Niederberger, Verena; Sperr, W R; Valent, Peter; Kahlert, Helga; Fiebig, Helmut; Verdino, Petra; Keller, Walter; Ebner, Christof; Spitzauer, Susanne; Valenta, Rudolf; Singh, Mohan B

2002-01-01

More than 400 million individuals are sensitized to grass pollen allergens. Group 5 allergens represent the most potent grass pollen allergens recognized by more than 80 % of grass pollen allergic patients. The aim of our study was to reduce the allergenic activity of group 5 allergens for specific immunotherapy of grass pollen allergy. Based on B- and T-cell epitope mapping studies and on sequence comparison of group 5 allergens from different grasses, point mutations were introduced by site-directed mutagenesis in highly conserved sequence domains of Lol p 5, the group 5 allergen from ryegrass. We obtained Lol p 5 mutants with low IgE-binding capacity and reduced allergenic activity as determined by basophil histamine release and by skin prick testing in allergic patients. Circular dichroism analysis showed that these mutants exhibited an overall structural fold similar to the recombinant Lol p 5 wild-type allergen. In addition, Lol p 5 mutants retained the ability to induce proliferation of group 5 allergen-specific T cell lines and clones. Our results demonstrate that a few point mutations in the Lol p 5 sequence yield mutants with reduced allergenic activity that represent potential vaccine candidates for immunotherapy of grass pollen allergy.

Prediction of genetic gains by selection indices using mixed models in elephant grass for energy purposes.

Science.gov (United States)

Silva, V B; Daher, R F; Araújo, M S B; Souza, Y P; Cassaro, S; Menezes, B R S; Gravina, L M; Novo, A A C; Tardin, F D; Júnior, A T Amaral

2017-09-27

Genetically improved cultivars of elephant grass need to be adapted to different ecosystems with a faster growth speed and lower seasonality of biomass production over the year. This study aimed to use selection indices using mixed models (REML/BLUP) for selecting families and progenies within full-sib families of elephant grass (Pennisetum purpureum) for biomass production. One hundred and twenty full-sib progenies were assessed from 2014 to 2015 in a randomized block design with three replications. During this period, the traits dry matter production, the number of tillers, plant height, stem diameter, and neutral detergent fiber were assessed. Families 3 and 1 were the best classified, being the most indicated for selection effect. Progenies 40, 45, 46, and 49 got the first positions in the three indices assessed in the first cut. The gain for individual 40 was 161.76% using Mulamba and Mock index. The use of selection indices using mixed models is advantageous in elephant grass since they provide high gains with the selection, which are distributed among all the assessed traits in the most appropriate situation to breeding programs.

Intensity stabilisation of optical pulse sequences for coherent control of laser-driven qubits

Science.gov (United States)

Thom, Joseph; Yuen, Ben; Wilpers, Guido; Riis, Erling; Sinclair, Alastair G.

2018-05-01

We demonstrate a system for intensity stabilisation of optical pulse sequences used in laser-driven quantum control of trapped ions. Intensity instability is minimised by active stabilisation of the power (over a dynamic range of > 104) and position of the focused beam at the ion. The fractional Allan deviations in power were found to be logic gates to be below 10^{-6} per gate.

Complete primary structure of a Lolium perenne (perennial rye grass) pollen allergen, Lol p III: comparison with known Lol p I and II sequences.

Science.gov (United States)

Ansari, A A; Shenbagamurthi, P; Marsh, D G

1989-10-17

The complete amino acid sequence of a Lolium perenne (rye grass) pollen allergen, Lol p III, determined by the automated Edman degradation of the protein and its selected fragments, is reported in this paper. Cleavage by enzymatic and chemical techniques established unambiguously the sequence for this 97-residue protein (Mr = 10,909), which lacks cysteine and shows no evidence of glycosylation. The sequence of Lol p III is very similar to that of another L. perenne allergen, Lol p II, which was sequenced recently; of the 97 positions in the two proteins, 57 are occupied by identical amino acids (59% identity). In addition, both allergens share a similar structure with an antibody-binding fragment of a third L. perenne allergen, Lol p I. Since human antibody responsiveness to all these three allergens is associated with HLA-DR3, and since the structure common to the three molecules shows high degrees of amphipathicity in Lol p II and III, we speculate that this common segment in the three molecules might contain or contribute to the respectively Ia/T-cell sites.

Treatment with grass allergen peptides improves symptoms of grass pollen-induced allergic rhinoconjunctivitis.

Science.gov (United States)

Ellis, Anne K; Frankish, Charles W; O'Hehir, Robyn E; Armstrong, Kristen; Steacy, Lisa; Larché, Mark; Hafner, Roderick P

2017-08-01

Synthetic peptide immunoregulatory epitopes are a new class of immunotherapy to treat allergic rhinoconjunctivitis (ARC). Grass allergen peptides, comprising 7 synthetic T-cell epitopes derived from Cyn d 1, Lol p 5, Dac g 5, Hol l 5, and Phl p 5, is investigated for treatment of grass pollen-induced ARC. We sought to evaluate the efficacy, safety, and tolerability of intradermally administered grass allergen peptides. A multicenter, randomized, double-blind, placebo-controlled study evaluated 3 regimens of grass allergen peptides versus placebo in patients with grass pollen-induced allergy (18-65 years). After a 4-day baseline challenge to rye grass in the environmental exposure unit (EEU), subjects were randomized to receive grass allergen peptides at 6 nmol at 2-week intervals for a total of 8 doses (8x6Q2W), grass allergen peptides at 12 nmol at 4-week intervals for a total of 4 doses (4x12Q4W), or grass allergen peptides at 12 nmol at 2-week intervals for a total of 8 doses (8x12Q2W) or placebo and treated before the grass pollen season. The primary efficacy end point was change from baseline in total rhinoconjunctivitis symptom score across days 2 to 4 of a 4-day posttreatment challenge (PTC) in the EEU after the grass pollen season. Secondary efficacy end points and safety were also assessed. Two hundred eighty-two subjects were randomized. Significantly greater improvement (reduction of total rhinoconjunctivitis symptom score from baseline to PTC) occurred across days 2 to 4 with grass allergen peptide 8x6Q2W versus placebo (-5.4 vs -3.8, respectively; P = .0346). Greater improvement at PTC also occurred for grass allergen peptide 8x6Q2W versus placebo (P = .0403) in patients with more symptomatic ARC. No safety signals were detected. Grass allergen peptide 8x6Q2W significantly improved ARC symptoms after rye grass allergen challenge in an EEU with an acceptable safety profile. Copyright © 2017 American Academy of Allergy, Asthma & Immunology

An integral projection model with YY-males and application to evaluating grass carp control

Science.gov (United States)

Erickson, Richard A.; Eager, Eric A.; Brey, Marybeth; Hansen, Michael J.; Kocovsky, Patrick

2017-01-01

Invasive fish species disrupt ecosystems and cause economic damage. Several methods have been discussed to control populations of invasive fish including the release of YY-males. YY-males are fish that have 2 male chromosomes compared to a XY-male. When YY-males mate, they only produce male (XY) offspring. This decreases the female proportion of the population and can, in theory, eradicate local populations by biasing the sex-ratio. YY-males have been used as a population control tool for brook trout in montane streams and lakes in Idaho, USA. The YY-male control method has been discussed for grass carp in Lake Erie, North America. We developed and presented an integral projection model for grass carp to model the use of YY-males as a control method for populations in this lake. Using only the YY-male control method, we found that high levels of YY-males would need to be release annually to control the species. Specifically, these levels were the same order of magnitude as the baseline adult population (e.g., 1000 YY-males needed to be released annual for 20 years to control a baseline adult population of 2500 grass carp). These levels may not be reasonable or obtainable for fisheries managers given the impacts of YY-males on aquatic vegetation and other constraints of natural resource management.

Spatiotemporal Variation in the Environmental Controls of C4-Grass Origin and Ecology: Insights from Grass-Pollen δ13C Data

Science.gov (United States)

Nelson, D. M.; Urban, M.; Hu, F.

2014-12-01

Understanding the environmental factors controlling the origin and shifting abundance of C4 grasses in Earth's history is useful for projecting the response of C4-grass dominated grasslands to future environmental change. Unfortunately, grass pollen is typically morphologically indistinct, making palynological analysis a blunt tool for studying C4-grasses in the paleorecord. δ13C of individual grass-pollen grains using a spooling wire microcombustion device interfaced with an isotope ratio mass spectrometer (Single Pollen Isotope Ratio AnaLysis, SPIRAL) overcomes this challenge and the potential biases of δ13C data from other substrates (e.g. leaf waxes). To assess the presence and relative abundance of C3- and C4-grass pollen in samples of unknown composition, we developed a hierarchical Bayesian model, trained with ~1,900 δ13C values from pollen grains of 31 grass species. Surface-sediment data from Africa, Australia, and North America demonstrate the reliability of this technique for quantifying C4-grass abundance on the landscape. To investigate the timing and control of the origin of C4-grasses we analyzed samples from the Oligocene-Miocene from Europe and from the Eocene from North America. Results indicate that C4 grasses appeared on the landscape of southwest Europe no later than the early Oligocene, implying that low atmospheric pCO2 may not have been the main driver and/or precondition for the development of C4 photosynthesis in the grass family. In contrast, we found no evidence for C4 grasses in the southeast United States before pCO2 fell. In application of SPIRAL to the late Quaternary, we found that shifts in pCO2 and moisture balance exerted key controls on the relative abundance of C3 and C4 grasses in Africa and Australia. Overall, our results imply that as in the past, future changes in the C3/C4 composition of grass-dominated ecosystems will likely exhibit striking spatiotemporal variability as a result of differing combinations of

Napier grass stunt disease prevalence, incidence, severity and genetic variability of the associated phytoplasma in Uganda

DEFF Research Database (Denmark)

Kawube, Geofrey; Talwana, Herbert; Nicolaisen, Mogens

2015-01-01

The prevalence, incidence and severity of Napier grass stunt disease (NGSD) caused by phytoplasma on Pennisetum purpureum, the main fodder for livestock under intensive and semi-intensive management systems in Uganda were determined following a field survey carried out in 17 districts. A total...... of 298 Napier grass fields were visited and NGSD status visually assessed and 1192 samples collected for identification and confirmation of the phytoplasma by polymerase chain reaction (PCR) assays using universal primers P1/P6 nested with R16F2n/R16R2n and, tuf primers 890/340 nested with 835 and 400....... From these, 221 PCR products were sequenced and sequences aligned. Napier grass stunt disease is widely spread at an epidemic proportion, with the districts at different risk levels. The most affected districts are in central, East and North parts of the country while those in the west are least...

Cloning and sequencing of Lol pI, the major allergenic protein of rye-grass pollen.

Science.gov (United States)

Griffith, I J; Smith, P M; Pollock, J; Theerakulpisut, P; Avjioglu, A; Davies, S; Hough, T; Singh, M B; Simpson, R J; Ward, L D

1991-02-25

We have isolated a full length cDNA clone encoding the major glycoprotein allergen Lol pI. The clone was selected using a combination of immunological screening of a cDNA expression library and PCR amplification of Lol pI-specific transcripts. Lol pI expressed in bacteria as a fusion protein shows recognition by specific IgE antibodies present in sera of grass pollen-allergic subjects. Northern analysis has shown that the Lol pI transcripts are expressed only in pollen of rye-grass. Molecular cloning of Lol pI provides a molecular genetic approach to study the structure-function relationship of allergens.

Modeled Changes in Potential Grassland Productivity and in Grass-Fed Ruminant Livestock Density in Europe over 1961–2010

Science.gov (United States)

Chang, Jinfeng; Viovy, Nicolas; Vuichard, Nicolas; Ciais, Philippe; Campioli, Matteo; Klumpp, Katja; Martin, Raphaël; Leip, Adrian; Soussana, Jean-François

2015-01-01

%) per decade was found: 97% of this increase was attributed to the rise in CO2, -3% to climate trends and 15% to trends in nitrogen fertilization and deposition. When compared with statistical data, ORCHIDEE-GM captures well the observed phase of climate-driven interannual variability in grassland production well, whereas the magnitude of the interannual variability in modeled productivity is larger than the statistical data. Regional grass-fed livestock numbers can be reproduced by ORCHIDEE-GM based on its simple assumptions and parameterization about productivity being the only limiting factor to define the sustainable number of animals per unit area. Causes for regional model-data misfits are discussed, including uncertainties in farming practices (e.g., nitrogen fertilizer application, and mowing and grazing intensity) and in ruminant diet composition, as well as uncertainties in the statistical data and in model parameter values. PMID:26018186

Using a prescribed fire to test custom and standard fuel models for fire behaviour prediction in a non-native, grass-invaded tropical dry shrubland

Science.gov (United States)

Andrew D. Pierce; Sierra McDaniel; Mark Wasser; Alison Ainsworth; Creighton M. Litton; Christian P. Giardina; Susan Cordell; Ralf Ohlemuller

2014-01-01

Questions: Do fuel models developed for North American fuel types accurately represent fuel beds found in grass-invaded tropical shrublands? Do standard or custom fuel models for firebehavior models with in situ or RAWS measured fuel moistures affect the accuracy of predicted fire behavior in grass-invaded tropical shrublands? Location: Hawai’i Volcanoes National...

Methods for performing crosses in Setaria viridis, a new model system for the grasses.

Science.gov (United States)

Jiang, Hui; Barbier, Hugues; Brutnell, Thomas

2013-10-01

Setaria viridis is an emerging model system for C4 grasses. It is closely related to the bioenergy feed stock switchgrass and the grain crop foxtail millet. Recently, the 510 Mb genome of foxtail millet, S. italica, has been sequenced (1,2) and a 25x coverage genome sequence of the weedy relative S. viridis is in progress. S. viridis has a number of characteristics that make it a potentially excellent model genetic system including a rapid generation time, small stature, simple growth requirements, prolific seed production (3) and developed systems for both transient and stable transformation (4). However, the genetics of S. viridis is largely unexplored, in part, due to the lack of detailed methods for performing crosses. To date, no standard protocol has been adopted that will permit rapid production of seeds from controlled crosses. The protocol presented here is optimized for performing genetic crosses in S. viridis, accession A10.1. We have employed a simple heat treatment with warm water for emasculation after pruning the panicle to retain 20-30 florets and labeling of flowers to eliminate seeds resulting from newly developed flowers after emasculation. After testing a series of heat treatments at permissive temperatures and varying the duration of dipping, we have established an optimum temperature and time range of 48 °C for 3-6 min. By using this method, a minimum of 15 crosses can be performed by a single worker per day and an average of 3-5 outcross progeny per panicle can be recovered. Therefore, an average of 45-75 outcross progeny can be produced by one person in a single day. Broad implementation of this technique will facilitate the development of recombinant inbred line populations of S. viridis X S. viridis or S. viridis X S. italica, mapping mutations through bulk segregant analysis and creating higher order mutants for genetic analysis.

Foundations of Sequence-to-Sequence Modeling for Time Series

OpenAIRE

Kuznetsov, Vitaly; Mariet, Zelda

2018-01-01

The availability of large amounts of time series data, paired with the performance of deep-learning algorithms on a broad class of problems, has recently led to significant interest in the use of sequence-to-sequence models for time series forecasting. We provide the first theoretical analysis of this time series forecasting framework. We include a comparison of sequence-to-sequence modeling to classical time series models, and as such our theory can serve as a quantitative guide for practiti...

Enhanced precipitation variability decreases grass- and increases shrub-productivity

Science.gov (United States)

Gherardi, Laureano A.; Sala, Osvaldo E.

2015-01-01

Although projections of precipitation change indicate increases in variability, most studies of impacts of climate change on ecosystems focused on effects of changes in amount of precipitation, overlooking precipitation variability effects, especially at the interannual scale. Here, we present results from a 6-y field experiment, where we applied sequences of wet and dry years, increasing interannual precipitation coefficient of variation while maintaining a precipitation amount constant. Increased precipitation variability significantly reduced ecosystem primary production. Dominant plant-functional types showed opposite responses: perennial-grass productivity decreased by 81%, whereas shrub productivity increased by 67%. This pattern was explained by different nonlinear responses to precipitation. Grass productivity presented a saturating response to precipitation where dry years had a larger negative effect than the positive effects of wet years. In contrast, shrubs showed an increasing response to precipitation that resulted in an increase in average productivity with increasing precipitation variability. In addition, the effects of precipitation variation increased through time. We argue that the differential responses of grasses and shrubs to precipitation variability and the amplification of this phenomenon through time result from contrasting root distributions of grasses and shrubs and competitive interactions among plant types, confirmed by structural equation analysis. Under drought conditions, grasses reduce their abundance and their ability to absorb water that then is transferred to deep soil layers that are exclusively explored by shrubs. Our work addresses an understudied dimension of climate change that might lead to widespread shrub encroachment reducing the provisioning of ecosystem services to society. PMID:26417095

Homogenous stands of a wetland grass harbour diverse consortia of arbuscular mycorrhizal fungi.

Science.gov (United States)

Wirsel, Stefan G R

2004-05-01

A molecular approach was applied to investigate the colonisation of arbuscular mycorrhizal fungi (AMF) on the wetland grass Phragmites australis. A PCR assay targeting the traditional families of the Glomeromycota yielded products that were used to construct libraries of 18S rDNA. Five hundred and forty six clones were typed by restriction analysis and 76 representatives were sequenced. The majority corresponded to a wide range of taxa within Glomus group A, a few belonged to the "Diversisporaceae" and none to the genera Scutellospora or Acaulospora. Among these sequences, some were very similar to those reported earlier, e.g. Glomus mosseae and G. fasciculatum, other pointed to various new taxa. Although this wetland habitat harboured just one single plant species, phylogenetic analysis exhibited 21 AMF phylotypes, which is in the same range as reported for other natural ecosystems composed of more diverse host communities. Diversity indices supported the perception that the AMF mycoflora associated with this natural grass "monoculture" is not depauperate as it had been described for grasses of crop monocultures. Soil conditions determined the mycorrhizal state of the host, since AMF were not detected at the lakeward front of the reed belt, which is permanently waterlogged.

A grass molecular identification system for forensic botany: a critical evaluation of the strengths and limitations.

Science.gov (United States)

Ward, Jodie; Gilmore, Simon R; Robertson, James; Peakall, Rod

2009-11-01

Plant material is frequently encountered in criminal investigations but often overlooked as potential evidence. We designed a DNA-based molecular identification system for 100 Australian grasses that consisted of a series of polymerase chain reaction assays that enabled the progressive identification of grasses to different taxonomic levels. The identification system was based on DNA sequence variation at four chloroplast and two mitochondrial loci. Seventeen informative indels and 68 single-nucleotide polymorphisms were utilized as molecular markers for subfamily to species-level identification. To identify an unknown sample to subfamily level required a minimum of four markers or nine markers for species identification. The accuracy of the system was confirmed by blind tests. We have demonstrated "proof of concept" of a molecular identification system for trace botanical samples. Our evaluation suggests that the adoption of a system that combines this approach with DNA sequencing could assist the morphological identification of grasses found as forensic evidence.

Distribution, Diversity, and Long-Term Retention of Grass Short Interspersed Nuclear Elements (SINEs).

Science.gov (United States)

Mao, Hongliang; Wang, Hao

2017-08-01

Instances of highly conserved plant short interspersed nuclear element (SINE) families and their enrichment near genes have been well documented, but little is known about the general patterns of such conservation and enrichment and underlying mechanisms. Here, we perform a comprehensive investigation of the structure, distribution, and evolution of SINEs in the grass family by analyzing 14 grass and 5 other flowering plant genomes using comparative genomics methods. We identify 61 SINE families composed of 29,572 copies, in which 46 families are first described. We find that comparing with other grass TEs, grass SINEs show much higher level of conservation in terms of genomic retention: The origin of at least 26% families can be traced to early grass diversification and these families are among most abundant SINE families in 86% species. We find that these families show much higher level of enrichment near protein coding genes than families of relatively recent origin (51%:28%), and that 40% of all grass SINEs are near gene and the percentage is higher than other types of grass TEs. The pattern of enrichment suggests that differential removal of SINE copies in gene-poor regions plays an important role in shaping the genomic distribution of these elements. We also identify a sequence motif located at 3' SINE end which is shared in 17 families. In short, this study provides insights into structure and evolution of SINEs in the grass family. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Nonparametric combinatorial sequence models.

Science.gov (United States)

Wauthier, Fabian L; Jordan, Michael I; Jojic, Nebojsa

2011-11-01

This work considers biological sequences that exhibit combinatorial structures in their composition: groups of positions of the aligned sequences are "linked" and covary as one unit across sequences. If multiple such groups exist, complex interactions can emerge between them. Sequences of this kind arise frequently in biology but methodologies for analyzing them are still being developed. This article presents a nonparametric prior on sequences which allows combinatorial structures to emerge and which induces a posterior distribution over factorized sequence representations. We carry out experiments on three biological sequence families which indicate that combinatorial structures are indeed present and that combinatorial sequence models can more succinctly describe them than simpler mixture models. We conclude with an application to MHC binding prediction which highlights the utility of the posterior distribution over sequence representations induced by the prior. By integrating out the posterior, our method compares favorably to leading binding predictors.

Model-driven software engineering

NARCIS (Netherlands)

Amstel, van M.F.; Brand, van den M.G.J.; Protic, Z.; Verhoeff, T.; Hamberg, R.; Verriet, J.

2014-01-01

Software plays an important role in designing and operating warehouses. However, traditional software engineering methods for designing warehouse software are not able to cope with the complexity, size, and increase of automation in modern warehouses. This chapter describes Model-Driven Software

Semantic Web and Model-Driven Engineering

CERN Document Server

Parreiras, Fernando S

2012-01-01

The next enterprise computing era will rely on the synergy between both technologies: semantic web and model-driven software development (MDSD). The semantic web organizes system knowledge in conceptual domains according to its meaning. It addresses various enterprise computing needs by identifying, abstracting and rationalizing commonalities, and checking for inconsistencies across system specifications. On the other side, model-driven software development is closing the gap among business requirements, designs and executables by using domain-specific languages with custom-built syntax and se

EBIPM | Finding the Tools to Manage Invasive Annual Grasses

Science.gov (United States)

management decisions for a given landscape based on ecological principles. Take a look at our video " Grass Management How much could prevention save you? Guidelines to Implement EBIPM Weed Prevention Areas Grass Facts/ID The EBIPM Model Crooked River Weed Management Area Guide Tools for Educators EBIPM High

Genetic modification of wetland grasses for phytoremediation

Energy Technology Data Exchange (ETDEWEB)

Czako, M.; Liang Dali; Marton, L. [Dept. of Biological Sciences, Univ. of South Carolina, Columbia, SC (United States); Feng Xianzhong; He Yuke [National Lab. of Plant Molecular Genetics, Shanghai Inst. of Plant Physiology, Chinese Academy of Sciences, Shanghai, SH (China)

2005-04-01

Wetland grasses and grass-like monocots are very important natural remediators of pollutants. Their genetic improvement is an important task because introduction of key transgenes can dramatically improve their remediation potential. Tissue culture is prerequisite for genetic manipulation, and methods are reported here for in vitro culture and micropropagation of a number of wetland plants of various ecological requirements such as salt marsh, brackish water, riverbanks, and various zones of lakes and ponds, and bogs. The monocots represent numerous genera in various families such as Poaceae, Cyperaceae, Juncaceae, and Typhaceae. The reported species are in various stages of micropropagation and Arundo donax is scaled for mass propagation for selecting elite lines for pytoremediation. Transfer of key genes for mercury phytoremediation into the salt marsh cordgrass (Spartina alterniflora) is also reported here. All but one transgenic lines contained both the organomercurial lyase (merB) and mercuric reductase (merA) sequences showing that co-introduction into Spartina of two genes from separate Agrobacterium strains is possible. (orig.)

Environmental performance assessment of Napier grass for bioenergy production

DEFF Research Database (Denmark)

Nimmanterdwong, Prathana; Chalermsinsuwan, Benjapon; Østergård, Hanne

2017-01-01

equivalence. This idea provides the quantitative indicators involving the resource use and the percent renewability of the systems. For the proposed biorefinery model, Napier grass (Pennisetum purpureum) grown in Thailand was used as lignocellulosic feedstock. An emergy assessment was performed in two parts...... cultivation and biorefinery stages. For Napier grass cultivation, most of the emergy support came from local resources in term of evapotranspiration of Napier grass (33%) and the diesel consumption during the cultivation process (21%). The emergy sustainability indicator of the cultivation was 0...

Optimal pulse sequence for ferumoxides-enhanced MR imaging used in the detection of hepatocellular carcinoma: a comparative study using seven pulse sequences

International Nuclear Information System (INIS)

Kim, Seung Hoon; Choi, Dongil; Lim, Jae Hoon; Lee, Won Jae; Jang, Hyun Jung; Lim, Kyo Keun; Lee, Soon Jin; Cho, Jae Min; Kim, Seung Kwon; Kim, Gab Chul

2002-01-01

To identify the optimal pulse sequence for ferumoxides-enhanced magnetic resonance (MR) imaging in the detection of hepatocelluar carcinomas (HCCs). Sixteen patients with 25 HCCs underwent MR imaging following intravenous infusion of ferumoxides. All MR studies were performed on a 1.5-T MR system, using a phased-array coil. Ferumoxides (Feridex IV) at a dose of 15 μmol/Kg was slowly infused intravenously, and axial images of seven sequences were obtained 30 minutes after the end of infusion. The MR protocol included fast spin-echo (FSE) with two echo times (TR3333-8571/TE18 and 90-117), singleshot FSE (SSFSE) with two echo times (TR∞/TE39 and 98), T2-weighted gradient-recalled acquisition in the steady state (GRASS) (TR216/TE20), T2-weighted fast multiplanar GRASS (FMPGR) (TR130/TE8.4-9.5), and T2-weighted fast multiplanar spoiled GRASS (FMPSPGR) (TR130/TE8.4-9.5). Contrast-to-noise ratios (CNRs) of HCCs determined during the imaging sequences formed the basis of quantitative analysis, and images were qualitatively assessed in terms of lesion conspicuity and image artifacts. The diagnostic accuracy of all sequences was assessed using receiver operating characteristic (ROC) analysis. Quantitative analysis revealed that the CNRs of T2-weighted FMPGR and T2-weighted FMPSPGR were significantly higher than those of the other sequences, while qualitative analysis showed that image artifacts were prominent at T2-weighted GRASS imaging. Lesion conspicuity was statistically significantly less clear at SSFSE imaging. In term of lesion detection, T-weighted FMPGR, T2- weighted FMPSPGR, and proton density FSE imaging were statistically superior to the others. T2-weighted FMPGR, T2- weighted FMPSPGR, and proton density FSE appear to be the optimal pulse sequences for ferumoxidesenhanced MR imaging in the detection of HCCs

SQ grass sublingual allergy immunotherapy tablet for disease-modifying treatment of grass pollen allergic rhinoconjunctivitis

DEFF Research Database (Denmark)

Dahl, Ronald; Roberts, Graham; de Blic, Jacques

2016-01-01

BACKGROUND: Allergy immunotherapy is a treatment option for allergic rhinoconjunctivitis (ARC). It is unique compared with pharmacotherapy in that it modifies the immunologic pathways that elicit an allergic response. The SQ Timothy grass sublingual immunotherapy (SLIT) tablet is approved in North...... America and throughout Europe for the treatment of adults and children (≥5 years old) with grass pollen-induced ARC. OBJECTIVE: The clinical evidence for the use of SQ grass SLIT-tablet as a disease-modifying treatment for grass pollen ARC is discussed in this review. METHODS: The review included...... the suitability of SQ grass SLIT-tablet for patients with clinically relevant symptoms to multiple Pooideae grass species, single-season efficacy, safety, adherence, coseasonal initiation, and cost-effectiveness. The data from the long-term SQ grass SLIT-tablet clinical trial that evaluated a clinical effect 2...

A molecular identification system for grasses: a novel technology for forensic botany.

Science.gov (United States)

Ward, J; Peakall, R; Gilmore, S R; Robertson, J

2005-09-10

Our present inability to rapidly, accurately and cost-effectively identify trace botanical evidence remains the major impediment to the routine application of forensic botany. Grasses are amongst the most likely plant species encountered as forensic trace evidence and have the potential to provide links between crime scenes and individuals or other vital crime scene information. We are designing a molecular DNA-based identification system for grasses consisting of several PCR assays that, like a traditional morphological taxonomic key, provide criteria that progressively identify an unknown grass sample to a given taxonomic rank. In a prior study of DNA sequences across 20 phylogenetically representative grass species, we identified a series of potentially informative indels in the grass mitochondrial genome. In this study we designed and tested five PCR assays spanning these indels and assessed the feasibility of these assays to aid identification of unknown grass samples. We confirmed that for our control set of 20 samples, on which the design of the PCR assays was based, the five primer combinations produced the expected results. Using these PCR assays in a 'blind test', we were able to identify 25 unknown grass samples with some restrictions. Species belonging to genera represented in our control set were all correctly identified to genus with one exception. Similarly, genera belonging to tribes in the control set were correctly identified to the tribal level. Finally, for those samples for which neither the tribal or genus specific PCR assays were designed, we could confidently exclude these samples from belonging to certain tribes and genera. The results confirmed the utility of the PCR assays and the feasibility of developing a robust full-scale usable grass identification system for forensic purposes.

Molecular basis of IgE-recognition of Lol p 5, a major allergen of rye-grass pollen.

Science.gov (United States)

Suphioglu, C; Blaher, B; Rolland, J M; McCluskey, J; Schäppi, G; Kenrick, J; Singh, M B; Knox, R B

1998-04-01

Grass pollen, especially of rye-grass (Lolium perenne). represents an important cause of type I allergy. Identification of IgE-binding (allergenic) epitopes of major grass pollen allergens is essential for understanding the molecular basis of interaction between allergens and human IgE antibodies and therefore facilitates the devising of safer and more effective diagnostic and immunotherapy reagents. The aim of this study was to identify the allergenic epitopes of Lol p 5, a major allergen of rye-grass pollen, immunodissect these epitopes further so that the amino acid residues critical for antibody binding can be determined and investigate the conservation and nature of these epitopes within the context of the natural grass pollen allergens. Peptides, 12-13 amino acid residues long and overlapping each other by 4 amino acid residues, based on the entire deduced amino acid sequence of the coding region of Lol p 5, were synthesised and assayed for IgE-binding. Two strong IgE-binding epitopes (Lol p 5 (49-60) and (265-276), referred to as peptides 7 and 34, respectively) were identified. These epitopes were further resolved by truncated peptides and amino acid replacement studies and the amino acid residues critical for IgE-binding determined (Lol p 5 (49-60) residue Lys57 and (265-276) residue Lys275). Sequences of these epitopes were conserved in related allergens and may form the conserved allergenic domains responsible for the cross-reactivity observed between pollen allergens of taxonomically related grasses. Furthermore, due to its strong IgE-reactivity, synthetic peptide Lol p 5 (265-276) was used to affinity-purify specific IgE antibodies which recognised proteins of other clinically important grass pollens. further indicating presence of allergenic cross-reactivity at the level of allergenic epitope. Moreover, Lol p 5 (265 276) demonstrated a strong capacity to inhibit IgE-binding to natural rye-grass pollen proteins highlighting the antibody accessibility

Brachypodium distachyon. A New Model System for Functional Genomics in Grasses1

Science.gov (United States)

Draper, John; Mur, Luis A.J.; Jenkins, Glyn; Ghosh-Biswas, Gadab C.; Bablak, Pauline; Hasterok, Robert; Routledge, Andrew P.M.

2001-01-01

A new model for grass functional genomics is described based on Brachypodium distachyon, which in the evolution of the Pooideae diverged just prior to the clade of “core pooid” genera that contain the majority of important temperate cereals and forage grasses. Diploid ecotypes of B. distachyon (2n = 10) have five easily distinguishable chromosomes that display high levels of chiasma formation at meiosis. The B. distachyon nuclear genome was indistinguishable in size from that of Arabidopsis, making it the simplest genome described in grasses to date. B. distachyon is a self-fertile, inbreeding annual with a life cycle of less than 4 months. These features, coupled with its small size (approximately 20 cm at maturity), lack of seed-head shatter, and undemanding growth requirements should make it amenable to high-throughput genetics and mutant screens. Immature embryos exhibited a high capacity for plant regeneration via somatic embryogenesis. Regenerated plants display very low levels of albinism and have normal fertility. A simple transformation system has been developed based on microprojectile bombardment of embryogenic callus and hygromycin selection. Selected B. distachyon ecotypes were resistant to all tested cereal-adapted Blumeria graminis species and cereal brown rusts (Puccinia reconditia). In contrast, different ecotypes displayed resistance or disease symptoms following challenge with the rice blast pathogen (Magnaporthe grisea) and wheat/barley yellow stripe rusts (Puccinia striformis). Despite its small stature, B. distachyon has large seeds that should prove useful for studies on grain filling. Such biological characteristics represent important traits for study in temperate cereals. PMID:11743099

Model-driven Service Engineering with SoaML

Science.gov (United States)

Elvesæter, Brian; Carrez, Cyril; Mohagheghi, Parastoo; Berre, Arne-Jørgen; Johnsen, Svein G.; Solberg, Arnor

This chapter presents a model-driven service engineering (MDSE) methodology that uses OMG MDA specifications such as BMM, BPMN and SoaML to identify and specify services within a service-oriented architecture. The methodology takes advantage of business modelling practices and provides a guide to service modelling with SoaML. The presentation is case-driven and illuminated using the telecommunication example. The chapter focuses in particular on the use of the SoaML modelling language as a means for expressing service specifications that are aligned with business models and can be realized in different platform technologies.

GUI development for GRASS GIS

Directory of Open Access Journals (Sweden)

Martin Landa

2007-12-01

Full Text Available This article discusses GUI development for GRASS GIS. Sophisticated native GUI for GRASS is one of the key points (besides the new 2D/3D raster library, vector architecture improvements, etc. for the future development of GRASS. In 2006 the GRASS development team decided to start working on the new generation of GUI instead of improving the current GUI based on Tcl/Tk.

Optical modeling of induction-linac driven free-electron lasers

International Nuclear Information System (INIS)

Scharlemann, E.T.; Fawley, W.M.

1986-01-01

The free-electron laser (FEL) simulation code FRED, developed at Lawrence Livermore National Laboratory (LLNL) primarily to model single-pass FEL amplifiers driven by induction linear accelerators, is described. The main emphasis is on the modeling of optical propagation in the laser and on the differences between the requirements for modeling rf-linac-driven vs. induction-linac-driven FELs. Examples of optical guiding and mode cleanup are presented for a 50 μm FEL

GRASS GIS: The first Open Source Temporal GIS

Science.gov (United States)

Gebbert, Sören; Leppelt, Thomas

2015-04-01

over temporal aggregation, temporal accumulation, spatio-temporal statistics, spatio-temporal sampling, temporal algebra, temporal topology analysis, time series animation and temporal topology visualization to time series import and export capabilities with support for NetCDF and VTK data formats. We will present several temporal modules that support parallel processing of raster and 3D raster time series. [1] GRASS GIS Open Source Approaches in Spatial Data Handling In Open Source Approaches in Spatial Data Handling, Vol. 2 (2008), pp. 171-199, doi:10.1007/978-3-540-74831-19 by M. Neteler, D. Beaudette, P. Cavallini, L. Lami, J. Cepicky edited by G. Brent Hall, Michael G. Leahy [2] Gebbert, S., Pebesma, E., 2014. A temporal GIS for field based environmental modeling. Environ. Model. Softw. 53, 1-12. [3] Zambelli, P., Gebbert, S., Ciolli, M., 2013. Pygrass: An Object Oriented Python Application Programming Interface (API) for Geographic Resources Analysis Support System (GRASS) Geographic Information System (GIS). ISPRS Intl Journal of Geo-Information 2, 201-219. [4] Löwe, P., Klump, J., Thaler, J. (2012): The FOSS GIS Workbench on the GFZ Load Sharing Facility compute cluster, (Geophysical Research Abstracts Vol. 14, EGU2012-4491, 2012), General Assembly European Geosciences Union (Vienna, Austria 2012). [5] Akhter, S., Aida, K., Chemin, Y., 2010. "GRASS GIS on High Performance Computing with MPI, OpenMP and Ninf-G Programming Framework". ISPRS Conference, Kyoto, 9-12 August 2010

Effect of high-sugar grasses on methane emissions simulated using a dynamic model

NARCIS (Netherlands)

St-Pierre, J.L.; Dijkstra, J.; France, J.; Parsons, A.J.; Edwards, G.R.; Rasmussen, S.; Kebreab, E.; Bannink, A.

2012-01-01

High-sugar grass varieties have received considerable attention for their potential ability to decrease N excretion in cattle. However, feeding high-sugar grasses alters the pattern of rumen fermentation, and no in vivo studies to date have examined this strategy with respect to another

Modelling the effectiveness of grass buffer strips in managing muddy floods under a changing climate

Science.gov (United States)

Mullan, Donal; Vandaele, Karel; Boardman, John; Meneely, John; Crossley, Laura H.

2016-10-01

Muddy floods occur when rainfall generates runoff on agricultural land, detaching and transporting sediment into the surrounding natural and built environment. In the Belgian Loess Belt, muddy floods occur regularly and lead to considerable economic costs associated with damage to property and infrastructure. Mitigation measures designed to manage the problem have been tested in a pilot area within Flanders and were found to be cost-effective within three years. This study assesses whether these mitigation measures will remain effective under a changing climate. To test this, the Water Erosion Prediction Project (WEPP) model was used to examine muddy flooding diagnostics (precipitation, runoff, soil loss and sediment yield) for a case study hillslope in Flanders where grass buffer strips are currently used as a mitigation measure. The model was run for present day conditions and then under 33 future site-specific climate scenarios. These future scenarios were generated from three earth system models driven by four representative concentration pathways and downscaled using quantile mapping and the weather generator CLIGEN. Results reveal that under the majority of future scenarios, muddy flooding diagnostics are projected to increase, mostly as a consequence of large scale precipitation events rather than mean changes. The magnitude of muddy flood events for a given return period is also generally projected to increase. These findings indicate that present day mitigation measures may have a reduced capacity to manage muddy flooding given the changes imposed by a warming climate with an enhanced hydrological cycle. Revisions to the design of existing mitigation measures within existing policy frameworks are considered the most effective way to account for the impacts of climate change in future mitigation planning.

The Orion GN and C Data-Driven Flight Software Architecture for Automated Sequencing and Fault Recovery

Science.gov (United States)

King, Ellis; Hart, Jeremy; Odegard, Ryan

2010-01-01

The Orion Crew Exploration Vehicle (CET) is being designed to include significantly more automation capability than either the Space Shuttle or the International Space Station (ISS). In particular, the vehicle flight software has requirements to accommodate increasingly automated missions throughout all phases of flight. A data-driven flight software architecture will provide an evolvable automation capability to sequence through Guidance, Navigation & Control (GN&C) flight software modes and configurations while maintaining the required flexibility and human control over the automation. This flexibility is a key aspect needed to address the maturation of operational concepts, to permit ground and crew operators to gain trust in the system and mitigate unpredictability in human spaceflight. To allow for mission flexibility and reconfrgurability, a data driven approach is being taken to load the mission event plan as well cis the flight software artifacts associated with the GN&C subsystem. A database of GN&C level sequencing data is presented which manages and tracks the mission specific and algorithm parameters to provide a capability to schedule GN&C events within mission segments. The flight software data schema for performing automated mission sequencing is presented with a concept of operations for interactions with ground and onboard crew members. A prototype architecture for fault identification, isolation and recovery interactions with the automation software is presented and discussed as a forward work item.

Insects traversing grass-like vertical compliant beams

Science.gov (United States)

Li, Chen; Fearing, Ronald; Full, Robert

2014-03-01

Small running animals encounter many challenging terrains. These terrains can be filled with 3D, multi-component obstacles. Here, we study cockroaches (Blaberus discoidalis) moving through grass-like vertical compliant beams during escape. We created an apparatus to control and vary geometric parameters and mechanical properties of model grass including height, width, thickness, lateral and fore-aft spacings, angle, number of layers, stiffness, and damping. We observed a suite of novel locomotor behaviors not previously described on simpler 2D ground. When model grass height was >2 × body length and lateral spacing was test our hypothesis, we modified body shape by adding either a rectangular or an oval plate onto its dorsal surface, and found that P dropped by an order of magnitude and t more than doubled. Upon removal of either plate, both P and t recovered. Locomotor kinematics and geometry effectively coupled to terrain properties enables negotiation of 3D, multi-component obstacles, and provides inspiration for small robots to navigate such terrain with minimal sensing and control.

Dynamic MR imaging of the temporomandibular joint arthrosis using spoiled GRASS sequence

International Nuclear Information System (INIS)

Suenaga, Shigeaki; Hamamoto, Sadatoshi; Kawano, Kazunori

1994-01-01

The purpose of this study was to quantitatively evaluate contrast enhancement effects of the posterior disk attachment in the temporomandibular joint arthrosis using dynamic MRI with bilateral surface coils. One hundred twenty-four temporomandibular joints in 96 symptomatic patients and 27 control subjects were examined with a spoiled GRASS pulse sequence (TR: 35 ms, TE: 8 ms, flip angle: 60deg). One sagittal scan was performed prior to injection, then 0.1 mmol/kg of Gd-DTPA was given as a rapid bolus injection, immediately after which scans were performed at 30 seconds intervals for a period of 5 minutes. Signal intensity (SI) was measured from the ROI of the posterior disk attachment region. The contrast enhancement effects may be calculated by SI ratio (SIR) = ( SI post -SI pre )/SI pre , where SI post and SI pre were the signal intensities after and before administration of contrast medium. The time intensity curve of SIR versus time after injection was obtained on each symptoms. Join pain group (85 joints) tended to show a rapid enhancement pattern, while control group (54 joints), joint sound or opening limitation group (39 joints), and asymptomatic group (68 joints) showed a relatively gradual enhancement pattern. The drop of SIR in four groups were hardly observed during examination. Mean peak SIR of control group, joint pain group, joint sound or opening limitation group, and asymptomatic group was 0.62±0.24 (SD), 1.53±0.69, 0.73±0.38 and 0.78±0.44 respectively. The mean SIR of pain group was significantly (P<0.001, t-test) higher than that of other groups. These results suggested that dynamic MRI of the temporomandibular joint may effectively depict the inflammatory changes of the posterior disk attachment. (author)

Dynamic MR imaging of the temporomandibular joint arthrosis using spoiled GRASS sequence

Energy Technology Data Exchange (ETDEWEB)

Suenaga, Shigeaki; Hamamoto, Sadatoshi; Kawano, Kazunori (Kagoshima Univ. (Japan). Dental School) (and others)

1994-07-01

The purpose of this study was to quantitatively evaluate contrast enhancement effects of the posterior disk attachment in the temporomandibular joint arthrosis using dynamic MRI with bilateral surface coils. One hundred twenty-four temporomandibular joints in 96 symptomatic patients and 27 control subjects were examined with a spoiled GRASS pulse sequence (TR: 35 ms, TE: 8 ms, flip angle: 60deg). One sagittal scan was performed prior to injection, then 0.1 mmol/kg of Gd-DTPA was given as a rapid bolus injection, immediately after which scans were performed at 30 seconds intervals for a period of 5 minutes. Signal intensity (SI) was measured from the ROI of the posterior disk attachment region. The contrast enhancement effects may be calculated by SI ratio (SIR) = ( SI[sup post]-SI[sup pre])/SI[sup pre], where SI[sup post] and SI[sup pre] were the signal intensities after and before administration of contrast medium. The time intensity curve of SIR versus time after injection was obtained on each symptoms. Join pain group (85 joints) tended to show a rapid enhancement pattern, while control group (54 joints), joint sound or opening limitation group (39 joints), and asymptomatic group (68 joints) showed a relatively gradual enhancement pattern. The drop of SIR in four groups were hardly observed during examination. Mean peak SIR of control group, joint pain group, joint sound or opening limitation group, and asymptomatic group was 0.62[+-]0.24 (SD), 1.53[+-]0.69, 0.73[+-]0.38 and 0.78[+-]0.44 respectively. The mean SIR of pain group was significantly (P<0.001, t-test) higher than that of other groups. These results suggested that dynamic MRI of the temporomandibular joint may effectively depict the inflammatory changes of the posterior disk attachment. (author).

Effects of field-grown genetically modified Zoysia grass on bacterial community structure.

Science.gov (United States)

Lee, Yong-Eok; Yang, Sang-Hwan; Bae, Tae-Woong; Kang, Hong-Gyu; Lim, Pyung-Ok; Lee, Hyo-Yeon

2011-04-01

Herbicide-tolerant Zoysia grass has been previously developed through Agrobacterium-mediated transformation. We investigated the effects of genetically modified (GM) Zoysia grass and the associated herbicide application on bacterial community structure by using culture-independent approaches. To assess the possible horizontal gene transfer (HGT) of transgenic DNA to soil microorganisms, total soil DNAs were amplified by PCR with two primer sets for the bar and hpt genes, which were introduced into the GM Zoysia grass by a callus-type transformation. The transgenic genes were not detected from the total genomic DNAs extracted from 1.5 g of each rhizosphere soils of GM and non-GM Zoysia grasses. The structures and diversities of the bacterial communities in rhizosphere soils of GM and non-GM Zoysia grasses were investigated by constructing 16S rDNA clone libraries. Classifier, provided in the RDP II, assigned 100 clones in the 16S rRNA gene sequences library into 11 bacterial phyla. The most abundant phyla in both clone libraries were Acidobacteria and Proteobacteria. The bacterial diversity of the GM clone library was lower than that of the non- GM library. The former contained four phyla, whereas the latter had seven phyla. Phylogenetic trees were constructed to confirm these results. Phylogenetic analyses of the two clone libraries revealed considerable difference from each other. The significance of difference between clone libraries was examined with LIBSHUFF statistics. LIBSHUFF analysis revealed that the two clone libraries differed significantly (P〈0.025), suggesting alterations in the composition of the microbial community associated with GM Zoysia grass.

Analyzing rasters, vectors and time series using new Python interfaces in GRASS GIS 7

Science.gov (United States)

Petras, Vaclav; Petrasova, Anna; Chemin, Yann; Zambelli, Pietro; Landa, Martin; Gebbert, Sören; Neteler, Markus; Löwe, Peter

2015-04-01

GRASS GIS 7 is a free and open source GIS software developed and used by many scientists (Neteler et al., 2012). While some users of GRASS GIS prefer its graphical user interface, significant part of the scientific community takes advantage of various scripting and programing interfaces offered by GRASS GIS to develop new models and algorithms. Here we will present different interfaces added to GRASS GIS 7 and available in Python, a popular programming language and environment in geosciences. These Python interfaces are designed to satisfy the needs of scientists and programmers under various circumstances. PyGRASS (Zambelli et al., 2013) is a new object-oriented interface to GRASS GIS modules and libraries. The GRASS GIS libraries are implemented in C to ensure maximum performance and the PyGRASS interface provides an intuitive, pythonic access to their functionality. GRASS GIS Python scripting library is another way of accessing GRASS GIS modules. It combines the simplicity of Bash and the efficiency of the Python syntax. When full access to all low-level and advanced functions and structures from GRASS GIS library is required, Python programmers can use an interface based on the Python ctypes package. Ctypes interface provides complete, direct access to all functionality as it would be available to C programmers. GRASS GIS provides specialized Python library for managing and analyzing spatio-temporal data (Gebbert and Pebesma, 2014). The temporal library introduces space time datasets representing time series of raster, 3D raster or vector maps and allows users to combine various spatio-temporal operations including queries, aggregation, sampling or the analysis of spatio-temporal topology. We will also discuss the advantages of implementing scientific algorithm as a GRASS GIS module and we will show how to write such module in Python. To facilitate the development of the module, GRASS GIS provides a Python library for testing (Petras and Gebbert, 2014) which

Sequence modelling and an extensible data model for genomic database

Energy Technology Data Exchange (ETDEWEB)

Li, Peter Wei-Der [California Univ., San Francisco, CA (United States); Univ. of California, Berkeley, CA (United States)

1992-01-01

The Human Genome Project (HGP) plans to sequence the human genome by the beginning of the next century. It will generate DNA sequences of more than 10 billion bases and complex marker sequences (maps) of more than 100 million markers. All of these information will be stored in database management systems (DBMSs). However, existing data models do not have the abstraction mechanism for modelling sequences and existing DBMS`s do not have operations for complex sequences. This work addresses the problem of sequence modelling in the context of the HGP and the more general problem of an extensible object data model that can incorporate the sequence model as well as existing and future data constructs and operators. First, we proposed a general sequence model that is application and implementation independent. This model is used to capture the sequence information found in the HGP at the conceptual level. In addition, abstract and biological sequence operators are defined for manipulating the modelled sequences. Second, we combined many features of semantic and object oriented data models into an extensible framework, which we called the ``Extensible Object Model``, to address the need of a modelling framework for incorporating the sequence data model with other types of data constructs and operators. This framework is based on the conceptual separation between constructors and constraints. We then used this modelling framework to integrate the constructs for the conceptual sequence model. The Extensible Object Model is also defined with a graphical representation, which is useful as a tool for database designers. Finally, we defined a query language to support this model and implement the query processor to demonstrate the feasibility of the extensible framework and the usefulness of the conceptual sequence model.

Sequence modelling and an extensible data model for genomic database

Energy Technology Data Exchange (ETDEWEB)

Li, Peter Wei-Der (California Univ., San Francisco, CA (United States) Lawrence Berkeley Lab., CA (United States))

1992-01-01

The Human Genome Project (HGP) plans to sequence the human genome by the beginning of the next century. It will generate DNA sequences of more than 10 billion bases and complex marker sequences (maps) of more than 100 million markers. All of these information will be stored in database management systems (DBMSs). However, existing data models do not have the abstraction mechanism for modelling sequences and existing DBMS's do not have operations for complex sequences. This work addresses the problem of sequence modelling in the context of the HGP and the more general problem of an extensible object data model that can incorporate the sequence model as well as existing and future data constructs and operators. First, we proposed a general sequence model that is application and implementation independent. This model is used to capture the sequence information found in the HGP at the conceptual level. In addition, abstract and biological sequence operators are defined for manipulating the modelled sequences. Second, we combined many features of semantic and object oriented data models into an extensible framework, which we called the Extensible Object Model'', to address the need of a modelling framework for incorporating the sequence data model with other types of data constructs and operators. This framework is based on the conceptual separation between constructors and constraints. We then used this modelling framework to integrate the constructs for the conceptual sequence model. The Extensible Object Model is also defined with a graphical representation, which is useful as a tool for database designers. Finally, we defined a query language to support this model and implement the query processor to demonstrate the feasibility of the extensible framework and the usefulness of the conceptual sequence model.

Differentiation of plant age in grasses using remote sensing

Science.gov (United States)

Knox, Nichola M.; Skidmore, Andrew K.; van der Werff, Harald M. A.; Groen, Thomas A.; de Boer, Willem F.; Prins, Herbert H. T.; Kohi, Edward; Peel, Mike

2013-10-01

Phenological or plant age classification across a landscape allows for examination of micro-topographical effects on plant growth, improvement in the accuracy of species discrimination, and will improve our understanding of the spatial variation in plant growth. In this paper six vegetation indices used in phenological studies (including the newly proposed PhIX index) were analysed for their ability to statistically differentiate grasses of different ages in the sequence of their development. Spectra of grasses of different ages were collected from a greenhouse study. These were used to determine if NDVI, NDWI, CAI, EVI, EVI2 and the newly proposed PhIX index could sequentially discriminate grasses of different ages, and subsequently classify grasses into their respective age category. The PhIX index was defined as: (AVNIRn+log(ASWIR2n))/(AVNIRn-log(ASWIR2n)), where AVNIRn and ASWIR2n are the respective normalised areas under the continuum removed reflectance curve within the VNIR (500-800 nm) and SWIR2 (2000-2210 nm) regions. The PhIX index was found to produce the highest phenological classification accuracy (Overall Accuracy: 79%, and Kappa Accuracy: 75%) and similar to the NDVI, EVI and EVI2 indices it statistically sequentially separates out the developmental age classes. Discrimination between seedling and dormant age classes and the adult and flowering classes was problematic for most of the tested indices. Combining information from the visible near infrared (VNIR) and shortwave infrared region (SWIR) region into a single phenological index captures the phenological changes associated with plant pigments and the ligno-cellulose absorption feature, providing a robust method to discriminate the age classes of grasses. This work provides a valuable contribution into mapping spatial variation and monitoring plant growth across savanna and grassland ecosystems.

Transcriptomic Identification of Drought-Related Genes and SSR Markers in Sudan Grass Based on RNA-Seq

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Yongqun Zhu

2017-05-01

Full Text Available Sudan grass (Sorghum sudanense is an annual warm-season gramineous forage grass that is widely used as pasture, hay, and silage. However, drought stress severely impacts its yield, and there is limited information about the mechanisms of drought tolerance in Sudan grass. In this study, we used next-generation sequencing to identify differentially expressed genes (DEGs in the Sudan grass variety Wulate No.1, and we developed simple sequence repeat (SSR markers associated with drought stress. From 852,543,826 raw reads, nearly 816,854,366 clean reads were identified and used for analysis. A total of 80,686 unigenes were obtained via de novo assembly of the clean reads including 45,065 unigenes (55.9% that were identified as coding sequences (CDSs. According to Gene Ontology analysis, 31,444 unigenes were annotated, 11,778 unigenes were identified to 25 categories in the clusters of orthologous groups of proteins (KOG classification, and 11,223 unigenes were assigned to 280 Kyoto Encyclopedia of Genes and Genomes (KEGG pathways. Additionally, there were 2,329 DEGs under a short-term of 25% polyethylene glycol (PEG treatment, while 5,101 DEGs were identified under the long-term of 25% PEG treatment. DEGs were enriched in pathways of carbon fixation in photosynthetic organisms and plant hormone signal transduction which played a leading role in short-term of drought stress. However, DEGs were mainly enriched in pathway of plant hormone signal transduction that played an important role under long-term of drought stress. To increase accuracy, we excluded all the DEGs of all controls, specifically, five DEGs that were associated with high PEG concentrations were found through RNA-Seq. All five genes were up-regulated under drought stress, but the functions of the genes remain unclear. In addition, we identified 17,548 SSRs obtained from 80,686 unigenes. The newly identified drought tolerance DEGs will contribute to transgenic breeding efforts, while

An idealized model for tree-grass coexistence in savannas : The role of life stage structure and fire disturbances

NARCIS (Netherlands)

Baudena, Mara|info:eu-repo/dai/nl/340303867; D'Andrea, Fabio; Provenzale, A.

2010-01-01

1. We discuss a simple implicit-space model for the competition of trees and grasses in an idealized savanna environment. The model represents patch occupancy dynamics within the habitat and introduces life stage structure in the tree population, namely adults and seedlings. A tree can be

Grass-specific CD4+ T-cells exhibit varying degrees of cross-reactivity, implications for allergen-specific immunotherapy

Science.gov (United States)

Archila, LD; DeLong, JH; Wambre, E; James, EA; Robinson, DM; Kwok, WW

2014-01-01

Background Conceptually, allergic responses may involve cross-reactivity by antibodies or T-cells. While IgE cross-reactivity amongst grass pollen allergens has been observed, cross-reactivity at the allergen-specific T-cell level has been less documented. Identification of the patterns of cross-reactivity may improve our understanding, allowing optimization of better immunotherapy strategies. Objectives We use Phleum pratense as model for the studying of cross-reactivity at the allergen-specific CD4+ T cell level amongst DR04:01 restricted Pooideae grass pollen T-cell epitopes. Methods After In vitro culture of blood mononucleated cells from Grass-pollen allergic subjects with specific Pooideae antigenic epitopes, dual tetramer staining with APC-labeled DR04:01/Phleum pratense tetramers and PE-labeled DR04:01/Pooideae grass homolog tetramers was assessed to identify cross-reactivity amongst allergen-specific DR04:01-restricted T-cells in 6 subjects. Direct ex vivo staining enabled the comparison of frequency and phenotype of different Pooideae grass pollen reactive T-cells. Intracellular cytokine staining (ICS) assays were also used to examine phenotypes of these T-cells. Results T-cells with various degree of cross reactive profiles could be detected. Poa p 1 97-116, Lol p 1 221-240, Lol p 5a 199-218, and Poa p 5a 199-218 were identified as minimally-cross-reactive T-cell epitopes that do not show cross reactivity to Phl p 1 and Phl p 5a epitopes. Ex vivo tetramer staining assays demonstrated T-cells that recognized these minimally-cross reactive T-cell epitopes are present in Grass-pollen allergic subjects. Conclusions Our results suggest that not all Pooideae grass epitopes with sequence homology are cross-reactive. Non-cross reactive T-cells with comparable frequency, phenotype and functionality to Phl p-specific T-cells, suggest that a multiple allergen system should be considered for immunotherapy instead of a mono allergen system. PMID:24708411

Grass-specific CD4(+) T-cells exhibit varying degrees of cross-reactivity, implications for allergen-specific immunotherapy.

Science.gov (United States)

Archila, L D; DeLong, J H; Wambre, E; James, E A; Robinson, D M; Kwok, W W

2014-07-01

Conceptually, allergic responses may involve cross-reactivity by antibodies or T-cells. While IgE cross-reactivity among grass-pollen allergens has been observed, cross-reactivity at the allergen-specific T-cell level has been less documented. Identification of the patterns of cross-reactivity may improve our understanding, allowing optimization of better immunotherapy strategies. We use Phleum pratense as model for the studying of cross-reactivity at the allergen-specific CD4(+) T cell level among DR04:01 restricted Pooideae grass-pollen T-cell epitopes. After in vitro culture of blood mono-nucleated cells from grass-pollen-allergic subjects with specific Pooideae antigenic epitopes, dual tetramer staining with APC-labelled DR04:01/Phleum pratense tetramers and PE-labelled DR04:01/Pooideae grass homolog tetramers was assessed to identify cross-reactivity among allergen-specific DR04:01-restricted T-cells in six subjects. Direct ex vivo staining enabled the comparison of frequency and phenotype of different Pooideae grass-pollen reactive T-cells. Intracellular cytokine staining (ICS) assays were also used to examine phenotypes of these T-cells. T-cells with various degrees of cross-reactive profiles could be detected. Poa p 1 97-116 , Lol p 1 221-240 , Lol p 5a 199-218 , and Poa p 5a 199-218 were identified as minimally cross-reactive T-cell epitopes that do not show cross-reactivity to Phl p 1 and Phl p 5a epitopes. Ex vivo tetramer staining assays demonstrated T-cells that recognized these minimally cross-reactive T-cell epitopes are present in Grass-pollen-allergic subjects. Our results suggest that not all Pooideae grass epitopes with sequence homology are cross-reactive. Non-cross-reactive T-cells with comparable frequency, phenotype and functionality to Phl p-specific T-cells suggest that a multiple allergen system should be considered for immunotherapy instead of a mono-allergen system. © 2014 John Wiley & Sons Ltd.

High-biomass C4 grasses-Filling the yield gap.

Science.gov (United States)

Mullet, John E

2017-08-01

A significant increase in agricultural productivity will be required by 2050 to meet the needs of an expanding and rapidly developing world population, without allocating more land and water resources to agriculture, and despite slowing rates of grain yield improvement. This review examines the proposition that high-biomass C 4 grasses could help fill the yield gap. High-biomass C 4 grasses exhibit high yield due to C 4 photosynthesis, long growth duration, and efficient capture and utilization of light, water, and nutrients. These C 4 grasses exhibit high levels of drought tolerance during their long vegetative growth phase ideal for crops grown in water-limited regions of agricultural production. The stems of some high-biomass C 4 grasses can accumulate high levels of non-structural carbohydrates that could be engineered to enhance biomass yield and utility as feedstocks for animals and biofuels production. The regulatory pathway that delays flowering of high-biomass C 4 grasses in long days has been elucidated enabling production and deployment of hybrids. Crop and landscape-scale modeling predict that utilization of high-biomass C 4 grass crops on land and in regions where water resources limit grain crop yield could increase agricultural productivity. Copyright © 2017 Elsevier B.V. All rights reserved.

PRODUCTION OF PRINTING AND WRITING PAPER GRADE PULP FROM ELEPHANT GRASS

Directory of Open Access Journals (Sweden)

Marcela Freitas Andrade

2016-09-01

Full Text Available The main goal of this study was to characterize chemically and morphologically elephant grass (Pennisetum purpureum, and evaluate the potential of its fibers for production of printing and writing paper grade pulp. The elephant grass was chemically and morphologically characterized and cooked by the soda process to two different degrees of delignification (kappa 17.5 and 10.6. The resulting pulps were fully bleached by the O-D*-(EP-D sequence and characterized for their beatability, drainability and physical-mechanical properties. The lignin content (20.2% was low, indicating that this grass should be easier to pulp. The morphological analyses of the elephant grass indicated a short fiber material, similar to hardwoods. The soda pulp from elephant grass cooked to kappa number 17.5 presented higher screened yield than 10.6 kappa pulp, with alkali demands of 15.0% and 20.0%, respectively. The total active chlorine required by the 17.5 and 10.6 kappa pulps, were 42.1 and 35.1 kg/odt pulp, respectively, to achieve an ISO brightness of approximately 90.0%. The bleached soda pulps cooked to 17.5 and 10.6 kappa number showed similar refinability and resistance to drainage, but the tensile and burst index were highest for the 17.5 kappa pulp at beating energy consumptions in the range of 0-6 Wh. It was concluded that both 10.6 and 17.5 kappa pulps from elephant grass are suitable for the production of printing and writing paper grade pulps, but the highest kappa 17.5 pulp is more economically attractive given its highest pulping yield, despite the significantly increased of chemical demand for bleaching A produção de papel para impressão e escrita Grau de celulose a partir de capim-elefante.

QTLs for resistance to the false brome rust Puccinia brachypodii in the model grass Brachypodium distachyon L.

NARCIS (Netherlands)

Barbieri, M.; Marcel, T.C.; Niks, R.E.; Francia, E.; Pasquariello, M.; Mazzamurro, V.; Garvin, D.F.; Pecchioni, N.

2012-01-01

The potential of the model grass Brachypodium distachyon L. (Brachypodium) for studying grass–pathogen interactions is still underexploited. We aimed to identify genomic regions in Brachypodium associated with quantitative resistance to the false brome rust fungus Puccinia brachypodii. The inbred

Nutritive value of Tanzania grass for dairy cows under rotational grazing

Directory of Open Access Journals (Sweden)

Alberto Magno Fernandes

2014-08-01

Full Text Available A nutritional analysis of Tanzania grass (Megathyrsus maximus Jacquin cv. Tanzânia was conducted. Pasture was managed in a rotational grazing system with a 30-day resting period, three days of paddock occupation and two grazing cycles. Ten Holstein × Zebu crossbred cows were kept within a 2-ha area divided into 11 paddocks ha-1. Cows were fed 2 kg of corn meal daily and performance was evaluated by weighing the animals every 14 days and by recording milk production twice a day. Nutritional composition of the Tanzania grass was determined from forage (extrusa samples collected by esophageal fistulae from two animals. The nutritive value of Tanzania grass was estimated according to a modification of the CNCPS evaluation model. Tanzania grass supplemented with 2 kg of corn meal supplied 33.2% more net energy for lactation than required by the animals to produce 13.7 kg of milk day-1. Nevertheless, the amount of metabolizable protein met the daily protein requirement of the animals. Although the model used in the study requires adjustments, Tanzania grass has the potential to produce milk in a rotational grazing system.

Molecular features of grass allergens and development of biotechnological approaches for allergy prevention.

Science.gov (United States)

Devis, Deborah L; Davies, Janet M; Zhang, Dabing

2017-09-01

Allergic diseases are characterized by elevated allergen-specific IgE and excessive inflammatory cell responses. Among the reported plant allergens, grass pollen and grain allergens, derived from agriculturally important members of the Poaceae family such as rice, wheat and barley, are the most dominant and difficult to prevent. Although many allergen homologs have been predicted from species such as wheat and timothy grass, fundamental aspects such as the evolution and function of plant pollen allergens remain largely unclear. With the development of genetic engineering and genomics, more primary sequences, functions and structures of plant allergens have been uncovered, and molecular component-based allergen-specific immunotherapies are being developed. In this review, we aim to provide an update on (i) the distribution and importance of pollen and grain allergens of the Poaceae family, (ii) the origin and evolution, and functional aspects of plant pollen allergens, (iii) developments of allergen-specific immunotherapy for pollen allergy using biotechnology and (iv) development of less allergenic plants using gene engineering techniques. We also discuss future trends in revealing fundamental aspects of grass pollen allergens and possible biotechnological approaches to reduce the amount of pollen allergens in grasses. Copyright © 2017. Published by Elsevier Inc.

Envisioning the future of collaborative model-driven software engineering

NARCIS (Netherlands)

Di Ruscio, Davide; Franzago, Mirco; Malavolta, Ivano; Muccini, Henry

2017-01-01

The adoption of Model-driven Software Engineering (MDSE) to develop complex software systems in application domains like automotive and aerospace is being supported by the maturation of model-driven platforms and tools. However, empirical studies show that a wider adoption of MDSE technologies is

Ecophysiological responses of native and invasive grasses to simulated warming and drought

Science.gov (United States)

Ravi, S.; Law, D. J.; Wiede, A.; Barron-Gafford, G. A.; Breshears, D. D.; Dontsova, K.; Huxman, T. E.

2011-12-01

Climate models predict that many arid regions around the world - including the North American deserts - may become affected more frequently by recurrent droughts. At the same time, these regions are experiencing rapid vegetation transformations such as invasion by exotic grasses. Thus, understanding the ecophysiological processes accompanying exotic grass invasion in the context of rising temperatures and recurrent droughts is fundamental to global change research. Under ambient and warmer (+ 4° C) conditions inside the Biosphere 2 facility, we compared the ecophysiological responses (e.g. photosynthesis, stomatal conductance, pre-dawn leaf water potential, light & CO2 response functions, biomass) of a native grass - Heteropogan contortus (Tangle head) and an invasive grass - Pennisetum ciliare (Buffel grass) growing in single and mixed communities. Further, we monitored the physiological responses and mortality of these plant communities under moisture stress conditions, simulating a global change-type-drought. The results indicate that the predicted warming scenarios may enhance the invasibility of desert landscapes by exotic grasses. In this study, buffel grass assimilated more CO2 per unit leaf area and out-competed native grasses more efficiently in a warmer environment. However, scenarios involving a combination of drought and warming proved disastrous to both the native and invasive grasses, with drought-induced grass mortality occurring at much shorter time scales under warmer conditions.

The Arizona Universities Library Consortium patron-driven e-book model

Directory of Open Access Journals (Sweden)

Jeanne Richardson

2013-03-01

Full Text Available Building on Arizona State University's patron-driven acquisitions (PDA initiative in 2009, the Arizona Universities Library Consortium, in partnership with the Ingram Content Group, created a cooperative patron-driven model to acquire electronic books (e-books. The model provides the opportunity for faculty and students at the universities governed by the Arizona Board of Regents (ABOR to access a core of e-books made accessible through resource discovery services and online catalogs. These books are available for significantly less than a single ABOR university would expend for the same materials. The patron-driven model described is one of many evolving models in digital scholarship, and, although the Arizona Universities Library Consortium reports a successful experience, patron-driven models pose questions to stakeholders in the academic publishing industry.

Data-driven models of dominantly-inherited Alzheimer's disease progression.

Science.gov (United States)

Oxtoby, Neil P; Young, Alexandra L; Cash, David M; Benzinger, Tammie L S; Fagan, Anne M; Morris, John C; Bateman, Randall J; Fox, Nick C; Schott, Jonathan M; Alexander, Daniel C

2018-03-22

Dominantly-inherited Alzheimer's disease is widely hoped to hold the key to developing interventions for sporadic late onset Alzheimer's disease. We use emerging techniques in generative data-driven disease progression modelling to characterize dominantly-inherited Alzheimer's disease progression with unprecedented resolution, and without relying upon familial estimates of years until symptom onset. We retrospectively analysed biomarker data from the sixth data freeze of the Dominantly Inherited Alzheimer Network observational study, including measures of amyloid proteins and neurofibrillary tangles in the brain, regional brain volumes and cortical thicknesses, brain glucose hypometabolism, and cognitive performance from the Mini-Mental State Examination (all adjusted for age, years of education, sex, and head size, as appropriate). Data included 338 participants with known mutation status (211 mutation carriers in three subtypes: 163 PSEN1, 17 PSEN2, and 31 APP) and a baseline visit (age 19-66; up to four visits each, 1.1 ± 1.9 years in duration; spanning 30 years before, to 21 years after, parental age of symptom onset). We used an event-based model to estimate sequences of biomarker changes from baseline data across disease subtypes (mutation groups), and a differential equation model to estimate biomarker trajectories from longitudinal data (up to 66 mutation carriers, all subtypes combined). The two models concur that biomarker abnormality proceeds as follows: amyloid deposition in cortical then subcortical regions (∼24 ± 11 years before onset); phosphorylated tau (17 ± 8 years), tau and amyloid-β changes in cerebrospinal fluid; neurodegeneration first in the putamen and nucleus accumbens (up to 6 ± 2 years); then cognitive decline (7 ± 6 years), cerebral hypometabolism (4 ± 4 years), and further regional neurodegeneration. Our models predicted symptom onset more accurately than predictions that used familial estimates: root mean squared error of 1

Substrate-driven mapping of the degradome by comparison of sequence logos.

Directory of Open Access Journals (Sweden)

Julian E Fuchs

Full Text Available Sequence logos are frequently used to illustrate substrate preferences and specificity of proteases. Here, we employed the compiled substrates of the MEROPS database to introduce a novel metric for comparison of protease substrate preferences. The constructed similarity matrix of 62 proteases can be used to intuitively visualize similarities in protease substrate readout via principal component analysis and construction of protease specificity trees. Since our new metric is solely based on substrate data, we can engraft the protease tree including proteolytic enzymes of different evolutionary origin. Thereby, our analyses confirm pronounced overlaps in substrate recognition not only between proteases closely related on sequence basis but also between proteolytic enzymes of different evolutionary origin and catalytic type. To illustrate the applicability of our approach we analyze the distribution of targets of small molecules from the ChEMBL database in our substrate-based protease specificity trees. We observe a striking clustering of annotated targets in tree branches even though these grouped targets do not necessarily share similarity on protein sequence level. This highlights the value and applicability of knowledge acquired from peptide substrates in drug design of small molecules, e.g., for the prediction of off-target effects or drug repurposing. Consequently, our similarity metric allows to map the degradome and its associated drug target network via comparison of known substrate peptides. The substrate-driven view of protein-protein interfaces is not limited to the field of proteases but can be applied to any target class where a sufficient amount of known substrate data is available.

Analysis of the soil food web structure under grass and grass clover

NARCIS (Netherlands)

Eekeren, van N.J.M.; Smeding, F.W.; Vries, de F.T.; Bloem, J.

2006-01-01

The below ground biodiversity of soil organisms plays an important role in the functioning of the the soil ecosystem, and consequently the above ground plant production. The objective of this study is to investigate the effect of grass or grass-clover in combination with fertilisation on the soil

Robust biological nitrogen fixation in a model grass-bacterial association.

Science.gov (United States)

Pankievicz, Vânia C S; do Amaral, Fernanda P; Santos, Karina F D N; Agtuca, Beverly; Xu, Youwen; Schueller, Michael J; Arisi, Ana Carolina M; Steffens, Maria B R; de Souza, Emanuel M; Pedrosa, Fábio O; Stacey, Gary; Ferrieri, Richard A

2015-03-01

Nitrogen-fixing rhizobacteria can promote plant growth; however, it is controversial whether biological nitrogen fixation (BNF) from associative interaction contributes to growth promotion. The roots of Setaria viridis, a model C4 grass, were effectively colonized by bacterial inoculants resulting in a significant enhancement of growth. Nitrogen-13 tracer studies provided direct evidence for tracer uptake by the host plant and incorporation into protein. Indeed, plants showed robust growth under nitrogen-limiting conditions when inoculated with an ammonium-excreting strain of Azospirillum brasilense. (11)C-labeling experiments showed that patterns in central carbon metabolism and resource allocation exhibited by nitrogen-starved plants were largely reversed by bacterial inoculation, such that they resembled plants grown under nitrogen-sufficient conditions. Adoption of S. viridis as a model should promote research into the mechanisms of associative nitrogen fixation with the ultimate goal of greater adoption of BNF for sustainable crop production. © 2015 The Authors The Plant Journal © 2015 John Wiley & Sons Ltd.

FmMDb: a versatile database of foxtail millet markers for millets and bioenergy grasses research.

Directory of Open Access Journals (Sweden)

Venkata Suresh B

Full Text Available The prominent attributes of foxtail millet (Setaria italica L. including its small genome size, short life cycle, inbreeding nature, and phylogenetic proximity to various biofuel crops have made this crop an excellent model system to investigate various aspects of architectural, evolutionary and physiological significances in Panicoid bioenergy grasses. After release of its whole genome sequence, large-scale genomic resources in terms of molecular markers were generated for the improvement of both foxtail millet and its related species. Hence it is now essential to congregate, curate and make available these genomic resources for the benefit of researchers and breeders working towards crop improvement. In view of this, we have constructed the Foxtail millet Marker Database (FmMDb; http://www.nipgr.res.in/foxtail.html, a comprehensive online database for information retrieval, visualization and management of large-scale marker datasets with unrestricted public access. FmMDb is the first database which provides complete marker information to the plant science community attempting to produce elite cultivars of millet and bioenergy grass species, thus addressing global food insecurity.

Model Driven Architecture: Foundations and Applications

NARCIS (Netherlands)

Rensink, Arend

The OMG's Model Driven Architecture (MDA) initiative has been the focus of much attention in both academia and industry, due to its promise of more rapid and consistent software development through the increased use of models. In order for MDA to reach its full potential, the ability to manipulate

GRASS-SST, Fission Products Gas Release and Fuel Swelling in Steady-State and Transients

International Nuclear Information System (INIS)

Zawadzki, S.

2001-01-01

1 - Description of program or function: GRASS-SST is a comprehensive, mechanistic model for the prediction of fission-gas behaviour in UO 2 -base fuels during steady-state and transient conditions. GRASS-SST treats fission-gas release and fuel swelling on an equal basis and simultaneously treats all major mechanisms that influence fission-gas behaviour. Models are included for intra- and inter-granular fission-gas bubble behaviour as well as a mechanistic description of the role of grain-edge inter-linked porosity on fission-gas release and swelling. GRASS-SST calculations include the effects of gas production from fissioning uranium atoms, bubble nucleation, a realistic equation of state for xenon, lattice bubble diffusivities based on experimental observations, bubble migration, bubble coalescence, re-solution, temperature and temperature gradients, inter-linked porosity, and fission-gas interaction with structural defects (dislocations and grain boundaries) on both the distribution of fission-gas within the fuel and on the amount of fission-gas released from the fuel. GRASS-SST includes the effects of the degree of nonequilibrium in the UO 2 lattice on fission-gas bubble mobility and bubble coalescence and also accounts for the observed formation of grain-surface channels. GRASS-SST also includes mechanistic models for grain-growth/grain boundary sweeping and for the behaviour of fission gas during liquefaction/dissolution and fuel melting conditions. 2 - Method of solution: A system of coupled equations for the evolution of the fission-gas bubble-size distributions in the lattice, on dislocations, on grain faces, and grain edges is derived based on the GRASS-SST models. Given a set of operating conditions, GRASS-SST calculates the bubble radii for the size classes of bubbles under consideration using a realistic equation of state for xenon as well as a generalised capillary relation. 3 - Restrictions on the complexity of the problem: Maxima of : 1 axial section

A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions

Science.gov (United States)

Burke, Sean V.; Wysocki, William P.; Clark, Lynn G.

2018-01-01

The systematics of grasses has advanced through applications of plastome phylogenomics, although studies have been largely limited to subfamilies or other subgroups of Poaceae. Here we present a plastome phylogenomic analysis of 250 complete plastomes (179 genera) sampled from 44 of the 52 tribes of Poaceae. Plastome sequences were determined from high throughput sequencing libraries and the assemblies represent over 28.7 Mbases of sequence data. Phylogenetic signal was characterized in 14 partitions, including (1) complete plastomes; (2) protein coding regions; (3) noncoding regions; and (4) three loci commonly used in single and multi-gene studies of grasses. Each of the four main partitions was further refined, alternatively including or excluding positively selected codons and also the gaps introduced by the alignment. All 76 protein coding plastome loci were found to be predominantly under purifying selection, but specific codons were found to be under positive selection in 65 loci. The loci that have been widely used in multi-gene phylogenetic studies had among the highest proportions of positively selected codons, suggesting caution in the interpretation of these earlier results. Plastome phylogenomic analyses confirmed the backbone topology for Poaceae with maximum bootstrap support (BP). Among the 14 analyses, 82 clades out of 309 resolved were maximally supported in all trees. Analyses of newly sequenced plastomes were in agreement with current classifications. Five of seven partitions in which alignment gaps were removed retrieved Panicoideae as sister to the remaining PACMAD subfamilies. Alternative topologies were recovered in trees from partitions that included alignment gaps. This suggests that ambiguities in aligning these uncertain regions might introduce a false signal. Resolution of these and other critical branch points in the phylogeny of Poaceae will help to better understand the selective forces that drove the radiation of the BOP and PACMAD

Turbulent transfer characteristics of radioiodine effluents from air to grass

Energy Technology Data Exchange (ETDEWEB)

Markee, E. H. [ARFRO, Environmental Science Services Administration, Idaho Falls, Idaho (United States)

1967-07-01

A total of 20 controlled field releases of radioiodine have been performed at the National Reactor Testing Station in Idaho as a portion of a program to study the transmission of gaseous radioiodine through the air-vegetation-cow-milk-human chain. Most of the releases were conducted over typical pasture grasses during different wind and stability conditions. Radioiodine adherence to grass and carbon plates was measured during most of the tests. Vertical air concentration profiles and turbulence parameters were measured to determine flux characteristics. Analysis of the data reveals the complex interdisciplinary nature of transfer of radioiodine from air to a natural surface. The data are in reasonable agreement with the deposition models of Sheppard and Chamberlain when corrections for the physical and biological receptiveness of the grass and grass density are made. The average ratios of momentum to mass flux were found to be 0.9 in stable conditions and 1.4 in unstable conditions. These ratios demonstrate the effect on mass flux in the lowest 4m by a surface that acts as a partial sink for gaseous effluents. This series of releases indicates the need for further research on the biological receptiveness of grass and turbulent transfer within a grass canopy. (author)

Automated Testing of Event-Driven Applications

DEFF Research Database (Denmark)

Jensen, Casper Svenning

may be tested by selecting an interesting input (i.e. a sequence of events), and deciding if a failure occurs when the selected input is applied to the event-driven application under test. Automated testing promises to reduce the workload for developers by automatically selecting interesting inputs...... and detect failures. However, it is non-trivial to conduct automated testing of event-driven applications because of, for example, infinite input spaces and the absence of specifications of correct application behavior. In this PhD dissertation, we identify a number of specific challenges when conducting...... automated testing of event-driven applications, and we present novel techniques for solving these challenges. First, we present an algorithm for stateless model-checking of event-driven applications with partial-order reduction, and we show how this algorithm may be used to systematically test web...

Meadow-grass gall midge

DEFF Research Database (Denmark)

Hansen, Lars Monrad

The area with meadow-grass (Poa pratensis, L.) grown for seed production in Den-mark is a significant proportion of the entire seed production. The meadow-grass gall midge (Mayetiola schoberi, Barnes 1958) is of considerable economic importance since powerful attacks can reduce the yield...

HLA-D gene studies in relation to immune responsiveness to a grass allergen Lol p III.

Science.gov (United States)

Ansari, A A; Shinomiya, N; Zwollo, P; Marsh, D G

1991-01-01

The grass pollen allergen Lol p III (Mr 11,000) is a well-characterized antigen that has been found useful in immunogenetic studies of human immune responsiveness. Since immune responsiveness to this allergen is associated with HLA-DR3, we investigated whether there was any sequence in the HLA-D region that would render a person "susceptible" [antibody (Ab)-positive] to the allergen. By sequence-specific oligonucleotide (SSO) slot-blot and sequence analyses of polymerase chain reaction (PCR)-amplified genomic DNA from Lol p III responder and nonresponder subjects, Ab responsiveness was found to be strongly associated with the sequence Glu-Tyr-Ser-Thr-Ser (EYSTS), present in the first polymorphic regions of DR beta I polypeptide chains of DR3, DR11 (split of DR5), and DRw6. Of the 41 grass-allergic subjects investigated, 19 had the EYSTS sequence, of whom 18 (95%) were Lol p III immunoglobulin G (IgG) Ab responders; among the 22 EYSTS- subjects, ten were Lol p III responders (P = 0.001, relative risk = 21.6). No such association was found with any polymorphic sequences in other DR beta chains, or in DQ alpha I and DQ beta I chains. These findings suggest that the EYSTS sequence is important in the presentation of an epitope of Lol p III; other sequence(s) may be involved in the presentation of other epitope(s). To our knowledge, this is the first demonstration of a strong association between a specific HLA sequence and immune responsiveness to a well-defined antigen. The paper shows that presence of the EYSTS sequence classifies subjects as Lol p III responders in 18/19 cases.

Consistent model driven architecture

Science.gov (United States)

Niepostyn, Stanisław J.

2015-09-01

The goal of the MDA is to produce software systems from abstract models in a way where human interaction is restricted to a minimum. These abstract models are based on the UML language. However, the semantics of UML models is defined in a natural language. Subsequently the verification of consistency of these diagrams is needed in order to identify errors in requirements at the early stage of the development process. The verification of consistency is difficult due to a semi-formal nature of UML diagrams. We propose automatic verification of consistency of the series of UML diagrams originating from abstract models implemented with our consistency rules. This Consistent Model Driven Architecture approach enables us to generate automatically complete workflow applications from consistent and complete models developed from abstract models (e.g. Business Context Diagram). Therefore, our method can be used to check practicability (feasibility) of software architecture models.

Estimating the content of clover and grass in the sward using a consumer camera and image processing

DEFF Research Database (Denmark)

Mortensen, Anders Krogh; Karstoft, Henrik; Søegaard, Karen

the dry matter ratio of clover and grass in clover grass fields from sparse close up images. First, the light conditions is determined, which is used for selecting model parameters to estimate the coverage of both clover and grass. Next, the clover and grass coverage are transformed to give the dry matter...

Sequence-based novel genomic microsatellite markers for robust genotyping purposes in foxtail millet [Setaria italica (L.) P. Beauv].

Science.gov (United States)

Gupta, Sarika; Kumari, Kajal; Sahu, Pranav Pankaj; Vidapu, Sudhakar; Prasad, Manoj

2012-02-01

The unavailability of microsatellite markers and saturated genetic linkage map has restricted the genetic improvement of foxtail millet [Setaria italica (L.) P. Beauv.], despite the fact that in recent times it has been documented as a new model species for biofuel grasses. With the objective to generate a good number of microsatellite markers in foxtail millet cultivar 'Prasad', 690 clones were sequenced which generated 112.95 kb high quality sequences obtained from three genomic libraries each enriched with different microsatellite repeat motifs. Microsatellites were identified in 512 (74.2%) of the 690 positive clones and 172 primer pairs (pp) were successfully designed from 249 (48.6%) unique SSR-containing clones. The efficacies of the microsatellite containing genomic sequences were established by superior primer designing ability (69%), PCR amplification efficiency (85.5%) and polymorphic potential (52%) in the parents of F(2) mapping population. Out of 172 pp, functional 147 markers showed high level of cross-species amplification (~74%) in six grass species. Higher polymorphism rate and broad range of genetic diversity (0.30-0.69 averaging 0.58) obtained in constructed phylogenetic tree using 52 microsatellite markers, demonstrated the utility of markers in germplasm characterizations. In silico comparative mapping of 147 foxtail millet microsatellite containing sequences against the mapping data of sorghum (~18%), maize (~16%) and rice (~5%) indicated the presence of orthologous sequences of the foxtail millet in the respective species. The result thus demonstrates the applicability of microsatellite markers in various genotyping applications, determining phylogenetic relationships and comparative mapping in several important grass species.

Nutritional value of cabbage and kikuyu grass as food for grass carp ...

African Journals Online (AJOL)

and digestibility coefficients were obtained for the protein, fibre, ash and fat contents of both ... Cabbage is a superior feed compared to grass for raising grass carp and a suitable low-cost alternative ... Materials and Methods ... from jumping out and was fitted with an air lift under- .... In: Aquatic weeds in South East Asia.

High green fodder yielding new grass varieties

OpenAIRE

C. Babu, K. Iyanar and A. Kalamani

2014-01-01

Two high biomass yielding forage grass varieties one each in Cumbu Napier hybrid and Guinea grass have been evolved at the Department of Forage Crops, Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore and identified for release at national (All India) level as Cumbu Napier hybrid grass CO (BN) 5 and Guinea grass CO (GG) 3 during 2012 and 2013 respectively. Cumbu Napier hybrid grass CO (BN) 5 secured first rank at all national level with reference to green ...

Evolutionary relationships between Rhynchosporium lolii sp. nov. and other Rhynchosporium species on grasses.

Directory of Open Access Journals (Sweden)

Kevin M King

Full Text Available The fungal genus Rhynchosporium (causative agent of leaf blotch contains several host-specialised species, including R. commune (colonising barley and brome-grass, R. agropyri (couch-grass, R. secalis (rye and triticale and the more distantly related R. orthosporum (cocksfoot. This study used molecular fingerprinting, multilocus DNA sequence data, conidial morphology, host range tests and scanning electron microscopy to investigate the relationship between Rhynchosporium species on ryegrasses, both economically important forage grasses and common wild grasses in many cereal growing areas, and other plant species. Two different types of Rhynchosporium were found on ryegrasses in the UK. Firstly, there were isolates of R. commune that were pathogenic to both barley and Italian ryegrass. Secondly, there were isolates of a new species, here named R. lolii, that were pathogenic only to ryegrass species. R. lolii was most closely related to R. orthosporum, but exhibited clear molecular, morphological and host range differences. The species was estimated to have diverged from R. orthosporum ca. 5735 years before the present. The colonisation strategy of all of the different Rhynchosporium species involved extensive hyphal growth in the sub-cuticular regions of the leaves. Finally, new species-specific PCR diagnostic tests were developed that could distinguish between these five closely related Rhynchosporium species.

Energy sorghum--a genetic model for the design of C4 grass bioenergy crops.

Science.gov (United States)

Mullet, John; Morishige, Daryl; McCormick, Ryan; Truong, Sandra; Hilley, Josie; McKinley, Brian; Anderson, Robert; Olson, Sara N; Rooney, William

2014-07-01

Sorghum is emerging as an excellent genetic model for the design of C4 grass bioenergy crops. Annual energy Sorghum hybrids also serve as a source of biomass for bioenergy production. Elucidation of Sorghum's flowering time gene regulatory network, and identification of complementary alleles for photoperiod sensitivity, enabled large-scale generation of energy Sorghum hybrids for testing and commercial use. Energy Sorghum hybrids with long vegetative growth phases were found to accumulate more than twice as much biomass as grain Sorghum, owing to extended growing seasons, greater light interception, and higher radiation use efficiency. High biomass yield, efficient nitrogen recycling, and preferential accumulation of stem biomass with low nitrogen content contributed to energy Sorghum's elevated nitrogen use efficiency. Sorghum's integrated genetics-genomics-breeding platform, diverse germplasm, and the opportunity for annual testing of new genetic designs in controlled environments and in multiple field locations is aiding fundamental discovery, and accelerating the improvement of biomass yield and optimization of composition for biofuels production. Recent advances in wide hybridization between Sorghum and other C4 grasses could allow the deployment of improved genetic designs of annual energy Sorghums in the form of wide-hybrid perennial crops. The current trajectory of energy Sorghum genetic improvement indicates that it will be possible to sustainably produce biofuels from C4 grass bioenergy crops that are cost competitive with petroleum-based transportation fuels. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

A Model-Driven Development Method for Management Information Systems

Science.gov (United States)

Mizuno, Tomoki; Matsumoto, Keinosuke; Mori, Naoki

Traditionally, a Management Information System (MIS) has been developed without using formal methods. By the informal methods, the MIS is developed on its lifecycle without having any models. It causes many problems such as lack of the reliability of system design specifications. In order to overcome these problems, a model theory approach was proposed. The approach is based on an idea that a system can be modeled by automata and set theory. However, it is very difficult to generate automata of the system to be developed right from the start. On the other hand, there is a model-driven development method that can flexibly correspond to changes of business logics or implementing technologies. In the model-driven development, a system is modeled using a modeling language such as UML. This paper proposes a new development method for management information systems applying the model-driven development method to a component of the model theory approach. The experiment has shown that a reduced amount of efforts is more than 30% of all the efforts.

Model-Driven Development of Context-Aware Services

NARCIS (Netherlands)

Andrade Almeida, João; Iacob, Maria Eugenia; Jonkers, Henk; Quartel, Dick; Eliassen, Frank; Montresor, Alberto

2006-01-01

In this paper, we define a model-driven design trajectory for context-aware services consisting of three levels of models with different degrees of abstraction and platform independence. The models at the highest level of platform independence describe the behaviour of a context-aware service and

Different techniques to study rumen fermentation characteristics of maturing grass and grass silage

NARCIS (Netherlands)

Cone, J.W.; Gelder, van A.H.; Soliman, I.A.; Visser, de H.; Vuuren, van A.M.

1999-01-01

Grass samples were harvested during the 1993 growing season after a precut on April 27, 1993 and were stored frozen or left to ensile in 30-L buckets. Effects on chemical composition and fermentation kinetics of the maturation of the grass and of ensiling were investigated. Chemical composition and

Estimation of grass to cow's milk transfer coefficients for emergency situations

International Nuclear Information System (INIS)

Ujwal, P.; Karunakara, N.; Yashodhara, I.; Rao, Chetan; Kumara, Sudeep; Dileep, B.N.; Ravi, P.M.

2012-01-01

Several studies have been reported on soil to grass equilibrium transfer factors and grass to cow's milk transfer coefficients for 137 Cs for the environs of different nuclear power plants of both India and other parts of the world. In such studies, the activity concentration of 137 Cs is measured in grass collected from different places. Cow's milk samples are collected from nearby localities or from milk dairies and analyzed for 137 Cs and the grass to cow's milk transfer coefficient is estimated. In situation where 137 Cs is not present in measurable activity concentrations, its stable counterpart (Cs) is measured for the estimation of transfer coefficients. These transfer coefficient values are generally used in theoretical models to estimate the dose to the population for hypothetical situation of emergency. It should be noted that the transfer coefficients obtained for equilibrium conditions may not be totally applicable for emergency situation. However, studies aimed at evaluating transfer coefficients for emergency situations are sparse because nuclear power plants do not release 137 Cs during normal operating situations and therefore simulating situation of emergency release is not possible. Hence, the only method to estimate the grass to milk transfer coefficient for emergency situation is to spike the grass with small quantity of stable Cs. This paper reports the results of grass to milk transfer coefficients for stable isotope of Cesium (Cs) for emergency situation

Bending of Euler-Bernoulli nanobeams based on the strain-driven and stress-driven nonlocal integral models: a numerical approach

Science.gov (United States)

Oskouie, M. Faraji; Ansari, R.; Rouhi, H.

2018-04-01

Eringen's nonlocal elasticity theory is extensively employed for the analysis of nanostructures because it is able to capture nanoscale effects. Previous studies have revealed that using the differential form of the strain-driven version of this theory leads to paradoxical results in some cases, such as bending analysis of cantilevers, and recourse must be made to the integral version. In this article, a novel numerical approach is developed for the bending analysis of Euler-Bernoulli nanobeams in the context of strain- and stress-driven integral nonlocal models. This numerical approach is proposed for the direct solution to bypass the difficulties related to converting the integral governing equation into a differential equation. First, the governing equation is derived based on both strain-driven and stress-driven nonlocal models by means of the minimum total potential energy. Also, in each case, the governing equation is obtained in both strong and weak forms. To solve numerically the derived equations, matrix differential and integral operators are constructed based upon the finite difference technique and trapezoidal integration rule. It is shown that the proposed numerical approach can be efficiently applied to the strain-driven nonlocal model with the aim of resolving the mentioned paradoxes. Also, it is able to solve the problem based on the strain-driven model without inconsistencies of the application of this model that are reported in the literature.

Small mammal use of native warm-season and non-native cool-season grass forage fields

Science.gov (United States)

Ryan L Klimstra,; Christopher E Moorman,; Converse, Sarah J.; Royle, J. Andrew; Craig A Harper,

2015-01-01

Recent emphasis has been put on establishing native warm-season grasses for forage production because it is thought native warm-season grasses provide higher quality wildlife habitat than do non-native cool-season grasses. However, it is not clear whether native warm-season grass fields provide better resources for small mammals than currently are available in non-native cool-season grass forage production fields. We developed a hierarchical spatially explicit capture-recapture model to compare abundance of hispid cotton rats (Sigmodon hispidus), white-footed mice (Peromyscus leucopus), and house mice (Mus musculus) among 4 hayed non-native cool-season grass fields, 4 hayed native warm-season grass fields, and 4 native warm-season grass-forb ("wildlife") fields managed for wildlife during 2 summer trapping periods in 2009 and 2010 of the western piedmont of North Carolina, USA. Cotton rat abundance estimates were greater in wildlife fields than in native warm-season grass and non-native cool-season grass fields and greater in native warm-season grass fields than in non-native cool-season grass fields. Abundances of white-footed mouse and house mouse populations were lower in wildlife fields than in native warm-season grass and non-native cool-season grass fields, but the abundances were not different between the native warm-season grass and non-native cool-season grass fields. Lack of cover following haying in non-native cool-season grass and native warm-season grass fields likely was the key factor limiting small mammal abundance, especially cotton rats, in forage fields. Retention of vegetation structure in managed forage production systems, either by alternately resting cool-season and warm-season grass forage fields or by leaving unharvested field borders, should provide refugia for small mammals during haying events.

Sequence-Specific Model for Peptide Retention Time Prediction in Strong Cation Exchange Chromatography.

Science.gov (United States)

Gussakovsky, Daniel; Neustaeter, Haley; Spicer, Victor; Krokhin, Oleg V

2017-11-07

The development of a peptide retention prediction model for strong cation exchange (SCX) separation on a Polysulfoethyl A column is reported. Off-line 2D LC-MS/MS analysis (SCX-RPLC) of S. cerevisiae whole cell lysate was used to generate a retention dataset of ∼30 000 peptides, sufficient for identifying the major sequence-specific features of peptide retention mechanisms in SCX. In contrast to RPLC/hydrophilic interaction liquid chromatography (HILIC) separation modes, where retention is driven by hydrophobic/hydrophilic contributions of all individual residues, SCX interactions depend mainly on peptide charge (number of basic residues at acidic pH) and size. An additive model (incorporating the contributions of all 20 residues into the peptide retention) combined with a peptide length correction produces a 0.976 R 2 value prediction accuracy, significantly higher than the additive models for either HILIC or RPLC. Position-dependent effects on peptide retention for different residues were driven by the spatial orientation of tryptic peptides upon interaction with the negatively charged surface functional groups. The positively charged N-termini serve as a primary point of interaction. For example, basic residues (Arg, His, Lys) increase peptide retention when located closer to the N-terminus. We also found that hydrophobic interactions, which could lead to a mixed-mode separation mechanism, are largely suppressed at 20-30% of acetonitrile in the eluent. The accuracy of the final Sequence-Specific Retention Calculator (SSRCalc) SCX model (∼0.99 R 2 value) exceeds all previously reported predictors for peptide LC separations. This also provides a solid platform for method development in 2D LC-MS protocols in proteomics and peptide retention prediction filtering of false positive identifications.

Breeding for Grass Seed Yield

DEFF Research Database (Denmark)

Boelt, Birte; Studer, Bruno

2010-01-01

Seed yield is a trait of major interest for many fodder and amenity grass species and has received increasing attention since seed multiplication is economically relevant for novel grass cultivars to compete in the commercial market. Although seed yield is a complex trait and affected...... by agricultural practices as well as environmental factors, traits related to seed production reveal considerable genetic variation, prerequisite for improvement by direct or indirect selection. This chapter first reports on the biological and physiological basics of the grass reproduction system, then highlights...... important aspects and components affecting the seed yield potential and the agronomic and environmental aspects affecting the utilization and realization of the seed yield potential. Finally, it discusses the potential of plant breeding to sustainably improve total seed yield in fodder and amenity grasses....

Data-driven modeling of nano-nose gas sensor arrays

DEFF Research Database (Denmark)

Alstrøm, Tommy Sonne; Larsen, Jan; Nielsen, Claus Højgård

2010-01-01

We present a data-driven approach to classification of Quartz Crystal Microbalance (QCM) sensor data. The sensor is a nano-nose gas sensor that detects concentrations of analytes down to ppm levels using plasma polymorized coatings. Each sensor experiment takes approximately one hour hence...... the number of available training data is limited. We suggest a data-driven classification model which work from few examples. The paper compares a number of data-driven classification and quantification schemes able to detect the gas and the concentration level. The data-driven approaches are based on state...

Data–driven modeling of nano-nose gas sensor arrays

DEFF Research Database (Denmark)

Alstrøm, Tommy Sonne; Larsen, Jan; Nielsen, Claus Højgård

2010-01-01

We present a data-driven approach to classification of Quartz Crystal Microbalance (QCM) sensor data. The sensor is a nano-nose gas sensor that detects concentrations of analytes down to ppm levels using plasma polymorized coatings. Each sensor experiment takes approximately one hour hence...... the number of available training data is limited. We suggest a data-driven classification model which work from few examples. The paper compares a number of data-driven classification and quantification schemes able to detect the gas and the concentration level. The data-driven approaches are based on state...

Post-ruminal digestibility of crude protein from grass and grass silages in cows

NARCIS (Netherlands)

Cone, J.W.; Gelder, van A.H.; Mathijssen-Kamman, A.A.; Hindle, V.A.

2006-01-01

Grass samples were grown on a clay or sandy soil, fertilised with 150 or 300 kg N/ha per year, and harvested on different days during two consecutive growing seasons. The grass samples were stored frozen or ensiled after wilting to approximately 250 or 450 g DM/kg. The recoveries of crude protein

In silico sequence analysis and homology modeling of predicted beta-amylase 7-like protein in Brachypodium distachyon L.

Directory of Open Access Journals (Sweden)

ERTUĞRUL FILIZ

2014-04-01

Full Text Available Beta-amylase (β-amylase, EC 3.2.1.2 is an enzyme that catalyses hydrolysis of glucosidic bonds in polysaccharides. In this study, we analyzed protein sequence of predicted beta-amylase 7-like protein in Brachypodium distachyon. pI (isoelectric point value was found as 5.23 in acidic character, while the instability index (II was found as 50.28 with accepted unstable protein. The prediction of subcellular localization was revealed that the protein may reside in chloroplast by using CELLO v.2.5. The 3D structure of protein was performed using comparative homology modeling with SWISS-MODEL. The accuracy of the predicted 3D structure was checked using Ramachandran plot analysis showed that 95.4% in favored region. The results of our study contribute to understanding of β-amylase protein structure in grass species and will be scientific base for 3D modeling of beta-amylase proteins in further studies.

Associative diazotrophic bacteria in grass roots and soils from heavy metal contaminated sites.

Science.gov (United States)

Moreira, Fátima M S; Lange, Anderson; Klauberg-Filho, Osmar; Siqueira, José O; Nóbrega, Rafaela S A; Lima, Adriana S

2008-12-01

This work aimed to evaluate density of associative diazotrophic bacteria populations in soil and grass root samples from heavy metal contaminated sites, and to characterize isolates from these populations, both, phenotypically (Zinc, Cadmium and NaCl tolerance in vitro, and protein profiles) and genotypically (16S rDNA sequencing), as compared to type strains of known diazotrophic species. Densities were evaluated by using NFb, Fam and JNFb media, commonly used for enrichment cultures of diazotrophic bacteria. Bacterial densities found in soil and grass root samples from contaminated sites were similar to those reported for agricultural soils. Azospirillum spp. isolates from contaminated sites and type strains from non-contaminated sites varied substantially in their in vitro tolerance to Zn+2 and Cd+2, being Cd+2 more toxic than Zn+2. Among the most tolerant isolates (UFLA 1S, 1R, S181, S34 and S22), some (1R, S34 and S22) were more tolerant to heavy metals than rhizobia from tropical and temperate soils. The majority of the isolates tolerant to heavy metals were also tolerant to salt stress as indicated by their ability to grow in solid medium supplemented with 30 g L(-1) NaCl. Five isolates exhibited high dissimilarity in protein profiles, and the 16S rDNA sequence analysis of two of them revealed new sequences for Azospirillum.

The Sorghum bicolor genome and the diversification of grasses

Energy Technology Data Exchange (ETDEWEB)

Paterson, Andrew H.; Bowers, John E.; Bruggmann, Remy; dubchak, Inna; Grimwood, Jane; Gundlach, Heidrun; Haberer, Georg; Hellsten, Uffe; Mitros, Therese; Poliakov, Alexander; Schmutz, Jeremy; Spannagl, Manuel; Tang, Haibo; Wang, Xiyin; Wicker, Thomas; Bharti, Arvind K.; Chapman, Jarrod; Feltus, F. Alex; Gowik, Udo; Grigoriev, Igor V.; Lyons, Eric; Maher, Christopher A.; Martis, Mihaela; Marechania, Apurva; Otillar, Robert P.; Penning, Bryan W.; Salamov, Asaf. A.; Wang, Yu; Zhang, Lifang; Carpita, Nicholas C.; Freeling, Michael; Gingle, Alan R.; hash, C. Thomas; Keller, Beat; Klein, Patricia; Kresovich, Stephen; McCann, Maureen C.; Ming, Ray; Peterson, Daniel G.; ur-Rahman, Mehboob-; Ware, Doreen; Westhoff, Peter; Mayer, Klaus F. X.; Messing, Joachim; Rokhsar, Daniel S.

2008-08-20

Sorghum, an African grass related to sugar cane and maize, is grown for food, feed, fibre and fuel. We present an initial analysis of the approx730-megabase Sorghum bicolor (L.) Moench genome, placing approx98percent of genes in their chromosomal context using whole-genome shotgun sequence validated by genetic, physical and syntenic information. Genetic recombination is largely confined to about one-third of the sorghum genome with gene order and density similar to those of rice. Retrotransposon accumulation in recombinationally recalcitrant heterochromatin explains the approx75percent larger genome size of sorghum compared with rice. Although gene and repetitive DNA distributions have been preserved since palaeopolyploidization approx70 million years ago, most duplicated gene sets lost one member before the sorghum rice divergence. Concerted evolution makes one duplicated chromosomal segment appear to be only a few million years old. About 24percent of genes are grass-specific and 7percent are sorghum-specific. Recent gene and microRNA duplications may contribute to sorghum's drought tolerance.

Semi-Empirical Models for Buoyancy-Driven Ventilation

DEFF Research Database (Denmark)

Terpager Andersen, Karl

2015-01-01

A literature study is presented on the theories and models dealing with buoyancy-driven ventilation in rooms. The models are categorised into four types according to how the physical process is conceived: column model, fan model, neutral plane model and pressure model. These models are analysed...... and compared with a reference model. Discrepancies and differences are shown, and the deviations are discussed. It is concluded that a reliable buoyancy model based solely on the fundamental flow equations is desirable....

Grass pollen immunotherapy induces highly cross-reactive IgG antibodies to group V allergen from different grass species

NARCIS (Netherlands)

van Ree, R.; Brewczyński, P. Z.; Tan, K. Y.; Mulder-Willems, H. J.; Widjaja, P.; Stapel, S. O.; Aalberse, R. C.; Kroon, A. M.

1995-01-01

Sera from two groups of patients receiving grass pollen immunotherapy were tested on IgG reactivity with group V allergen from six different grass species. One group of patients was treated with a mixture of 10 grass species, and the other with a mixture of five. Only Lolium perenne, Dactylis

Simulating efficiently the evolution of DNA sequences.

Science.gov (United States)

Schöniger, M; von Haeseler, A

1995-02-01

Two menu-driven FORTRAN programs are described that simulate the evolution of DNA sequences in accordance with a user-specified model. This general stochastic model allows for an arbitrary stationary nucleotide composition and any transition-transversion bias during the process of base substitution. In addition, the user may define any hypothetical model tree according to which a family of sequences evolves. The programs suggest the computationally most inexpensive approach to generate nucleotide substitutions. Either reproducible or non-repeatable simulations, depending on the method of initializing the pseudo-random number generator, can be performed. The corresponding options are offered by the interface menu.

Plastid phylogenomics of the cool-season grass subfamily: clarification of relationships among early-diverging tribes.

Science.gov (United States)

Saarela, Jeffery M; Wysocki, William P; Barrett, Craig F; Soreng, Robert J; Davis, Jerrold I; Clark, Lynn G; Kelchner, Scot A; Pires, J Chris; Edger, Patrick P; Mayfield, Dustin R; Duvall, Melvin R

2015-05-04

Whole plastid genomes are being sequenced rapidly from across the green plant tree of life, and phylogenetic analyses of these are increasing resolution and support for relationships that have varied among or been unresolved in earlier single- and multi-gene studies. Pooideae, the cool-season grass lineage, is the largest of the 12 grass subfamilies and includes important temperate cereals, turf grasses and forage species. Although numerous studies of the phylogeny of the subfamily have been undertaken, relationships among some 'early-diverging' tribes conflict among studies, and some relationships among subtribes of Poeae have not yet been resolved. To address these issues, we newly sequenced 25 whole plastomes, which showed rearrangements typical of Poaceae. These plastomes represent 9 tribes and 11 subtribes of Pooideae, and were analysed with 20 existing plastomes for the subfamily. Maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) robustly resolve most deep relationships in the subfamily. Complete plastome data provide increased nodal support compared with protein-coding data alone at nodes that are not maximally supported. Following the divergence of Brachyelytrum, Phaenospermateae, Brylkinieae-Meliceae and Ampelodesmeae-Stipeae are the successive sister groups of the rest of the subfamily. Ampelodesmeae are nested within Stipeae in the plastome trees, consistent with its hybrid origin between a phaenospermatoid and a stipoid grass (the maternal parent). The core Pooideae are strongly supported and include Brachypodieae, a Bromeae-Triticeae clade and Poeae. Within Poeae, a novel sister group relationship between Phalaridinae and Torreyochloinae is found, and the relative branching order of this clade and Aveninae, with respect to an Agrostidinae-Brizinae clade, are discordant between MP and ML/BI trees. Maximum likelihood and Bayesian analyses strongly support Airinae and Holcinae as the successive sister groups of a Dactylidinae

The ModelCC Model-Driven Parser Generator

Directory of Open Access Journals (Sweden)

Fernando Berzal

2015-01-01

Full Text Available Syntax-directed translation tools require the specification of a language by means of a formal grammar. This grammar must conform to the specific requirements of the parser generator to be used. This grammar is then annotated with semantic actions for the resulting system to perform its desired function. In this paper, we introduce ModelCC, a model-based parser generator that decouples language specification from language processing, avoiding some of the problems caused by grammar-driven parser generators. ModelCC receives a conceptual model as input, along with constraints that annotate it. It is then able to create a parser for the desired textual syntax and the generated parser fully automates the instantiation of the language conceptual model. ModelCC also includes a reference resolution mechanism so that ModelCC is able to instantiate abstract syntax graphs, rather than mere abstract syntax trees.

Sequence homology: A poor predictive value for profilins cross-reactivity

Directory of Open Access Journals (Sweden)

Pazouki Nazanin

2005-09-01

Full Text Available Summary Background Profilins are highly cross-reactive allergens which bind IgE antibodies of almost 20% of plant-allergic patients. This study is aimed at investigating cross-reactivity of melon profilin with other plant profilins and the role of the linear and conformational epitopes in human IgE cross-reactivity. Methods Seventeen patients with melon allergy were selected based on clinical history and a positive skin prick test to melon extract. Melon profilin has been cloned and expressed in E. coli. The IgE binding and cross-reactivity of the recombinant profilin were measured by ELISA and inhibition ELISA. The amino acid sequence of melon profilin was compared with other profilin sequences. A combination of chemical cleavage and immunoblotting techniques were used to define the role of conformational and linear epitopes in IgE binding. Comparative modeling was used to construct three-dimensional models of profilins and to assess theoretical impact of amino acid differences on conformational structure. Results Profilin was identified as a major IgE-binding component of melon. Alignment of amino acid sequences of melon profilin with other profilins showed the most identity with watermelon profilin. This melon profilin showed substantial cross-reactivity with the tomato, peach, grape and Cynodon dactylon (Bermuda grass pollen profilins. Cantaloupe, watermelon, banana and Poa pratensis (Kentucky blue grass displayed no notable inhibition. Our experiments also indicated human IgE only react with complete melon profilin. Immunoblotting analysis with rabbit polyclonal antibody shows the reaction of the antibody to the fragmented and complete melon profilin. Although, the well-known linear epitope of profilins were identical in melon and watermelon, comparison of three-dimensional models of watermelon and melon profilins indicated amino acid differences influence the electric potential and accessibility of the solvent-accessible surface of

Grass leaves as potential hominin dietary resources.

Science.gov (United States)

Paine, Oliver C C; Koppa, Abigale; Henry, Amanda G; Leichliter, Jennifer N; Codron, Daryl; Codron, Jacqueline; Lambert, Joanna E; Sponheimer, Matt

2018-04-01

Discussions about early hominin diets have generally excluded grass leaves as a staple food resource, despite their ubiquity in most early hominin habitats. In particular, stable carbon isotope studies have shown a prevalent C 4 component in the diets of most taxa, and grass leaves are the single most abundant C 4 resource in African savannas. Grass leaves are typically portrayed as having little nutritional value (e.g., low in protein and high in fiber) for hominins lacking specialized digestive systems. It has also been argued that they present mechanical challenges (i.e., high toughness) for hominins with bunodont dentition. Here, we compare the nutritional and mechanical properties of grass leaves with the plants growing alongside them in African savanna habitats. We also compare grass leaves to the leaves consumed by other hominoids and demonstrate that many, though by no means all, compare favorably with the nutritional and mechanical properties of known primate foods. Our data reveal that grass leaves exhibit tremendous variation and suggest that future reconstructions of hominin dietary ecology take a more nuanced approach when considering grass leaves as a potential hominin dietary resource. Copyright © 2017. Published by Elsevier Ltd.

Unified Deep Learning Architecture for Modeling Biology Sequence.

Science.gov (United States)

Wu, Hongjie; Cao, Chengyuan; Xia, Xiaoyan; Lu, Qiang

2017-10-09

Prediction of the spatial structure or function of biological macromolecules based on their sequence remains an important challenge in bioinformatics. When modeling biological sequences using traditional sequencing models, characteristics, such as long-range interactions between basic units, the complicated and variable output of labeled structures, and the variable length of biological sequences, usually lead to different solutions on a case-by-case basis. This study proposed the use of bidirectional recurrent neural networks based on long short-term memory or a gated recurrent unit to capture long-range interactions by designing the optional reshape operator to adapt to the diversity of the output labels and implementing a training algorithm to support the training of sequence models capable of processing variable-length sequences. Additionally, the merge and pooling operators enhanced the ability to capture short-range interactions between basic units of biological sequences. The proposed deep-learning model and its training algorithm might be capable of solving currently known biological sequence-modeling problems through the use of a unified framework. We validated our model on one of the most difficult biological sequence-modeling problems currently known, with our results indicating the ability of the model to obtain predictions of protein residue interactions that exceeded the accuracy of current popular approaches by 10% based on multiple benchmarks.

Lol p XI, a new major grass pollen allergen, is a member of a family of soybean trypsin inhibitor-related proteins.

Science.gov (United States)

van Ree, R; Hoffman, D R; van Dijk, W; Brodard, V; Mahieu, K; Koeleman, C A; Grande, M; van Leeuwen, W A; Aalberse, R C

1995-05-01

Monoclonal antibodies were obtained against an unknown allergen from Lolium perenne grass pollen. The allergen had an apparent molecular mass of 18 kd on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Earlier immunoblotting studies had shown that carbohydrate-specific IgG antibodies recognize an antigen of similar size. We sought to characterize the allergen biochemically and immunologically. The amino acid sequence of the allergen was determined by automated Edman degradation, and its monosaccharide composition was determined by gas chromatographic analysis. A panel of 270 grass pollen-positive sera was assessed in a RAST with the purified allergen. Protease digestion (proteinase K) and chemical deglycosylation (trifluoromethane sulfonic acid) were used to distinguish between carbohydrate and peptide epitopes for IgE antibodies. The allergen was shown to be a glycoprotein with a molecular mass of 16 kd, of which 8% is carbohydrate. Its amino acid sequence shares 32% homology with soybean trypsin inhibitor (Kunitz) but lacks its active site. No homology was found with known grass pollen allergens, hence it was designated Lol p XI. A high degree of homology (44%) was found with a tree pollen allergen, Ole e I, the major allergen of olive pollen. More than 65% of grass pollen-positive sera had IgE against Lol p XI. IgE reactivity was demonstrated both with the carbohydrate moiety and the peptide backbone. Lol p XI is a new major grass pollen allergen carrying an IgE-binding carbohydrate determinant. Lol p XI is structurally related to the major allergen from olive pollen.

Data-Driven Problems in Elasticity

Science.gov (United States)

Conti, S.; Müller, S.; Ortiz, M.

2018-01-01

We consider a new class of problems in elasticity, referred to as Data-Driven problems, defined on the space of strain-stress field pairs, or phase space. The problem consists of minimizing the distance between a given material data set and the subspace of compatible strain fields and stress fields in equilibrium. We find that the classical solutions are recovered in the case of linear elasticity. We identify conditions for convergence of Data-Driven solutions corresponding to sequences of approximating material data sets. Specialization to constant material data set sequences in turn establishes an appropriate notion of relaxation. We find that relaxation within this Data-Driven framework is fundamentally different from the classical relaxation of energy functions. For instance, we show that in the Data-Driven framework the relaxation of a bistable material leads to material data sets that are not graphs.

Advances in Setaria genomics for genetic improvement of cereals and bioenergy grasses.

Science.gov (United States)

Muthamilarasan, Mehanathan; Prasad, Manoj

2015-01-01

Recent advances in Setaria genomics appear promising for genetic improvement of cereals and biofuel crops towards providing multiple securities to the steadily increasing global population. The prominent attributes of foxtail millet (Setaria italica, cultivated) and green foxtail (S. viridis, wild) including small genome size, short life-cycle, in-breeding nature, genetic close-relatedness to several cereals, millets and bioenergy grasses, and potential abiotic stress tolerance have accentuated these two Setaria species as novel model system for studying C4 photosynthesis, stress biology and biofuel traits. Considering this, studies have been performed on structural and functional genomics of these plants to develop genetic and genomic resources, and to delineate the physiology and molecular biology of stress tolerance, for the improvement of millets, cereals and bioenergy grasses. The release of foxtail millet genome sequence has provided a new dimension to Setaria genomics, resulting in large-scale development of genetic and genomic tools, construction of informative databases, and genome-wide association and functional genomic studies. In this context, this review discusses the advancements made in Setaria genomics, which have generated a considerable knowledge that could be used for the improvement of millets, cereals and biofuel crops. Further, this review also shows the nutritional potential of foxtail millet in providing health benefits to global population and provides a preliminary information on introgressing the nutritional properties in graminaceous species through molecular breeding and transgene-based approaches.

Molecular cloning, expression and immunological characterisation of Lol p 5C, a novel allergen isoform of rye grass pollen demonstrating high IgE reactivity.

Science.gov (United States)

Suphioglu, C; Mawdsley, D; Schäppi, G; Gruehn, S; de Leon, M; Rolland, J M; O'Hehir, R E

1999-12-03

A novel isoform of a major rye grass pollen allergen Lol p 5 was isolated from a cDNA expression library. The new isoform, Lol p 5C, shares 95% amino acid sequence identity with Lol p 5A. Both isoforms demonstrated shared antigenic activity but different allergenic activities. Recombinant Lol p 5C demonstrated 100% IgE reactivity in 22 rye grass pollen sensitive patients. In comparison, recombinant Lol p 5A showed IgE reactivity in less than 64% of the patients. Therefore, Lol p 5C represents a novel and highly IgE-reactive isoform allergen of rye grass pollen.

EFFECT OF MULCH AND MIXED CROPPING GRASS - LEGUME AT SALINE SOIL ON GROWTH, FORAGE YIELD AND NUTRITIONAL QUALITY OF GUINEA GRASS

Directory of Open Access Journals (Sweden)

F. Kusmiyati

2014-10-01

Full Text Available The research was conducted to evaluate the effect of mulch and mixed cropping grass – legume atsaline soil on growth, forage yield and nutritional quality of guinea grass. Saline soil used in thisresearch was classified into strongly saline soil with low soil fertility. The research was arrranged inrandomized complete block design with 3 blocks. The treatments were : M1 = guinea grassmonoculture, without mulch; M2 = guinea grass monoculture, 3 ton/ha mulch; M3 = guinea grassmonoculture, 6 ton/ha mulch, M4 = mixed cropping grass with Sesbania grandiflora, without mulch;M5 = mixed cropping grass with Sesbania grandiflora, 3 ton/ha mulch; M6 = mixed cropping grass withSesbania grandiflora, 6 ton/ha mulch. Data were analyzed using analysis of variance, then followed byDuncan's Multiple Range Test. The highest soil moisture content was achieved at mixed cropping grasslegumewith 6 ton/ha of mulch. The effect of mulch at saline soil significantly increased plant growth,forage yield and nutritional quality of guinea grass. Application of 3 ton/ha mulch increased plantgrowth, forage yield and nutritional quality of guinea grass. Plant growth, forage yield and nutritionalquality of guinea grass were not affected by monoculture or mixed cropping with Sesbania at saline soil.

Gene discovery and molecular marker development, based on high-throughput transcript sequencing of Paspalum dilatatum Poir.

Directory of Open Access Journals (Sweden)

Andrea Giordano

Full Text Available BACKGROUND: Paspalum dilatatum Poir. (common name dallisgrass is a native grass species of South America, with special relevance to dairy and red meat production. P. dilatatum exhibits higher forage quality than other C4 forage grasses and is tolerant to frost and water stress. This species is predominantly cultivated in an apomictic monoculture, with an inherent high risk that biotic and abiotic stresses could potentially devastate productivity. Therefore, advanced breeding strategies that characterise and use available genetic diversity, or assess germplasm collections effectively are required to deliver advanced cultivars for production systems. However, there are limited genomic resources available for this forage grass species. RESULTS: Transcriptome sequencing using second-generation sequencing platforms has been employed using pooled RNA from different tissues (stems, roots, leaves and inflorescences at the final reproductive stage of P. dilatatum cultivar Primo. A total of 324,695 sequence reads were obtained, corresponding to c. 102 Mbp. The sequences were assembled, generating 20,169 contigs of a combined length of 9,336,138 nucleotides. The contigs were BLAST analysed against the fully sequenced grass species of Oryza sativa subsp. japonica, Brachypodium distachyon, the closely related Sorghum bicolor and foxtail millet (Setaria italica genomes as well as against the UniRef 90 protein database allowing a comprehensive gene ontology analysis to be performed. The contigs generated from the transcript sequencing were also analysed for the presence of simple sequence repeats (SSRs. A total of 2,339 SSR motifs were identified within 1,989 contigs and corresponding primer pairs were designed. Empirical validation of a cohort of 96 SSRs was performed, with 34% being polymorphic between sexual and apomictic biotypes. CONCLUSIONS: The development of genetic and genomic resources for P. dilatatum will contribute to gene discovery and expression

Genotyping-by-sequencing data of 272 crested wheatgrass (Agropyron cristatum genotypes

Directory of Open Access Journals (Sweden)

Pingchuan Li

2017-12-01

Full Text Available Crested wheatgrass [Agropyron cristatum L. (Gaertn.] is an important cool-season forage grass widely used for early spring grazing. However, the genomic resources for this non-model plant are still lacking. Our goal was to generate the first set of next generation sequencing data using the genotyping-by-sequencing technique. A total of 272 crested wheatgrass plants representing seven breeding lines, five cultivars and five geographically diverse accessions were sequenced with an Illumina MiSeq instrument. These sequence datasets were processed using different bioinformatics tools to generate contigs for diploid and tetraploid plants and SNPs for diploid plants. Together, these genomic resources form a fundamental basis for genomic studies of crested wheatgrass and other wheatgrass species. The raw reads were deposited into Sequence Read Archive (SRA database under NCBI accession SRP115373 (https://www.ncbi.nlm.nih.gov/sra?term=SRP115373 and the supplementary datasets are accessible in Figshare (10.6084/m9.figshare.5345092. Keywords: Crested wheatgrass, Genotyping-by-sequencing, Diploid, Tetraploid, Raw sequence data

Evaluating grasses as a long-term energy resource

Energy Technology Data Exchange (ETDEWEB)

Christian, D.G.; Riche, A.B.

2001-07-01

The work reported here is part of an ongoing project that aims to evaluate the yields of three perennial rhizomatous grasses and determine their suitability as bio-energy crops. The work began in 1993, and the grasses have been monitored continuously since that time. This report covers the period 1999/2000, and includes: the performance of plots of the energy grasses Miscanthus grass, switchgrass and reed canary grass seven years after they were planted; assessment of the yield of 15 genotypes of Miscanthus planted in 1997; monitoring all the species throughout the growing period for the presence of pests, weeds and diseases; measurement of the amount of nitrate leached from below Miscanthus grass; investigating the occurrence of lodging in switchgrass. (Author)

Recombinant pollen allergens from Dactylis glomerata: preliminary evidence that human IgE cross-reactivity between Dac g II and Lol p I/II is increased following grass pollen immunotherapy.

Science.gov (United States)

Roberts, A M; Van Ree, R; Cardy, S M; Bevan, L J; Walker, M R

1992-07-01

We previously described the isolation of three identical complementary DNA (cDNA) clones, constructed from Orchard/Cocksfoot grass (Dactylis glomerata) anther messenger RNA (mRNA), expressing a 140,000 MW beta-galactosidase fusion protein recognized by IgE antibodies in atopic sera. Partial nucleotide sequencing and inferred amino acid sequence showed greater than 90% homology with the group II allergen from Lolium perenne (Lol II) indicating they encode the group II equivalent, Dac g II. Western blot immunoprobing of recombinant lysates with rabbit polyclonal, mouse monoclonal and human polyclonal antisera demonstrates immunological identity between recombinant Dac g II, Lol p I and Lol p II. Similar cross-identity is observed with pollen extracts from three other grass species: Festuca rubra, Phleum pratense and Anthoxanthum odoratum. Recombinant Dac g II was recognized by species- and group-cross-reactive human IgE antibodies in 33% (4/12) of sera randomly selected from grass-sensitive individuals and in 67% (14/21) of sera from patients receiving grass pollen immunotherapy, whilst 0/4 sera from patients receiving venom immunotherapy alone contained Dac g II cross-reactive IgE. Cross-reactive IgG4 antibodies were detectable in 95% of sera from grass pollen immunotherapy patients. These preliminary data suggest that conventional grass pollen allergoid desensitization immunotherapy may induce IgE responses to a cross-reactive epitope(s) co-expressed by grass pollen groups I and II (and possibly group III) allergens.

Managing business compliance using model-driven security management

Science.gov (United States)

Lang, Ulrich; Schreiner, Rudolf

Compliance with regulatory and governance standards is rapidly becoming one of the hot topics of information security today. This is because, especially with regulatory compliance, both business and government have to expect large financial and reputational losses if compliance cannot be ensured and demonstrated. One major difficulty of implementing such regulations is caused the fact that they are captured at a high level of abstraction that is business-centric and not IT centric. This means that the abstract intent needs to be translated in a trustworthy, traceable way into compliance and security policies that the IT security infrastructure can enforce. Carrying out this mapping process manually is time consuming, maintenance-intensive, costly, and error-prone. Compliance monitoring is also critical in order to be able to demonstrate compliance at any given point in time. The problem is further complicated because of the need for business-driven IT agility, where IT policies and enforcement can change frequently, e.g. Business Process Modelling (BPM) driven Service Oriented Architecture (SOA). Model Driven Security (MDS) is an innovative technology approach that can solve these problems as an extension of identity and access management (IAM) and authorization management (also called entitlement management). In this paper we will illustrate the theory behind Model Driven Security for compliance, provide an improved and extended architecture, as well as a case study in the healthcare industry using our OpenPMF 2.0 technology.

Distributed simulation a model driven engineering approach

CERN Document Server

Topçu, Okan; Oğuztüzün, Halit; Yilmaz, Levent

2016-01-01

Backed by substantive case studies, the novel approach to software engineering for distributed simulation outlined in this text demonstrates the potent synergies between model-driven techniques, simulation, intelligent agents, and computer systems development.

Genetic compatibility determines endophyte-grass combinations.

Directory of Open Access Journals (Sweden)

Kari Saikkonen

Full Text Available Even highly mutually beneficial microbial-plant interactions, such as mycorrhizal- and rhizobial-plant exchanges, involve selfishness, cheating and power-struggles between the partners, which depending on prevailing selective pressures, lead to a continuum of interactions from antagonistic to mutualistic. Using manipulated grass-endophyte combinations in a five year common garden experiment, we show that grass genotypes and genetic mismatches constrain genetic combinations between the vertically (via host seeds transmitted endophytes and the out-crossing host, thereby reducing infections in established grass populations. Infections were lost in both grass tillers and seedlings in F(1 and F(2 generations, respectively. Experimental plants were collected as seeds from two different environments, i.e., meadows and nearby riverbanks. Endophyte-related benefits to the host included an increased number of inflorescences, but only in meadow plants and not until the last growing season of the experiment. Our results illustrate the importance of genetic host specificity and trans-generational maternal effects on the genetic structure of a host population, which act as destabilizing forces in endophyte-grass symbioses. We propose that (1 genetic mismatches may act as a buffering mechanism against highly competitive endophyte-grass genotype combinations threatening the biodiversity of grassland communities and (2 these mismatches should be acknowledged, particularly in breeding programmes aimed at harnessing systemic and heritable endophytes to improve the agriculturally valuable characteristics of cultivars.

Mechanical pretreatment at harvesting increases the bioenergy output from marginal land grasses

DEFF Research Database (Denmark)

Tsapekos, Panagiotis; Kougias, Panagiotis; Egelund, H.

2017-01-01

Meadow grass has recently gained increased attention as a substrate for full-scale biogas reactors. However, to increase its biodegradability, pretreatment is needed. In the present work, different harvesting machines were compared in order to assess their effect on biogas production. Specifically...... the methane yield of meadow grass by 20% compared to a classical Disc-mower. The positive effect was also validated by three kinetic model equations. The modified Gompertz model was the most capable of determining the kinetics of anaerobic digestion process, pointing out also the superiority of Excoriator...

Fluid-driven normal faulting earthquake sequences in the Taiwan orogen

Science.gov (United States)

Wang, Ling-hua; Rau, Ruey-Juin; Lee, En-Jui

2017-04-01

Seismicity in the Central Range of Taiwan shows normal faulting mechanisms with T-axes directing NE, subparallel to the strike of the mountain belt. We analyze earthquake sequences occurred within 2012-2015 in the Nanshan area of northern Taiwan which indicating swarm behavior and migration characteristics. We select events larger than 2.0 from Central Weather Bureau catalog and use the double-difference relocation program hypoDD with waveform cross-correlation in the Nanshan area. We obtained a final count of 1406 (95%) relocated earthquakes. Moreover, we compute focal mechanisms using USGS program HASH by P-wave first motion and S/P ratio picking and 114 fault plane solutions with M 3.0-5.87 were determined. To test for fluid diffusion, we model seismicity using the equation of Shapiro et al. (1997) by fitting earthquake diffusing rate D during the migration period. According to the relocation result, seismicity in the Taiwan orogenic belt present mostly N25E orientation parallel to the mountain belt with the same direction of the tension axis. In addition, another seismic fracture depicted by seismicity rotated 35 degree counterclockwise to the NW direction. Nearly all focal mechanisms are normal fault type. In the Nanshan area, events show N10W distribution with a focal depth range from 5-12 km and illustrate fault plane dipping about 45-60 degree to SW. Three months before the M 5.87 mainshock which occurred in March, 2013, there were some foreshock events occurred in the shallow part of the fault plane of the mainshock. Half a year following the mainshock, earthquakes migrated to the north and south, respectively with processes matched the diffusion model at a rate of 0.2-0.6 m2/s. This migration pattern and diffusion rate offer an evidence of 'fluid-driven' process in the fault zone. We also find the upward migration of earthquakes in the mainshock source region. These phenomena are likely caused by the opening of the permeable conduit due to the M 5

Sonoran Desert ecosystem transformation by a C4 grass without the grass/fire cycle

Science.gov (United States)

Olsson, Aaryn D.; Betancourt, Julio; McClaran, Mitchel P.; Marsh, Stuart E.

2012-01-01

Aim Biological invasions facilitate ecosystem transformation by altering the structure and function, diversity, dominance and disturbance regimes. A classic case is the grass–fire cycle in which grass invasion increases the frequency, scale and/or intensity of wildfires and promotes the continued invasion of invasive grasses. Despite wide acceptance of the grass–fire cycle, questions linger about the relative roles that interspecific plant competition and fire play in ecosystem transformations. Location Sonoran Desert Arizona Upland of the Santa Catalina Mountains, Arizona, USA. Methods We measured species cover, density and saguaro (Carnegiea gigantea) size structure along gradients of Pennisetum ciliare invasion at 10 unburned/ungrazed P. ciliare patches. Regression models quantified differences in diversity, cover and density with respect to P. ciliare cover, and residence time and a Fisher's exact test detected demographic changes in saguaro populations. Because P. ciliare may have initially invaded locations that were both more invasible and less diverse, we ran analyses with and without the plots in which initial infestations were located. Results Richness and diversity decreased with P. ciliare cover as did cover and density of most dominant species. Richness and diversity declined with increasing time since invasion, suggesting an ongoing transformation. The proportion of old-to-young Carnegiea gigantea was significantly lower in plots with dominant P. ciliare cover. Main conclusions Rich desert scrub (15–25 species per plot) was transformed into depauperate grassland (2–5 species per plot) within 20 years following P. ciliare invasion without changes to the fire regime. While the onset of a grass–fire cycle may drive ecosystem change in the later stages and larger scales of grass invasions of arid lands, competition by P. ciliare can drive small-scale transformations earlier in the invasion. Linking competition-induced transformation rates with

Preliminary Results of Clover and Grass Coverage and Total Dry Matter Estimation in Clover-Grass Crops Using Image Analysis

Directory of Open Access Journals (Sweden)

Anders K. Mortensen

2017-12-01

Full Text Available The clover-grass ratio is an important factor in composing feed ratios for livestock. Cameras in the field allow the user to estimate the clover-grass ratio using image analysis; however, current methods assume the total dry matter is known. This paper presents the preliminary results of an image analysis method for non-destructively estimating the total dry matter of clover-grass. The presented method includes three steps: (1 classification of image illumination using a histogram of the difference in excess green and excess red; (2 segmentation of clover and grass using edge detection and morphology; and (3 estimation of total dry matter using grass coverage derived from the segmentation and climate parameters. The method was developed and evaluated on images captured in a clover-grass plot experiment during the spring growing season. The preliminary results are promising and show a high correlation between the image-based total dry matter estimate and the harvested dry matter ( R 2 = 0.93 with an RMSE of 210 kg ha − 1 .

Tree-grass interaction dynamics and pulsed fires : mathematical and numerical studies

OpenAIRE

Tamen, A. T.; Dumont, Y.; Tewa, J. J.; Bowong, S.; Couteron, Pierre

2016-01-01

Savannas are dynamical systems where grasses and trees can either dominate or coexist. Fires are known to be central in the functioning of the savanna biome although their characteristics are expected to vary along the rainfall gradients as observed in Sub-Saharan Africa. In this paper, we model the tree-grass dynamics using impulsive differential equations that consider fires as discrete events. This framework allows us to carry out a comprehensive qualitative mathematical analysis that reve...

Tree-Grass interactions dynamics and Pulse Fires: mathematical and numerical studies

OpenAIRE

Tamen, A. Tchuinté; Dumont, Y.; Bowong, S.; Tewa, J. J.; Couteron, P.

2015-01-01

Savannas are dynamical systems where grasses and trees can either dominate or coexist. Fires are known to be central in the functioning of the savanna biome though their characteristics are expected to vary along the rainfall gradients as observed in Sub-Saharan Africa. In this paper, we model the tree-grass dynamics using impulsive differential equations that consider fires as discrete events. This framework allows us to carry out a comprehensive qualitative mathematical analysis that reveal...

Data mining, knowledge discovery and data-driven modelling

NARCIS (Netherlands)

Solomatine, D.P.; Velickov, S.; Bhattacharya, B.; Van der Wal, B.

2003-01-01

The project was aimed at exploring the possibilities of a new paradigm in modelling - data-driven modelling, often referred as "data mining". Several application areas were considered: sedimentation problems in the Port of Rotterdam, automatic soil classification on the basis of cone penetration

Development of SSR Markers Linked to Low Hydrocyanic Acid Content in Sorghum-Sudan Grass Hybrid Based on BSA Method.

Science.gov (United States)

Xiao-Xia, Yu; Zhi-Hua, Liu; Zhuo, Yu; Yue, Shi; Xiao-Yu, Li

2016-01-01

Sorghum-Sudan grass hybrid containing high hydrocyanic acid content can cause hydrocyanic acid poisoning to the livestock and limit the popularization of this forage crop. Molecular markers associated with low hydrocyanic acid content can speed up the process of identification of genotypes with low hydrocyanic acid content. In the present study, 11 polymorphic SSR primers were screened and used for bulked segregant analysis and single marker analysis. Three SSR markers Xtxp7230, Xtxp7375 and Bnlg667960 associated with low hydrocyanic acid content were rapidly identified by BSA. In single marker analysis, six markers Xtxp7230, Xtxp7375, Bnlg667960, Xtxp67-11, Xtxp295-7 and Xtxp12-9 were linked to low hydrocyanic acid content, which explained the proportion of phenotypic variation from 7.6 % to 41.2 %. The markers identified by BSA were also verified by single marker analysis. The three SSR marker bands were then cloned and sequenced for sequence homology analysis in NCBI. It is the first report on the development of molecular markers associated with low hydrocyanic acid content in sorghum- Sudan grass hybrid. These markers will be useful for genetic improvement of low hydrocyanic acid sorghum-Sudan grass hybrid by marker-assisted breeding.

Menthor Editor: An Ontology-Driven Conceptual Modeling Platform

NARCIS (Netherlands)

Moreira, João Luiz; Sales, Tiago Prince; Guerson, John; Braga, Bernardo F.B; Brasileiro, Freddy; Sobral, Vinicius

2016-01-01

The lack of well-founded constructs in ontology tools can lead to the construction of non-intended models. In this demonstration we present the Menthor Editor, an ontology-driven conceptual modelling platform which incorporates the theories of the Unified Foundational Ontology (UFO). We illustrate

Grass Biomethane for Agriculture and Energy

DEFF Research Database (Denmark)

Korres, N.E.; Thamsiriroj, T.; Smith, B.

2011-01-01

have advanced the role of grassland as a renewable source of energy in grass biomethane production with various environmental and socio-economic benefits. It is underlined that the essential question whether the gaseous biofuel meets the EU sustainability criteria of 60% greenhouse gas emission savings...... by 2020 can be met since savings up to 89.4% under various scenarios can be achieved. Grass biomethane production compared to other liquid biofuels either when these are produced by indigenous of imported feedstocks is very promising. Grass biomethane, given the mature and well known technology...

Quantitative system validation in model driven design

DEFF Research Database (Denmark)

Hermanns, Hilger; Larsen, Kim Guldstrand; Raskin, Jean-Francois

2010-01-01

The European STREP project Quasimodo1 develops theory, techniques and tool components for handling quantitative constraints in model-driven development of real-time embedded systems, covering in particular real-time, hybrid and stochastic aspects. This tutorial highlights the advances made, focus...

Determining the regional potential for a grass biomethane industry

International Nuclear Information System (INIS)

Smyth, Beatrice M.; Smyth, Henry; Murphy, Jerry D.

2011-01-01

Research highlights: → We identified assessment criteria for determining the regional potential for grass biomethane. → Grass biomethane is distributed via the natural gas grid. → The criteria include: land use; grass yields; gas grid coverage; availability of co-substrates. → The county with the highest potential can fuel 50% of cars or supply 130% of domestic gas consumption. - Abstract: Grass biogas/biomethane has been put forward as a renewable energy solution and it has been shown to perform well in terms of energy balance, greenhouse gas emissions and policy constraints. Biofuel and energy crop solutions are country-specific and grass biomethane has strong potential in countries with temperate climates and a high proportion of grassland, such as Ireland. For a grass biomethane industry to develop in a country, suitable regions (i.e. those with the highest potential) must be identified. In this paper, factors specifically related to the assessment of the potential of a grass biogas/biomethane industry are identified and analysed. The potential for grass biogas and grass biomethane is determined on a county-by-county basis using multi-criteria decision analysis. Values are assigned to each county and ratings and weightings applied to determine the overall county potential. The potential for grass biomethane with co-digestion of slaughter waste (belly grass) is also determined. The county with the highest potential (Limerick) is analysed in detail and is shown to have ready potential for production of gaseous biofuel to meet either 50% of the vehicle fleet or 130% of the domestic natural gas demand, through 25 facilities at a scale of ca. 30 kt yr -1 of feedstock. The assessment factors developed in this paper can be used in other resource studies into grass biomethane or other energy crops.

[Mechanisms of grass in slope erosion control in Loess sandy soil region of Northwest China].

Science.gov (United States)

Zhao, Chun-Hong; Gao, Jian-En; Xu, Zhen

2013-01-01

By adopting the method of simulated precipitation and from the viewpoint of slope hydrodynamics, in combining with the analysis of soil resistance to erosion, a quantitative study was made on the mechanisms of grass in controlling the slope erosion in the cross area of wind-water erosion in Loess Plateau of Northwest China under different combinations of rainfall intensity and slope gradient, aimed to provide basis to reveal the mechanisms of vegetation in controlling soil erosion and to select appropriate vegetation for the soil and water conservation in Loess Plateau. The grass Astragalus adsurgens with the coverage about 40% could effectively control the slope erosion. This grass had an efficiency of more than 70% in reducing sediment, and the grass root had a greater effect than grass canopy. On bare slope and on the slopes with the grass plant or only the grass root playing effect, there existed a functional relation between the flow velocity on the slopes and the rainfall intensity and slope gradient (V = DJ(0.33 i 0.5), where V is flow velocity, D is the comprehensive coefficient which varies with different underlying surfaces, i is rainfall intensity, and J is slope gradient). Both the grass root and the grass canopy could markedly decrease the flow velocity on the slopes, and increase the slope resistance, but the effect of grass root in decreasing flow velocity was greater while the effect in increasing resistance was smaller than that of grass canopy. The effect of grass root in increasing slope resistance was mainly achieved by increasing the sediment grain resistance, while the effect of canopy was mainly achieved by increasing the slope form resistance and wave resistance. The evaluation of the soil resistance to erosion by using a conceptual model of sediment generation by overland flow indicated that the critical shear stress value of bare slope and of the slopes with the grass plant or only the grass root playing effect was 0.533, 1.672 and 0

A neurocomputational model of automatic sequence production.

Science.gov (United States)

Helie, Sebastien; Roeder, Jessica L; Vucovich, Lauren; Rünger, Dennis; Ashby, F Gregory

2015-07-01

Most behaviors unfold in time and include a sequence of submovements or cognitive activities. In addition, most behaviors are automatic and repeated daily throughout life. Yet, relatively little is known about the neurobiology of automatic sequence production. Past research suggests a gradual transfer from the associative striatum to the sensorimotor striatum, but a number of more recent studies challenge this role of the BG in automatic sequence production. In this article, we propose a new neurocomputational model of automatic sequence production in which the main role of the BG is to train cortical-cortical connections within the premotor areas that are responsible for automatic sequence production. The new model is used to simulate four different data sets from human and nonhuman animals, including (1) behavioral data (e.g., RTs), (2) electrophysiology data (e.g., single-neuron recordings), (3) macrostructure data (e.g., TMS), and (4) neurological circuit data (e.g., inactivation studies). We conclude with a comparison of the new model with existing models of automatic sequence production and discuss a possible new role for the BG in automaticity and its implication for Parkinson's disease.

Post-treatment efficacy of discontinuous treatment with 300IR 5-grass pollen sublingual tablet in adults with grass pollen-induced allergic rhinoconjunctivitis

DEFF Research Database (Denmark)

Didier, A; Malling, H-J; Worm, Marcel

2013-01-01

Sustained efficacy over three pollen seasons of pre- and co-seasonal treatment with 300IR 5-grass pollen sublingual tablet has been demonstrated in adults with moderate-severe grass pollen-associated allergic rhinoconjunctivitis.......Sustained efficacy over three pollen seasons of pre- and co-seasonal treatment with 300IR 5-grass pollen sublingual tablet has been demonstrated in adults with moderate-severe grass pollen-associated allergic rhinoconjunctivitis....

Immunochemical Analysis of Paxilline and Ergot Alkaloid Mycotoxins in Grass Seeds and Plants.

Science.gov (United States)

Bauer, Julia I; Gross, Madeleine; Cramer, Benedikt; Humpf, Hans-Ulrich; Hamscher, Gerd; Usleber, Ewald

2018-01-10

Limited availability of toxin standards for lolitrem B and ergovaline impedes routine control of grasses for endophyte toxins. This study aimed at assessing the applicability of an enzyme immunoassay (EIA) for the indole-diterpene mycotoxin paxilline, in combination with a generic EIA for ergot alkaloids, as alternative parameters for screening purposes. Analysis of grass seeds and model pastures of four different grass species showed that both EIAs yielded highly positive results for paxilline and ergot alkaloids in perennial ryegrass seeds. Furthermore, evidence for natural occurrence of paxilline in grass in Germany was obtained. High performance liquid chromatography-tandem mass spectrometry analysis qualitatively confirmed the paxilline EIA results but showed that paxilline analogues 1'-O-acetylpaxilline and 13-desoxypaxilline were the predominant compounds in seeds and grass. In the absence of easily accessible reference standards for specific analysis of some major endophyte toxins, analysis of paxilline and ergot alkaloids by EIA may be suitable substitute parameters. The major advantage of this approach is its ease of use and speed, providing an analytical tool which could enhance routine screening for endophyte toxins in pasture.

Mathematical modeling of compression processes in air-driven boosters

International Nuclear Information System (INIS)

Li Zeyu; Zhao Yuanyang; Li Liansheng; Shu Pengcheng

2007-01-01

The compressed air in normal pressure is used as the source of power of the air-driven booster. The continuous working of air-driven boosters relies on the difference of surface area between driven piston and driving piston, i.e., the different forces acting on the pistons. When the working surface area of the driving piston for providing power is greater than that of the driven piston for compressing gas, the gas in compression chamber will be compressed. On the basis of the first law of thermodynamics, the motion regulation of piston is analyzed and the mathematical model of compression processes is set up. Giving a calculating example, the vary trends of gas pressure and pistons' move in working process of booster have been gotten. The change of parameters at different working conditions is also calculated and compared. And the corresponding results can be referred in the design of air-driven boosters

Viral pathogen production in a wild grass host driven by host growth and soil nitrogen.

Science.gov (United States)

Whitaker, Briana K; Rúa, Megan A; Mitchell, Charles E

2015-08-01

Nutrient limitation is a basic ecological constraint that has received little attention in studies on virus production and disease dynamics. Nutrient availability could directly limit the production of viral nucleic acids and proteins, or alternatively limit host growth and thus indirectly limit metabolic pathways necessary for viral replication. In order to compare direct and indirect effects of nutrient limitation on virus production within hosts, we manipulated soil nitrogen (N) and phosphorus (P) availability in a glasshouse for the wild grass host Bromus hordeaceus and the viral pathogen Barley yellow dwarf virus-PAV. We found that soil N additions increased viral concentrations within host tissues, and the effect was mediated by host growth. Specifically, in statistical models evaluating the roles of host biomass production, leaf N and leaf P, viral production depended most strongly on host biomass, rather than the concentration of either nutrient. Furthermore, at low soil N, larger plants supported greater viral concentrations than smaller ones, whereas at high N, smaller plants supported greater viral concentrations. Our results suggest that enhanced viral productivity under N enrichment is an indirect consequence of nutrient stimulation to host growth rate. Heightened pathogen production in plants has important implications for a world facing increasing rates of nutrient deposition. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Grasses for energy production: hydrological guidelines

Energy Technology Data Exchange (ETDEWEB)

Hall, R.L.

2003-07-01

This report provides hydrological guidelines for growers, land and water resource managers, environmental groups and other parties interested in utilising grasses for energy production. The aim of the report is to help interested parties decide if a location is suitable for planting energy grasses by considering whether potential hydrological impacts will have an adverse effect on crop productivity and yield. The guidelines consider: the water use of energy grasses compared with other crops; the factors governing water use; the water requirements for a productive crop; and the likely impacts on the availability and quantity of water. The report points out that there are still gaps in our knowledge of the processes controlling the water use and growth of energy grasses and notes that, in some situations, there will be considerable uncertainty in predictions of water use and the magnitude of the associated hydrological impacts.

Genetics and physiology of cell wall polysaccharides in the model C4 grass, Setaria viridis spp.

Science.gov (United States)

Ermawar, Riksfardini A; Collins, Helen M; Byrt, Caitlin S; Henderson, Marilyn; O'Donovan, Lisa A; Shirley, Neil J; Schwerdt, Julian G; Lahnstein, Jelle; Fincher, Geoffrey B; Burton, Rachel A

2015-10-02

Setaria viridis has emerged as a model species for the larger C4 grasses. Here the cellulose synthase (CesA) superfamily has been defined, with an emphasis on the amounts and distribution of (1,3;1,4)-β-glucan, a cell wall polysaccharide that is characteristic of the grasses and is of considerable value for human health. Orthologous relationship of the CesA and Poales-specific cellulose synthase-like (Csl) genes among Setaria italica (Si), Sorghum bicolor (Sb), Oryza sativa (Os), Brachypodium distachyon (Bradi) and Hordeum vulgare (Hv) were compared using bioinformatics analysis. Transcription profiling of Csl gene families, which are involved in (1,3;1,4)-β-glucan synthesis, was performed using real-time quantitative PCR (Q-PCR). The amount of (1,3;1,4)-β-glucan was measured using a modified Megazyme assay. The fine structures of the (1,3;1,4)-β-glucan, as denoted by the ratio of cellotriosyl to cellotetraosyl residues (DP3:DP4 ratio) was assessed by chromatography (HPLC and HPAEC-PAD). The distribution and deposition of the MLG was examined using the specific antibody BG-1 and captured using fluorescence and transmission electron microscopy (TEM). The cellulose synthase gene superfamily contains 13 CesA and 35 Csl genes in Setaria. Transcript profiling of CslF, CslH and CslJ gene families across a vegetative tissue series indicated that SvCslF6 transcripts were the most abundant relative to all other Csl transcripts. The amounts of (1,3;1,4)-β-glucan in Setaria vegetative tissues ranged from 0.2% to 2.9% w/w with much smaller amounts in developing grain (0.003% to 0.013% w/w). In general, the amount of (1,3;1,4)-β-glucan was greater in younger than in older tissues. The DP3:DP4 ratios varied between tissue types and across developmental stages, and ranged from 2.4 to 3.0:1. The DP3:DP4 ratios in developing grain ranged from 2.5 to 2.8:1. Micrographs revealing the distribution of (1,3;1,4)-β-glucan in walls of different cell types and the data were

Towards a sufficiency-driven business model : Experiences and opportunities

NARCIS (Netherlands)

Bocken, N.M.P.; Short, SW

2016-01-01

Business model innovation is an important lever for change to tackle pressing sustainability issues. In this paper, ‘sufficiency’ is proposed as a driver of business model innovation for sustainability. Sufficiency-driven business models seek to moderate overall resource consumption by curbing

Improving our understanding of environmental controls on the distribution of C3 and C4 grasses.

Science.gov (United States)

Pau, Stephanie; Edwards, Erika J; Still, Christopher J

2013-01-01

A number of studies have demonstrated the ecological sorting of C3 and C4 grasses along temperature and moisture gradients. However, previous studies of C3 and C4 grass biogeography have often inadvertently compared species in different and relatively unrelated lineages, which are associated with different environmental settings and distinct adaptive traits. Such confounded comparisons of C3 and C4 grasses may bias our understanding of ecological sorting imposed strictly by photosynthetic pathway. Here, we used MaxEnt species distribution modeling in combination with satellite data to understand the functional diversity of C3 and C4 grasses by comparing both large clades and closely related sister taxa. Similar to previous work, we found that C4 grasses showed a preference for regions with higher temperatures and lower precipitation compared with grasses using the C3 pathway. However, air temperature differences were smaller (2 °C vs. 4 °C) and precipitation and % tree cover differences were larger (1783 mm vs. 755 mm, 21.3% vs. 7.7%, respectively) when comparing C3 and C4 grasses within the same clade vs. comparing all C4 and all C3 grasses (i.e., ignoring phylogenetic structure). These results were due to important differences in the environmental preferences of C3 BEP and PACMAD clades (the two main grass clades). Winter precipitation was found to be more important for understanding the distribution and environmental niche of C3 PACMADs in comparison with both C3 BEPs and C4 taxa, for which temperature was much more important. Results comparing closely related C3 -C4 sister taxa supported the patterns derived from our modeling of the larger clade groupings. Our findings, which are novel in comparing the distribution and niches of clades, demonstrate that the evolutionary history of taxa is important for understanding the functional diversity of C3 and C4 grasses, and should have implications for how grasslands will respond to global change. © 2012

A Model-Driven Approach to e-Course Management

Science.gov (United States)

Savic, Goran; Segedinac, Milan; Milenkovic, Dušica; Hrin, Tamara; Segedinac, Mirjana

2018-01-01

This paper presents research on using a model-driven approach to the development and management of electronic courses. We propose a course management system which stores a course model represented as distinct machine-readable components containing domain knowledge of different course aspects. Based on this formally defined platform-independent…

Complete chloroplast genome sequence of green foxtail (Setaria viridis), a promising model system for C4 photosynthesis.

Science.gov (United States)

Wang, Shuo; Gao, Li-Zhi

2016-09-01

The complete chloroplast genome of green foxtail (Setaria viridis), a promising model system for C4 photosynthesis, is first reported in this study. The genome harbors a large single copy (LSC) region of 81 016 bp and a small single copy (SSC) region of 12 456  bp separated by a pair of inverted repeat (IRa and IRb) regions of 22 315 bp. GC content is 38.92%. The proportion of coding sequence is 57.97%, comprising of 111 (19 duplicated in IR regions) unique genes, 71 of which are protein-coding genes, four are rRNA genes, and 36 are tRNA genes. Phylogenetic analysis indicated that S. viridis was clustered with its cultivated species S. italica in the tribe Paniceae of the family Poaceae. This newly determined chloroplast genome will provide valuable genetic resources to assist future studies on C4 photosynthesis in grasses.

Translating message sequence charts to other process languages using process mining

NARCIS (Netherlands)

Lassen, K.B.; Dongen, van B.F.; Jensen, K.; Aalst, van der W.M.P.; Billington, J.

2008-01-01

Message Sequence Charts (MSCs) are often used by software analysts when discussing the behavior of a system with different stakeholders. Often such discussions lead to more complete behavioral models in the form of, e.g., Event-driven Process Chains (EPCs), Unified Modeling Language (UML), activity

Competition between trees and grasses for both soil water and mineral nitrogen in dry savannas.

Science.gov (United States)

Donzelli, D; De Michele, C; Scholes, R J

2013-09-07

The co-existence of trees and grasses in savannas in general can be the result of processes involving competition for resources (e.g. water and nutrients) or differential response to disturbances such as fire, animals and human activities; or a combination of both broad mechanisms. In moist savannas, the tree-grass coexistence is mainly attributed to of disturbances, while in dry savannas, limiting resources are considered the principal mechanism of co-existence. Virtually all theoretical explorations of tree-grass dynamics in dry savannas consider only competition for soil water. Here we investigate whether coexistence could result from a balanced competition for two resources, namely soil water and mineral nitrogen. We introduce a simple dynamical resource-competition model for trees and grasses. We consider two alternative hypotheses: (1) trees are the superior competitors for nitrogen while grasses are superior competitors for water, and (2) vice-versa. We study the model properties under the two hypotheses and test each hypothesis against data from 132 dry savannas in Africa using Kendall's test of independence. We find that Hypothesis 1 gets much more support than Hypothesis 2, and more support than the null hypothesis that neither is operative. We further consider gradients of rainfall and nitrogen availability and find that the Hypothesis 1 model reproduces the observed patterns in nature. We do not consider our results to definitively show that tree-grass coexistence in dry savannas is due to balanced competition for water and nitrogen, but show that this mechanism is a possibility, which cannot be a priori excluded and should thus be considered along with the more traditional explanations. Copyright © 2013 Elsevier Ltd. All rights reserved.

Data and Dynamics Driven Approaches for Modelling and Forecasting the Red Sea Chlorophyll

KAUST Repository

Dreano, Denis

2017-01-01

concentration and have practical applications for fisheries operation and harmful algae blooms monitoring. Modelling approaches can be divided between physics- driven (dynamical) approaches, and data-driven (statistical) approaches. Dynamical models are based

Model-Driven Development of Safety Architectures

Science.gov (United States)

Denney, Ewen; Pai, Ganesh; Whiteside, Iain

2017-01-01

We describe the use of model-driven development for safety assurance of a pioneering NASA flight operation involving a fleet of small unmanned aircraft systems (sUAS) flying beyond visual line of sight. The central idea is to develop a safety architecture that provides the basis for risk assessment and visualization within a safety case, the formal justification of acceptable safety required by the aviation regulatory authority. A safety architecture is composed from a collection of bow tie diagrams (BTDs), a practical approach to manage safety risk by linking the identified hazards to the appropriate mitigation measures. The safety justification for a given unmanned aircraft system (UAS) operation can have many related BTDs. In practice, however, each BTD is independently developed, which poses challenges with respect to incremental development, maintaining consistency across different safety artifacts when changes occur, and in extracting and presenting stakeholder specific information relevant for decision making. We show how a safety architecture reconciles the various BTDs of a system, and, collectively, provide an overarching picture of system safety, by considering them as views of a unified model. We also show how it enables model-driven development of BTDs, replete with validations, transformations, and a range of views. Our approach, which we have implemented in our toolset, AdvoCATE, is illustrated with a running example drawn from a real UAS safety case. The models and some of the innovations described here were instrumental in successfully obtaining regulatory flight approval.

Data-Driven Model Order Reduction for Bayesian Inverse Problems

KAUST Repository

Cui, Tiangang; Youssef, Marzouk; Willcox, Karen

2014-01-01

One of the major challenges in using MCMC for the solution of inverse problems is the repeated evaluation of computationally expensive numerical models. We develop a data-driven projection- based model order reduction technique to reduce

Model-driven software migration a methodology

CERN Document Server

Wagner, Christian

2014-01-01

Today, reliable software systems are the basis of any business or company. The continuous further development of those systems is the central component in software evolution. It requires a huge amount of time- man power- as well as financial resources. The challenges are size, seniority and heterogeneity of those software systems. Christian Wagner addresses software evolution: the inherent problems and uncertainties in the process. He presents a model-driven method which leads to a synchronization between source code and design. As a result the model layer will be the central part in further e

Profile-driven regression for modeling and runtime optimization of mobile networks

DEFF Research Database (Denmark)

McClary, Dan; Syrotiuk, Violet; Kulahci, Murat

2010-01-01

Computer networks often display nonlinear behavior when examined over a wide range of operating conditions. There are few strategies available for modeling such behavior and optimizing such systems as they run. Profile-driven regression is developed and applied to modeling and runtime optimization...... of throughput in a mobile ad hoc network, a self-organizing collection of mobile wireless nodes without any fixed infrastructure. The intermediate models generated in profile-driven regression are used to fit an overall model of throughput, and are also used to optimize controllable factors at runtime. Unlike...

Modeling of Prepregs during Automated Draping Sequences

DEFF Research Database (Denmark)

Krogh, Christian; Glud, Jens Ammitzbøll; Jakobsen, Johnny

2017-01-01

algorithm used to generate target points on the mold which are used as input to a draping sequence planner. The draping sequence planner prescribes the displacement history for each gripper in the drape tool and these displacements are then applied to each gripper in a transient model of the draping...... sequence. The model is based on a transient finite element analysis with the material’s constitutive behavior currently being approximated as linear elastic orthotropic. In-plane tensile and bias-extension tests as well as bending tests are conducted and used as input for the model. The virtual draping...

DNA sequence modeling based on context trees

NARCIS (Netherlands)

Kusters, C.J.; Ignatenko, T.; Roland, J.; Horlin, F.

2015-01-01

Genomic sequences contain instructions for protein and cell production. Therefore understanding and identification of biologically and functionally meaningful patterns in DNA sequences is of paramount importance. Modeling of DNA sequences in its turn can help to better understand and identify such

Model Driven Integrated Decision-Making in Manufacturing Enterprises

Directory of Open Access Journals (Sweden)

Richard H. Weston

2012-01-01

Full Text Available Decision making requirements and solutions are observed in four world class Manufacturing Enterprises (MEs. Observations made focus on deployed methods of complexity handling that facilitate multi-purpose, distributed decision making. Also observed are examples of partially deficient “integrated decision making” which stem from lack of understanding about how ME structural relations enable and/or constrain reachable ME behaviours. To begin to address this deficiency the paper outlines the use of a “reference model of ME decision making” which can inform the structural design of decision making systems in MEs. Also outlined is a “systematic model driven approach to modelling ME systems” which can particularise the reference model in specific case enterprises and thereby can “underpin integrated ME decision making”. Coherent decomposition and representational mechanisms have been incorporated into the model driven approach to systemise complexity handling. The paper also describes in outline an application of the modelling method in a case study ME and explains how its use has improved the integration of previously distinct planning functions. The modelling approach is particularly innovative in respect to the way it structures the coherent creation and experimental re-use of “fit for purpose” discrete event (predictive simulation models at the multiple levels of abstraction.

VAM populations in relation to grass invasion associated with forest decline.

Science.gov (United States)

Vosatka, M; Cudlin, P; Mejstrik, V

1991-01-01

Spruce stands in Northern Bohemia forests, damaged to various degrees by industrial pollution, have shown establishment of grass cover following tree defoliation. Populations of vesicular-arbuscular mycorrhizal (VAM) fungi were studied under this grass cover in four permanent plots with spruce under different levels of pollution stress. Soil and root samples were collected in April and June within each plot as follows: (1) sites without grass, (2) sites with initial stages of grass invasion, and (3) sites with fully developed grass cover. In all plots, the highest number of propagules were recovered from samples taken from sites having full grass cover. Mycorrhizal infection of grass was highest in the plot with the severest pollution damage and lowest in the least damaged plot. The development of grass cover and VAM infection of grass increased with tree defoliation caused by air pollution.

Grass survey of the Itremo Massif records endemic central highland ...

African Journals Online (AJOL)

Twenty species are endemic to the central highlands, and a further 1 4 species are restricted to Madagascar. Five ecological groups of grasses were identified in the Itremo Massif: shade species in gallery forests, open wet area species, fire grasses, anthropogenic disturbance associated grasses and rock-dwelling grasses.

Selective logging and fire as drivers of alien grass invasion in a Bolivian tropical dry forest

NARCIS (Netherlands)

Veldman, J.W.; Mostacedo, B.; Peña-Claros, M.; Putz, F.E.

2009-01-01

Logging is an integral component of most conceptual models that relate human land-use and climate change to tropical deforestation via positive-feedbacks involving fire. Given that grass invasions can substantially alter fire regimes, we studied grass distributions in a tropical dry forest 1-5 yr

Rumen escape protein in grass and grass silage deterimened with a nylon bag and an enzymatic technique

NARCIS (Netherlands)

Cone, J.W.; Gelder, van A.H.; Mathijssen-Kamman, A.A.; Hindle, V.A.

2004-01-01

Rumen escape protein (REP) was determined for six grasses and 16 grass silages using a nylon bag technique and an in vitro technique using a proteolytic enzyme preparation of Streptomyces griseus. In vitro, the samples were incubated for 0, 1, 6 and 24 h. The highest correlation observed between

EroGRASS : Failure of grass cover layers at seaward and shoreward dike slopes. design, construction and performance

NARCIS (Netherlands)

Verhagen, H.J.; Verheij, H.J.; Cao, T.M.; Dassanayake, D.; Roelvink, D.; Piontkowitz, T.

2009-01-01

A large number of the dikes in the North Sea and Baltic Sea regions are covered with grass that is exposed to hydraulic loading from waves and currents during storm surges. During previous storm surges the grass cover layers often showed large strength and remained undamaged. A clear physical

Chaos game representation (CGR)-walk model for DNA sequences

International Nuclear Information System (INIS)

Jie, Gao; Zhen-Yuan, Xu

2009-01-01

Chaos game representation (CGR) is an iterative mapping technique that processes sequences of units, such as nucleotides in a DNA sequence or amino acids in a protein, in order to determine the coordinates of their positions in a continuous space. This distribution of positions has two features: one is unique, and the other is source sequence that can be recovered from the coordinates so that the distance between positions may serve as a measure of similarity between the corresponding sequences. A CGR-walk model is proposed based on CGR coordinates for the DNA sequences. The CGR coordinates are converted into a time series, and a long-memory ARFIMA (p, d, q) model, where ARFIMA stands for autoregressive fractionally integrated moving average, is introduced into the DNA sequence analysis. This model is applied to simulating real CGR-walk sequence data of ten genomic sequences. Remarkably long-range correlations are uncovered in the data, and the results from these models are reasonably fitted with those from the ARFIMA (p, d, q) model. (cross-disciplinary physics and related areas of science and technology)

Linking Microbial Community Structure and Function During the Acidified Anaerobic Digestion of Grass

Directory of Open Access Journals (Sweden)

Aoife Joyce

2018-03-01

Full Text Available Harvesting valuable bioproducts from various renewable feedstocks is necessary for the critical development of a sustainable bioeconomy. Anaerobic digestion is a well-established technology for the conversion of wastewater and solid feedstocks to energy with the additional potential for production of process intermediates of high market values (e.g., carboxylates. In recent years, first-generation biofuels typically derived from food crops have been widely utilized as a renewable source of energy. The environmental and socioeconomic limitations of such strategy, however, have led to the development of second-generation biofuels utilizing, amongst other feedstocks, lignocellulosic biomass. In this context, the anaerobic digestion of perennial grass holds great promise for the conversion of sustainable renewable feedstock to energy and other process intermediates. The advancement of this technology however, and its implementation for industrial applications, relies on a greater understanding of the microbiome underpinning the process. To this end, microbial communities recovered from replicated anaerobic bioreactors digesting grass were analyzed. The bioreactors leachates were not buffered and acidic pH (between 5.5 and 6.3 prevailed at the time of sampling as a result of microbial activities. Community composition and transcriptionally active taxa were examined using 16S rRNA sequencing and microbial functions were investigated using metaproteomics. Bioreactor fraction, i.e., grass or leachate, was found to be the main discriminator of community analysis across the three molecular level of investigation (DNA, RNA, and proteins. Six taxa, namely Bacteroidia, Betaproteobacteria, Clostridia, Gammaproteobacteria, Methanomicrobia, and Negativicutes accounted for the large majority of the three datasets. The initial stages of grass hydrolysis were carried out by Bacteroidia, Gammaproteobacteria, and Negativicutes in the grass biofilms, in addition to

Linking Microbial Community Structure and Function During the Acidified Anaerobic Digestion of Grass.

Science.gov (United States)

Joyce, Aoife; Ijaz, Umer Z; Nzeteu, Corine; Vaughan, Aoife; Shirran, Sally L; Botting, Catherine H; Quince, Christopher; O'Flaherty, Vincent; Abram, Florence

2018-01-01

Harvesting valuable bioproducts from various renewable feedstocks is necessary for the critical development of a sustainable bioeconomy. Anaerobic digestion is a well-established technology for the conversion of wastewater and solid feedstocks to energy with the additional potential for production of process intermediates of high market values (e.g., carboxylates). In recent years, first-generation biofuels typically derived from food crops have been widely utilized as a renewable source of energy. The environmental and socioeconomic limitations of such strategy, however, have led to the development of second-generation biofuels utilizing, amongst other feedstocks, lignocellulosic biomass. In this context, the anaerobic digestion of perennial grass holds great promise for the conversion of sustainable renewable feedstock to energy and other process intermediates. The advancement of this technology however, and its implementation for industrial applications, relies on a greater understanding of the microbiome underpinning the process. To this end, microbial communities recovered from replicated anaerobic bioreactors digesting grass were analyzed. The bioreactors leachates were not buffered and acidic pH (between 5.5 and 6.3) prevailed at the time of sampling as a result of microbial activities. Community composition and transcriptionally active taxa were examined using 16S rRNA sequencing and microbial functions were investigated using metaproteomics. Bioreactor fraction, i.e., grass or leachate, was found to be the main discriminator of community analysis across the three molecular level of investigation (DNA, RNA, and proteins). Six taxa, namely Bacteroidia, Betaproteobacteria, Clostridia, Gammaproteobacteria, Methanomicrobia, and Negativicutes accounted for the large majority of the three datasets. The initial stages of grass hydrolysis were carried out by Bacteroidia, Gammaproteobacteria, and Negativicutes in the grass biofilms, in addition to Clostridia in the

Investigation of Desso GrassMaster® as application in hydraulic engineering

NARCIS (Netherlands)

Steeg, van der P.; Paulissen, M.P.C.P.; Roex, E.; Mommer, L.

2015-01-01

Dessa GrassMaster® is a reinforced grass system which is applied successfully on sports fields and enables to use a sports field more intensively than a normal grass field. In this report the possibility of an application of Dessa GrassMaster®in hydraulic conditions, with a focus on grass dikes, is

A sequence-dependent rigid-base model of DNA

Science.gov (United States)

Gonzalez, O.; Petkevičiutė, D.; Maddocks, J. H.

2013-02-01

A novel hierarchy of coarse-grain, sequence-dependent, rigid-base models of B-form DNA in solution is introduced. The hierarchy depends on both the assumed range of energetic couplings, and the extent of sequence dependence of the model parameters. A significant feature of the models is that they exhibit the phenomenon of frustration: each base cannot simultaneously minimize the energy of all of its interactions. As a consequence, an arbitrary DNA oligomer has an intrinsic or pre-existing stress, with the level of this frustration dependent on the particular sequence of the oligomer. Attention is focussed on the particular model in the hierarchy that has nearest-neighbor interactions and dimer sequence dependence of the model parameters. For a Gaussian version of this model, a complete coarse-grain parameter set is estimated. The parameterized model allows, for an oligomer of arbitrary length and sequence, a simple and explicit construction of an approximation to the configuration-space equilibrium probability density function for the oligomer in solution. The training set leading to the coarse-grain parameter set is itself extracted from a recent and extensive database of a large number of independent, atomic-resolution molecular dynamics (MD) simulations of short DNA oligomers immersed in explicit solvent. The Kullback-Leibler divergence between probability density functions is used to make several quantitative assessments of our nearest-neighbor, dimer-dependent model, which is compared against others in the hierarchy to assess various assumptions pertaining both to the locality of the energetic couplings and to the level of sequence dependence of its parameters. It is also compared directly against all-atom MD simulation to assess its predictive capabilities. The results show that the nearest-neighbor, dimer-dependent model can successfully resolve sequence effects both within and between oligomers. For example, due to the presence of frustration, the model can

A sequence-dependent rigid-base model of DNA.

Science.gov (United States)

Gonzalez, O; Petkevičiūtė, D; Maddocks, J H

2013-02-07

A novel hierarchy of coarse-grain, sequence-dependent, rigid-base models of B-form DNA in solution is introduced. The hierarchy depends on both the assumed range of energetic couplings, and the extent of sequence dependence of the model parameters. A significant feature of the models is that they exhibit the phenomenon of frustration: each base cannot simultaneously minimize the energy of all of its interactions. As a consequence, an arbitrary DNA oligomer has an intrinsic or pre-existing stress, with the level of this frustration dependent on the particular sequence of the oligomer. Attention is focussed on the particular model in the hierarchy that has nearest-neighbor interactions and dimer sequence dependence of the model parameters. For a Gaussian version of this model, a complete coarse-grain parameter set is estimated. The parameterized model allows, for an oligomer of arbitrary length and sequence, a simple and explicit construction of an approximation to the configuration-space equilibrium probability density function for the oligomer in solution. The training set leading to the coarse-grain parameter set is itself extracted from a recent and extensive database of a large number of independent, atomic-resolution molecular dynamics (MD) simulations of short DNA oligomers immersed in explicit solvent. The Kullback-Leibler divergence between probability density functions is used to make several quantitative assessments of our nearest-neighbor, dimer-dependent model, which is compared against others in the hierarchy to assess various assumptions pertaining both to the locality of the energetic couplings and to the level of sequence dependence of its parameters. It is also compared directly against all-atom MD simulation to assess its predictive capabilities. The results show that the nearest-neighbor, dimer-dependent model can successfully resolve sequence effects both within and between oligomers. For example, due to the presence of frustration, the model can

Editorial - Special Issue on Model-driven Service-oriented architectures

NARCIS (Netherlands)

Andrade Almeida, João; Ferreira Pires, Luis; van Sinderen, Marten J.; Steen, M.W.A.

2009-01-01

Model-driven approaches to software development have proliferated in recent years owing to the availability of techniques based on metamodelling and model transformations, such as the meta-object facility (MOF) and the query view transformation (QVT) standards. During the same period,

Data-driven non-Markovian closure models

Science.gov (United States)

Kondrashov, Dmitri; Chekroun, Mickaël D.; Ghil, Michael

2015-03-01

This paper has two interrelated foci: (i) obtaining stable and efficient data-driven closure models by using a multivariate time series of partial observations from a large-dimensional system; and (ii) comparing these closure models with the optimal closures predicted by the Mori-Zwanzig (MZ) formalism of statistical physics. Multilayer stochastic models (MSMs) are introduced as both a generalization and a time-continuous limit of existing multilevel, regression-based approaches to closure in a data-driven setting; these approaches include empirical model reduction (EMR), as well as more recent multi-layer modeling. It is shown that the multilayer structure of MSMs can provide a natural Markov approximation to the generalized Langevin equation (GLE) of the MZ formalism. A simple correlation-based stopping criterion for an EMR-MSM model is derived to assess how well it approximates the GLE solution. Sufficient conditions are derived on the structure of the nonlinear cross-interactions between the constitutive layers of a given MSM to guarantee the existence of a global random attractor. This existence ensures that no blow-up can occur for a broad class of MSM applications, a class that includes non-polynomial predictors and nonlinearities that do not necessarily preserve quadratic energy invariants. The EMR-MSM methodology is first applied to a conceptual, nonlinear, stochastic climate model of coupled slow and fast variables, in which only slow variables are observed. It is shown that the resulting closure model with energy-conserving nonlinearities efficiently captures the main statistical features of the slow variables, even when there is no formal scale separation and the fast variables are quite energetic. Second, an MSM is shown to successfully reproduce the statistics of a partially observed, generalized Lotka-Volterra model of population dynamics in its chaotic regime. The challenges here include the rarity of strange attractors in the model's parameter

Beginning SQL Server Modeling Model-driven Application Development in SQL Server

CERN Document Server

Weller, Bart

2010-01-01

Get ready for model-driven application development with SQL Server Modeling! This book covers Microsoft's SQL Server Modeling (formerly known under the code name "Oslo") in detail and contains the information you need to be successful with designing and implementing workflow modeling. Beginning SQL Server Modeling will help you gain a comprehensive understanding of how to apply DSLs and other modeling components in the development of SQL Server implementations. Most importantly, after reading the book and working through the examples, you will have considerable experience using SQL M

Established native perennial grasses out-compete an invasive annual grass regardless of soil water and nutrient availability

Science.gov (United States)

Christopher M. McGlone; Carolyn Hull Sieg; Thomas E. Kolb; Ty Nietupsky

2012-01-01

Competition and resource availability influence invasions into native perennial grasslands by nonnative annual grasses such as Bromus tectorum. In two greenhouse experiments we examined the influence of competition, water availability, and elevated nitrogen (N) and phosphorus (P) availability on growth and reproduction of the invasive annual grass B. tectorum and two...

The NTeQ ISD Model: A Tech-Driven Model for Digital Natives (DNs)

Science.gov (United States)

Williams, C.; Anekwe, J. U.

2017-01-01

Integrating Technology for enquiry (NTeQ) instructional development model (ISD), is believed to be a technology-driven model. The authors x-rayed the ten-step model to reaffirm the ICT knowledge demand of the learner and the educator; hence computer-based activities at various stages of the model are core elements. The model also is conscious of…

Reflection of a Year Long Model-Driven Business and UI Modeling Development Project

Science.gov (United States)

Sukaviriya, Noi; Mani, Senthil; Sinha, Vibha

Model-driven software development enables users to specify an application at a high level - a level that better matches problem domain. It also promises the users with better analysis and automation. Our work embarks on two collaborating domains - business process and human interactions - to build an application. Business modeling expresses business operations and flows then creates business flow implementation. Human interaction modeling expresses a UI design, its relationship with business data, logic, and flow, and can generate working UI. This double modeling approach automates the production of a working system with UI and business logic connected. This paper discusses the human aspects of this modeling approach after a year long of building a procurement outsourcing contract application using the approach - the result of which was deployed in December 2008. The paper discusses in multiple areas the happy endings and some heartache. We end with insights on how a model-driven approach could do better for humans in the process.

The Prospect of Market-Driven Improvements in Animal Welfare: Lessons from the Case of Grass Milk in Denmark

Directory of Open Access Journals (Sweden)

Peter Sandøe

2013-06-01

Full Text Available Citizens in many European countries urge that the welfare of farm animals should be improved. Policy-makers propose that this could, at least to some extent, be achieved through increased consumption of animal products produced under labeling schemes guaranteeing higher standards of animal welfare. Yet considerable uncertainties exist about the ability of the market to promote animal welfare. So far the consumption of most welfare-friendly products has been limited, and the impact of driving and limiting factors is poorly understood. Reviewing market studies, we identify the factors that have shaped the relatively successful market for grass milk in Denmark. We conclude that the positive drivers such as an appealing animal welfare attribute and animal welfare being bundled with other qualities are essentially the same as those operating in connection with less successful animal welfare-friendly products. It is therefore to be expected that other animal welfare-friendly food products marketed via “natural behaviors” in the farm animals will catch the interest of consumers. However, grass milk consumption has been supported by proper labeling, ready availability and low price premiums as well as multifaceted public support. This suggests that successful cases require the joint presence of a number of positive drivers as well as low consumption barriers.

Germination of Themeda triandra (Kangaroo grass) as affected by ...

African Journals Online (AJOL)

Low rainfall in range areas restricts germination, growth and development of majority of range grasses. However, germination and establishment potential of forage grasses vary and depends on environmental conditions. Themeda triandra is an excellent known grass to grow under different environmental conditions.

The importance of cross-reactivity in grass pollen allergy

Directory of Open Access Journals (Sweden)

Aleksić Ivana

2014-01-01

Full Text Available According to the data obtained from in vivo and in vitro testing in Serbia, a significant number of patients have allergic symptoms caused by grass pollen. We examined the protein composition of grass pollens (Dactylis glomerata, Lolium perenne and Phleum pratense and cross-reactivity in patients allergic to grass pollen from our region. The grass pollen allergen extract was characterized by SDS-PAGE, while cross-reactivity of single grass pollens was revealed by immunoblot analysis. A high degree of cross-reactivity was demonstrated for all three single pollens in the sera of allergic patients compared to the grass pollen extract mixture. Confirmation of the existence of cross-reactivity between different antigenic sources facilitates the use of monovalent vaccines, which are easier to standardize and at the same time prevent further sensitization of patients and reduces adverse reactions. [Projekat Ministarstva nauke Republike Srbije, br. 172049 i br. 172024

Diversification of C(4) grasses (Poaceae) does not coincide with their ecological dominance.

Science.gov (United States)

Bouchenak-Khelladi, Yanis; Slingsby, Jasper A; Verboom, G Anthony; Bond, William J

2014-02-01

The radiation of a lineage and its rise to ecological dominance are distinct phenomena and driven by different processes. For example, paleoecological data has been used to show that the Cretaceous angiosperm radiation did not coincide with their rise to dominance. Using a phylogenetic approach, we here explored the evolution of C4 grasses and evaluated whether the diversification of this group and its rise to ecological dominance in the late Miocene were decoupled. We assembled a matrix including 675 grass species of the PACMAD clade and 2784 characters (ITS and ndhF) to run a molecular dating analysis using three fossils as reference calibrations. We coded species as C3 vs. C4 and reconstructed ancestral states under maximum likelihood. We used the program BiSSE to test whether rates of diversification are correlated with photosynthetic pathway and whether the radiation of C4 lineages preceded or coincided with their rise to ecological dominance from ∼10 Ma. C4 grass lineages first originated around 35 Ma at the time of the Eocene-Oligocene transition. Accelerated diversification of C4 lineages did not coincide with their rise to ecological dominance. C4-dominated grasslands have expanded only since the Late Miocene and Pliocene. The initial diversification of their biotic elements can be tracked back as far as the Eocene-Oligocene transition. We suggest that shifts in taxonomic diversification and ecological dominance were stimulated by different factors, as in the case of the early angiosperms in the Cretaceous.

Thermogravimetric analysis of forest understory grasses

Science.gov (United States)

Thomas Elder; John S. Kush; Sharon M. Hermann

2011-01-01

Forest understory grasses are of significance in the initiation, establishment and maintenance of fire, whether used as a management tool or when occurring as wildfire. The fundamental thermal properties of such grasses are critical to their behavior in fire situations and have been investigated in the current work by the application of thermogravimetric analysis (TGA...

A GRASS GIS application for vertical sorting of sediments analysis in River Dynamics

Directory of Open Access Journals (Sweden)

Annalisa Minelli

2012-03-01

Full Text Available The extreme versatility in different research fields of GRASS GIS is well known. A tool for the vertical sorting of sediments in river dynamics analysis is illustrated in this work.In particular, a GRASS GIS python module has been written which implements a forecasting sorting model by Blom&Parker (2006 to analyze river bed composition’s evolution in depth in terms of grainsize.The module takes a DEM and information relative to the bed load transport composition as input. It works in two different and consecutive phases: the first one uses the GRASS capabilities in analyzing geometrical features of the river bed along a chosen river reach, the second phase is the "numerical" one and implements the forecasting model itself, then executes statistical analyses and draws graphs, by the means of matplotlib library.Moreover, a specific procedure for the import of a laser scanner cloud of points is implemented, in case the raster DEM map is not available.At the moment, the module has been applied using flumes data from Saint Anthony Falls Laboratory (Minneapolis, MN and some first results have been obtained, but the "testing" phase on other flume’s data is still in progress. Moreover the module has been written for GRASS 65 on a Ubuntu Linux machine, even if the debugging of a GRASS 64, Windowsversion, is also in progress.The final aim of this work is the application of the model on natural rivers, but there are still some drawbacks. First of all the need of a high resolution DEM in input, secondly the number and type of data in input (for example the bed load composition in volume fraction per each size considered which is not easily obtainable, so the best solution is represented by testing the model on a well instrumented river reach to export in future the forecasting method to un-instrumented reaches.

Quality management using model-driven engineering: an overview

OpenAIRE

Ruiz-Rube, Iván; Escalona, María José

2014-01-01

Quality Management (QM) is one of the critical points of any software development process. In recent years, several proposals have emerged on this issue, mainly with regard to maturity models, quality standards and best practices collections. Besides, Model Driven Engineering (MDE) aims to build software systems through the construction and transformation of models. However, MDE might be used for other different tasks. In this poster, we summarize the main contributions abou...

Names of Southern African grasses: Name changes and additional ...

African Journals Online (AJOL)

The main reasons for changes in botanical names are briefly reviewed, with examples from the lists. At this time, about 1040 grass species and subspecific taxa are recognized in the subcontinent. Keywords: botanical research; botanical research institute; botany; grass; grasses; identification; name change; nomenclature; ...

Model-driven dependability assessment of software systems

CERN Document Server

Bernardi, Simona; Petriu, Dorina C

2013-01-01

In this book, the authors present cutting-edge model-driven techniques for modeling and analysis of software dependability. Most of them are based on the use of UML as software specification language. From the software system specification point of view, such techniques exploit the standard extension mechanisms of UML (i.e., UML profiling). UML profiles enable software engineers to add non-functional properties to the software model, in addition to the functional ones. The authors detail the state of the art on UML profile proposals for dependability specification and rigorously describe the t

The effectiveness and efficiency of model driven game design

NARCIS (Netherlands)

Dormans, Joris

2012-01-01

In order for techniques from Model Driven Engineering to be accepted at large by the game industry, it is critical that the effectiveness and efficiency of these techniques are proven for game development. There is no lack of game design models, but there is no model that has surfaced as an industry

Construction of UML class diagram with Model-Driven Development

Directory of Open Access Journals (Sweden)

Tomasz Górski

2016-03-01

Full Text Available Model transformations play a key role in software development projects based on Model--Driven Development (MDD principles. Transformations allow for automation of repetitive and well-defined steps, thus shortening design time and reducing a number of errors. In the object-oriented approach, the key elements are use cases. They are described, modelled and later designed until executable application code is obtained. The aim of the paper is to present transformation of a model-to-model type, Communication-2-Class, which automates construction of Unified Modelling Language (UML class diagram in the context of the analysis/design model. An UML class diagram is created based on UML communication diagram within use case realization. As a result, a class diagram shows all of the classes involved in the use case realization and the relationships among them. The plug-in which implements Communication-2-Class transformation was implemented in the IBM Rational Software Architect. The article presents the tests results of developed plug-in, which realizes Communication-2-Class transformation, showing capabilities of shortening use case realization’s design time.[b]Keywords[/b]: Model-Driven Development, transformations, Unified Modelling Language, analysis/design model, UML class diagram, UML communication diagram

Host status of false brome grass to the leaf rust fungus Puccinia brachypodii and the stripe rust fungus P. Striiformis

NARCIS (Netherlands)

Barbieri, M.; Marcel, T.C.; Niks, R.E.

2011-01-01

Purple false brome grass (Brachypodium distachyon) has recently emerged as a model system for temperate grasses and is also a potential model plant to investigate plant interactions with economically important pathogens such as rust fungi. We determined the host status of five Brachypodium species

Modeling of laser-driven hydrodynamics experiments

Science.gov (United States)

di Stefano, Carlos; Doss, Forrest; Rasmus, Alex; Flippo, Kirk; Desjardins, Tiffany; Merritt, Elizabeth; Kline, John; Hager, Jon; Bradley, Paul

2017-10-01

Correct interpretation of hydrodynamics experiments driven by a laser-produced shock depends strongly on an understanding of the time-dependent effect of the irradiation conditions on the flow. In this talk, we discuss the modeling of such experiments using the RAGE radiation-hydrodynamics code. The focus is an instability experiment consisting of a period of relatively-steady shock conditions in which the Richtmyer-Meshkov process dominates, followed by a period of decaying flow conditions, in which the dominant growth process changes to Rayleigh-Taylor instability. The use of a laser model is essential for capturing the transition. also University of Michigan.

Model-Driven Policy Framework for Data Centers

DEFF Research Database (Denmark)

Caba, Cosmin Marius; Kentis, Angelos Mimidis; Soler, José

2016-01-01

. Moreover, the lack of simple solutions for managing the configuration and behavior of the DC components makes the DC hard to configure and slow in adapting to changes in business needs. In this paper, we propose a model-driven framework for policy-based management for DCs, to simplify not only the service...

Mathematical modelling of digesta passage rate, mean retention time and in vivo apparent digestibility of two different lengths of hay and big-bale grass silage in ponies.

Science.gov (United States)

Moore-Colyer, M J S; Morrow, H J; Longland, A C

2003-07-01

Welsh-cross pony geldings (about 300 kg live weight) were used in a 4x4 Latin square experiment to determine the rate of passage and apparent digestibility of unchopped big-bale grass silage (BBL), chopped big-bale grass silage (BBS), unchopped grass hay (HL) and chopped grass hay (HS) offered at approximately 15 g/kg live weight per d. On day 1 of collection weeks, ponies were fed 85 g ytterbium chloride hexahydrate-marked feed 1.5 h after the morning meal. Total faecal collections commenced 8 h later and continued for 168 h. Apparent digestibilities of feed DM, organic matter (OM), crude protein (CP, Nx6.25), acid-detergent fibre (ADF) and neutral-detergent fibre (NDF) were also determined. Faecal excretion data were subjected to the models of Pond et al. (1988) and digesta mean retention time (MRT) calculated from these models and using the algebraic method of Thielmans et al. (1978). Silage had significantly (Peffect. All the models of Pond et al. (1988) accurately described (R(2)>0.8) the pattern of faecal marker excretion. MRT of BBL (29.0 h)>BBS(27 h)>HS and HL (26 h). Compartmental analysis using the G3 model of Pond et al. (1988) showed BBL and HS diets had longer MRT in the time-dependent compartment, whereas BBS and HL had longer MRT in the time-independent compartment. Results from this experiment indicate that BBL and BBS are readily accepted and digested by ponies. While Yb is a successful external marker for determining total tract MRT and for modelling faecal excretion curves in horses, the results did not allow any definite conclusions to be drawn on digesta MRT within the different compartments of the equid gut.

Bud-bank and tiller dynamics of co-occurring C3 caespitose grasses in mixed-grass prairie.

Science.gov (United States)

Ott, Jacqueline P; Hartnett, David C

2015-09-01

Tiller recruitment from the belowground bud bank of caespitose grasses influences their ability to monopolize local resources and, hence, their genet fitness. Differences in bud production and outgrowth among tiller types within a genet and among species may explain co-occurrence of caespitose grasses. This study aimed to characterize genet bud-bank and tiller production and dynamics in two co-occurring species and compare their vegetative reproductive strategies. Bud-bank and tiller dynamics of Hesperostipa comata and Nassella viridula, dominant C3 caespitose grasses in the northern mixed-grass prairie of North America, were assessed throughout an annual cycle. The two species showed similar strategies, maintaining polycyclic tillers and thus creating mixed-age genet bud banks comprising multiple bud cohorts produced in different years. Vegetative tillers produced the majority of buds, whereas flowering tillers contributed little to the bud bank. Buds lived for at least 2 yr and were maintained in multiple developmental stages throughout the year. Because bud longevity rarely exceeded tiller longevity, tiller longevity drove turnover within the bud bank. Tiller population dynamics, more than bud production per tiller, determined the differential contribution of tiller types to the bud bank. Nassella viridula had higher bud production per tiller, a consistent annual tiller recruitment density, and greater longevity of buds on senesced and flowering tillers than H. comata. Co-occurring C3 caespitose grasses had similar bud-bank and tiller dynamics contributing to genet persistence but differed in bud characteristics that could affect genet longevity and species coexistence. © 2015 Botanical Society of America.

Selecting elephant grass families and progenies to produce bioenergy through mixed models (REML/BLUP).

Science.gov (United States)

Rodrigues, E V; Daher, R F; Dos Santos, A; Vivas, M; Machado, J C; Gravina, G do A; de Souza, Y P; Vidal, A K; Rocha, A Dos S; Freitas, R S

2017-05-18

Brazil has great potential to produce bioenergy since it is located in a tropical region that receives high incidence of solar energy and presents favorable climatic conditions for such purpose. However, the use of bioenergy in the country is below its productivity potential. The aim of the current study was to select full-sib progenies and families of elephant grass (Pennisetum purpureum S.) to optimize phenotypes relevant to bioenergy production through mixed models (REML/BLUP). The circulating diallel-based crossing of ten elephant grass genotypes was performed. An experimental design using the randomized block methodology, with three repetitions, was set to assess both the hybrids and the parents. Each plot comprised 14-m rows, 1.40 m spacing between rows, and 1.40 m spacing between plants. The number of tillers, plant height, culm diameter, fresh biomass production, dry biomass rate, and the dry biomass production were assessed. Genetic-statistical analyses were performed through mixed models (REML/BLUP). The genetic variance in the assessed families was explained through additive genetic effects and dominance genetic effects; the dominance variance was prevalent. Families such as Capim Cana D'África x Guaçu/I.Z.2, Cameroon x Cuba-115, CPAC x Cuba-115, Cameroon x Guaçu/I.Z.2, and IAC-Campinas x CPAC showed the highest dry biomass production. The family derived from the crossing between Cana D'África and Guaçu/I.Z.2 showed the largest number of potential individuals for traits such as plant height, culm diameter, fresh biomass production, dry biomass production, and dry biomass rate. The individual 5 in the family Cana D'África x Guaçu/I.Z.2, planted in blocks 1 and 2, showed the highest dry biomass production.

Dose-response relationship of a new Timothy grass pollen allergoid in comparison with a 6-grass pollen allergoid.

Science.gov (United States)

Pfaar, O; Hohlfeld, J M; Al-Kadah, B; Hauswald, B; Homey, B; Hunzelmann, N; Schliemann, S; Velling, P; Worm, M; Klimek, L

2017-11-01

Subcutaneous allergen immunotherapy with grass pollen allergoids has been proven to be effective and safe in the treatment of patients with allergic rhinoconjunctivitis. Based on the extensive cross-reactivity among Pooideae species, it has been suggested that grass pollen extracts could be prepared from a single species, rather than from a multiple species mixture. To find the optimal dose of a Phleum pratense (P. pratense) allergoid preparation and compare its efficacy and safety to a 6-grass pollen allergoid preparation. In this double-blind, placebo-controlled study (EudraCT: 2011-000674-58), three doses of P. pratense allergoid (1800 therapeutic units (TU), standard-dose 6000 TU and 18 000 TU) were compared with placebo and the marketed 6-grass pollen allergoid (6000 TU). In a pre-seasonal dosing regimen, 102 patients were randomized to five treatment groups and received nine subcutaneous injections. The primary efficacy endpoint was the change in weal size (late-phase reaction [LPR]) in response to the intracutaneous testing (ICT) before and after treatment, comparing the active allergoids to placebo. Secondary outcomes were the change in Total Nasal Symptom Score (TNSS) assessed in the allergen exposure chamber (AEC), the changes in P. pratense-serum-specific IgG 4 and the incidence of adverse events (AEs). All three doses of the P. pratense and the 6-grass pollen allergoid preparations were significantly superior to placebo for the primary outcome, whereas there were no significant differences in the change in TNSS. Compared to the standard-dose, the high-dose of P. pratense did not produce any additional significant benefit, but showed a slight increase in AEs. Yet this increase in AEs was lower than for the 6-grass pollen preparation. The standard-dose of the new P. pratense allergoid was comparable to the marketed 6-grass pollen preparation at equal dose for the parameters measured. © 2017 The Authors. Clinical & Experimental Allergy Published by John

Automatic pre-processing for an object-oriented distributed hydrological model using GRASS-GIS

Science.gov (United States)

Sanzana, P.; Jankowfsky, S.; Branger, F.; Braud, I.; Vargas, X.; Hitschfeld, N.

2012-04-01

Landscapes are very heterogeneous, which impact the hydrological processes occurring in the catchments, especially in the modeling of peri-urban catchments. The Hydrological Response Units (HRUs), resulting from the intersection of different maps, such as land use, soil types and geology, and flow networks, allow the representation of these elements in an explicit way, preserving natural and artificial contours of the different layers. These HRUs are used as model mesh in some distributed object-oriented hydrological models, allowing the application of a topological oriented approach. The connectivity between polygons and polylines provides a detailed representation of the water balance and overland flow in these distributed hydrological models, based on irregular hydro-landscape units. When computing fluxes between these HRUs, the geometrical parameters, such as the distance between the centroid of gravity of the HRUs and the river network, and the length of the perimeter, can impact the realism of the calculated overland, sub-surface and groundwater fluxes. Therefore, it is necessary to process the original model mesh in order to avoid these numerical problems. We present an automatic pre-processing implemented in the open source GRASS-GIS software, for which several Python scripts or some algorithms already available were used, such as the Triangle software. First, some scripts were developed to improve the topology of the various elements, such as snapping of the river network to the closest contours. When data are derived with remote sensing, such as vegetation areas, their perimeter has lots of right angles that were smoothed. Second, the algorithms more particularly address bad-shaped elements of the model mesh such as polygons with narrow shapes, marked irregular contours and/or the centroid outside of the polygons. To identify these elements we used shape descriptors. The convexity index was considered the best descriptor to identify them with a threshold

Tag-Driven Online Novel Recommendation with Collaborative Item Modeling

Directory of Open Access Journals (Sweden)

Fenghuan Li

2018-04-01

Full Text Available Online novel recommendation recommends attractive novels according to the preferences and characteristics of users or novels and is increasingly touted as an indispensable service of many online stores and websites. The interests of the majority of users remain stable over a certain period. However, there are broad categories in the initial recommendation list achieved by collaborative filtering (CF. That is to say, it is very possible that there are many inappropriately recommended novels. Meanwhile, most algorithms assume that users can provide an explicit preference. However, this assumption does not always hold, especially in online novel reading. To solve these issues, a tag-driven algorithm with collaborative item modeling (TDCIM is proposed for online novel recommendation. Online novel reading is different from traditional book marketing and lacks preference rating. In addition, collaborative filtering frequently suffers from the Matthew effect, leading to ignored personalized recommendations and serious long tail problems. Therefore, item-based CF is improved by latent preference rating with a punishment mechanism based on novel popularity. Consequently, a tag-driven algorithm is constructed by means of collaborative item modeling and tag extension. Experimental results show that online novel recommendation is improved greatly by a tag-driven algorithm with collaborative item modeling.

MACRO NUTRIENTS UPTAKE OF FORAGE GRASSES AT DIFFERENT SALINITY STRESSES

Directory of Open Access Journals (Sweden)

F. Kusmiyati

2014-10-01

Full Text Available The high concentration of sodium chloride (NaCl in saline soils has negative effects on the growth ofmost plants. The experiment was designed to evaluate macro nutrient uptake (Nitrogen, Phosphorus andPotassium of forage grasses at different NaCl concentrations in growth media. The experiment wasconducted in a greenhouse at Forage Crops Laboratory of Animal Agriculture Faculty, Diponegoro University.Split plot design was used to arrange the experiment. The main plot was forage grasses (Elephant grass(Pennisetum purpureum and King grass (Pennisetum hybrida. The sub plot was NaCl concentrationin growth media (0, 150, and 300 mM. The nitrogen (N, phosphorus (P and potassium (K uptake in shootand root of plant were measured. The result indicated increasing NaCl concentration in growth mediasignificantly decreased the N, P and K uptake in root and shoot of the elephant grass and king grass. Thepercentage reduction percentage of N, P and K uptake at 150 mM and 300 mM were high in elephant grassand king grass. It can be concluded that based on nitrogen, phosphorus and potassium uptake, elephantgrass and king grass are not tolerant to strong and very strong saline soil.

Data-Driven Model Order Reduction for Bayesian Inverse Problems

KAUST Repository

Cui, Tiangang

2014-01-06

One of the major challenges in using MCMC for the solution of inverse problems is the repeated evaluation of computationally expensive numerical models. We develop a data-driven projection- based model order reduction technique to reduce the computational cost of numerical PDE evaluations in this context.

Database-driven primary analysis of raw sequencing data

DEFF Research Database (Denmark)

2014-01-01

The present invention relates to methods for identifying the source of a biological sequence containing sample from raw sequencing reads. The method may be used to identify the source of unknown DNA and can be used for diagnostic, biodefense, food safety and quality, and hygiene applications...

Factors influencing the grass carp gut microbiome and its effect on metabolism.

Science.gov (United States)

Ni, Jiajia; Yan, Qingyun; Yu, Yuhe; Zhang, Tanglin

2014-03-01

Gut microbiota have attracted extensive attention recently because of their important role in host metabolism, immunity and health maintenance. The present study focused on factors affecting the gut microbiome of grass carp (Ctenopharyngodon idella) and further explored the potential effect of the gut microbiome on metabolism. Totally, 43.39 Gb of screened metagenomic sequences obtained from 24 gut samples were fully analysed. We detected 1228 phylotypes (116 Archaea and 1112 Bacteria), most of which belonged to the phyla Firmicutes, Proteobacteria and Fusobacteria. Totally, 41335 of the detected open reading frames (ORFs) were matched to Kyoto Encyclopedia of Genes and Genomes pathways, and carbohydrate and amino acid metabolism was the main matched pathway deduced from the annotated ORFs. Redundancy analysis based on the phylogenetic composition and gene composition of the gut microbiome indicated that gut fullness and feeding (i.e. ryegrass vs. commercial feed, and pond-cultured vs. wild) were significantly related to the gut microbiome. Moreover, many biosynthesis and metabolism pathways of carbohydrates, amino acids and lipids were significantly enhanced by the gut microbiome in ryegrass-fed grass carp. These findings suggest that the metabolic role played by the gut microbiome in grass carp can be affected by feeding. These findings contribute to the field of fish gut microbial ecology and also provide a basis for follow-up functional studies. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Modeling the Thermosphere as a Driven-Dissipative Thermodynamic System

Science.gov (United States)

2013-03-01

8 Figure 2: Illustration of the geocentric solar magnetospheric coordinate system............15 Figure 3: Diagram of the...to test new methods of modeling the thermospheric environment. Thermosphere as a Driven-Dissipative Thermodynamic System One approach for modeling... approach uses empirical coupling and relaxation constants to model the 4 input of energy to the thermosphere from the solar wind during

Grasses as invasive plants in South Africa revisited: Patterns, pathways and management

Directory of Open Access Journals (Sweden)

Vernon Visser

2017-03-01

Full Text Available Background: In many countries around the world, the most damaging invasive plant species are grasses. However, the status of grass invasions in South Africa has not been documented recently. Objectives: To update Sue Milton’s 2004 review of grasses as invasive alien plants in South Africa, provide the first detailed species level inventory of alien grasses in South Africa and assess the invasion dynamics and management of the group. Method: We compiled the most comprehensive inventory of alien grasses in South Africa to date using recorded occurrences of alien grasses in the country from various literature and database sources. Using historical literature, we reviewed past efforts to introduce alien grasses into South Africa. We sourced information on the origins, uses, distributions and minimum residence times to investigate pathways and patterns of spatial extent. We identified alien grasses in South Africa that are having environmental and economic impacts and determined whether management options have been identified, and legislation created, for these species. Results: There are at least 256 alien grass species in the country, 37 of which have become invasive. Alien grass species richness increased most dramatically from the late 1800s to about 1940. Alien grass species that are not naturalised or invasive have much shorter residence times than those that have naturalised or become invasive. Most grasses were probably introduced for forage purposes, and a large number of alien grass species were trialled at pasture research stations. A large number of alien grass species in South Africa are of Eurasian origin, although more recent introductions include species from elsewhere in Africa and from Australasia. Alien grasses are most prevalent in the south-west of the country, and the Fynbos Biome has the most alien grasses and the most widespread species. We identified 11 species that have recorded environmental and economic impacts in the

Towards a multi-stakeholder-driven model for excellence in higher ...

African Journals Online (AJOL)

The model is further based on significant NQF and OBE alignment of all learning ... form the foundation of this strategic-driven model for curriculum development. ... of quality planning, quality management system implementation and quality

Lessons learned in managing alfalfa-grass mixtures

Science.gov (United States)

Grass-alfalfa mixtures have a number of benefits that make them attractive to producers. However, they can be problematic to establish and maintain. Research programs have made progress in understanding the benefits and challenges of alfalfa-grass mixtures. Mixtures may have greater winter survival ...

Variation in important pasture grasses: I. Morphological and ...

African Journals Online (AJOL)

Variation in important pasture grasses: I. Morphological and geographical variation. ... Seven species are important pasture grasses throughout the western Transvaal, Orange Free State, northern Cape and Natal. ... Language: English.

Old Faithful Model for Radiolytic Gas-Driven Cryovolcanism at Enceladus

Science.gov (United States)

Cooper, John F.; Cooper, Paul D.; Sittler, Edward; Sturner, Steven J.; Rymer, Abigail M.

2009-01-01

A new model is presented on how chemically driven cryovolcanism might contribute to episodic outgassing at the icy moon Enceladus and potentially elsewhere including Europa and Kuiper Belt Objects. Exposed water ices can become oxidized from radiolytic chemical alteration of near-surface water ice by space environment irradiation. In contact with primordially abundant reductants such as NH3, CH4, and other hydrocarbons, the product oxidants can react exothermically to produce volatile gases driving cryovolcanism via gas-piston forces on any subsurface liquid reservoirs. Radiolytic oxidants such as H2O2 and O2 can continuously accumulate deep in icy regoliths and be conveyed by rheological flows to subsurface chemical reaction zones over million-year time scales indicated by cratering ages for active regions of Enceladus and Europa. Surface blanketing with cryovolcanic plume ejecta would further accelerate regolith burial of radiolytic oxidants. Episodic heating from transient gravitational tides, radioisotope decay, impacts, or other geologic events might occasionally accelerate chemical reaction rates and ignite the exothermic release of cumulative radiolytic oxidant energy. The time history for the suggested "Old Faithful" model of radiolytic gas-driven cryovolcanism at Enceladus and elsewhere therefore consists of long periods of chemical energy accumulation punctuated by much briefer episodes of cryovolcanic activity. The most probable sequence for detection of activity in the current epoch is a long evolutionary phase of slow but continuous oxidant accumulation over billions of years followed by continuous but variable high activity over the past 10(exp 7)-10(exp 8) years. Detectable cryovolcanic activity could then later decline due to near-total oxidation of the rheologically accessible ice crust and depletion the accessible reductant abundances, as may have already occurred for Europa in the more intense radiation environment of Jupiter's magnetosphere

Water use, root activity and deep drainage within a perennial legume-grass pasture: A case study in southern inland Queensland, Australia

Directory of Open Access Journals (Sweden)

A. Nahuel A. Pachas

2016-09-01

Full Text Available Water use and depth of water extraction of leucaena (Leucaena leucocephala and Rhodes grass (Chloris gayana pasture, irrigated with desalinated coal seam water (a by-product of the coal seam gas industry, were monitored to provide background information on root activity, spatial and temporal water use and deep drainage over a 757-day period from August 2011 to August 2013. Methodology comprised measurement of soil water from surface to 4 m depth using 8 EnviroSCAN probes connected to dataloggers positioned within leucaena twin rows and within the Rhodes grass inter-row. Just over 581,000 individual moisture measurements were collated and are reported here. Water extraction (and by inference root activity of leucaena and Rhodes grass showed marked seasonal fluctuation with deepest and highest water extraction occurring during the first growing season; water extraction was greatly diminished during the following drier and cooler seasons due to the negative influences of lower soil moisture contents, lower temperatures and increased defoliation on pasture growth. The highest values of deep drainage below 4 m depth occurred when high rainfall events corresponded with high soil water storage in the entire profile (0–4 m depth. Given that water usage by both leucaena and Rhodes grass was greatest in the upper layers of soil (<1.5 m, future research should focus on how the level of competitive interaction might be managed by choice of row spacing and frequency of irrigation. Further studies are needed, including: (a physical sampling to determine the depth of active roots; (b how defoliation affects rooting behaviours and water use of leucaena; and (c modelling of the water and salt balances of leucaena and grass inter-row systems using data from this study, with various levels of irrigation, to investigate the risks of deep drainage over an extended climate sequence.Keywords: Active rooting depth, agroforestry, Chloris gayana, Leucaena leucocephala

Data to Decisions: Creating a Culture of Model-Driven Drug Discovery.

Science.gov (United States)

Brown, Frank K; Kopti, Farida; Chang, Charlie Zhenyu; Johnson, Scott A; Glick, Meir; Waller, Chris L

2017-09-01

Merck & Co., Inc., Kenilworth, NJ, USA, is undergoing a transformation in the way that it prosecutes R&D programs. Through the adoption of a "model-driven" culture, enhanced R&D productivity is anticipated, both in the form of decreased attrition at each stage of the process and by providing a rational framework for understanding and learning from the data generated along the way. This new approach focuses on the concept of a "Design Cycle" that makes use of all the data possible, internally and externally, to drive decision-making. These data can take the form of bioactivity, 3D structures, genomics, pathway, PK/PD, safety data, etc. Synthesis of high-quality data into models utilizing both well-established and cutting-edge methods has been shown to yield high confidence predictions to prioritize decision-making and efficiently reposition resources within R&D. The goal is to design an adaptive research operating plan that uses both modeled data and experiments, rather than just testing, to drive project decision-making. To support this emerging culture, an ambitious information management (IT) program has been initiated to implement a harmonized platform to facilitate the construction of cross-domain workflows to enable data-driven decision-making and the construction and validation of predictive models. These goals are achieved through depositing model-ready data, agile persona-driven access to data, a unified cross-domain predictive model lifecycle management platform, and support for flexible scientist-developed workflows that simplify data manipulation and consume model services. The end-to-end nature of the platform, in turn, not only supports but also drives the culture change by enabling scientists to apply predictive sciences throughout their work and over the lifetime of a project. This shift in mindset for both scientists and IT was driven by an early impactful demonstration of the potential benefits of the platform, in which expert-level early discovery

LHC-GCS a model-driven approach for automatic PLC and SCADA code generation

CERN Document Server

Thomas, Geraldine; Barillère, Renaud; Cabaret, Sebastien; Kulman, Nikolay; Pons, Xavier; Rochez, Jacques

2005-01-01

The LHC experiments’ Gas Control System (LHC GCS) project [1] aims to provide the four LHC experiments (ALICE, ATLAS, CMS and LHCb) with control for their 23 gas systems. To ease the production and maintenance of 23 control systems, a model-driven approach has been adopted to generate automatically the code for the Programmable Logic Controllers (PLCs) and for the Supervision Control And Data Acquisition (SCADA) systems. The first milestones of the project have been achieved. The LHC GCS framework [4] and the generation tools have been produced. A first control application has actually been generated and is in production, and a second is in preparation. This paper describes the principle and the architecture of the model-driven solution. It will in particular detail how the model-driven solution fits with the LHC GCS framework and with the UNICOS [5] data-driven tools.

Efficient and Accurate Log-Levy Approximations of Levy-Driven LIBOR Models

DEFF Research Database (Denmark)

Papapantoleon, Antonis; Schoenmakers, John; Skovmand, David

2012-01-01

The LIBOR market model is very popular for pricing interest rate derivatives but is known to have several pitfalls. In addition, if the model is driven by a jump process, then the complexity of the drift term grows exponentially fast (as a function of the tenor length). We consider a Lévy-driven ...... ratchet caps show that the approximations perform very well. In addition, we also consider the log-Lévy approximation of annuities, which offers good approximations for high-volatility regimes....

Utilization of grasses for potential biofuel production and phytoremediation of heavy metal contaminated soils.

Science.gov (United States)

Balsamo, Ronald A; Kelly, William J; Satrio, Justinus A; Ruiz-Felix, M Nydia; Fetterman, Marisa; Wynn, Rodd; Hagel, Kristen

2015-01-01

This research focuses on investigating the use of common biofuel grasses to assess their potential as agents of long-term remediation of contaminated soils using lead as a model heavy metal ion. We present evidence demonstrating that switch grass and Timothy grass may be potentially useful for long-term phytoremediation of heavy metal contaminated soils and describe novel techniques to track and remove contaminants from inception to useful product. Enzymatic digestion and thermochemical approaches are being used to convert this lignocellulosic feedstock into useful product (sugars, ethanol, biocrude oil+biochar). Preliminary studies on enzymatic hydrolysis and fast pyrolysis of the Switchgrass materials that were grown in heavy metal contaminated soil and non-contaminated soils show that the presence of lead in the Switchgrass material feedstock does not adversely affect the outcomes of the conversion processes. These results indicate that the modest levels of contaminant uptake allow these grass species to serve as phytoremediation agents as well as feedstocks for biofuel production in areas degraded by industrial pollution.

Molecular fingerprinting of complex grass allergoids: size assessments reveal new insights in epitope repertoires and functional capacities.

Science.gov (United States)

Starchenka, S; Bell, A J; Mwange, J; Skinner, M A; Heath, M D

2017-01-01

Subcutaneous allergen immunotherapy (SCIT) is a well-documented treatment for allergic disease which involves injections of native allergen or modified (allergoid) extracts. The use of allergoid vaccines is a growing sector of the allergy immunotherapy market, associated with shorter-course therapy. The aim of this study was the structural and immunological characterisation of group 1 (Lol p 1) IgG-binding epitopes within a complex mix grass allergoid formulation containing rye grass. HP-SEC was used to resolve a mix grass allergoid preparation of high molecular weight into several distinct fractions with defined molecular weight and elution profiles. Allergen verification of the HP-SEC allergoid fractions was confirmed by mass spectrometry analysis. IgE and IgG immunoreactivity of the allergoid preparations was explored and Lol p 1 specific IgG-binding epitopes mapped by SPOT synthesis technology (PepSpot™) with structural analysis based on a Lol p 1 homology model. Grass specific IgE reactivity of the mix grass modified extract (allergoid) was diminished in comparison with the mix grass native extract. A difference in IgG profiles was observed between an intact mix grass allergoid preparation and HP-SEC allergoid fractions, which indicated enhancement of accessible reactive IgG epitopes across size distribution profiles of the mix grass allergoid formulation. Detailed analysis of the epitope specificity showed retention of six Lol p 1 IgG-binding epitopes in the mix grass modified extract. The structural and immunological changes which take place following the grass allergen modification process was further unravelled revealing distinct IgG immunological profiles. All epitopes were mapped on the solvent exposed area of Lol p 1 homology model accessible for IgG binding. One of the epitopes was identified as an 'immunodominant' Lol p 1 IgG-binding epitope (62-IFKDGRGCGSCFEIK-76) and classified as a novel epitope. The results from this study support the concept

Observer and data-driven model based fault detection in Power Plant Coal Mills

DEFF Research Database (Denmark)

Fogh Odgaard, Peter; Lin, Bao; Jørgensen, Sten Bay

2008-01-01

model with motor power as the controlled variable, data-driven methods for fault detection are also investigated. Regression models that represent normal operating conditions (NOCs) are developed with both static and dynamic principal component analysis and partial least squares methods. The residual...... between process measurement and the NOC model prediction is used for fault detection. A hybrid approach, where a data-driven model is employed to derive an optimal unknown input observer, is also implemented. The three methods are evaluated with case studies on coal mill data, which includes a fault......This paper presents and compares model-based and data-driven fault detection approaches for coal mill systems. The first approach detects faults with an optimal unknown input observer developed from a simplified energy balance model. Due to the time-consuming effort in developing a first principles...

Genome-Wide Analysis of Syntenic Gene Deletion in the Grasses

Science.gov (United States)

Schnable, James C.; Freeling, Michael; Lyons, Eric

2012-01-01

The grasses, Poaceae, are one of the largest and most successful angiosperm families. Like many radiations of flowering plants, the divergence of the major grass lineages was preceded by a whole-genome duplication (WGD), although these events are not rare for flowering plants. By combining identification of syntenic gene blocks with measures of gene pair divergence and different frequencies of ancient gene loss, we have separated the two subgenomes present in modern grasses. Reciprocal loss of duplicated genes or genomic regions has been hypothesized to reproductively isolate populations and, thus, speciation. However, in contrast to previous studies in yeast and teleost fishes, we found very little evidence of reciprocal loss of homeologous genes between the grasses, suggesting that post-WGD gene loss may not be the cause of the grass radiation. The sets of homeologous and orthologous genes and predicted locations of deleted genes identified in this study, as well as links to the CoGe comparative genomics web platform for analyzing pan-grass syntenic regions, are provided along with this paper as a resource for the grass genetics community. PMID:22275519

Kinetics of the pyrolysis of arundo, sawdust, corn stover and switch grass biomass by thermogravimetric analysis using a multi-stage model.

Science.gov (United States)

Biney, Paul O; Gyamerah, Michael; Shen, Jiacheng; Menezes, Bruna

2015-03-01

A new multi-stage kinetic model has been developed for TGA pyrolysis of arundo, corn stover, sawdust and switch grass that accounts for the initial biomass weight (W0). The biomass were decomposed in a nitrogen atmosphere from 23°C to 900°C in a TGA at a single 20°C/min ramp rate in contrast with the isoconversion technique. The decomposition was divided into multiple stages based on the absolute local minimum values of conversion derivative, (dx/dT), obtained from DTG curves. This resulted in three decomposition stages for arundo, corn stover and sawdust and four stages for switch grass. A linearized multi-stage model was applied to the TGA data for each stage to determine the pre-exponential factor, activation energy, and reaction order. The activation energies ranged from 54.7 to 60.9 kJ/mol, 62.9 to 108.7 kJ/mol, and 18.4 to 257.9 kJ/mol for the first, second and the third decomposition stages respectively. Copyright © 2014 Elsevier Ltd. All rights reserved.

Grass-on-grass competition along a catenal gradient in mesic ...

African Journals Online (AJOL)

Three aboveground treatments (full light competition, no light competition and clipping to simulate grazing), and two belowground treatments (full belowground competition and belowground competition excluded by a root tube), were used. On all soil depths the three grass species differed in mean mass, with E. racemosa ...

Results from the 5-year SQ grass sublingual immunotherapy tablet asthma prevention (GAP) trial in children with grass pollen allergy.

Science.gov (United States)

Valovirta, Erkka; Petersen, Thomas H; Piotrowska, Teresa; Laursen, Mette K; Andersen, Jens S; Sørensen, Helle F; Klink, Rabih

2018-02-01

Allergy immunotherapy targets the immunological cause of allergic rhinoconjunctivitis and allergic asthma and has the potential to alter the natural course of allergic disease. The primary objective was to investigate the effect of the SQ grass sublingual immunotherapy tablet compared with placebo on the risk of developing asthma. A total of 812 children (5-12 years), with a clinically relevant history of grass pollen allergic rhinoconjunctivitis and no medical history or signs of asthma, were included in the randomized, double-blind, placebo-controlled trial, comprising 3 years of treatment and 2 years of follow-up. There was no difference in time to onset of asthma, defined by prespecified asthma criteria relying on documented reversible impairment of lung function (primary endpoint). Treatment with the SQ grass sublingual immunotherapy tablet significantly reduced the risk of experiencing asthma symptoms or using asthma medication at the end of trial (odds ratio = 0.66, P year posttreatment follow-up, and during the entire 5-year trial period. Also, grass allergic rhinoconjunctivitis symptoms were 22% to 30% reduced (P years). At the end of the trial, the use of allergic rhinoconjunctivitis pharmacotherapy was significantly less (27% relative difference to placebo, P < .001). Total IgE, grass pollen-specific IgE, and skin prick test reactivity to grass pollen were all reduced compared to placebo. Treatment with the SQ grass sublingual immunotherapy tablet reduced the risk of experiencing asthma symptoms and using asthma medication, and had a positive, long-term clinical effect on rhinoconjunctivitis symptoms and medication use but did not show an effect on the time to onset of asthma. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Arbuscular mycorrhizal assemblages in native plant roots change in the presence of invasive exotic grasses

Science.gov (United States)

Hawkes, C.V.; Belnap, J.; D'Antonio, C.; Firestone, M.K.

2006-01-01

Plant invasions have the potential to significantly alter soil microbial communities, given their often considerable aboveground effects. We examined how plant invasions altered the arbuscular mycorrhizal fungi of native plant roots in a grassland site in California and one in Utah. In the California site, we used experimentally created plant communities composed of exotic (Avena barbata, Bromus hordeaceus) and native (Nassella pulchra, Lupinus bicolor) monocultures and mixtures. In the Utah semi-arid grassland, we took advantage of invasion by Bromus tectorum into long-term plots dominated by either of two native grasses, Hilaria jamesii or Stipa hymenoides. Arbuscular mycorrhizal fungi colonizing roots were characterized with PCR amplification of the ITS region, cloning, and sequencing. We saw a significant effect of the presence of exotic grasses on the diversity of mycorrhizal fungi colonizing native plant roots. In the three native grasses, richness of mycorrhizal fungi decreased; in the native forb at the California site, the number of fungal RFLP patterns increased in the presence of exotics. The exotic grasses also caused the composition of the mycorrhizal community in native roots to shift dramatically both in California, with turnover of Glomus spp., and Utah, with replacement of Glomus spp. by apparently non-mycorrhizal fungi. Invading plants may be able to influence the network of mycorrhizal fungi in soil that is available to natives through either earlier root activity or differential carbon provision compared to natives. Alteration of the soil microbial community by plant invasion can provide a mechanism for both successful invasion and the resulting effects of invaders on the ecosystem. ?? Springer 2006.

Optimization of Lead Removal via Napier Grass in Synthetic Brackish Water using Response Surface Model

Science.gov (United States)

Hongsawat, P.; Suttiarporn, P.; Wutsanthia, K.; Kongsiri, G.

2018-03-01

The efficiency of the lead (Pb) phytoremediation by Napier grass was studied on the plant’s growth and plant’s tolerance on the Pb toxicity in synthetic brackish water. It was found that the plant was high tolerance to high level of Pb concentration (10 mg/l) in synthetic brackish water. Which revealed on the possibilities of plant’s growth under the presence of Pb contaminated condition. According to the Pb removal efficiency, the highest one (88.63±4.9%) was found at 10 ppm Pb concentration, 0.3 g/l NaCl concentration during the period 45 day. However, this study investigated the optimum condition for lead (Pb) removal from synthetic brackish water using phytoremediation treatment with Napier grass through a Box-Behnken Design. Three operational variables, i.e. Pb concentration (1, 5.5, 10 mg/l), NaCl (0.1, 0.3, 0.5 g/l) and period time (7, 26, 45 day), were determined. The results were provided evidence that the highest Pb removal efficiency (93.56%) from synthetic brackish water via Napier grass was Pb and NaCl concentration at 10 mg/l and 0.5 g/l during 45 day.

Natural lactic acid bacteria population of tropical grasses and their fermentation factor analysis of silage prepared with cellulase and inoculant.

Science.gov (United States)

Khota, Waroon; Pholsen, Suradej; Higgs, David; Cai, Yimin

2016-12-01

Natural lactic acid bacteria (LAB) populations in tropical grasses and their fermentation characteristics on silage prepared with cellulase enzyme and LAB inoculants were studied. A commercial inoculant Lactobacillus plantarum Chikuso 1 (CH), a local selected strain Lactobacillus casei TH14 (TH14), and 2 cellulases, Acremonium cellulase (AC) and Maicelase (MC; Meiji Seika Pharma Co. Ltd., Tokyo, Japan), were used as additives to silage preparation with fresh and wilted (6 h) Guinea grass and Napier grass. Silage was prepared using a laboratory-scale fermentation system. Treatments were CH, TH14, AC at 0.01% fresh matter, AC 0.1%, MC 0.01%, MC 0.1%, CH+AC 0.01%, CH+AC 0.1%, CH+MC 0.01%, CH+MC 0.1%, TH14+AC 0.1%, TH14+AC 0.01%, TH14+MC 0.1%, and TH14+MC 0.01%. Microorganism counts of Guinea grass and Napier grass before ensiling were 10 2 LAB and 10 6 aerobic bacteria; these increased during wilting. Based on morphological and biochemical characteristics, and 16S rRNA gene sequence analysis, natural strains from both grasses were identified as L. plantarum, L. casei, Lactobacillus acidipiscis, Leuconostoc pseudomesenteroides, Leuconostoc garlicum, Weissella confusa, and Lactococcus lactis. Lactobacillus plantarum and L. casei are the dominant species and could grow at lower pH and produce more lactic acid than the other isolates. Crude protein and neutral detergent fiber were 5.8 and 83.7% of dry matter (DM) for Guinea grass, and 7.5 and 77.1% of DM for Napier grass. Guinea grass had a low level of water-soluble carbohydrates (0.39% of DM). Guinea grass silage treated with cellulase had a lower pH and higher lactic acid content than control and LAB treatments. The 0.1% AC and MC treatments had the best result for fermentation quality. All high water-soluble carbohydrate (2.38% DM) Napier grass silages showed good fermentation quality. Compared with control and LAB-inoculated silage, the cellulase-treated silages had significantly higher crude protein content and

Convex relationships in ecosystems containing mixtures of trees and grass

CSIR Research Space (South Africa)

Scholes, RJ

2003-12-01

Full Text Available The relationship between grass production and the quantity of trees in mixed tree-grass ecosystems (savannas) is convex for all or most of its range. In other words, the grass production declines more steeply per unit increase in tree quantity...

Model morphing and sequence assignment after molecular replacement

Energy Technology Data Exchange (ETDEWEB)

Terwilliger, Thomas C., E-mail: terwilliger@lanl.gov [Los Alamos National Laboratory, Mail Stop M888, Los Alamos, NM 87545 (United States); Read, Randy J. [University of Cambridge, Cambridge Institute for Medical Research, Cambridge CB2 0XY (United Kingdom); Adams, Paul D. [Lawrence Berkeley National Laboratory, One Cyclotron Road, Bldg 64R0121, Berkeley, CA 94720 (United States); Brunger, Axel T. [Stanford University, 318 Campus Drive West, Stanford, CA 94305 (United States); Afonine, Pavel V. [Lawrence Berkeley National Laboratory, One Cyclotron Road, Bldg 64R0121, Berkeley, CA 94720 (United States); Hung, Li-Wei [Los Alamos National Laboratory, Mail Stop M888, Los Alamos, NM 87545 (United States)

2013-11-01

A procedure for model building is described that combines morphing a model to match a density map, trimming the morphed model and aligning the model to a sequence. A procedure termed ‘morphing’ for improving a model after it has been placed in the crystallographic cell by molecular replacement has recently been developed. Morphing consists of applying a smooth deformation to a model to make it match an electron-density map more closely. Morphing does not change the identities of the residues in the chain, only their coordinates. Consequently, if the true structure differs from the working model by containing different residues, these differences cannot be corrected by morphing. Here, a procedure that helps to address this limitation is described. The goal of the procedure is to obtain a relatively complete model that has accurate main-chain atomic positions and residues that are correctly assigned to the sequence. Residues in a morphed model that do not match the electron-density map are removed. Each segment of the resulting trimmed morphed model is then assigned to the sequence of the molecule using information about the connectivity of the chains from the working model and from connections that can be identified from the electron-density map. The procedure was tested by application to a recently determined structure at a resolution of 3.2 Å and was found to increase the number of correctly identified residues in this structure from the 88 obtained using phenix.resolve sequence assignment alone (Terwilliger, 2003 ▶) to 247 of a possible 359. Additionally, the procedure was tested by application to a series of templates with sequence identities to a target structure ranging between 7 and 36%. The mean fraction of correctly identified residues in these cases was increased from 33% using phenix.resolve sequence assignment to 47% using the current procedure. The procedure is simple to apply and is available in the Phenix software package.

Model morphing and sequence assignment after molecular replacement

International Nuclear Information System (INIS)

Terwilliger, Thomas C.; Read, Randy J.; Adams, Paul D.; Brunger, Axel T.; Afonine, Pavel V.; Hung, Li-Wei

2013-01-01

A procedure for model building is described that combines morphing a model to match a density map, trimming the morphed model and aligning the model to a sequence. A procedure termed ‘morphing’ for improving a model after it has been placed in the crystallographic cell by molecular replacement has recently been developed. Morphing consists of applying a smooth deformation to a model to make it match an electron-density map more closely. Morphing does not change the identities of the residues in the chain, only their coordinates. Consequently, if the true structure differs from the working model by containing different residues, these differences cannot be corrected by morphing. Here, a procedure that helps to address this limitation is described. The goal of the procedure is to obtain a relatively complete model that has accurate main-chain atomic positions and residues that are correctly assigned to the sequence. Residues in a morphed model that do not match the electron-density map are removed. Each segment of the resulting trimmed morphed model is then assigned to the sequence of the molecule using information about the connectivity of the chains from the working model and from connections that can be identified from the electron-density map. The procedure was tested by application to a recently determined structure at a resolution of 3.2 Å and was found to increase the number of correctly identified residues in this structure from the 88 obtained using phenix.resolve sequence assignment alone (Terwilliger, 2003 ▶) to 247 of a possible 359. Additionally, the procedure was tested by application to a series of templates with sequence identities to a target structure ranging between 7 and 36%. The mean fraction of correctly identified residues in these cases was increased from 33% using phenix.resolve sequence assignment to 47% using the current procedure. The procedure is simple to apply and is available in the Phenix software package

Establishing native warm season grasses on Eastern Kentucky strip mines

Energy Technology Data Exchange (ETDEWEB)

Barnes, T.G.; Larkin, J.L.; Arnett, M.B. [Univ. of Kentucky, Lexington, KY (United States). Dept. of Forestry

1998-12-31

The authors evaluated various methods of establishing native warm season grasses on two reclaimed Eastern Kentucky mines from 1994--1997. Most current reclamation practices incorporate the use of tall fescue (Festuca arundinacea) and other cool-season grasses/legumes that provide little wildlife habitats. The use of native warm season grasses will likely improve wildlife habitat on reclaimed strip mines. Objectives of this study were to compare the feasibility of establishing these grasses during fall, winter, or spring using a native rangeland seeder or hydroseeding; a fertilizer application at planting; or cold-moist stratification prior to hydroseeding. Vegetative cover, bare ground, species richness, and biomass samples were collected at the end of each growing season. Native warm season grass plantings had higher plant species richness compared to cool-season reclamation mixtures. There was no difference in establishment of native warm season grasses as a result of fertilization or seeding technique. Winter native warm season grass plantings were failures and cold-moist stratification did not increase plant establishment during any season. As a result of a drought during 1997, both cool-season and warm season plantings were failures. Cool-season reclamation mixtures had significantly more vegetative cover and biomass compared to native warm season grass mixtures and the native warm season grass plantings did not meet vegetative cover requirements for bond release. Forbs and legumes that established well included pale purple coneflower (Echinacea pallida), lance-leaf coreopsis (Coreopsis lanceolata), round-headed lespedeza (Lespedeza capitata), partridge pea (Cassia fasiculata), black-eyed susan (Rudbeckia hirta), butterfly milkweed (Asclepias tuberosa), and bergamot (Monarda fistulosa). Results from two demonstration plots next to research plots indicate it is possible to establish native warm season grasses on Eastern Kentucky strip mines for wildlife habitat.

Establishing native warm season grasses on Eastern Kentucky strip mines

International Nuclear Information System (INIS)

Barnes, T.G.; Larkin, J.L.; Arnett, M.B.

1998-01-01

The authors evaluated various methods of establishing native warm season grasses on two reclaimed Eastern Kentucky mines from 1994--1997. Most current reclamation practices incorporate the use of tall fescue (Festuca arundinacea) and other cool-season grasses/legumes that provide little wildlife habitats. The use of native warm season grasses will likely improve wildlife habitat on reclaimed strip mines. Objectives of this study were to compare the feasibility of establishing these grasses during fall, winter, or spring using a native rangeland seeder or hydroseeding; a fertilizer application at planting; or cold-moist stratification prior to hydroseeding. Vegetative cover, bare ground, species richness, and biomass samples were collected at the end of each growing season. Native warm season grass plantings had higher plant species richness compared to cool-season reclamation mixtures. There was no difference in establishment of native warm season grasses as a result of fertilization or seeding technique. Winter native warm season grass plantings were failures and cold-moist stratification did not increase plant establishment during any season. As a result of a drought during 1997, both cool-season and warm season plantings were failures. Cool-season reclamation mixtures had significantly more vegetative cover and biomass compared to native warm season grass mixtures and the native warm season grass plantings did not meet vegetative cover requirements for bond release. Forbs and legumes that established well included pale purple coneflower (Echinacea pallida), lance-leaf coreopsis (Coreopsis lanceolata), round-headed lespedeza (Lespedeza capitata), partridge pea (Cassia fasiculata), black-eyed susan (Rudbeckia hirta), butterfly milkweed (Asclepias tuberosa), and bergamot (Monarda fistulosa). Results from two demonstration plots next to research plots indicate it is possible to establish native warm season grasses on Eastern Kentucky strip mines for wildlife habitat

Ontology Driven Meta-Modeling of Service Oriented Architecture

African Journals Online (AJOL)

pc

2018-03-05

Mar 5, 2018 ... #Department of Computer Applications, National Institute of ... *5Department of Computer Science, Winona State University, MN, USA ..... Further, it has aided in service .... Software: A Research Roadmap”, Workshop on the Future of ... and A. Solberg, “Model-driven service engineering with SoaML”, in.

Optimisation of logistics processes of energy grass collection

Science.gov (United States)

Bányai, Tamás.

2010-05-01

The collection of energy grass is a logistics-intensive process [1]. The optimal design and control of transportation and collection subprocesses is a critical point of the supply chain. To avoid irresponsible decisions by right of experience and intuition, the optimisation and analysis of collection processes based on mathematical models and methods is the scientific suggestible way. Within the frame of this work, the author focuses on the optimisation possibilities of the collection processes, especially from the point of view transportation and related warehousing operations. However the developed optimisation methods in the literature [2] take into account the harvesting processes, county-specific yields, transportation distances, erosion constraints, machinery specifications, and other key variables, but the possibility of more collection points and the multi-level collection were not taken into consideration. The possible areas of using energy grass is very wide (energetically use, biogas and bio alcohol production, paper and textile industry, industrial fibre material, foddering purposes, biological soil protection [3], etc.), so not only a single level but also a multi-level collection system with more collection and production facilities has to be taken into consideration. The input parameters of the optimisation problem are the followings: total amount of energy grass to be harvested in each region; specific facility costs of collection, warehousing and production units; specific costs of transportation resources; pre-scheduling of harvesting process; specific transportation and warehousing costs; pre-scheduling of processing of energy grass at each facility (exclusive warehousing). The model take into consideration the following assumptions: (1) cooperative relation among processing and production facilties, (2) capacity constraints are not ignored, (3) the cost function of transportation is non-linear, (4) the drivers conditions are ignored. The

New chloroplast microsatellite markers suitable for assessing genetic diversity of Lolium perenne and other related grass species.

Science.gov (United States)

Diekmann, Kerstin; Hodkinson, Trevor R; Barth, Susanne

2012-11-01

Lolium perenne (perennial ryegrass) is the most important forage grass species of temperate regions. We have previously released the chloroplast genome sequence of L. perenne 'Cashel'. Here nine chloroplast microsatellite markers are published, which were designed based on knowledge about genetically variable regions within the L. perenne chloroplast genome. These markers were successfully used for characterizing the genetic diversity in Lolium and different grass species. Chloroplast genomes of 14 Poaceae taxa were screened for mononucleotide microsatellite repeat regions and primers designed for their amplification from nine loci. The potential of these markers to assess genetic diversity was evaluated on a set of 16 Irish and 15 European L. perenne ecotypes, nine L. perenne cultivars, other Lolium taxa and other grass species. All analysed Poaceae chloroplast genomes contained more than 200 mononucleotide repeats (chloroplast simple sequence repeats, cpSSRs) of at least 7 bp in length, concentrated mainly in the large single copy region of the genome. Nucleotide composition varied considerably among subfamilies (with Pooideae biased towards poly A repeats). The nine new markers distinguish L. perenne from all non-Lolium taxa. TeaCpSSR28 was able to distinguish between all Lolium species and Lolium multiflorum due to an elongation of an A(8) mononucleotide repeat in L. multiflorum. TeaCpSSR31 detected a considerable degree of microsatellite length variation and single nucleotide polymorphism. TeaCpSSR27 revealed variation within some L. perenne accessions due to a 44-bp indel and was hence readily detected by simple agarose gel electrophoresis. Smaller insertion/deletion events or single nucleotide polymorphisms detected by these new markers could be visualized by polyacrylamide gel electrophoresis or DNA sequencing, respectively. The new markers are a valuable tool for plant breeding companies, seed testing agencies and the wider scientific community due to

Modeling of prepregs during automated draping sequences

Science.gov (United States)

Krogh, Christian; Glud, Jens A.; Jakobsen, Johnny

2017-10-01

The behavior of wowen prepreg fabric during automated draping sequences is investigated. A drape tool under development with an arrangement of grippers facilitates the placement of a woven prepreg fabric in a mold. It is essential that the draped configuration is free from wrinkles and other defects. The present study aims at setting up a virtual draping framework capable of modeling the draping process from the initial flat fabric to the final double curved shape and aims at assisting the development of an automated drape tool. The virtual draping framework consists of a kinematic mapping algorithm used to generate target points on the mold which are used as input to a draping sequence planner. The draping sequence planner prescribes the displacement history for each gripper in the drape tool and these displacements are then applied to each gripper in a transient model of the draping sequence. The model is based on a transient finite element analysis with the material's constitutive behavior currently being approximated as linear elastic orthotropic. In-plane tensile and bias-extension tests as well as bending tests are conducted and used as input for the model. The virtual draping framework shows a good potential for obtaining a better understanding of the drape process and guide the development of the drape tool. However, results obtained from using the framework on a simple test case indicate that the generation of draping sequences is non-trivial.

Investigation of mircroorganisms colonising activated zeolites during anaerobic biogas production from grass silage.

Science.gov (United States)

Weiss, S; Zankel, A; Lebuhn, M; Petrak, S; Somitsch, W; Guebitz, G M

2011-03-01

The colonisation of activated zeolites (i.e. clinoptilolites) as carriers for microorganisms involved in the biogas process was investigated. Zeolite particle sizes of 1.0-2.5mm were introduced to anaerobic laboratory batch-cultures and to continuously operated bioreactors during biogas production from grass silage. Incubation over 5-84 days led to the colonisation of zeolite surfaces in small batch-cultures (500 ml) and even in larger scaled and flow-through disturbed bioreactors (28 l). Morphological insights were obtained by using scanning electron microscopy (SEM). Single strand conformation polymorphism (SSCP) analysis based on amplification of bacterial and archaeal 16S rRNA fragments demonstrated structurally distinct populations preferring zeolite as operational environment. via sequence analysis conspicuous bands from SSCP patterns were identified. Populations immobilised on zeolite (e.g. Ruminofilibacter xylanolyticum) showed pronounced hydrolytic enzyme activity (xylanase) shortly after re-incubation in sterilised sludge on model substrate. In addition, the presence of methanogenic archaea on zeolite particles was demonstrated. Copyright © 2010 Elsevier Ltd. All rights reserved.

Model-Driven Engineering of Machine Executable Code

Science.gov (United States)

Eichberg, Michael; Monperrus, Martin; Kloppenburg, Sven; Mezini, Mira

Implementing static analyses of machine-level executable code is labor intensive and complex. We show how to leverage model-driven engineering to facilitate the design and implementation of programs doing static analyses. Further, we report on important lessons learned on the benefits and drawbacks while using the following technologies: using the Scala programming language as target of code generation, using XML-Schema to express a metamodel, and using XSLT to implement (a) transformations and (b) a lint like tool. Finally, we report on the use of Prolog for writing model transformations.

Modelling of two-zone accelerator-driven systems

Directory of Open Access Journals (Sweden)

V. A. Babenko

2012-09-01

Full Text Available Neutron-physical modelings of two-zone subcritical reactor driven by high-intensity neutron generator are considered. The cascade principle in subcritical reactors, the use of which can hypothetically substantially amplify the neutron flux from the external source is discussed in this article. The theoretical preconditions of the cascade principle are discussed, and the directions of practical realization of the cascade subcritical system are considered, namely the possible methods of neutron feedback between reactor sections elimination. The results of Monte Carlo neutron-physical modeling of the cascade subcritical systems are presented and discussed.

Reconstructing the Evolutionary History of Paralogous APETALA1/FRUITFULL-Like Genes in Grasses (Poaceae)

Science.gov (United States)

Preston, Jill C.; Kellogg, Elizabeth A.

2006-01-01

Gene duplication is an important mechanism for the generation of evolutionary novelty. Paralogous genes that are not silenced may evolve new functions (neofunctionalization) that will alter the developmental outcome of preexisting genetic pathways, partition ancestral functions (subfunctionalization) into divergent developmental modules, or function redundantly. Functional divergence can occur by changes in the spatio-temporal patterns of gene expression and/or by changes in the activities of their protein products. We reconstructed the evolutionary history of two paralogous monocot MADS-box transcription factors, FUL1 and FUL2, and determined the evolution of sequence and gene expression in grass AP1/FUL-like genes. Monocot AP1/FUL-like genes duplicated at the base of Poaceae and codon substitutions occurred under relaxed selection mostly along the branch leading to FUL2. Following the duplication, FUL1 was apparently lost from early diverging taxa, a pattern consistent with major changes in grass floral morphology. Overlapping gene expression patterns in leaves and spikelets indicate that FUL1 and FUL2 probably share some redundant functions, but that FUL2 may have become temporally restricted under partial subfunctionalization to particular stages of floret development. These data have allowed us to reconstruct the history of AP1/FUL-like genes in Poaceae and to hypothesize a role for this gene duplication in the evolution of the grass spikelet. PMID:16816429

A model for information retrieval driven by conceptual spaces

OpenAIRE

Tanase, D.

2015-01-01

A retrieval model describes the transformation of a query into a set of documents. The question is: what drives this transformation? For semantic information retrieval type of models this transformation is driven by the content and structure of the semantic models. In this case, Knowledge Organization Systems (KOSs) are the semantic models that encode the meaning employed for monolingual and cross-language retrieval. The focus of this research is the relationship between these meanings’ repre...

Oxygen isotope fractionations across individual leaf carbohydrates in grass and tree species.

Science.gov (United States)

Lehmann, Marco M; Gamarra, Bruno; Kahmen, Ansgar; Siegwolf, Rolf T W; Saurer, Matthias

2017-08-01

Almost no δ 18 O data are available for leaf carbohydrates, leaving a gap in the understanding of the δ 18 O relationship between leaf water and cellulose. We measured δ 18 O values of bulk leaf water (δ 18 O LW ) and individual leaf carbohydrates (e.g. fructose, glucose and sucrose) in grass and tree species and δ 18 O of leaf cellulose in grasses. The grasses were grown under two relative humidity (rH) conditions. Sucrose was generally 18 O-enriched compared with hexoses across all species with an apparent biosynthetic fractionation factor (ε bio ) of more than 27‰ relative to δ 18 O LW , which might be explained by isotopic leaf water and sucrose synthesis gradients. δ 18 O LW and δ 18 O values of carbohydrates and cellulose in grasses were strongly related, indicating that the leaf water signal in carbohydrates was transferred to cellulose (ε bio  = 25.1‰). Interestingly, damping factor p ex p x , which reflects oxygen isotope exchange with less enriched water during cellulose synthesis, responded to rH conditions if modelled from δ 18 O LW but not if modelled directly from δ 18 O of individual carbohydrates. We conclude that δ 18 O LW is not always a good substitute for δ 18 O of synthesis water due to isotopic leaf water gradients. Thus, compound-specific δ 18 O analyses of individual carbohydrates are helpful to better constrain (post-)photosynthetic isotope fractionation processes in plants. © 2017 John Wiley & Sons Ltd.

Estimating grass-clover ratio variations caused by traffic intensities using image analysis

DEFF Research Database (Denmark)

Jørgensen, Rasmus Nyholm; Sørensen, Claus Grøn; Green, Ole

Grass and especially clover have a negative yield response as a function of  traffic intensity.  Conventional grass-clover production for silage have high traffic intensity due to fertilizing with slurry, cutting the grass, rolling the grass into swaths, and collecting and chopping the grass...... to fulfill the aim [1]http://www.ruralni.gov.uk/index/publications/press_articles/dairy-2/role-of-clover.htm...

Controlling grass weeds on hard surfaces

DEFF Research Database (Denmark)

Rask, Anne Merete; Kristoffersen, Palle; Andreasen, Christian

2012-01-01

An experiment was conducted on a specially designed hard surface to study the impact of time interval between flaming treatments on the regrowth and flower production of two grass weeds. The goal of this experiment was to optimize the control of annual bluegrass and perennial ryegrass, both species...... that are very difficult to control without herbicides. Aboveground biomass from 72 plants per treatment was harvested and dry weights were recorded at regular intervals to investigate how the plants responded to flaming. Regrowth of the grasses was measured by harvesting aboveground biomass 2 wk after......, as they did not increase the reduction of aboveground biomass compared with the 7-d treatment interval. Knowledge on the regrowth of grass weeds after flaming treatments provided by this study can help improve recommendations given to road keepers and park managers for management on these weeds. Nomenclature...

Microbial protein synthesis, digestion and lactation responses of cows to grass or grass-red clover silage diet supplemented with barley or oats

Directory of Open Access Journals (Sweden)

A. VANHATALO

2008-12-01

Full Text Available The study was conducted to evaluate effects of silage type (grass-red clover vs. pure grass and grain supplement (oats vs. barley on rumen fermentation, post-ruminal nutrient flows, diet digestion and milk production. Four primiparous Finnish Ayrshire cows fitted with cannulae in the rumen and duodenum were used in a 4 × 4 Latin square experiment with four 28-d experimental periods and 2 × 2 factorial arrangements of treatments. Using red clover-containing (40% silage rather than pure grass silage had minor effects on rumen fermentation or diet digestion but increased non-ammonia nitrogen (N flow in terms of increased flows of microbial and dietary N entering to the small intestine. This was reflected as a reduced ruminal N degradability on grass-red clover diets. Furthermore, grass-red clover diets in comparison to grass silage diets increased milk lactose concentration and yields of milk, protein and lactose. Feeding oats in replacement for barley had minor effects on rumen fermentation or post-ruminal non-ammonia N flows but reduced digestibility of organic matter and neutral detergent fibre in the diet. Using oats rather than barley increased yields of milk and lactose but reduced milk protein concentration. Oats also increased proportions of C18:0 and C18:1 in milk fat and reduced those of C10:0 to C16:0. It is concluded that inclusion of red clover and replacement of barley with oats in grass silage based diets have beneficial effects in dairy cow production.;

Divergent evapotranspiration partition dynamics between shrubs and grasses in a shrub-encroached steppe ecosystem.

Science.gov (United States)

Wang, Pei; Li, Xiao-Yan; Wang, Lixin; Wu, Xiuchen; Hu, Xia; Fan, Ying; Tong, Yaqin

2018-06-04

Previous evapotranspiration (ET) partitioning studies have usually neglected competitions and interactions between antagonistic plant functional types. This study investigated whether shrubs and grasses have divergent ET partition dynamics impacted by different water-use patterns, canopy structures, and physiological properties in a shrub-encroached steppe ecosystem in Inner Mongolia, China. The soil water-use patterns of shrubs and grasses have been quantified by an isotopic tracing approach and coupled into an improved multisource energy balance model to partition ET fluxes into soil evaporation, grass transpiration, and shrub transpiration. The mean fractional contributions to total ET were 24 ± 13%, 20 ± 4%, and 56 ± 16% for shrub transpiration, grass transpiration, and soil evaporation respectively during the growing season. Difference in ecohydrological connectivity and leaf development both contributed to divergent transpiration partitioning between shrubs and grasses. Shrub-encroachment processes result in larger changes in the ET components than in total ET flux, which could be well explained by changes in canopy resistance, an ecosystem function dominated by the interaction of soil water-use patterns and ecosystem structure. The analyses presented here highlight the crucial effects of vegetation structural changes on the processes of land-atmosphere interaction and climate feedback. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

Towards Product Lining Model-Driven Development Code Generators

OpenAIRE

Roth, Alexander; Rumpe, Bernhard

2015-01-01

A code generator systematically transforms compact models to detailed code. Today, code generation is regarded as an integral part of model-driven development (MDD). Despite its relevance, the development of code generators is an inherently complex task and common methodologies and architectures are lacking. Additionally, reuse and extension of existing code generators only exist on individual parts. A systematic development and reuse based on a code generator product line is still in its inf...

Is the Grass Always Greener? Comparing the Environmental Impact of Conventional, Natural and Grass-Fed Beef Production Systems

Directory of Open Access Journals (Sweden)

Judith L. Capper

2012-04-01

Full Text Available This study compared the environmental impact of conventional, natural and grass-fed beef production systems. A deterministic model based on the metabolism and nutrient requirements of the beef population was used to quantify resource inputs and waste outputs per 1.0 × 109 kg of hot carcass weight beef in conventional (CON, natural (NAT and grass-fed (GFD production systems. Production systems were modeled using characteristic management practices, population dynamics and production data from U.S. beef production systems. Increased productivity (slaughter weight and growth rate in the CON system reduced the cattle population size required to produce 1.0 × 109 kg of beef compared to the NAT or GFD system. The CON system required 56.3% of the animals, 24.8% of the water, 55.3% of the land and 71.4% of the fossil fuel energy required to produce 1.0 × 109 kg of beef compared to the GFD system. The carbon footprint per 1.0 × 109 kg of beef was lowest in the CON system (15,989 × 103 t, intermediate in the NAT system (18,772 × 103 t and highest in the GFD system (26,785 × 103 t. The challenge to the U.S beef industry is to communicate differences in system environmental impacts to facilitate informed dietary choice.

The effects of energy grass plantations on biodiversity

Energy Technology Data Exchange (ETDEWEB)

Semere, T; Slater, F

2005-07-01

The ecological impact on local wildlife of biomass plantations of three different species of grasses has been monitored in the years 2002 to 2004 inclusive at farms in Herefordshire UK. Two of the grasses were not native to Britain. Wildlife monitored included ground flora, beetles, insects, birds, small mammals, butterflies, bees and hoverflies. The results provide a baseline of biodiversity data from biomass farms in England, although due to poor crop growth, the data from the switch-grass plantation was incomplete. The surveys were carried out by Cardiff University supported financially by the DTI.

The effects of energy grass plantations on biodiversity

International Nuclear Information System (INIS)

Semere, T.; Slater, F.

2005-01-01

The ecological impact on local wildlife of biomass plantations of three different species of grasses has been monitored in the years 2002 to 2004 inclusive at farms in Herefordshire UK. Two of the grasses were not native to Britain. Wildlife monitored included ground flora, beetles, insects, birds, small mammals, butterflies, bees and hoverflies. The results provide a baseline of biodiversity data from biomass farms in England, although due to poor crop growth, the data from the switch-grass plantation was incomplete. The surveys were carried out by Cardiff University supported financially by the DTI

Hidden Markov models for labeled sequences

DEFF Research Database (Denmark)

Krogh, Anders Stærmose

1994-01-01

A hidden Markov model for labeled observations, called a class HMM, is introduced and a maximum likelihood method is developed for estimating the parameters of the model. Instead of training it to model the statistics of the training sequences it is trained to optimize recognition. It resembles MMI...

A model for an acoustically driven microbubble inside a rigid tube

KAUST Repository

Qamar, Adnan; Samtaney, Ravi

2014-01-01

A theoretical framework to model the dynamics of acoustically driven microbubble inside a rigid tube is presented. The proposed model is not a variant of the conventional Rayleigh-Plesset category of models. It is derived from the reduced Navier

Continuous Online Sequence Learning with an Unsupervised Neural Network Model.

Science.gov (United States)

Cui, Yuwei; Ahmad, Subutar; Hawkins, Jeff

2016-09-14

The ability to recognize and predict temporal sequences of sensory inputs is vital for survival in natural environments. Based on many known properties of cortical neurons, hierarchical temporal memory (HTM) sequence memory recently has been proposed as a theoretical framework for sequence learning in the cortex. In this letter, we analyze properties of HTM sequence memory and apply it to sequence learning and prediction problems with streaming data. We show the model is able to continuously learn a large number of variableorder temporal sequences using an unsupervised Hebbian-like learning rule. The sparse temporal codes formed by the model can robustly handle branching temporal sequences by maintaining multiple predictions until there is sufficient disambiguating evidence. We compare the HTM sequence memory with other sequence learning algorithms, including statistical methods: autoregressive integrated moving average; feedforward neural networks-time delay neural network and online sequential extreme learning machine; and recurrent neural networks-long short-term memory and echo-state networks on sequence prediction problems with both artificial and real-world data. The HTM model achieves comparable accuracy to other state-of-the-art algorithms. The model also exhibits properties that are critical for sequence learning, including continuous online learning, the ability to handle multiple predictions and branching sequences with high-order statistics, robustness to sensor noise and fault tolerance, and good performance without task-specific hyperparameter tuning. Therefore, the HTM sequence memory not only advances our understanding of how the brain may solve the sequence learning problem but is also applicable to real-world sequence learning problems from continuous data streams.

Test-driven verification/validation of model transformations

Institute of Scientific and Technical Information of China (English)

László LENGYEL; Hassan CHARAF

2015-01-01

Why is it important to verify/validate model transformations? The motivation is to improve the quality of the trans-formations, and therefore the quality of the generated software artifacts. Verified/validated model transformations make it possible to ensure certain properties of the generated software artifacts. In this way, verification/validation methods can guarantee different requirements stated by the actual domain against the generated/modified/optimized software products. For example, a verified/ validated model transformation can ensure the preservation of certain properties during the model-to-model transformation. This paper emphasizes the necessity of methods that make model transformation verified/validated, discusses the different scenarios of model transformation verification and validation, and introduces the principles of a novel test-driven method for verifying/ validating model transformations. We provide a solution that makes it possible to automatically generate test input models for model transformations. Furthermore, we collect and discuss the actual open issues in the field of verification/validation of model transformations.

Sequence Tree Modeling for Combined Accident and Feed-and-Bleed Operation

International Nuclear Information System (INIS)

Kim, Bo Gyung; Kang Hyun Gook; Yoon, Ho Joon

2016-01-01

In order to address this issue, this study suggests the sequence tree model to analyze accident sequence systematically. Using the sequence tree model, all possible scenarios which need a specific safety action to prevent the core damage can be identified and success conditions of safety action under complicated situation such as combined accident will be also identified. Sequence tree is branch model to divide plant condition considering the plant dynamics. Since sequence tree model can reflect the plant dynamics, arising from interaction of different accident timing and plant condition and from the interaction between the operator action, mitigation system, and the indicators for operation, sequence tree model can be used to develop the dynamic event tree model easily. Target safety action for this study is a feed-and-bleed (F and B) operation. A F and B operation directly cools down the reactor cooling system (RCS) using the primary cooling system when residual heat removal by the secondary cooling system is not available. In this study, a TLOFW accident and a TLOFW accident with LOCA were the target accidents. Based on the conventional PSA model and indicators, the sequence tree model for a TLOFW accident was developed. If sampling analysis is performed, practical accident sequences can be identified based on the sequence analysis. If a realistic distribution for the variables can be obtained for sampling analysis, much more realistic accident sequences can be described. Moreover, if the initiating event frequency under a combined accident can be quantified, the sequence tree model can translate into a dynamic event tree model based on the sampling analysis results

Sequence Tree Modeling for Combined Accident and Feed-and-Bleed Operation

Energy Technology Data Exchange (ETDEWEB)

Kim, Bo Gyung; Kang Hyun Gook [KAIST, Daejeon (Korea, Republic of); Yoon, Ho Joon [Khalifa University of Science, Abu Dhabi (United Arab Emirates)

2016-05-15

In order to address this issue, this study suggests the sequence tree model to analyze accident sequence systematically. Using the sequence tree model, all possible scenarios which need a specific safety action to prevent the core damage can be identified and success conditions of safety action under complicated situation such as combined accident will be also identified. Sequence tree is branch model to divide plant condition considering the plant dynamics. Since sequence tree model can reflect the plant dynamics, arising from interaction of different accident timing and plant condition and from the interaction between the operator action, mitigation system, and the indicators for operation, sequence tree model can be used to develop the dynamic event tree model easily. Target safety action for this study is a feed-and-bleed (F and B) operation. A F and B operation directly cools down the reactor cooling system (RCS) using the primary cooling system when residual heat removal by the secondary cooling system is not available. In this study, a TLOFW accident and a TLOFW accident with LOCA were the target accidents. Based on the conventional PSA model and indicators, the sequence tree model for a TLOFW accident was developed. If sampling analysis is performed, practical accident sequences can be identified based on the sequence analysis. If a realistic distribution for the variables can be obtained for sampling analysis, much more realistic accident sequences can be described. Moreover, if the initiating event frequency under a combined accident can be quantified, the sequence tree model can translate into a dynamic event tree model based on the sampling analysis results.

Quantum tunneling in the periodically driven SU(2) model

International Nuclear Information System (INIS)

Arvieu, R.

1991-01-01

The tunneling rate is investigated in the quantum and classical limits using an exactly soluble, periodically driven SU(2) model. The tunneling rate is obtained by solving the time-dependent Schroedinger equation and projecting the exact wave-function on the space of coherent states using the Husimi distribution. The oscillatory, coherent tunneling of the wave-function between two Hartree-Fock minima is observed. The driving plays an important role increasing the tunneling rate by orders of magnitude as compared to the semiclassical results. This is due to the dominant role of excited states in the driven quantum tunneling. (author) 15 refs., 4 figs

Functional immunoglobulin E cross-reactivity between Pas n 1 of Bahia grass pollen and other group 1 grass pollen allergens.

Science.gov (United States)

Davies, J M; Dang, T D; Voskamp, A; Drew, A C; Biondo, M; Phung, M; Upham, J W; Rolland, J M; O'Hehir, R E

2011-02-01

Grass pollens are major triggers of allergic rhinitis and asthma, but the immunological relationships between pollen allergens of the subtropical Bahia grass, Paspalum notatum, and temperate grasses are unresolved. To assess serum IgE cross-reactivity between subtropical P. notatum and temperate Lolium perenne (Ryegrass) pollen allergens. Serum IgE reactivities of grass pollen-allergic patients with P. notatum, L. perenne and Cynodon dactylon (Bermuda grass) pollen extracts and their respective purified group 1 allergens, Pas n 1, Lol p 1 and Cyn d 1, were compared by immunoblotting, ELISA and basophil activation. In a cohort of 51 patients from a temperate region, a high frequency of IgE reactivity with each grass pollen was detected, but reactivity with L. perenne pollen was substantially greater than with P. notatum and C. dactylon pollen. Similarly, serum IgE reactivity with Lol p 1 was greater than with Pas n 1 or Cyn d 1. For seven of eight sera studied in detail, asymmetric serum IgE cross-reactivity was observed; L. perenne pollen inhibited IgE reactivity with P. notatum pollen but not the converse, and IgE reactivity with Pas n 1 was inhibited by Lol p 1 but IgE reactivity with Lol p 1 was not inhibited by Pas n 1 or Cyn d 1. Importantly, P. notatum pollen and Pas n 1 activated basophils in grass pollen-allergic patients from a temperate region, although stimulation was greater by pollen of L. perenne than P. notatum or C. dactylon, and by Lol p 1 than Pas n 1 or Cyn d 1. In contrast, a cohort of 47 patients from a subtropical region showed similar IgE reactivity with P. notatum and L. perenne pollen, and reciprocal cross-inhibition of IgE reactivity between L. perenne and P. notatum. Pollen allergens of the subtropical P. notatum, including Pas n 1, show clinically relevant IgE cross-reactivity with pollen allergens of L. perenne but also species-specific IgE reactivity. © 2011 Blackwell Publishing Ltd.

Model Driven Development of Data Sensitive Systems

DEFF Research Database (Denmark)

Olsen, Petur

2014-01-01

storage systems, where the actual values of the data is not relevant for the behavior of the system. For many systems the values are important. For instance the control flow of the system can be dependent on the input values. We call this type of system data sensitive, as the execution is sensitive...... to the values of variables. This theses strives to improve model-driven development of such data-sensitive systems. This is done by addressing three research questions. In the first we combine state-based modeling and abstract interpretation, in order to ease modeling of data-sensitive systems, while allowing...... efficient model-checking and model-based testing. In the second we develop automatic abstraction learning used together with model learning, in order to allow fully automatic learning of data-sensitive systems to allow learning of larger systems. In the third we develop an approach for modeling and model-based...

Development of NIR calibration models to assess year-to-year variation in total non-structural carbohydrates in grasses using PLSR

DEFF Research Database (Denmark)

Shetty, Nisha; Gislum, René; Jensen, Anne Mette Dahl

2012-01-01

Near-infrared (NIR) spectroscopy was used in combination with chemometrics to quantify total nonstructural carbohydrates (TNC) in grass samples in order to overcome year-to-year variation. A total of 1103 above-ground plant and root samples were collected from different field and pot experiments...... and with various experimental designs in the period from 2001 to 2005. A calibration model was developed using partial least squares regression (PLSR). The calibration model on a large data set spanning five years demonstrated that quantification of TNC using NIR spectroscopy was possible with an acceptable low...

Grass Rooting the System

Science.gov (United States)

Perlman, Janice E.

1976-01-01

Suggests a taxonomy of the grass roots movement and gives a general descriptive over view of the 60 groups studied with respect to origin, constituency, size, funding, issues, and ideology. (Author/AM)

Hilly grasses and leaves: a promising unconventional feed resource for livestock.

OpenAIRE

Hossain M.E.; Karim M.H.; Ahmed M.I.; Sultana S.A.

2016-01-01

The study was undertaken to find out the chemical composition of different hilly grasses and leaves available in Bandarban areas of Bangladesh. Total 10 different hilly grasses and leaves such as Bottle gourd leaf (Lagenaria siceraria), Castor bean leaf (Ricinus communis), Cogon grass (Imperata cylindrica), Dhol kolmi (Ipomoea carnea), Giant reed leaf (Arundo donax), Hilly grass (Cynodon dactylon), Pithraj leaf (Aphanamixis polystachya), Sal leaf (Shorea robusta), Shegun leaf (Tectona grandis...

Data driven CAN node reliability assessment for manufacturing system

Science.gov (United States)

Zhang, Leiming; Yuan, Yong; Lei, Yong

2017-01-01

The reliability of the Controller Area Network(CAN) is critical to the performance and safety of the system. However, direct bus-off time assessment tools are lacking in practice due to inaccessibility of the node information and the complexity of the node interactions upon errors. In order to measure the mean time to bus-off(MTTB) of all the nodes, a novel data driven node bus-off time assessment method for CAN network is proposed by directly using network error information. First, the corresponding network error event sequence for each node is constructed using multiple-layer network error information. Then, the generalized zero inflated Poisson process(GZIP) model is established for each node based on the error event sequence. Finally, the stochastic model is constructed to predict the MTTB of the node. The accelerated case studies with different error injection rates are conducted on a laboratory network to demonstrate the proposed method, where the network errors are generated by a computer controlled error injection system. Experiment results show that the MTTB of nodes predicted by the proposed method agree well with observations in the case studies. The proposed data driven node time to bus-off assessment method for CAN networks can successfully predict the MTTB of nodes by directly using network error event data.

Effect of machinery wheel load on grass yield

DEFF Research Database (Denmark)

Green, Ole; Jørgensen, Rasmus Nyholm; Kristensen, Kristian

2010-01-01

Effect of machinery wheel load on grass   Ole Green1, Rasmus N. Jørgensen2, Kristian Kristensen3, René Gislum3, Dionysis Bochtis1, & Claus G. Sørensen1   1University of Aarhus, Dept. of Agricultural Engineering 2University of Southern Denmark, Inst. of Chemical Eng., Biotechnology and Environmental...... 3University of Aarhus, Dept. of Genetics and Biotechnology   Corresponding author: Ole Green Address & e-mail: Research Centre Foulum, Blichers Allé 20, 8830 Tjele. Ole.Green@agrsci.dk     Abstract   Different traffic intensities have been shown to have a negative influence on the yield of grass...... and clover. A full scale grass-clover field trial was established to estimate the effect on clover-grass yields as a function of different wheel loads and tire pressures. The trial comprised 16 different traffic intensities with 35 replicates and 1 traffic free treatment with 245 replicates, totalling 17...

Alley cropping of legumes with grasses as forages : Effect of different grass species and row spacing of gliricidia on the growth and biomass production of forages

Directory of Open Access Journals (Sweden)

Siti Yuhaeni

1998-12-01

Full Text Available A study to evaluate the effect of different grass species and row spacing of gliricidia (Gliricidia sepium on the growth and biomass production of forages in an alley cropping system was conducted in two different agroclimatical zones i.e. Bogor, located at 500 m a .s .l . with an average annual rainfall of 3,112 nun/year and Sukabumi located at 900 m a .s .l . with an average annual rainfall of 1,402 mm/year . Both locations have low N, P, and K content and the soil is classified as acidic. The experimental design used was a split plot design with 3 replicates . The main plots were different grass species i.e. king grass (Pennisetum purpureum x P. typhoides and elephant grass (P. purpureum. The sub plots were the row spacing of gliricidia at 2, 3, 4, 6 m (1 hedgerows and 4 m (2 hedgerows. The results indicated that the growth and biomass production of grasses were significantly affected (P<0 .05 by the treatments in Bogor. The highest biomass productions was obtained from the 2 m row spacing which gave the highest dry matter production of grasses (1 .65 kg/hill and gliricidia (0 .086 kg/tree . In Sukabumi the growth and biomass production of grasses and gliricidia were also significantly affected by the treatments . The highest dry matter production was obtained with 2 m row spacing (dry matter of grasses and gliricidia were 1 .12 kg/hill and 0 .026 kg/tree, respectively . The result further indicated that biomass production of forages increased with the increase in gliricidia population. The alley cropping system wich is suitable for Bogor was the 2 m row spacing of gliricidia intercropped with either king or elephant grass and for Sukabumi 2 and 4 m (2 rows of gliricidia row spacing intercropped with king or elephant grass .

Lessons Learned from Stakeholder-Driven Modeling in the Western Lake Erie Basin

Science.gov (United States)

Muenich, R. L.; Read, J.; Vaccaro, L.; Kalcic, M. M.; Scavia, D.

2017-12-01

Lake Erie's history includes a great environmental success story. Recognizing the impact of high phosphorus loads from point sources, the United States and Canada 1972 Great Lakes Water Quality Agreement set load reduction targets to reduce algae blooms and hypoxia. The Lake responded quickly to those reductions and it was declared a success. However, since the mid-1990s, Lake Erie's algal blooms and hypoxia have returned, and this time with a dominant algae species that produces toxins. Return of the algal blooms and hypoxia is again driven by phosphorus loads, but this time a major source is the agriculturally-dominated Maumee River watershed that covers NW Ohio, NE Indiana, and SE Michigan, and the hypoxic extent has been shown to be driven by Maumee River loads plus those from the bi-national and multiple land-use St. Clair - Detroit River system. Stakeholders in the Lake Erie watershed have a long history of engagement with environmental policy, including modeling and monitoring efforts. This talk will focus on the application of interdisciplinary, stakeholder-driven modeling efforts aimed at understanding the primary phosphorus sources and potential pathways to reduce these sources and the resulting algal blooms and hypoxia in Lake Erie. We will discuss the challenges, such as engaging users with different goals, benefits to modeling, such as improvements in modeling data, and new research questions emerging from these modeling efforts that are driven by end-user needs.

Perspectives of data-driven LPV modeling of high-purity distillation columns

NARCIS (Netherlands)

Bachnas, A.A.; Toth, R.; Mesbah, A.; Ludlage, J.H.A.

2013-01-01

Abstract—This paper investigates data-driven, Linear- Parameter-Varying (LPV) modeling of a high-purity distillation column. Two LPV modeling approaches are studied: a local approach, corresponding to the interpolation of Linear Time- Invariant (LTI) models identified at steady-state purity levels,

Satellite Phenology Observations Inform Peak Season of Allergenic Grass Pollen Aerobiology across Two Continents

Science.gov (United States)

Huete, A. R.; Devadas, R.; Davies, J.

2015-12-01

Pollen exposure and prevalence of allergenic diseases have increased in many parts of the world during the last 30 years, with exposure to aeroallergen grass pollen expected to intensify with climate change, raising increased concerns for allergic diseases. The primary contributing factors to higher allergenic plant species presence are thought to be climate change, land conversion, and biotic mixing of species. Conventional methods for monitoring airborne pollen are hampered by a lack of sampling sites and heavily rely on meteorology with less attention to land cover updates and monitoring of key allergenic species phenology stages. Satellite remote sensing offers an alternative method to overcome the restrictive coverage afforded by in situ pollen networks by virtue of its synoptic coverage and repeatability of measurements that enable timely updates of land cover and land use information and monitoring landscape dynamics and interactions with human activity and climate. In this study, we assessed the potential of satellite observations of urban/peri-urban environments to directly inform landscape conditions conducive to pollen emissions. We found satellite measurements of grass cover phenological evolution to be highly correlated with in situ aerobiological grass pollen concentrations in five urban centres located across two hemispheres (Australia and France). Satellite greenness data from the Moderate Resolution Imaging Spectroradiometer (MODIS) were found to be strongly synchronous with grass pollen aerobiology in both temperate grass dominated sites (France and Melbourne), as well as in Sydney, where multiple pollen peaks coincided with the presence of subtropical grasses. Employing general additive models (GAM), the satellite phenology data provided strong predictive capabilities to inform airborne pollen levels and forecast periods of grass pollen emissions at all five sites. Satellite phenology offer promising opportunities of improving public health risk

Energy evaluation of fresh grass in the diets of lactating dairy cows

NARCIS (Netherlands)

Bruinenberg, M.H.; Zom, R.L.G.; Valk, H.

2002-01-01

The discrepancy between the estimated feeding value of fresh grass and the output per kg grass in terms of milk and maintenance was studied by evaluating 12 experiments with grass-fed dairy cows. The percentage grass in the diets varied between 40 and 90. Intake and milk production were recorded

Spatially explicit integrated modeling and economic valuation of climate driven land use change and its indirect effects.

Science.gov (United States)

Bateman, Ian; Agarwala, Matthew; Binner, Amy; Coombes, Emma; Day, Brett; Ferrini, Silvia; Fezzi, Carlo; Hutchins, Michael; Lovett, Andrew; Posen, Paulette

2016-10-01

We present an integrated model of the direct consequences of climate change on land use, and the indirect effects of induced land use change upon the natural environment. The model predicts climate-driven shifts in the profitability of alternative uses of agricultural land. Both the direct impact of climate change and the induced shift in land use patterns will cause secondary effects on the water environment, for which agriculture is the major source of diffuse pollution. We model the impact of changes in such pollution on riverine ecosystems showing that these will be spatially heterogeneous. Moreover, we consider further knock-on effects upon the recreational benefits derived from water environments, which we assess using revealed preference methods. This analysis permits a multi-layered examination of the economic consequences of climate change, assessing the sequence of impacts from climate change through farm gross margins, land use, water quality and recreation, both at the individual and catchment scale. Copyright © 2016 Elsevier Ltd. All rights reserved.

The Potential of Cellulosic Ethanol Production from Grasses in Thailand

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Jinaporn Wongwatanapaiboon

2012-01-01

Full Text Available The grasses in Thailand were analyzed for the potentiality as the alternative energy crops for cellulosic ethanol production by biological process. The average percentage composition of cellulose, hemicellulose, and lignin in the samples of 18 types of grasses from various provinces was determined as 31.85–38.51, 31.13–42.61, and 3.10–5.64, respectively. The samples were initially pretreated with alkaline peroxide followed by enzymatic hydrolysis to investigate the enzymatic saccharification. The total reducing sugars in most grasses ranging from 500–600 mg/g grasses (70–80% yield were obtained. Subsequently, 11 types of grasses were selected as feedstocks for the ethanol production by simultaneous saccharification and cofermentation (SSCF. The enzymes, cellulase and xylanase, were utilized for hydrolysis and the yeasts, Saccharomyces cerevisiae and Pichia stipitis, were applied for cofermentation at 35°C for 7 days. From the results, the highest yield of ethanol, 1.14 g/L or 0.14 g/g substrate equivalent to 32.72% of the theoretical values was obtained from Sri Lanka ecotype vetiver grass. When the yields of dry matter were included in the calculations, Sri Lanka ecotype vetiver grass gave the yield of ethanol at 1,091.84 L/ha/year, whereas the leaves of dwarf napier grass showed the maximum yield of 2,720.55 L/ha/year (0.98 g/L or 0.12 g/g substrate equivalent to 30.60% of the theoretical values.

Towards an Experimental Framework for Measuring Usability of Model-Driven Tools

NARCIS (Netherlands)

Panach, Jose Ignacio; Condori-Fernandez, Nelly; Baar, Arthur; Vos, Tanja; Romeu, Ignacio; Pastor, Oscar; Campos, Pedro; Graham, Nicholas; Jorge, Joaquim; Nunes, Nuno; Palanque, Philippe; Winckler, Marco

2011-01-01

According to the Model-Driven Development (MDD) paradigm, analysts can substantially improve the software development process concentrating their efforts on a conceptual model, which can be transformed into code by means of transformation rules applied by a model compiler. However, MDD tools are not

Parameterized data-driven fuzzy model based optimal control of a semi-batch reactor.

Science.gov (United States)

Kamesh, Reddi; Rani, K Yamuna

2016-09-01

A parameterized data-driven fuzzy (PDDF) model structure is proposed for semi-batch processes, and its application for optimal control is illustrated. The orthonormally parameterized input trajectories, initial states and process parameters are the inputs to the model, which predicts the output trajectories in terms of Fourier coefficients. Fuzzy rules are formulated based on the signs of a linear data-driven model, while the defuzzification step incorporates a linear regression model to shift the domain from input to output domain. The fuzzy model is employed to formulate an optimal control problem for single rate as well as multi-rate systems. Simulation study on a multivariable semi-batch reactor system reveals that the proposed PDDF modeling approach is capable of capturing the nonlinear and time-varying behavior inherent in the semi-batch system fairly accurately, and the results of operating trajectory optimization using the proposed model are found to be comparable to the results obtained using the exact first principles model, and are also found to be comparable to or better than parameterized data-driven artificial neural network model based optimization results. Copyright © 2016 ISA. Published by Elsevier Ltd. All rights reserved.

Perennial Grass Bioenergy Cropping on Wet Marginal Land

NARCIS (Netherlands)

Das, Srabani; Teuffer, Karin; Stoof, Cathelijne R.; Walter, Michael F.; Walter, M.T.; Steenhuis, Tammo S.; Richards, Brian K.

2018-01-01

The control of soil moisture, vegetation type, and prior land use on soil health parameters of perennial grass cropping systems on marginal lands is not well known. A fallow wetness-prone marginal site in New York (USA) was converted to perennial grass bioenergy feedstock production. Quadruplicate

Diffusion tensor magnetic resonance imaging driven growth modeling for radiotherapy target definition in glioblastoma.

Science.gov (United States)

Jensen, Morten B; Guldberg, Trine L; Harbøll, Anja; Lukacova, Slávka; Kallehauge, Jesper F

2017-11-01

The clinical target volume (CTV) in radiotherapy is routinely based on gadolinium contrast enhanced T1 weighted (T1w + Gd) and T2 weighted fluid attenuated inversion recovery (T2w FLAIR) magnetic resonance imaging (MRI) sequences which have been shown to over- or underestimate the microscopic tumor cell spread. Gliomas favor spread along the white matter fiber tracts. Tumor growth models incorporating the MRI diffusion tensors (DTI) allow to account more consistently for the glioma growth. The aim of the study was to investigate the potential of a DTI driven growth model to improve target definition in glioblastoma (GBM). Eleven GBM patients were scanned using T1w, T2w FLAIR, T1w + Gd and DTI. The brain was segmented into white matter, gray matter and cerebrospinal fluid. The Fisher-Kolmogorov growth model was used assuming uniform proliferation and a difference in white and gray matter diffusion of a ratio of 10. The tensor directionality was tested using an anisotropy weighting parameter set to zero (γ0) and twenty (γ20). The volumetric comparison was performed using Hausdorff distance, Dice similarity coefficient (DSC) and surface area. The median of the standard CTV (CTVstandard) was 180 cm 3 . The median surface area of CTVstandard was 211 cm 2 . The median surface area of respective CTV γ0 and CTV γ20 significantly increased to 338 and 376 cm 2 , respectively. The Hausdorff distance was greater than zero and significantly increased for both CTV γ0 and CTV γ20 with respective median of 18.7 and 25.2 mm. The DSC for both CTV γ0 and CTV γ20 were significantly below one with respective median of 0.74 and 0.72, which means that 74 and 72% of CTVstandard were included in CTV γ0 and CTV γ20, respectively. DTI driven growth models result in CTVs with a significantly increased surface area, a significantly increased Hausdorff distance and decreased overlap between the standard and model derived volume.

UAV-imaging to model growth response of marram grass to sand burial: Implications for coastal dune development

Science.gov (United States)

Nolet, Corjan; van Puijenbroek, Marinka; Suomalainen, Juha; Limpens, Juul; Riksen, Michel

2018-04-01

Vegetated coastal dunes have the capacity to keep up with sea-level rise by accumulating and stabilizing wind-blown sand. In Europe, this is attributed to marram grass (Ammophila arenaria), a coastal grass species that combines two unique advantages for dune-building: (1) a very high tolerance to burial by wind-blown sand, and (2) more vigorous growth due to positive feedback to sand burial. However, while these vegetation characteristics have been demonstrated, observational data has not been used to model a function to describe the growth response of Ammophila to sand burial. Studies that model coastal dune development by incorporating positive feedback, as a result, may be hampered by growth functions that are unvalidated against field data. Therefore, this study aims to parameterize an empirical relationship to model the growth response of Ammophila to burial by wind-blown sand. A coastal foredune along a nourished beach in the Netherlands was monitored from April 2015 to April 2016. High-resolution geospatial data was acquired using an Unmanned Aerial Vehicle (UAV). Growth response of Ammophila, expressed by changes in Normalized Difference Vegetation Index (Δ NDVI) and vegetation cover (Δ Cover), is related to a sand burial gradient by fitting a Gaussian function using nonlinear quantile regression. The regression curves indicate an optimal burial rate for Ammophila of 0.31 m of sand per growing season, and suggest (by extrapolation of the data) a maximum burial tolerance for Ammophila between 0.78 (for Δ Cover) and 0.96 m (for Δ NDVI) of sand per growing season. These findings are advantageous to coastal management: maximizing the potential of Ammophila to develop dunes maximizes the potential of coastal dunes to provide coastal safety.

Evolutionary modes of emergence of short interspersed nuclear element (SINE) families in grasses.

Science.gov (United States)

Kögler, Anja; Schmidt, Thomas; Wenke, Torsten

2017-11-01

Short interspersed nuclear elements (SINEs) are non-autonomous transposable elements which are propagated by retrotransposition and constitute an inherent part of the genome of most eukaryotic species. Knowledge of heterogeneous and highly abundant SINEs is crucial for de novo (or improvement of) annotation of whole genome sequences. We scanned Poaceae genome sequences of six important cereals (Oryza sativa, Triticum aestivum, Hordeum vulgare, Panicum virgatum, Sorghum bicolor, Zea mays) and Brachypodium distachyon to examine the diversity and evolution of SINE populations. We comparatively analyzed the structural features, distribution, evolutionary relation and abundance of 32 SINE families and subfamilies within grasses, comprising 11 052 individual copies. The investigation of activity profiles within the Poaceae provides insights into their species-specific diversification and amplification. We found that Poaceae SINEs (PoaS) fall into two length categories: simple SINEs of up to 180 bp and dimeric SINEs larger than 240 bp. Detailed analysis at the nucleotide level revealed that multimerization of related and unrelated SINE copies is an important evolutionary mechanism of SINE formation. We conclude that PoaS families diversify by massive reshuffling between SINE families, likely caused by insertion of truncated copies, and provide a model for this evolutionary scenario. Twenty-eight of 32 PoaS families and subfamilies show significant conservation, in particular either in the 5' or 3' regions, across Poaceae species and share large sequence stretches with one or more other PoaS families. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

Tensile fracture properties of seven tropical grasses at different phenological stages

NARCIS (Netherlands)

Jacobs, A.A.A.; Scheper, J.A.; Benvenutti, M.A.; Gordon, I.J.; Poppi, D.P.; Elgersma, A.

2011-01-01

The intake of forage grasses by grazing ruminants is closely related to the mechanical fracture properties of grasses. The relationship between the tensile fracture properties of grasses and foraging behaviour is of particular importance in tropical reproductive swards composed of both stems and

Grass cell wall feruloylation: distribution of bound ferulate and candidate gene expression in Brachypodium distachyon

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Hugo Bruno Correa Molinari

2013-03-01

Full Text Available The cell walls of grasses such as wheat, maize, rice and sugar cane, contain large amounts of ferulate that is ester-linked to the cell wall polysaccharide glucuronoarabinoxylan (GAX. This ferulate is considered to limit the digestibility of polysaccharide in grass biomass as it forms covalent linkages between polysaccharide and lignin components. Candidate genes within a grass-specific clade of the BAHD acyl-coA transferase superfamily have been identified as being responsible for the ester linkage of ferulate to GAX. Manipulation of these BAHD genes may therefore be a biotechnological target for increasing efficiency of conversion of grass biomass into biofuel. Here, we describe the expression of these candidate genes and amounts of bound ferulate from various tissues and developmental stages of the model grass Brachypodium distachyon. BAHD candidate transcripts and significant amounts of bound ferulate were present in every tissue and developmental stage. We hypothesise that BAHD candidate genes similar to the recently described rice OsPMT gene (PMT sub-clade are principally responsible for the bound coumaric acid (pCA, and that other BAHD candidates (non-PMT sub-clade are responsible for bound ferulic acid (FA. There were some similarities with between the ratio of expression non-PMT / PMT genes and the ratio of bound FA / pCA between tissue types, compatible with this hypothesis. However, much further work to modify BAHD genes in grasses and to characterise the heterologously expressed proteins is required to demonstrate their function.

How much gas can we get from grass?

International Nuclear Information System (INIS)

Nizami, A.S.; Orozco, A.; Groom, E.; Dieterich, B.; Murphy, J.D.

2012-01-01

Highlights: ► We highlight the various results for biomethane potential that may be obtained from the same grass silage. ► The results indicated that methane potential varied from 350 to 493 L CH 4 kg −1 VS added for three different BMP procedures. ► We compare two distinct digestion systems using the same grass. ► A two stage wet system achieved 451 L CH 4 kg −1 VS added over a 50 day retention period. ► A two phase system achieved 341 L CH 4 kg −1 VS added at a 30 day retention time. -- Abstract: Grass biomethane has been shown to be a sustainable gaseous transport biofuel, with a good energy balance, and significant potential for economic viability. Of issue for the designer is the variation in characteristics of the grass depending on location of source, time of cut and species. Further confusion arises from the biomethane potential tests (BMP) which have a tendency to give varying results. This paper has dual ambitions. One of these is to highlight the various results for biomethane potential that may be obtained from the same grass silage. The results indicated that methane potential from the same grass silage varied from 350 to 493 L CH 4 kg −1 VS added for three different BMP procedures. The second ambition is to attempt to compare two distinct digestion systems again using the same grass: a two stage continuously stirred tank reactor (CSTR); and a sequentially fed leach bed reactor connected to an upflow anaerobic sludge blanket (SLBR–UASB). The two engineered systems were designed, fabricated, commissioned and operated at small pilot scale until stable optimal operating conditions were reached. The CSTR system achieved 451 L CH 4 kg −1 VS added over a 50 day retention period. The SLBR–UASB achieved 341 L CH 4 kg −1 VS added at a 30 day retention time.

Coefficients of resistance to cold-air-drainage winds on a grass-covered slope

International Nuclear Information System (INIS)

Komoda, H.; Kobayashi, T.; Mori, M.; Kaneko, T.

2006-01-01

The cold-air-drainage (CAD) wind is one of the most familiar local winds in Japan. It is driven by the surplus of density, or the deficit of potential temperature produced by radiative cooling in the surface air layer on a slope, and is resisted by the ground surface and the surrounding atmosphere. The coefficients of resistance of the ground surface and the surrounding atmosphere change with the CAD wind speed. The observations made on a grass-covered slope of Mt. Kuju showed that the resistance exerted by the surrounding atmosphere was much larger than that by the ground surface, and the sum of two coefficients of resistance decreased by one order of magnitude when the CAD wind speed exceeded some critical value

Nucleotide Sequence Diversity and Linkage Disequilibrium of Four Nuclear Loci in Foxtail Millet (Setaria italica.

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Shui-Lian He

Full Text Available Foxtail millet (Setaria italica (L. Beauv is one of the earliest domesticated grains, which has been cultivated in northern China by 8,700 years before present (YBP and across Eurasia by 4,000 YBP. Owing to a small genome and diploid nature, foxtail millet is a tractable model crop for studying functional genomics of millets and bioenergy grasses. In this study, we examined nucleotide sequence diversity, geographic structure, and levels of linkage disequilibrium at four nuclear loci (ADH1, G3PDH, IGS1 and TPI1 in representative samples of 311 landrace accessions across its cultivated range. Higher levels of nucleotide sequence and haplotype diversity were observed in samples from China relative to other sampled regions. Genetic assignment analysis classified the accessions into seven clusters based on nucleotide sequence polymorphisms. Intralocus LD decayed rapidly to half the initial value within ~1.2 kb or less.

Nucleotide Sequence Diversity and Linkage Disequilibrium of Four Nuclear Loci in Foxtail Millet (Setaria italica).

Science.gov (United States)

He, Shui-Lian; Yang, Yang; Morrell, Peter L; Yi, Ting-Shuang

2015-01-01

Foxtail millet (Setaria italica (L.) Beauv) is one of the earliest domesticated grains, which has been cultivated in northern China by 8,700 years before present (YBP) and across Eurasia by 4,000 YBP. Owing to a small genome and diploid nature, foxtail millet is a tractable model crop for studying functional genomics of millets and bioenergy grasses. In this study, we examined nucleotide sequence diversity, geographic structure, and levels of linkage disequilibrium at four nuclear loci (ADH1, G3PDH, IGS1 and TPI1) in representative samples of 311 landrace accessions across its cultivated range. Higher levels of nucleotide sequence and haplotype diversity were observed in samples from China relative to other sampled regions. Genetic assignment analysis classified the accessions into seven clusters based on nucleotide sequence polymorphisms. Intralocus LD decayed rapidly to half the initial value within ~1.2 kb or less.

UAVs and Machine Learning Revolutionising Invasive Grass and Vegetation Surveys in Remote Arid Lands

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Juan Sandino

2018-02-01

Full Text Available The monitoring of invasive grasses and vegetation in remote areas is challenging, costly, and on the ground sometimes dangerous. Satellite and manned aircraft surveys can assist but their use may be limited due to the ground sampling resolution or cloud cover. Straightforward and accurate surveillance methods are needed to quantify rates of grass invasion, offer appropriate vegetation tracking reports, and apply optimal control methods. This paper presents a pipeline process to detect and generate a pixel-wise segmentation of invasive grasses, using buffel grass (Cenchrus ciliaris and spinifex (Triodia sp. as examples. The process integrates unmanned aerial vehicles (UAVs also commonly known as drones, high-resolution red, green, blue colour model (RGB cameras, and a data processing approach based on machine learning algorithms. The methods are illustrated with data acquired in Cape Range National Park, Western Australia (WA, Australia, orthorectified in Agisoft Photoscan Pro, and processed in Python programming language, scikit-learn, and eXtreme Gradient Boosting (XGBoost libraries. In total, 342,626 samples were extracted from the obtained data set and labelled into six classes. Segmentation results provided an individual detection rate of 97% for buffel grass and 96% for spinifex, with a global multiclass pixel-wise detection rate of 97%. Obtained results were robust against illumination changes, object rotation, occlusion, background cluttering, and floral density variation.

Validation of rice genome sequence by optical mapping

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Pape Louise

2007-08-01

Full Text Available Abstract Background Rice feeds much of the world, and possesses the simplest genome analyzed to date within the grass family, making it an economically relevant model system for other cereal crops. Although the rice genome is sequenced, validation and gap closing efforts require purely independent means for accurate finishing of sequence build data. Results To facilitate ongoing sequencing finishing and validation efforts, we have constructed a whole-genome SwaI optical restriction map of the rice genome. The physical map consists of 14 contigs, covering 12 chromosomes, with a total genome size of 382.17 Mb; this value is about 11% smaller than original estimates. 9 of the 14 optical map contigs are without gaps, covering chromosomes 1, 2, 3, 4, 5, 7, 8 10, and 12 in their entirety – including centromeres and telomeres. Alignments between optical and in silico restriction maps constructed from IRGSP (International Rice Genome Sequencing Project and TIGR (The Institute for Genomic Research genome sequence sources are comprehensive and informative, evidenced by map coverage across virtually all published gaps, discovery of new ones, and characterization of sequence misassemblies; all totalling ~14 Mb. Furthermore, since optical maps are ordered restriction maps, identified discordances are pinpointed on a reliable physical scaffold providing an independent resource for closure of gaps and rectification of misassemblies. Conclusion Analysis of sequence and optical mapping data effectively validates genome sequence assemblies constructed from large, repeat-rich genomes. Given this conclusion we envision new applications of such single molecule analysis that will merge advantages offered by high-resolution optical maps with inexpensive, but short sequence reads generated by emerging sequencing platforms. Lastly, map construction techniques presented here points the way to new types of comparative genome analysis that would focus on discernment of

Effects of rye grass coverage on soil loss from loess slopes

Directory of Open Access Journals (Sweden)

Yuequn Dong

2015-09-01

Full Text Available Vegetative coverage is commonly used to reduce urban slope soil erosion. Laboratory experimental study on soil erosion under grass covered slopes is conventionally time and space consuming. In this study, a new method is suggested to study the influences of vegetation coverage on soil erosion from a sloped loess surface under three slope gradients of 5°, 15°, and 25°; four rye grass coverages of 0%, 25%, 50%, and 75%; and three rainfall intensities of 60, 90, and 120 mm/h with a silt-loamy loess soil. Rye grasses were planted in the field with the studied soil before being transplanted into a laboratory flume. Grass was allowed to resume growth for a period before the rain simulation experiment. Results showed that the grass cover reduced soil erosion by 63.90% to 92.75% and sediment transport rate by 80.59% to 96.17% under different slope gradients and rainfall intensities. The sediment concentration/sediment transport rate from bare slope was significantly higher than from a grass-covered slope. The sediment concentration/transport rate from grass-covered slopes decreased linearly with grass coverage and increased with rainfall intensity. The sediment concentration/transport rate from the bare slope increased as a power function of slope and reached the maximum value at the gradient of about 25°, whereas that from grass-covered slope increased linearly and at much lower levels. The results of this study can be used to estimate the effect of vegetation on soil erosion from loess slopes.

Devil's staircase and the absence of chaos in the dc- and ac-driven overdamped Frenkel-Kontorova model

Science.gov (United States)

Sokolović, I.; Mali, P.; Odavić, J.; Radošević, S.; Medvedeva, S. Yu.; Botha, A. E.; Shukrinov, Yu. M.; Tekić, J.

2017-08-01

The devil's staircase structure arising from the complete mode locking of an entirely nonchaotic system, the overdamped dc+ac driven Frenkel-Kontorova model with deformable substrate potential, was observed. Even though no chaos was found, a hierarchical ordering of the Shapiro steps was made possible through the use of a previously introduced continued fraction formula. The absence of chaos, deduced here from Lyapunov exponent analyses, can be attributed to the overdamped character and the Middleton no-passing rule. A comparative analysis of a one-dimensional stack of Josephson junctions confirmed the disappearance of chaos with increasing dissipation. Other common dynamic features were also identified through this comparison. A detailed analysis of the amplitude dependence of the Shapiro steps revealed that only for the case of a purely sinusoidal substrate potential did the relative sizes of the steps follow a Farey sequence. For nonsinusoidal (deformed) potentials, the symmetry of the Stern-Brocot tree, depicting all members of particular Farey sequence, was seen to be increasingly broken, with certain steps being more prominent and their relative sizes not following the Farey rule.

Integrating Usability Evaluation into Model-Driven Video Game Development

OpenAIRE

Fernandez , Adrian; Insfran , Emilio; Abrahão , Silvia; Carsí , José ,; Montero , Emanuel

2012-01-01

Part 3: Short Papers; International audience; The increasing complexity of video game development highlights the need of design and evaluation methods for enhancing quality and reducing time and cost. In this context, Model-Driven Development approaches seem to be very promising since a video game can be obtained by transforming platform-independent models into platform-specific models that can be in turn transformed into code. Although this approach is started to being used for video game de...

Modelling mono-digestion of grass silage in a 2-stage CSTR anaerobic digester using ADM1.

Science.gov (United States)

Thamsiriroj, T; Murphy, J D

2011-01-01

This paper examines 174 days of experimental data and modelling of mono-digestion of grass silage in a two stage wet process with recirculation of liquor; the two vessels have an effective volume of 312 L each. The organic loading rate is initiated at 0.5 kg VS m(-3) d(-1) (first 74 days) and subsequently increased to 1 kg VS m(-3) d(-1). The experimental data was used to generate a mathematical model (ADM1) which was calibrated over the first 74 days of operation. Good accuracy with experimental data was found for the subsequent 100 days. Results of the model would suggest starting the process without recirculation and thus building up the solids content of the liquor. As the level of VFA increases, recirculation should be employed to control VFA. Recirculation also controls solids content and pH. Methane production was estimated at 88% of maximum theoretical production. Copyright © 2010 Elsevier Ltd. All rights reserved.

Response of itchgrass and johnson grass to asulam/dalapon combinations

International Nuclear Information System (INIS)

Hook, B.J.

1986-01-01

Activities of asumlam [methyl[(4-aminophenyl)sulfonyl]carbamate], dalapon (2,2-dichloropropionic acid) and asulam/dalapon combinations on itchgrass (Rottboellia exaltata L.f.) and johnson grass [Sorghum halepense (L.) Pers.] were examined. When metabolism of 14 C-asulam was monitored, seven days after application, 97-100% of recovered 14 C co-chromatographed with 14 C-asulam. Itchgrass exhibited rapid uptake of 14 C-asulam within 8 hr after application. Asumlam concentrations remained constant in the plant between 8 and 72 hr. Johnson grass plants showed a differential response to asulam and asulam/dalapon treatments. Asulam-treated johnson grass absorbed 26-34% 14 C within 2 hr with no future significant increase in absorption in absorption through 72 hr. Treatment of johnson grass with asulam/dalapon enhanced 14 C absorption with time. At 24 and 72 hr 14 C levels were double that absorbed from treatment of asulam alone. Movement of 14 C-asulam in the apoplast and symplast of both itchgrass and johnson grass was noted. The highest radiolabel accumulated in the lower leaves of itchgrass and remained in the treated leaf of johnson grass

Native Grass Community Management Plan for the Oak Ridge Reservation

Energy Technology Data Exchange (ETDEWEB)

Ryon, Michael G [ORNL; Parr, Patricia Dreyer [ORNL; Cohen, Kari [ORNL

2007-06-01

Land managers at the Department of Energy's Oak Ridge National Laboratory in East Tennessee are restoring native warm-season grasses and wildflowers to various sites across the Oak Ridge Reservation (ORR). Some of the numerous benefits to planting native grasses and forbs include improved habitat quality for wildlife, improved aesthetic values, lower long-term maintenance costs, and compliance with Executive Order 13112 (Clinton 1999). Challenges to restoring native plants on the ORR include the need to gain experience in establishing and maintaining these communities and the potentially greater up-front costs of getting native grasses established. The goals of the native grass program are generally outlined on a fiscal-year basis. An overview of some of the issues associated with the successful and cost-effective establishment and maintenance of native grass and wildflower stands on the ORR is presented in this report.

Reversing land degradation through grasses: a systematic meta-analysis in the Indian tropics

Science.gov (United States)

Mandal, Debashis; Srivastava, Pankaj; Giri, Nishita; Kaushal, Rajesh; Cerda, Artemi; Meherul Alam, Nurnabi

2017-02-01

Although intensive agriculture is necessary to sustain the world's growing population, accelerated soil erosion contributes to a decrease in the environmental health of ecosystems at local, regional and global scales. Reversing the process of land degradation using vegetative measures is of utmost importance in such ecosystems. The present study critically analyzes the effect of grasses in reversing the process of land degradation using a systematic review. The collected information was segregated under three different land use and land management situations. Meta-analysis was applied to test the hypothesis that the use of grasses reduces runoff and soil erosion. The effect of grasses was deduced for grass strip and in combination with physical structures. Similarly, the effects of grasses were analyzed in degraded pasture lands. The overall result of the meta-analysis showed that infiltration capacity increased approximately 2-fold after planting grasses across the slopes in agricultural fields. Grazing land management through a cut-and-carry system increased conservation efficiencies by 42 and 63 % with respect to reduction in runoff and erosion, respectively. Considering the comprehensive performance index (CPI), it has been observed that hybrid Napier (Pennisetum purpureum) and sambuta (Saccharum munja) grass seem to posses the most desirable attributes as an effective grass barrier for the western Himalayas and Eastern Ghats, while natural grass (Dichanthium annulatum) and broom grass (Thysanolaena maxima) are found to be most promising grass species for the Konkan region of the Western Ghats and the northeastern Himalayan region, respectively. In addition to these benefits, it was also observed that soil carbon loss can be reduced by 83 % with the use of grasses. Overall, efficacy for erosion control of various grasses was more than 60 %; hence, their selection should be based on the production potential of these grasses under given edaphic and agro

Anaerobic co-digestion of sewage sludge with shredded grass from public green spaces.

Science.gov (United States)

Hidaka, Taira; Arai, Sayuri; Okamoto, Seiichiro; Uchida, Tsutomu

2013-02-01

Adding greenery from public spaces to the co-digestion process with sewage sludge was evaluated by shredding experiments and laboratory-scale batch and continuous mesophilic anaerobic fermentation experiments. The ratio of the shredded grass with 20mm or less in length by a commercially available shredder was 93%. The methane production was around 0.2NL/gVS-grass in the batch experiment. The continuous experiment fed with sewage sludge and shredded grass was stably operated for 81days. The average methane production was 0.09NL/gVS-grass when the TS ratio of the sewage sludge and the grass was 10:1. This value was smaller than those of other reports using grass silage, but the grass species in this study were not managed, and the collected grass was just shredded and not ensiled before feeding to the reactor for simple operation. The addition of grass to a digester can improve the carbon/nitrogen ratio, methane production and dewaterability. Copyright © 2013 Elsevier Ltd. All rights reserved.

Modelling exciton–phonon interactions in optically driven quantum dots

DEFF Research Database (Denmark)

Nazir, Ahsan; McCutcheon, Dara

2016-01-01

We provide a self-contained review of master equation approaches to modelling phonon effects in optically driven self-assembled quantum dots. Coupling of the (quasi) two-level excitonic system to phonons leads to dissipation and dephasing, the rates of which depend on the excitation conditions...

Simulating large-scale pedestrian movement using CA and event driven model: Methodology and case study

Science.gov (United States)

Li, Jun; Fu, Siyao; He, Haibo; Jia, Hongfei; Li, Yanzhong; Guo, Yi

2015-11-01

Large-scale regional evacuation is an important part of national security emergency response plan. Large commercial shopping area, as the typical service system, its emergency evacuation is one of the hot research topics. A systematic methodology based on Cellular Automata with the Dynamic Floor Field and event driven model has been proposed, and the methodology has been examined within context of a case study involving the evacuation within a commercial shopping mall. Pedestrians walking is based on Cellular Automata and event driven model. In this paper, the event driven model is adopted to simulate the pedestrian movement patterns, the simulation process is divided into normal situation and emergency evacuation. The model is composed of four layers: environment layer, customer layer, clerk layer and trajectory layer. For the simulation of movement route of pedestrians, the model takes into account purchase intention of customers and density of pedestrians. Based on evacuation model of Cellular Automata with Dynamic Floor Field and event driven model, we can reflect behavior characteristics of customers and clerks at the situations of normal and emergency evacuation. The distribution of individual evacuation time as a function of initial positions and the dynamics of the evacuation process is studied. Our results indicate that the evacuation model using the combination of Cellular Automata with Dynamic Floor Field and event driven scheduling can be used to simulate the evacuation of pedestrian flows in indoor areas with complicated surroundings and to investigate the layout of shopping mall.

Model morphing and sequence assignment after molecular replacement.

Science.gov (United States)

Terwilliger, Thomas C; Read, Randy J; Adams, Paul D; Brunger, Axel T; Afonine, Pavel V; Hung, Li-Wei

2013-11-01

A procedure termed `morphing' for improving a model after it has been placed in the crystallographic cell by molecular replacement has recently been developed. Morphing consists of applying a smooth deformation to a model to make it match an electron-density map more closely. Morphing does not change the identities of the residues in the chain, only their coordinates. Consequently, if the true structure differs from the working model by containing different residues, these differences cannot be corrected by morphing. Here, a procedure that helps to address this limitation is described. The goal of the procedure is to obtain a relatively complete model that has accurate main-chain atomic positions and residues that are correctly assigned to the sequence. Residues in a morphed model that do not match the electron-density map are removed. Each segment of the resulting trimmed morphed model is then assigned to the sequence of the molecule using information about the connectivity of the chains from the working model and from connections that can be identified from the electron-density map. The procedure was tested by application to a recently determined structure at a resolution of 3.2 Å and was found to increase the number of correctly identified residues in this structure from the 88 obtained using phenix.resolve sequence assignment alone (Terwilliger, 2003) to 247 of a possible 359. Additionally, the procedure was tested by application to a series of templates with sequence identities to a target structure ranging between 7 and 36%. The mean fraction of correctly identified residues in these cases was increased from 33% using phenix.resolve sequence assignment to 47% using the current procedure. The procedure is simple to apply and is available in the Phenix software package.

Model-driven design, simulation and implementation of service compositions in COSMO

NARCIS (Netherlands)

Quartel, Dick; Dirgahayu, T.; van Sinderen, Marten J.

2009-01-01

The success of software development projects to a large extent depends on the quality of the models that are produced in the development process, which in turn depends on the conceptual and practical support that is available for modelling, design and analysis. This paper focuses on model-driven

Morphogenetic, structural and productive traits of buffel grass under different irrigation regimes

Directory of Open Access Journals (Sweden)

Maria Janiele Ferreira Coutinho

2015-06-01

Full Text Available The water restriction conditions in the Brazilian semiarid region are one of the most limiting factors to the establishment and yield of forage grasses. This study aimed to evaluate the effect of different irrigation regimes on morphogenetic, structural and productive traits of buffel grass. Arandomized blocks design, with five treatments and six replications, was used. Treatments consisted of five irrigation regimes, corresponding to the intervals of 2, 4, 6, 8 and 10 days. The traits analyzed were: leaf emergence rate, phyllochron, leaf and stem elongation rate, leaf senescence rate, final leaf length, number of green leaves per tiller, number of tillers, stem height, leaf/stem ratio, leaf area index, dry mass of green leaf and stem, dry mass of green, dead and total forage, root dry mass, dry mass and green dry mass/dead dry mass ratio. The final leaf length and dead forage dry mass were not affected by the irrigation regimes. The leaf/stem ratio followed a quadratic model, maintaining the value of 0.51 up to the irrigation regime of four days. The other morphological, structural and productive traits decreased linearly with increasing irrigation frequencies. The irrigation intervals promoted reductions in the morphological, structural and productive parameters of buffel grass, when grown under greenhouse conditions. The irrigation regime of 2 days stands out as the least restrictive to the development of buffel grass.

Assessment of some macromineral concentration of a grass/ legume ...

African Journals Online (AJOL)

Assessment of some macromineral concentration of a grass/ legume sward in ... Bulletin of Animal Health and Production in Africa ... The study aimed to determine the concentration of some macromineral elements in the grass/legume pasture ...

Health economic comparison of SLIT allergen and SCIT allergoid immunotherapy in patients with seasonal grass-allergic rhinoconjunctivitis in Germany.

Science.gov (United States)

Verheggen, Bram G; Westerhout, Kirsten Y; Schreder, Carl H; Augustin, Matthias

2015-01-01

Allergoids are chemically modified allergen extracts administered to reduce allergenicity and to maintain immunogenicity. Oralair® (the 5-grass tablet) is a sublingual native grass allergen tablet for pre- and co-seasonal treatment. Based on a literature review, meta-analysis, and cost-effectiveness analysis the relative effects and costs of the 5-grass tablet versus a mix of subcutaneous allergoid compounds for grass pollen allergic rhinoconjunctivitis were assessed. A Markov model with a time horizon of nine years was used to assess the costs and effects of three-year immunotherapy treatment. Relative efficacy expressed as standardized mean differences was estimated using an indirect comparison on symptom scores extracted from available clinical trials. The Rhinitis Symptom Utility Index (RSUI) was applied as a proxy to estimate utility values for symptom scores. Drug acquisition and other medical costs were derived from published sources as well as estimates for resource use, immunotherapy persistence, and occurrence of asthma. The analysis was executed from the German payer's perspective, which includes payments of the Statutory Health Insurance (SHI) and additional payments by insurants. Comprehensive deterministic and probabilistic sensitivity analyses and different scenarios were performed to test the uncertainty concerning the incremental model outcomes. The applied model predicted a cost-utility ratio of the 5-grass tablet versus a market mix of injectable allergoid products of € 12,593 per QALY in the base case analysis. Predicted incremental costs and QALYs were € 458 (95% confidence interval, CI: € 220; € 739) and 0.036 (95% CI: 0.002; 0.078), respectively. Compared to the allergoid mix the probability of the 5-grass tablet being the most cost-effective treatment option was predicted to be 76% at a willingness-to-pay threshold of € 20,000. The results were most sensitive to changes in efficacy estimates, duration of the pollen season, and

Modeling a Sustainable Salt Tolerant Grass-Livestock Production System under Saline Conditions in the Western San Joaquin Valley of California

Directory of Open Access Journals (Sweden)

Stephen R. Kaffka

2013-09-01

Full Text Available Salinity and trace mineral accumulation threaten the sustainability of crop production in many semi-arid parts of the world, including California’s western San Joaquin Valley (WSJV. We used data from a multi-year field-scale trial in Kings County and related container trials to simulate a forage-grazing system under saline conditions. The model uses rainfall and irrigation water amounts, irrigation water quality, soil, plant, and atmospheric variables to predict Bermuda grass (Cynodon dactylon (L. Pers. growth, quality, and use by cattle. Simulations based on field measurements and a related container study indicate that although soil chemical composition is affected by irrigation water quality, irrigation timing and frequency can be used to mitigate salt and trace mineral accumulation. Bermuda grass yields of up to 12 Mg dry matter (DM·ha−1 were observed at the field site and predicted by the model. Forage yield and quality supports un-supplemented cattle stocking rates of 1.0 to 1.2 animal units (AU·ha−1. However, a balance must be achieved between stocking rate, desired average daily gain, accumulation of salts in the soil profile, and potential pollution of ground water from drainage and leaching. Using available weather data, crop-specific parameter values and field scale measurements of soil salinity and nitrogen levels, the model can be used by farmers growing forages on saline soils elsewhere, to sustain forage and livestock production under similarly marginal conditions.

Agricultural field reclamation utilizing native grass crop production

Science.gov (United States)

J. Cure

2013-01-01

Developing a method of agricultural field reclamation to native grasses in the Lower San Pedro Watershed could prove to be a valuable tool for educational and practical purposes. Agricultural field reclamation utilizing native grass crop production will address water table depletion, soil degradation and the economic viability of the communities within the watershed....

Classification of grass pollen through the quantitative analysis of surface ornamentation and texture.

Science.gov (United States)

Mander, Luke; Li, Mao; Mio, Washington; Fowlkes, Charless C; Punyasena, Surangi W

2013-11-07

Taxonomic identification of pollen and spores uses inherently qualitative descriptions of morphology. Consequently, identifications are restricted to categories that can be reliably classified by multiple analysts, resulting in the coarse taxonomic resolution of the pollen and spore record. Grass pollen represents an archetypal example; it is not routinely identified below family level. To address this issue, we developed quantitative morphometric methods to characterize surface ornamentation and classify grass pollen grains. This produces a means of quantifying morphological features that are traditionally described qualitatively. We used scanning electron microscopy to image 240 specimens of pollen from 12 species within the grass family (Poaceae). We classified these species by developing algorithmic features that quantify the size and density of sculptural elements on the pollen surface, and measure the complexity of the ornamentation they form. These features yielded a classification accuracy of 77.5%. In comparison, a texture descriptor based on modelling the statistical distribution of brightness values in image patches yielded a classification accuracy of 85.8%, and seven human subjects achieved accuracies between 68.33 and 81.67%. The algorithmic features we developed directly relate to biologically meaningful features of grass pollen morphology, and could facilitate direct interpretation of unsupervised classification results from fossil material.

De Novo Transcriptome Assembly and Identification of Gene Candidates for Rapid Evolution of Soil Al Tolerance in Anthoxanthum odoratum at the Long-Term Park Grass Experiment.

Directory of Open Access Journals (Sweden)

Billie Gould

Full Text Available Studies of adaptation in the wild grass Anthoxanthum odoratum at the Park Grass Experiment (PGE provided one of the earliest examples of rapid evolution in plants. Anthoxanthum has become locally adapted to differences in soil Al toxicity, which have developed there due to soil acidification from long-term experimental fertilizer treatments. In this study, we used transcriptome sequencing to identify Al stress responsive genes in Anthoxanhum and identify candidates among them for further molecular study of rapid Al tolerance evolution at the PGE. We examined the Al content of Anthoxanthum tissues and conducted RNA-sequencing of root tips, the primary site of Al induced damage. We found that despite its high tolerance Anthoxanthum is not an Al accumulating species. Genes similar to those involved in organic acid exudation (TaALMT1, ZmMATE, cell wall modification (OsSTAR1, and internal Al detoxification (OsNRAT1 in cultivated grasses were responsive to Al exposure. Expression of a large suite of novel loci was also triggered by early exposure to Al stress in roots. Three-hundred forty five transcripts were significantly more up- or down-regulated in tolerant vs. sensitive Anthoxanthum genotypes, providing important targets for future study of rapid evolution at the PGE.

De Novo Transcriptome Assembly and Identification of Gene Candidates for Rapid Evolution of Soil Al Tolerance in Anthoxanthum odoratum at the Long-Term Park Grass Experiment.

Science.gov (United States)

Gould, Billie; McCouch, Susan; Geber, Monica

2015-01-01

Studies of adaptation in the wild grass Anthoxanthum odoratum at the Park Grass Experiment (PGE) provided one of the earliest examples of rapid evolution in plants. Anthoxanthum has become locally adapted to differences in soil Al toxicity, which have developed there due to soil acidification from long-term experimental fertilizer treatments. In this study, we used transcriptome sequencing to identify Al stress responsive genes in Anthoxanhum and identify candidates among them for further molecular study of rapid Al tolerance evolution at the PGE. We examined the Al content of Anthoxanthum tissues and conducted RNA-sequencing of root tips, the primary site of Al induced damage. We found that despite its high tolerance Anthoxanthum is not an Al accumulating species. Genes similar to those involved in organic acid exudation (TaALMT1, ZmMATE), cell wall modification (OsSTAR1), and internal Al detoxification (OsNRAT1) in cultivated grasses were responsive to Al exposure. Expression of a large suite of novel loci was also triggered by early exposure to Al stress in roots. Three-hundred forty five transcripts were significantly more up- or down-regulated in tolerant vs. sensitive Anthoxanthum genotypes, providing important targets for future study of rapid evolution at the PGE.

Kinetic study of the catalytic pyrolysis of elephant grass using Ti-MCM-41

Energy Technology Data Exchange (ETDEWEB)

Fontes, Maria do Socorro Braga; Melo, Dulce Maria de Araujo; Rodrigues, Glicelia, E-mail: socorro.fontes@yahoo.com.br [Universidade Federal do Rio Grande do Norte (UFRN), Natal, RN (Brazil); Barros, Joana Maria de Farias [Universidade Federal de Campina Grande (UFCG), Cuite, PB (Brazil). Dept. de Quimica; Braga, Renata Martins [Universidade Federal da Paraiba (UFPB/CEAR/DEER), Joao Pessoa, PB (Brazil). Centro de Energias Alternativas e Renovaveis. Dept. de Engenharia de Energia Renovaveis

2014-08-15

This work aimed to study the kinetics of thermal and catalytic pyrolysis using Ti-MCM-41 as catalyst in order to assess the catalytic pyrolysis efficiency compared to thermal pyrolysis of elephant grass. Ti-MCM-41 molecular sieve was synthesized by hydrothermal method from hydrogel with the following molar composition: 1.00 CTMABr: 4.00 SiO{sub 2}:X TiO{sub 2}: 1 + X Na{sub 2}O: 200.00 H{sub 2}O, which structure template used was cetyltrimethylammonium bromide (CTMABr). The materials synthesized were characterized by X-ray diffraction, IR spectroscopy, thermogravimetric analysis and specific area by the BET method, for subsequent application in the biomass pyrolysis process. The kinetic models proposed by Vyazovkin and Flynn-Wall were used to determine the apparent activation energy involved in the thermal and catalytic pyrolysis of elephant grass and the results showed that the catalyst used was effective in reducing the apparent activation energy involved in the thermal decomposition of elephant grass. (author)

Phylogenetic analysis of the expansion of the MATH-BTB gene family in the grasses.

Science.gov (United States)

Juranić, Martina; Dresselhaus, Thomas

2014-01-01

MATH-BTB proteins are known to act as substrate-specific adaptors of cullin3 (CUL3)-based ubiquitin E3 ligases to target protein for ubiquitination. In a previous study we reported the presence of 31 MATH-BTB genes in the maize genome and determined the regulatory role of the MATH-BTB protein MAB1 during meiosis to mitosis transition. In contrast to maize, there are only 6 homologous genes in the model plant Arabidopsis, while this family has largely expanded in grasses. Here, we report a phylogenetic analysis of the MATH-BTB gene family in 9 land plant species including various mosses, eudicots, and grasses. We extend a previous classification of the plant MATH-BTB family and additionally arrange the expanded group into 5 grass-specific clades. Synteny studies indicate that expansion occurred to a large extent due to local gene duplications. Expression studies of 3 closely related MATH-BTB genes in maize (MAB1-3) indicate highly specific expression pattern. In summary, this work provides a solid base for further studies comparing genetic and functional information of the MATH-BTB family especially in the grasses.

Experiences in Teaching a Graduate Course on Model-Driven Software Development

Science.gov (United States)

Tekinerdogan, Bedir

2011-01-01

Model-driven software development (MDSD) aims to support the development and evolution of software intensive systems using the basic concepts of model, metamodel, and model transformation. In parallel with the ongoing academic research, MDSD is more and more applied in industrial practices. After being accepted both by a broad community of…

Data-driven modelling of LTI systems using symbolic regression

NARCIS (Netherlands)

Khandelwal, D.; Toth, R.; Van den Hof, P.M.J.

2017-01-01

The aim of this project is to automate the task of data-driven identification of dynamical systems. The underlying goal is to develop an identification tool that models a physical system without distinguishing between classes of systems such as linear, nonlinear or possibly even hybrid systems. Such

Prospects for Hybrid Breeding in Bioenergy Grasses

DEFF Research Database (Denmark)

Aguirre, Andrea Arias; Studer, Bruno; Frei, Ursula

2012-01-01

, we address crucial topics to implement hybrid breeding, such as the availability and development of heterotic groups, as well as biological mechanisms for hybridization control such as self-incompatibility (SI) and male sterility (MS). Finally, we present potential hybrid breeding schemes based on SI...... of different hybrid breeding schemes to optimally exploit heterosis for biomass yield in perennial ryegrass (Lolium perenne L.) and switchgrass (Panicum virgatum), two perennial model grass species for bioenergy production. Starting with a careful evaluation of current population and synthetic breeding methods...

Impact on Clover-Grass Yield from Wheel Load and Tyre Pressure

DEFF Research Database (Denmark)

Green, Ole; Jørgensen, Rasmus Nyholm; Sørensen, Claus Aage Grøn

2009-01-01

Traffic intensities have been shown to have a negative influence on the yield of grass and clover. A full scale grass-clover field trial was established to estimate the effect on clover-grass yields as a function of different wheel loads and tire pressures. The trial comprised 16 different traffi...

Data Driven Modelling of the Dynamic Wake Between Two Wind Turbines

DEFF Research Database (Denmark)

Knudsen, Torben; Bak, Thomas

2012-01-01

turbine. This paper establishes flow models relating the wind speeds at turbines in a farm. So far, research in this area has been mainly based on first principles static models and the data driven modelling done has not included the loading of the upwind turbine and its impact on the wind speed downwind......Wind turbines in a wind farm, influence each other through the wind flow. Downwind turbines are in the wake of upwind turbines and the wind speed experienced at downwind turbines is hence a function of the wind speeds at upwind turbines but also the momentum extracted from the wind by the upwind....... This paper is the first where modern commercial mega watt turbines are used for data driven modelling including the upwind turbine loading by changing power reference. Obtaining the necessary data is difficult and data is therefore limited. A simple dynamic extension to the Jensen wake model is tested...

Using maize as a model to study pollen tube growth and guidance, cross-incompatibility and sperm delivery in grasses.

Science.gov (United States)

Dresselhaus, Thomas; Lausser, Andreas; Márton, Mihaela L

2011-09-01

and growth of self-pollen to promote intraspecific outcrossing and to prevent fertilization by alien sperm cells. However, in the Poaceae, the underlying molecular mechanisms are still largely unknown. We propose to develop maize (Zea mays) as a model to investigate the above-described processes to understand the associated intra- and interspecific crossing barriers in grasses. Many genetic, cellular and biotechnological tools including the completion of a reference genome (inbred line B73) have been established in the last decade and many more maize inbred genomes are expected to be available soon. Moreover, a cellular marker line database as well as large transposon insertion collections and improved Agrobacterium transformation protocols are now available. Additionally, the processes described above are well studied at the morphological level and a number of mutants have been described already, awaiting disclosure of the relevant genes. The identification of the first key players in pollen tube growth, guidance and burst show maize to be an excellent grass model to investigate these processes in more detail. Here we provide an overview of our current understanding of these processes in Poaceae with a focus on maize, and also include relevant discoveries in eudicot model species.

Identification of grazed grasses using epidermal characters | R ...

African Journals Online (AJOL)

The use of anatomical features of the abaxial epidermis of grasses is discussed for the identification of fragments of epidermis present in samples of rumen. The reliability of this technique, and the variation of the epidermal characters in two widely distributed species of grass, is given. A "Key" to identity certain genera of ...

Rehabilitation experiment by phytoremediation using lawn grass

International Nuclear Information System (INIS)

2012-08-01

Measures against environmental contamination by radioactive materials originated from the Fukushima Nuclear Accident (May, 2011), are being conducted in Fukushima and surrounding prefectures. Regarding to the measures, a phytoremediation experiment with several types of lawn grasses in a field scale have been carried out. Lawn grasses are generally characterized by shallow rhizosphere, high density and root mat formation. Decontamination effectiveness of radioactive cesium by plant uptake and by sod removing was investigated. As a result, the range of decontamination factors by plant uptake was below than 1% because of low transfer rate form soil to plant. On the other hand, maximum decontamination factor by sod removing reached about 100%. Decontamination activities with various methods will be implemented according to the national decontamination policy and related plans in each municipality. The phytoremediation method with lawn grass would be applicable in limited circumstances. (author)

A Model-Driven Framework to Develop Personalized Health Monitoring

Directory of Open Access Journals (Sweden)

Algimantas Venčkauskas

2016-07-01

Full Text Available Both distributed healthcare systems and the Internet of Things (IoT are currently hot topics. The latter is a new computing paradigm to enable advanced capabilities in engineering various applications, including those for healthcare. For such systems, the core social requirement is the privacy/security of the patient information along with the technical requirements (e.g., energy consumption and capabilities for adaptability and personalization. Typically, the functionality of the systems is predefined by the patient’s data collected using sensor networks along with medical instrumentation; then, the data is transferred through the Internet for treatment and decision-making. Therefore, systems creation is indeed challenging. In this paper, we propose a model-driven framework to develop the IoT-based prototype and its reference architecture for personalized health monitoring (PHM applications. The framework contains a multi-layered structure with feature-based modeling and feature model transformations at the top and the application software generation at the bottom. We have validated the framework using available tools and developed an experimental PHM to test some aspects of the functionality of the reference architecture in real time. The main contribution of the paper is the development of the model-driven computational framework with emphasis on the synergistic effect of security and energy issues.

Zea mI, the maize homolog of the allergen-encoding Lol pI gene of rye grass.

Science.gov (United States)

Broadwater, A H; Rubinstein, A L; Chay, C H; Klapper, D G; Bedinger, P A

1993-09-15

Sequence analysis of a pollen-specific cDNA from maize has identified a homolog (Zea mI) of the gene (Lol pI) encoding the major allergen of rye-grass pollen. The protein encoded by the partial cDNA sequence is 59.3% identical and 72.7% similar to the comparable region of the reported amino acid sequence of Lol pIA. Southern analysis indicates that this cDNA represents a member of a small multigene family in maize. Northern analysis shows expression only in pollen, not in vegetative or female floral tissues. The timing of expression is developmentally regulated, occurring at a low level prior to the first pollen mitosis and at a high level after this postmeiotic division. Western analysis detects a protein in maize pollen lysates using polyclonal antiserum and monoclonal antibodies directed against purified Lolium perenne allergen.

A Model-Driven Approach for Telecommunications Network Services Definition

Science.gov (United States)

Chiprianov, Vanea; Kermarrec, Yvon; Alff, Patrick D.

Present day Telecommunications market imposes a short concept-to-market time for service providers. To reduce it, we propose a computer-aided, model-driven, service-specific tool, with support for collaborative work and for checking properties on models. We started by defining a prototype of the Meta-model (MM) of the service domain. Using this prototype, we defined a simple graphical modeling language specific for service designers. We are currently enlarging the MM of the domain using model transformations from Network Abstractions Layers (NALs). In the future, we will investigate approaches to ensure the support for collaborative work and for checking properties on models.

Integrating FMEA in a Model-Driven Methodology

Science.gov (United States)

Scippacercola, Fabio; Pietrantuono, Roberto; Russo, Stefano; Esper, Alexandre; Silva, Nuno

2016-08-01

Failure Mode and Effects Analysis (FMEA) is a well known technique for evaluating the effects of potential failures of components of a system. FMEA demands for engineering methods and tools able to support the time- consuming tasks of the analyst. We propose to make FMEA part of the design of a critical system, by integration into a model-driven methodology. We show how to conduct the analysis of failure modes, propagation and effects from SysML design models, by means of custom diagrams, which we name FMEA Diagrams. They offer an additional view of the system, tailored to FMEA goals. The enriched model can then be exploited to automatically generate FMEA worksheet and to conduct qualitative and quantitative analyses. We present a case study from a real-world project.

Sources of N2O in organic grass-clover pastures

OpenAIRE

Ambus, P.

2002-01-01

Organic farming practises, and in particular dairy production systems based on grass-clover pastures are becoming increasingly abundant within Danish agriculture. Grass-clover pastures may provide a mitigation option to reduce grassland nitrous oxide (N2O) emissions (Velthof et al. 1998). The objectives of this work was to examine the relationship between N2O emissions and transformations of inorganic N in organically managed grass-clover pastures of different ages. Results from the projec...

Modelling Laccoliths: Fluid-Driven Fracturing in the Lab

Science.gov (United States)

Ball, T. V.; Neufeld, J. A.

2017-12-01

Current modelling of the formation of laccoliths neglects the necessity to fracture rock layers for propagation to occur [1]. In magmatic intrusions at depth the idea of fracture toughness is used to characterise fracturing, however an analogue for near surface intrusions has yet to be explored [2]. We propose an analytical model for laccolith emplacement that accounts for the energy required to fracture at the tip of an intrusion. For realistic physical parameters we find that a lag region exists between the fluid magma front and the crack tip where large negative pressures in the tip cause volatiles to exsolve from the magma. Crucially, the dynamics of this tip region controls the spreading due to the competition between viscous forces and fracture energy. We conduct a series of complementary experiments to investigate fluid-driven fracturing of adhered layers and confirm the existence of two regimes: viscosity dominant spreading, controlled by the pressure in the lag region, and fracture energy dominant spreading, controlled by the energy required to fracture layers. Our experiments provide the first observations, and evolution, of a vapour tip. These experiments and our simplified model provide insight into the key physical processes in near surface magmatic intrusions with applications to fluid-driven fracturing more generally. Michaut J. Geophys. Res. 116(B5), B05205. Bunger & Cruden J. Geophys. Res. 116(B2), B02203.

Management techniques for the control of Melinis minutiflora P. Beauv. (molasses grass: ten years of research on an invasive grass species in the Brazilian Cerrado

Directory of Open Access Journals (Sweden)

Carlos Romero Martins

2017-09-01

Full Text Available ABSTRACT The invasion of exotic species is considered to be a major threat to the preservation of biodiversity. In the Parque Nacional de Brasília (National Park of Brasília, the invasive Melinis minutiflora (molasses grass occupies more than 10 % of the area of the park. The present, long-term, study compared two treatments of exposure to molasses grass: 1 fire and 2 integrated management (fire + herbicide sprays + manual removal. The aerial biomass of molasses grass in the experimental area initially represented ca. 55 % of the total aerial biomass, a percentage that apparently did not influence native plant species richness at this site. Fire alone was not sufficient to control molasses grass, which attained its pre-treatment biomass values after two years. Integrated management reduced, and maintained, biomass to less than 1 % of its original value after ten years, and maintained this level throughout the study, demonstrating that it is a promising strategy for the recovery of areas invaded by molasses grass in the Cerrado. However, because of the recolonization by molasses grass, long-term monitoring efforts are targeting outbreaks, which would require immediate intervention in order to maintain the native biological diversity of the region.

Development of a Stochastically-driven, Forward Predictive Performance Model for PEMFCs

Science.gov (United States)

Harvey, David Benjamin Paul

A one-dimensional multi-scale coupled, transient, and mechanistic performance model for a PEMFC membrane electrode assembly has been developed. The model explicitly includes each of the 5 layers within a membrane electrode assembly and solves for the transport of charge, heat, mass, species, dissolved water, and liquid water. Key features of the model include the use of a multi-step implementation of the HOR reaction on the anode, agglomerate catalyst sub-models for both the anode and cathode catalyst layers, a unique approach that links the composition of the catalyst layer to key properties within the agglomerate model and the implementation of a stochastic input-based approach for component material properties. The model employs a new methodology for validation using statistically varying input parameters and statistically-based experimental performance data; this model represents the first stochastic input driven unit cell performance model. The stochastic input driven performance model was used to identify optimal ionomer content within the cathode catalyst layer, demonstrate the role of material variation in potential low performing MEA materials, provide explanation for the performance of low-Pt loaded MEAs, and investigate the validity of transient-sweep experimental diagnostic methods.

DNA Methylation of T1R1 Gene in the Vegetarian Adaptation of Grass Carp Ctenopharyngodon idella.

Science.gov (United States)

Cai, Wenjing; He, Shan; Liang, Xu-Fang; Yuan, Xiaochen

2018-05-02

Although previous studies have indicated importance of taste receptors in food habits formation in mammals, little is known about those in fish. Grass carp is an excellent model for studying vegetarian adaptation, as it shows food habit transition from carnivore to herbivore. In the present study, pseudogenization or frameshift mutations of the umami receptors that hypothesized related to dietary switch in vertebrates, were not found in grass carp, suggesting other mechanisms for vegetarian adaptation in grass carp. T1R1 and T1R3 strongly responded to L-Arg and L-Lys, differing from those of zebrafish and medaka, contributing to high species specificity in amino acid preferences and diet selection of grass carp. After food habit transition of grass carp, DNA methylation levels were higher in CPG1 and CPG3 islands of upstream control region of T1R1 gene. Luciferase activity assay of upstream regulatory region of T1R1 (-2500-0 bp) without CPG1 or CPG3 indicated that CPG1 and CPG3 might be involved in transcriptional regulation of T1R1 gene. Subsequently, high DNA methylation decreased expression of T1R1 in intestinal tract. It could be a new mechanism to explain, at least partially, the vegetarian adaptation of grass carp by regulation of expression of umami receptor via epigenetic modification.

Drought resilience across ecologically dominant species: An experiment-model integration approach

Science.gov (United States)

Felton, A. J.; Warren, J.; Ricciuto, D. M.; Smith, M. D.

2017-12-01

Poorly understood are the mechanisms contributing to variability in ecosystem recovery following drought. Grasslands of the central U.S. are ecologically and economically important ecosystems, yet are also highly sensitive to drought. Although characteristics of these ecosystems change across gradients of temperature and precipitation, a consistent feature among these systems is the presence of highly abundant, dominant grass species that control biomass production. As a result, the incorporation of these species' traits into terrestrial biosphere models may constrain predictions amid increases in climatic variability. Here we report the results of a modeling-experiment (MODEX) research approach. We investigated the physiological, morphological and growth responses of the dominant grass species from each of the four major grasslands of the central U.S. (ranging from tallgrass prairie to desert grassland) following severe drought. Despite significant differences in baseline values, full recovery in leaf physiological function was evident across species, of which was consistently driven by the production of new leaves. Further, recovery in whole-plant carbon uptake tended to be driven by shifts in allocation from belowground to aboveground structures. However, there was clear variability among species in the magnitude of this dynamic as well as the relative allocation to stem versus leaf production. As a result, all species harbored the physiological capacity to recover from drought, yet we posit that variability in the recovery of whole-plant carbon uptake to be more strongly driven by variability in the sensitivity of species' morphology to soil moisture increases. The next step of this project will be to incorporate these and other existing data on these species and ecosystems into the community land model in an effort to test the sensitivity of this model to these data.

A Probabilistic Genome-Wide Gene Reading Frame Sequence Model

DEFF Research Database (Denmark)

Have, Christian Theil; Mørk, Søren

We introduce a new type of probabilistic sequence model, that model the sequential composition of reading frames of genes in a genome. Our approach extends gene finders with a model of the sequential composition of genes at the genome-level -- effectively producing a sequential genome annotation...... as output. The model can be used to obtain the most probable genome annotation based on a combination of i: a gene finder score of each gene candidate and ii: the sequence of the reading frames of gene candidates through a genome. The model --- as well as a higher order variant --- is developed and tested...... and are evaluated by the effect on prediction performance. Since bacterial gene finding to a large extent is a solved problem it forms an ideal proving ground for evaluating the explicit modeling of larger scale gene sequence composition of genomes. We conclude that the sequential composition of gene reading frames...

Web Services and Model-Driven Enterprise Information Services. Proceedings of the Joint Workshop on Web Services and Model-Driven Enterprise Information Services, WSMDEIS 2005.

NARCIS (Netherlands)

Bevinakoppa, S.; Ferreira Pires, Luis; Hammoudi, S.

2005-01-01

Web services and Model-driven development are two emerging research fields and have been receiving a lot of attention in the recent years. New approaches on these two areas can bring many benefits to the development of information systems, distribution flexibility, interoperability, maintainability

Data-driven remaining useful life prognosis techniques stochastic models, methods and applications

CERN Document Server

Si, Xiao-Sheng; Hu, Chang-Hua

2017-01-01

This book introduces data-driven remaining useful life prognosis techniques, and shows how to utilize the condition monitoring data to predict the remaining useful life of stochastic degrading systems and to schedule maintenance and logistics plans. It is also the first book that describes the basic data-driven remaining useful life prognosis theory systematically and in detail. The emphasis of the book is on the stochastic models, methods and applications employed in remaining useful life prognosis. It includes a wealth of degradation monitoring experiment data, practical prognosis methods for remaining useful life in various cases, and a series of applications incorporated into prognostic information in decision-making, such as maintenance-related decisions and ordering spare parts. It also highlights the latest advances in data-driven remaining useful life prognosis techniques, especially in the contexts of adaptive prognosis for linear stochastic degrading systems, nonlinear degradation modeling based pro...

A model-driven approach to information security compliance

Science.gov (United States)

Correia, Anacleto; Gonçalves, António; Teodoro, M. Filomena

2017-06-01

The availability, integrity and confidentiality of information are fundamental to the long-term survival of any organization. Information security is a complex issue that must be holistically approached, combining assets that support corporate systems, in an extended network of business partners, vendors, customers and other stakeholders. This paper addresses the conception and implementation of information security systems, conform the ISO/IEC 27000 set of standards, using the model-driven approach. The process begins with the conception of a domain level model (computation independent model) based on information security vocabulary present in the ISO/IEC 27001 standard. Based on this model, after embedding in the model mandatory rules for attaining ISO/IEC 27001 conformance, a platform independent model is derived. Finally, a platform specific model serves the base for testing the compliance of information security systems with the ISO/IEC 27000 set of standards.

Probabilistic topic modeling for the analysis and classification of genomic sequences

Science.gov (United States)

2015-01-01

Background Studies on genomic sequences for classification and taxonomic identification have a leading role in the biomedical field and in the analysis of biodiversity. These studies are focusing on the so-called barcode genes, representing a well defined region of the whole genome. Recently, alignment-free techniques are gaining more importance because they are able to overcome the drawbacks of sequence alignment techniques. In this paper a new alignment-free method for DNA sequences clustering and classification is proposed. The method is based on k-mers representation and text mining techniques. Methods The presented method is based on Probabilistic Topic Modeling, a statistical technique originally proposed for text documents. Probabilistic topic models are able to find in a document corpus the topics (recurrent themes) characterizing classes of documents. This technique, applied on DNA sequences representing the documents, exploits the frequency of fixed-length k-mers and builds a generative model for a training group of sequences. This generative model, obtained through the Latent Dirichlet Allocation (LDA) algorithm, is then used to classify a large set of genomic sequences. Results and conclusions We performed classification of over 7000 16S DNA barcode sequences taken from Ribosomal Database Project (RDP) repository, training probabilistic topic models. The proposed method is compared to the RDP tool and Support Vector Machine (SVM) classification algorithm in a extensive set of trials using both complete sequences and short sequence snippets (from 400 bp to 25 bp). Our method reaches very similar results to RDP classifier and SVM for complete sequences. The most interesting results are obtained when short sequence snippets are considered. In these conditions the proposed method outperforms RDP and SVM with ultra short sequences and it exhibits a smooth decrease of performance, at every taxonomic level, when the sequence length is decreased. PMID:25916734

Effects of conventional and grass-feeding systems on the nutrient composition of beef.

Science.gov (United States)

Leheska, J M; Thompson, L D; Howe, J C; Hentges, E; Boyce, J; Brooks, J C; Shriver, B; Hoover, L; Miller, M F

2008-12-01

The objectives of this study were to determine the nutrient composition of grass-fed beef in the United States for inclusion in the USDA National Nutrient Database for Standard Reference, and to compare the fatty acid composition of grass-fed and conventionally fed (control) beef. Ground beef (GB) and strip steaks (SS) were collected on 3 separate occasions from 15 grass-fed beef producers that represented 13 different states, whereas control beef samples were collected from 3 regions (Ohio, South Dakota, and Texas) of the United States on 3 separate occasions. Concentrations of minerals, choline, vitamin B(12), and thiamine were determined for grass-fed beef samples. Grass-fed GB samples had less Mg, P, and K (P < 0.05), and more Na, Zn, and vitamin B(12) (P < 0.05) than SS samples. Fat color, marbling, and pH were assessed for grass-fed and control SS. Subjective evaluation of the SS indicated that grass-fed beef had fat that was more yellow in color than control beef. Percentages of total fat, total cholesterol, and fatty acids along with trans fatty acids and CLA were determined for grass-fed and control SS and GB. Grass-fed SS had less total fat than control SS (P = 0.001), but both grass-fed and control SS were considered lean, because their total fat content was 4.3% or less. For both GB and SS, grass-fed beef had significantly less (P = 0.001 and P = 0.023, respectively) content of MUFA and a greater content of SFA, n-3 fatty acids, CLA, and trans-vaccenic acid than did the control samples. Concentrations of PUFA, trans fatty acids, n-6 fatty acids, and cholesterol did not differ between grass-fed and control ground beef. Trans-vaccenic acid (trans-11 18:1) made up the greatest concentration of the total trans fats in grass-fed beef, whereas CLA accounted for approximately 15% of the total trans fats. Although the fatty acid composition of grass-fed and conventionally fed beef was different, conclusions on the possible effects of these differences on human

Knowledge management driven leadership, culture and innovation success – an integrative model

OpenAIRE

Zieba, M.; Schivinski, Bruno

2015-01-01

Purpose - This article examines the relation between knowledge management (KM) driven leadership, culture and innovation success of knowledge-intensive small and medium sized companies. By building on the previously reported research on leadership, culture, innovation , and knowledge management, we synergistically integrate d KM-driven leadership and innovation success while exploring the meditational role of culture in that. Design/methodology/approach - A conceptual model comprising three c...

Data driven modelling of vertical atmospheric radiation

International Nuclear Information System (INIS)

Antoch, Jaromir; Hlubinka, Daniel

2011-01-01

In the Czech Hydrometeorological Institute (CHMI) there exists a unique set of meteorological measurements consisting of the values of vertical atmospheric levels of beta and gamma radiation. In this paper a stochastic data-driven model based on nonlinear regression and on nonhomogeneous Poisson process is suggested. In the first part of the paper, growth curves were used to establish an appropriate nonlinear regression model. For comparison we considered a nonhomogeneous Poisson process with its intensity based on growth curves. In the second part both approaches were applied to the real data and compared. Computational aspects are briefly discussed as well. The primary goal of this paper is to present an improved understanding of the distribution of environmental radiation as obtained from the measurements of the vertical radioactivity profiles by the radioactivity sonde system. - Highlights: → We model vertical atmospheric levels of beta and gamma radiation. → We suggest appropriate nonlinear regression model based on growth curves. → We compare nonlinear regression modelling with Poisson process based modeling. → We apply both models to the real data.

Biogas and Methane Yield from Rye Grass

Directory of Open Access Journals (Sweden)

Tomáš Vítěz

2015-01-01

Full Text Available Biogas production in the Czech Republic has expanded substantially, including marginal regions for maize cultivation. Therefore, there are increasingly sought materials that could partially replace maize silage, as a basic feedstock, while secure both biogas production and its quality.Two samples of rye grass (Lolium multiflorum var. westerwoldicum silage with different solids content 21% and 15% were measured for biogas and methane yield. Rye grass silage with solid content of 15% reached an average specific biogas yield 0.431 m3·kg−1 of organic dry matter and an average specific methane yield 0.249 m3·kg−1 of organic dry matter. Rye grass silage with solid content 21% reached an average specific biogas yield 0.654 m3·kg−1 of organic dry matter and an average specific methane yield 0.399 m3·kg−1 of organic dry matter.

Data and Dynamics Driven Approaches for Modelling and Forecasting the Red Sea Chlorophyll

KAUST Repository

Dreano, Denis

2017-05-31

Phytoplankton is at the basis of the marine food chain and therefore play a fundamental role in the ocean ecosystem. However, the large-scale phytoplankton dynamics of the Red Sea are not well understood yet, mainly due to the lack of historical in situ measurements. As a result, our knowledge in this area relies mostly on remotely-sensed observations and large-scale numerical marine ecosystem models. Models are very useful to identify the mechanisms driving the variations in chlorophyll concentration and have practical applications for fisheries operation and harmful algae blooms monitoring. Modelling approaches can be divided between physics- driven (dynamical) approaches, and data-driven (statistical) approaches. Dynamical models are based on a set of differential equations representing the transfer of energy and matter between different subsets of the biota, whereas statistical models identify relationships between variables based on statistical relations within the available data. The goal of this thesis is to develop, implement and test novel dynamical and statistical modelling approaches for studying and forecasting the variability of chlorophyll concentration in the Red Sea. These new models are evaluated in term of their ability to efficiently forecast and explain the regional chlorophyll variability. We also propose innovative synergistic strategies to combine data- and physics-driven approaches to further enhance chlorophyll forecasting capabilities and efficiency.

Effects of feeding dairy cows different legume-grass silages on milk phytoestrogen concentration

DEFF Research Database (Denmark)

Höjer, A; Adler, S; Purup, Stig

2012-01-01

interval of legume-grass silage on phytoestrogen intake and milk phytoestrogen concentrations. In one experiment, 15 Swedish Red dairy cows were fed 2- or 3-cut red clover-grass silage, or 2-cut birdsfoot trefoil-grass silage. In a second experiment, 16 Norwegian Red dairy cows were fed short-term ley...... red clover-grass silage diet (1,494μg/kg of milk). Because of the metabolism of biochanin A, genistein, and prunetin, their concentrations in milk and the apparent recovery were low. Coumestrol was detected in only short-term and long-term ley silage mixtures, and its milk concentration was low....... Concentrations of secoisolariciresinol and matairesinol were higher in 2-cut birdsfoot trefoil-grass and long-term ley silage mixtures, those with legume species other than red clover, and the highest grass proportions. The 2-cut birdsfoot trefoil-grass silage diet also resulted in higher enterolactone...

Results from the 5-year SQ grass sublingual immunotherapy tablet asthma prevention (GAP) trial in children with grass pollen allergy

DEFF Research Database (Denmark)

Valovirta, Erkka; Petersen, Thomas H; Piotrowska, Teresa

2018-01-01

BACKGROUND: Allergy immunotherapy targets the immunological cause of allergic rhinoconjunctivitis and allergic asthma and has the potential to alter the natural course of allergic disease. OBJECTIVE: The primary objective was to investigate the effect of the SQ grass sublingual immunotherapy tablet...... compared with placebo on the risk of developing asthma. METHODS: A total of 812 children (5-12 years), with a clinically relevant history of grass pollen allergic rhinoconjunctivitis and no medical history or signs of asthma, were included in the randomized, double-blind, placebo-controlled trial......, comprising 3 years of treatment and 2 years of follow-up. RESULTS: There was no difference in time to onset of asthma, defined by prespecified asthma criteria relying on documented reversible impairment of lung function (primary endpoint). Treatment with the SQ grass sublingual immunotherapy tablet...

A novel method to characterize silica bodies in grasses.

Science.gov (United States)

Dabney, Clemon; Ostergaard, Jason; Watkins, Eric; Chen, Changbin

2016-01-01

The deposition of silicon into epidermal cells of grass species is thought to be an important mechanism that plants use as a defense against pests and environmental stresses. There are a number of techniques available to study the size, density and distribution pattern of silica bodies in grass leaves. However, none of those techniques can provide a high-throughput analysis, especially for a great number of samples. We developed a method utilizing the autofluorescence of silica bodies to investigate their size and distribution, along with the number of carbon inclusions within the silica bodies of perennial grass species Koeleria macrantha. Fluorescence images were analyzed by image software Adobe Photoshop CS5 or ImageJ that remarkably facilitated the quantification of silica bodies in the dry ash. We observed three types of silica bodies or silica body related mineral structures. Silica bodies were detected on both abaxial and adaxial epidermis of K. macrantha leaves, although their sizes, density, and distribution patterns were different. No auto-fluorescence was detected from carbon inclusions. The combination of fluorescence microscopy and image processing software displayed efficient utilization in the identification and quantification of silica bodies in K. macrantha leaf tissues, which should applicable to biological, ecological and geological studies of grasses including forage, turf grasses and cereal crops.

Genetic engineering of grass cell wall polysaccharides for biorefining.

Science.gov (United States)

Bhatia, Rakesh; Gallagher, Joe A; Gomez, Leonardo D; Bosch, Maurice

2017-09-01

Grasses represent an abundant and widespread source of lignocellulosic biomass, which has yet to fulfil its potential as a feedstock for biorefining into renewable and sustainable biofuels and commodity chemicals. The inherent recalcitrance of lignocellulosic materials to deconstruction is the most crucial limitation for the commercial viability and economic feasibility of biomass biorefining. Over the last decade, the targeted genetic engineering of grasses has become more proficient, enabling rational approaches to modify lignocellulose with the aim of making it more amenable to bioconversion. In this review, we provide an overview of transgenic strategies and targets to tailor grass cell wall polysaccharides for biorefining applications. The bioengineering efforts and opportunities summarized here rely primarily on (A) reprogramming gene regulatory networks responsible for the biosynthesis of lignocellulose, (B) remodelling the chemical structure and substitution patterns of cell wall polysaccharides and (C) expressing lignocellulose degrading and/or modifying enzymes in planta. It is anticipated that outputs from the rational engineering of grass cell wall polysaccharides by such strategies could help in realizing an economically sustainable, grass-derived lignocellulose processing industry. © 2017 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

A Model-Driven Methodology for Big Data Analytics-as-a-Service

OpenAIRE

Damiani, Ernesto; Ardagna, Claudio Agostino; Ceravolo, Paolo; Bellandi, Valerio; Bezzi, Michele; Hebert, Cedric

2017-01-01

The Big Data revolution has promised to build a data-driven ecosystem where better decisions are supported by enhanced analytics and data management. However, critical issues still need to be solved in the road that leads to commodization of Big Data Analytics, such as the management of Big Data complexity and the protection of data security and privacy. In this paper, we focus on the first issue and propose a methodology based on Model Driven Engineering (MDE) that aims to substantially lowe...

Performance of Vetiver Grass (Vetiveria zizanioides for Phytoremediation of Contaminated Water

Directory of Open Access Journals (Sweden)

Syed Hasan Sharifah Nur Munirah

2017-01-01

Full Text Available In tolerance towards metal uptake, there is a need to evaluate the performance of vetiver grass for metal removal to reduce water impurity. This study was aimed to evaluate contaminant removal by vetiver grass at varying root length and plant density and determine the metal uptake in vetiver plant biomass. Pollutant uptake of vetiver grass was conducted in laboratory experiment and heavy metal analysis was done using acid digestion and Atomic Absorption Spectrometry. Findings indicated that the removal of heavy metal was decreased in seven days of the experiment where iron shows the highest percentage (96%; 0.42 ppm of removal due to iron is highly required for growth of vetiver grass. Removal rate of heavy metals in water by vetiver grass is ranked in the order of Fe>Zn>Pb>Mn>Cu. Results also demonstrated greater removal of heavy metals (Cu, Fe, Mn, Pb, Zn at greater root length and higher density of vetiver grass because it increased the surface area for metal absorption by plant root into vetiver plant from contaminated water. However, findings indicated that accumulation of heavy metals in plant biomass was higher in vetiver shoot than in root due to metal translocation from root to the shoot. Therefore, the findings have shown effective performance of vetiver grass for metal removal in the phytoremediation of contaminated water.

Brain transcriptome sequencing and assembly of three songbird model systems for the study of social behavior

Directory of Open Access Journals (Sweden)

Christopher N. Balakrishnan

2014-05-01

Full Text Available Emberizid sparrows (emberizidae have played a prominent role in the study of avian vocal communication and social behavior. We present here brain transcriptomes for three emberizid model systems, song sparrow Melospiza melodia, white-throated sparrow Zonotrichia albicollis, and Gambel’s white-crowned sparrow Zonotrichia leucophrys gambelii. Each of the assemblies covered fully or in part, over 89% of the previously annotated protein coding genes in the zebra finch Taeniopygia guttata, with 16,846, 15,805, and 16,646 unique BLAST hits in song, white-throated and white-crowned sparrows, respectively. As in previous studies, we find tissue of origin (auditory forebrain versus hypothalamus and whole brain as an important determinant of overall expression profile. We also demonstrate the successful isolation of RNA and RNA-sequencing from post-mortem samples from building strikes and suggest that such an approach could be useful when traditional sampling opportunities are limited. These transcriptomes will be an important resource for the study of social behavior in birds and for data driven annotation of forthcoming whole genome sequences for these and other bird species.

Model-driven development of smart grid services using SoaML

DEFF Research Database (Denmark)

Kosek, Anna Magdalena; Gehrke, Oliver

2014-01-01

This paper presents a model-driven software devel- opment process which can be applied to the design of smart grid services. The Service Oriented Architecture Modelling Language (SoaML) is used to describe the architecture as well as the roles and interactions between service participants....... The individual modelling steps and an example design of a SoaML model for a voltage control service are presented and explained. Finally, the paper discusses a proof-of-concept implementation of the modelled service in a smart grid testing laboratory....

Ice recrystallization inhibition proteins (IRIPs) and freeze tolerance in the cryophilic Antarctic hair grass Deschampsia antarctica E. Desv.

Science.gov (United States)

John, Ulrik P; Polotnianka, Renatam M; Sivakumaran, Kailayapillai A; Chew, Orinda; Mackin, Leanne; Kuiper, Micheal J; Talbot, Jonathan P; Nugent, Gregory D; Mautord, Julie; Schrauf, Gustavo E; Spangenberg, German C

2009-04-01

Antarctic hair grass (Deschampsia antarctica E. Desv.), the only grass indigenous to Antarctica, has well-developed freezing tolerance, strongly induced by cold acclimation. Here, we show that in response to low temperatures, D. antarctica expresses potent recrystallization inhibition (RI) activity that, inhibits the growth of small ice crystals into potentially damaging large ones, is proteinaceous and localized to the apoplasm. A gene family from D. antarctica encoding putative homologs of an ice recrystallization inhibition protein (IRIP) has been isolated and characterized. IRIPs are apoplastically targeted proteins with two potential ice-binding motifs: 1-9 leucine-rich repeats (LRRs) and c. 16 'IRIP' repeats. IRIP genes appear to be confined to the grass subfamily Pooideae and their products, exhibit sequence similarity to phytosulphokine receptors and are predicted to adopt conformations with two ice-binding surfaces. D. antarctica IRIP (DaIRIP) transcript levels are greatly enhanced in leaf tissue following cold acclimation. Transgenic Arabidopsis thaliana expressing a DaIRIP has novel RI activity, and purified DaIRIP, when added back to extracts of leaves from non-acclimated D. antarctica, can reconstitute the activity found in acclimated plants. We propose that IRIP-mediated RI activity may contribute to the cryotolerance of D. antarctica, and thus to its unique ability to have colonized Antarctica.

Modeling of Two-Wheeled Self-Balancing Robot Driven by DC Gearmotors

Science.gov (United States)

Frankovský, P.; Dominik, L.; Gmiterko, A.; Virgala, I.; Kurylo, P.; Perminova, O.

2017-08-01

This paper is aimed at modelling a two-wheeled self-balancing robot driven by the geared DC motors. A mathematical model consists of two main parts, the model of robot's mechanical structure and the model of the actuator. Linearized equations of motion are derived and the overall model of the two-wheeled self-balancing robot is represented in state-space realization for the purpose of state feedback controller design.

DNA analysis of herbarium Specimens of the grass weed Alopecurus myosuroides reveals herbicide resistance pre-dated herbicides.

Science.gov (United States)

Délye, Christophe; Deulvot, Chrystel; Chauvel, Bruno

2013-01-01

Acetyl-CoA carboxylase (ACCase) alleles carrying one point mutation that confers resistance to herbicides have been identified in arable grass weed populations where resistance has evolved under the selective pressure of herbicides. In an effort to determine whether herbicide resistance evolves from newly arisen mutations or from standing genetic variation in weed populations, we used herbarium specimens of the grass weed Alopecurus myosuroides to seek mutant ACCase alleles carrying an isoleucine-to-leucine substitution at codon 1781 that endows herbicide resistance. These specimens had been collected between 1788 and 1975, i.e., prior to the commercial release of herbicides inhibiting ACCase. Among the 734 specimens investigated, 685 yielded DNA suitable for PCR. Genotyping the ACCase locus using the derived Cleaved Amplified Polymorphic Sequence (dCAPS) technique identified one heterozygous mutant specimen that had been collected in 1888. Occurrence of a mutant codon encoding a leucine residue at codon 1781 at the heterozygous state was confirmed in this specimen by sequencing, clearly demonstrating that resistance to herbicides can pre-date herbicides in weeds. We conclude that point mutations endowing resistance to herbicides without having associated deleterious pleiotropic effects can be present in weed populations as part of their standing genetic variation, in frequencies higher than the mutation frequency, thereby facilitating their subsequent selection by herbicide applications.

Comprehensive Characterization of Napier Grass as a Feedstock for Thermochemical Conversion

Directory of Open Access Journals (Sweden)

Isah Y. Mohammed

2015-04-01

Full Text Available Study on Napier grass leaf (NGL, stem (NGS and leaf and stem (NGT was carried out. Proximate, ultimate and structural analyses were evaluated. Functional groups and crystalline components in the biomass were examined. Pyrolysis study was conducted in a thermogravimetric analyzer under nitrogen atmosphere of 20 mL/min at constant heating rate of 10 K/min. The results reveal that Napier grass biomass has high volatile matter, higher heating value, high carbon content and lower ash, nitrogen and sulfur contents. Structural analysis shows that the biomass has considerable cellulose and lignin contents which are good candidates for good quality bio-oil production. From the pyrolysis study, degradation of extractives, hemicellulose, cellulose and lignin occurred at temperature around 478, 543, 600 and above 600 K, respectively. Kinetics of the process was evaluated using reaction order model. New equations that described the process were developed using the kinetic parameters and data compared with experimental data. The results of the models fit well to the experimental data. The proposed models may be a reliable means for describing thermal decomposition of lignocellulosic biomass under nitrogen atmosphere at constant heating rate.

Soil nitrogen mineralization not affected by grass species traits

Science.gov (United States)

Maged Ikram Nosshi; Jack Butler; M. J. Trlica

2007-01-01

Species N use traits was evaluated as a mechanism whereby Bromus inermis (Bromus), an established invasive, might alter soil N supply in a Northern mixed-grass prairie. We compared soils under stands of Bromus with those from three representative native grasses of different litter C/N: Andropogon...

Factors affecting palatability of four submerged macrophytes for grass carp Ctenopharyngodon idella.

Science.gov (United States)

Sun, Jian; Wang, Long; Ma, Lin; Min, Fenli; Huang, Tao; Zhang, Yi; Wu, Zhenbin; He, Feng

2017-12-01

Grass carp can weaken the growth and reproductive capacity of submerged macrophytes by consuming valuable tissues, but factors affecting palatability of submerged macrophytes for grass carp rarely are considered. In this study, relative consumption rate of grass carp with regard to submerged macrophytes was in the following order: Hydrilla verticillata > Vallisneria natans > Ceratophyllum demersum > Myriophyllum spicatum. Firmness of macrophytes was in the following order: M. spicatum > C. demersum > H. verticillata = V. natans, whereas shear force was M. spicatum > C. demersum > H. verticillata > V. natans. After crude extracts of M. spicatum were combined with H. verticillata, grass carp fed on fewer macrophyte pellets that contained more plant secondary metabolites (PSMs). This indicated that structure and PSMs affected palatability of macrophytes.PSMs do not contribute to reduction in palatability through inhibition of intestinal proteinases activity, but they can cause a decrease in the abundance of Exiguobacterium, Acinetobacter-yielding proteases, lipases, and cellulose activity, which in turn can weaken the metabolic capacity of grass carp and adversely affect their growth. Thus, the disadvantages to the growth and development of grass carp caused by PSMs may drive grass carp to feed on palatable submerged macrophytes with lower PSMs.

The design and development of GRASS file reservation system

International Nuclear Information System (INIS)

Huang Qiulan; Zhu Suijiang; Cheng Yaodong; Chen Gang

2010-01-01

GFRS (GRASS File Reservation System) is designed to improve the file access performance of GRASS (Grid-enabled Advanced Storage System) which is a Hierarchical Storage Management (HSM) system developed at Computing Center, Institute of High Energy Physics. GRASS can provide massive storage management and data migration, but the data migration policy is simply based factors such as pool water level, the intervals for migration and so on, so it is short of precise control over files. As for that, we design GFRS to implement user-based file reservation which is to reserve and keep the required files on disks for High Energy physicists. CFRS can improve file access speed for users by avoiding migrating frequently accessed files to tapes. In this paper we first give a brief introduction of GRASS system and then detailed architecture and implementation of GFRS. Experiments results from GFRS have shown good performance and a simple analysis is made based on it. (authors)

Designing a New Raster Sub-System for GRASS-7

Directory of Open Access Journals (Sweden)

Martin Hruby

2012-03-01

Full Text Available The paper deals with a design of a new raster sub-system intended for modern GIS systems open for client and server operation, database connection and strong application interface (API. Motivation for such a design comes from the current state of API working in GRASS 6. If found attractive, the here presented design and its implementation (referred as RG7 may be integrated to the future new generation of the GRASS Geographical Information System version 7-8. The paper describes in details the concept of raster tiling, computer storage of rasters and basic raster access procedures. Finally, the paper gives a simple benchmarking experiment of random read access to raster files imported from the Spearfish dataset. The experiment compares the early implementation of RG7 with the current implementation of rasters in GRASS 6. As the result, the experiment shows the RG7 to be significantly faster than GRASS in random read access to large raster files.

Aspect-Oriented Model-Driven Software Product Line Engineering

Science.gov (United States)

Groher, Iris; Voelter, Markus

Software product line engineering aims to reduce development time, effort, cost, and complexity by taking advantage of the commonality within a portfolio of similar products. The effectiveness of a software product line approach directly depends on how well feature variability within the portfolio is implemented and managed throughout the development lifecycle, from early analysis through maintenance and evolution. This article presents an approach that facilitates variability implementation, management, and tracing by integrating model-driven and aspect-oriented software development. Features are separated in models and composed of aspect-oriented composition techniques on model level. Model transformations support the transition from problem to solution space models. Aspect-oriented techniques enable the explicit expression and modularization of variability on model, template, and code level. The presented concepts are illustrated with a case study of a home automation system.

A Local Poisson Graphical Model for inferring networks from sequencing data.

Science.gov (United States)

Allen, Genevera I; Liu, Zhandong

2013-09-01

Gaussian graphical models, a class of undirected graphs or Markov Networks, are often used to infer gene networks based on microarray expression data. Many scientists, however, have begun using high-throughput sequencing technologies such as RNA-sequencing or next generation sequencing to measure gene expression. As the resulting data consists of counts of sequencing reads for each gene, Gaussian graphical models are not optimal for this discrete data. In this paper, we propose a novel method for inferring gene networks from sequencing data: the Local Poisson Graphical Model. Our model assumes a Local Markov property where each variable conditional on all other variables is Poisson distributed. We develop a neighborhood selection algorithm to fit our model locally by performing a series of l1 penalized Poisson, or log-linear, regressions. This yields a fast parallel algorithm for estimating networks from next generation sequencing data. In simulations, we illustrate the effectiveness of our methods for recovering network structure from count data. A case study on breast cancer microRNAs (miRNAs), a novel application of graphical models, finds known regulators of breast cancer genes and discovers novel miRNA clusters and hubs that are targets for future research.

Input variable selection for data-driven models of Coriolis flowmeters for two-phase flow measurement

International Nuclear Information System (INIS)

Wang, Lijuan; Yan, Yong; Wang, Xue; Wang, Tao

2017-01-01

Input variable selection is an essential step in the development of data-driven models for environmental, biological and industrial applications. Through input variable selection to eliminate the irrelevant or redundant variables, a suitable subset of variables is identified as the input of a model. Meanwhile, through input variable selection the complexity of the model structure is simplified and the computational efficiency is improved. This paper describes the procedures of the input variable selection for the data-driven models for the measurement of liquid mass flowrate and gas volume fraction under two-phase flow conditions using Coriolis flowmeters. Three advanced input variable selection methods, including partial mutual information (PMI), genetic algorithm-artificial neural network (GA-ANN) and tree-based iterative input selection (IIS) are applied in this study. Typical data-driven models incorporating support vector machine (SVM) are established individually based on the input candidates resulting from the selection methods. The validity of the selection outcomes is assessed through an output performance comparison of the SVM based data-driven models and sensitivity analysis. The validation and analysis results suggest that the input variables selected from the PMI algorithm provide more effective information for the models to measure liquid mass flowrate while the IIS algorithm provides a fewer but more effective variables for the models to predict gas volume fraction. (paper)

Comparative growth analysis of cool- and warm-season grasses in a cool-temperate environment

International Nuclear Information System (INIS)

Belesky, D.P.; Fedders, J.M.

1995-01-01

Using both cool-season (C3) and warm-season (C4) species is a viable means of optimizing herbage productivity over varying climatic conditions in temperate environments. Despite well-documented differences in water, N, and radiation use, no consistent evidence demonstrates productivity differences among C3 and C4 perennial grass species under identical management. A field study was conducted to determine relative growth rates (RGR), nitrogen productivity (NP), and mean radiation productivity (RP) (dry matter production as a function of incident radiation) of cool- and warm-season grasses managed identically. Results were used to identify management practices thd could lead to optimal productivity in combinations or mixtures of cool- and warm-season grasses. Dry matter yields of warm-season grasses equaled or surpassed those of cool-season grasses, despite a 40% shorter growth interval. Certain cool- and warm-season grasses appear to be suitable for use in mixtures, based on distribution of herbage production; however, actual compatibility may be altered by defoliation management. Relative growth rates varied among years and were about 40% lower for canopies clipped to a 10-cm residue height each time 20-cm of growth accumulated compared with other treatments. The RGR of warm-season grasses was twice that of cool-season grasses Nitrogen productivity (g DM g-1 N d -1) and mean radiation productivity (g DM MJ-1) for warm-season grasses was also more than twice that of cool-season grasses. Radiation productivity of cool-season grasses was dependent on N, while this was not always the case for warm-season grasses. The superior production capability of certain warm-season compared with cool-season grasses in a cool-temperate environment can be sustained under a range of defoliation treatments and demonstrates suitability for use in frequently defoliated situations

Data-driven integration of genome-scale regulatory and metabolic network models

Science.gov (United States)

Imam, Saheed; Schäuble, Sascha; Brooks, Aaron N.; Baliga, Nitin S.; Price, Nathan D.

2015-01-01

Microbes are diverse and extremely versatile organisms that play vital roles in all ecological niches. Understanding and harnessing microbial systems will be key to the sustainability of our planet. One approach to improving our knowledge of microbial processes is through data-driven and mechanism-informed computational modeling. Individual models of biological networks (such as metabolism, transcription, and signaling) have played pivotal roles in driving microbial research through the years. These networks, however, are highly interconnected and function in concert—a fact that has led to the development of a variety of approaches aimed at simulating the integrated functions of two or more network types. Though the task of integrating these different models is fraught with new challenges, the large amounts of high-throughput data sets being generated, and algorithms being developed, means that the time is at hand for concerted efforts to build integrated regulatory-metabolic networks in a data-driven fashion. In this perspective, we review current approaches for constructing integrated regulatory-metabolic models and outline new strategies for future development of these network models for any microbial system. PMID:25999934

Single-particle model of a strongly driven, dense, nanoscale quantum ensemble

Science.gov (United States)

DiLoreto, C. S.; Rangan, C.

2018-01-01

We study the effects of interatomic interactions on the quantum dynamics of a dense, nanoscale, atomic ensemble driven by a strong electromagnetic field. We use a self-consistent, mean-field technique based on the pseudospectral time-domain method and a full, three-directional basis to solve the coupled Maxwell-Liouville equations. We find that interatomic interactions generate a decoherence in the state of an ensemble on a much faster time scale than the excited-state lifetime of individual atoms. We present a single-particle model of the driven, dense ensemble by incorporating interactions into a dephasing rate. This single-particle model reproduces the essential physics of the full simulation and is an efficient way of rapidly estimating the collective dynamics of a dense ensemble.

Development Policy in Thailand: From Top-down to Grass Roots.

Science.gov (United States)

Kelly, Matthew; Yutthaphonphinit, Phattaraphon; Seubsman, Sam-Ang; Sleigh, Adrian

2012-11-01

Top-down industrial development strategies initially dominated the developing world after the second World War but were eventually found to produce inequitable economic growth. For a decade or more, governments and international development agencies have embraced the idea of participatory grass roots development as a potential solution. Here we review Thailand's experience with development strategies and we examine the current focus on participatory approaches. Thai government planning agencies have adopted "people centred development" and a "sufficiency economy", particularly emphasised since the disruptions caused by the 1997 Asian financial crisis. They aim to address the inequitable sharing of the benefits of decades of rapid growth that was particularly unfair for the rural poor. Thai policies aim to decentralise power to the local level, allowing civil society and Non-Governmental Organisations (NGOs) more of a voice in national decision making and promoting sustainable farming practices aimed at enriching rural communities. An example of this change in Thai government policy is the Community Worker Accreditation Scheme which is aiming to develop human resources at the local level by training community based leaders and supporting networks of community organisations. This enables autonomous local development projects led by trained and accredited individuals and groups. The political tensions notable in Thailand at present are part of this modern transition driven by conflicting models of top-down (industrial) development and the bottom-up (participatory) development ideals described above. Once resolved, Thailand will have few obstacles to moving to a new economic level.

Using hidden Markov models to align multiple sequences.

Science.gov (United States)

Mount, David W

2009-07-01

A hidden Markov model (HMM) is a probabilistic model of a multiple sequence alignment (msa) of proteins. In the model, each column of symbols in the alignment is represented by a frequency distribution of the symbols (called a "state"), and insertions and deletions are represented by other states. One moves through the model along a particular path from state to state in a Markov chain (i.e., random choice of next move), trying to match a given sequence. The next matching symbol is chosen from each state, recording its probability (frequency) and also the probability of going to that state from a previous one (the transition probability). State and transition probabilities are multiplied to obtain a probability of the given sequence. The hidden nature of the HMM is due to the lack of information about the value of a specific state, which is instead represented by a probability distribution over all possible values. This article discusses the advantages and disadvantages of HMMs in msa and presents algorithms for calculating an HMM and the conditions for producing the best HMM.

Designing hybrid grass genomes to control runoff generation

Science.gov (United States)

MacLeod, C.; Binley, A.; Humphreys, M.; King, I. P.; O'Donovan, S.; Papadopoulos, A.; Turner, L. B.; Watts, C.; Whalley, W. R.; Haygarth, P.

2010-12-01

Sustainable management of water in landscapes requires balancing demands of agricultural production whilst moderating downstream effects like flooding. Pasture comprises 69% of global agricultural areas and is essential for producing food and fibre alongside environmental goods and services. Thus there is a need to breed forage grasses that deliver multiple benefits through increased levels of productivity whilst moderating fluxes of water. Here we show that a novel grass hybrid that combines the entire genomes of perennial ryegrass (Lolium perenne - the grass of choice for Europe’s forage agriculture) and meadow fescue (Festuca pratensis) has a significant role in flood prevention. Field plot experiments established differences in runoff generation with the hybrid cultivar reducing runoff by 50% compared to perennial ryegrass cultivar, and by 35% compared to a meadow fescue cultivar (34 events over two years, replicated randomized-block design, statistically significant differences). This important research outcome was the result of a project that combined plant genetics, soil physics and plot scale hydrology to identify novel grass genotypes that can reduce runoff from grassland systems. Through a coordinated series of experiments examining effects from the gene to plot scale, we have identified that the rapid growth and then turnover of roots in the L. perenne x F. pratensis hybrid is likely to be a key mechanism in reducing runoff generation. More broadly this is an exciting first step to realizing the potential to design grass genomes to achieve both food production, and to deliver flood control, a key ecosystem service.

A Model-driven and Service-oriented framework for the business process improvement

Directory of Open Access Journals (Sweden)

Andrea Delgado

2010-07-01

Full Text Available Business Process Management (BPM importance and benefits for organizations to focus on their business processes is nowadays broadly recognized, as business and technology areas are embracing and adopting the paradigm. The Service Oriented Computing (SOC paradigm bases software development on services to realize business processes. The implementation of business processes as services helps in reducing the gap between these two areas, easing the communication and understanding of business needs. The Model Driven Development (MDD paradigm bases software development in models, metamodels and languages that allow transformation between them. The automatic generation of service models from business process models is a key issue to support the separation of its definition from its technical implementation. In this article, we present MINERVA framework which applies Model Driven Development (MDD and Service Oriented Computing (SOC paradigms to business processes for the continuous business process improvement in organizations, giving support to the stages defined in the business process lifecycle from modeling to evaluation of its execution.

Validation of buoyancy driven spectral tensor model using HATS data

DEFF Research Database (Denmark)

Chougule, A.; Mann, Jakob; Kelly, Mark C.

2016-01-01

We present a homogeneous spectral tensor model for wind velocity and temperature fluctuations, driven by mean vertical shear and mean temperature gradient. Results from the model, including one-dimensional velocity and temperature spectra and the associated co-spectra, are shown in this paper....... The model also reproduces two-point statistics, such as coherence and phases, via cross-spectra between two points separated in space. Model results are compared with observations from the Horizontal Array Turbulence Study (HATS) field program (Horst et al. 2004). The spectral velocity tensor in the model...

DESIGN OF GRASS BRIQUETTE MACHINE

African Journals Online (AJOL)

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