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Sample records for model organism podospora

  1. A Genome-Wide Longitudinal Transcriptome Analysis of the Aging Model Podospora anserine

    PubMed Central

    Philipp, Oliver; Hamann, Andrea; Servos, Jörg; Werner, Alexandra; Koch, Ina; Osiewacz, Heinz D.

    2013-01-01

    Aging of biological systems is controlled by various processes which have a potential impact on gene expression. Here we report a genome-wide transcriptome analysis of the fungal aging model Podospora anserina. Total RNA of three individuals of defined age were pooled and analyzed by SuperSAGE (serial analysis of gene expression). A bioinformatics analysis identified different molecular pathways to be affected during aging. While the abundance of transcripts linked to ribosomes and to the proteasome quality control system were found to decrease during aging, those associated with autophagy increase, suggesting that autophagy may act as a compensatory quality control pathway. Transcript profiles associated with the energy metabolism including mitochondrial functions were identified to fluctuate during aging. Comparison of wild-type transcripts, which are continuously down-regulated during aging, with those down-regulated in the long-lived, copper-uptake mutant grisea, validated the relevance of age-related changes in cellular copper metabolism. Overall, we (i) present a unique age-related data set of a longitudinal study of the experimental aging model P. anserina which represents a reference resource for future investigations in a variety of organisms, (ii) suggest autophagy to be a key quality control pathway that becomes active once other pathways fail, and (iii) present testable predictions for subsequent experimental investigations. PMID:24376646

  2. Enzymatic synthesis of model substrates recognized by glucuronoyl esterases from Podospora anserina and Myceliophthora thermophila.

    PubMed

    Katsimpouras, Constantinos; Bénarouche, Anaïs; Navarro, David; Karpusas, Michael; Dimarogona, Maria; Berrin, Jean-Guy; Christakopoulos, Paul; Topakas, Evangelos

    2014-06-01

    Glucuronoyl esterases (GEs) are recently discovered enzymes that are suggested to cleave the ester bond between lignin alcohols and xylan-bound 4-O-methyl-D-glucuronic acid. Although their potential use for enhanced enzymatic biomass degradation and synthesis of valuable chemicals renders them attractive research targets for biotechnological applications, the difficulty to purify natural fractions of lignin-carbohydrate complexes hampers the characterization of fungal GEs. In this work, we report the synthesis of three aryl alkyl or alkenyl D-glucuronate esters using lipase B from Candida antarctica (CALB) and their use to determine the kinetic parameters of two GEs, StGE2 from the thermophilic fungus Myceliophthora thermophila (syn. Sporotrichum thermophile) and PaGE1 from the coprophilous fungus Podospora anserina. PaGE1 was functionally expressed in the methylotrophic yeast Pichia pastoris under the transcriptional control of the alcohol oxidase (AOX1) promoter and purified to its homogeneity (63 kDa). The three D-glucuronate esters contain an aromatic UV-absorbing phenol group that facilitates the quantification of their enzymatic hydrolysis by HPLC. Both enzymes were able to hydrolyze the synthetic esters with a pronounced preference towards the cinnamyl-D-glucuronate ester. The experimental results were corroborated by computational docking of the synthesized substrate analogues. We show that the nature of the alcohol portion of the hydrolyzed ester influences the catalytic efficiency of the two GEs. PMID:24531271

  3. Plant biomass degrading ability of the coprophilic ascomycete fungus Podospora anserina.

    PubMed

    Couturier, Marie; Tangthirasunun, Narumon; Ning, Xie; Brun, Sylvain; Gautier, Valérie; Bennati-Granier, Chloé; Silar, Philippe; Berrin, Jean-Guy

    2016-01-01

    The degradation of plant biomass is a major challenge towards the production of bio-based compounds and materials. As key lignocellulolytic enzyme producers, filamentous fungi represent a promising reservoir to tackle this challenge. Among them, the coprophilous ascomycete Podospora anserina has been used as a model organism to study various biological mechanisms because its genetics are well understood and controlled. In 2008, the sequencing of its genome revealed a great diversity of enzymes targeting plant carbohydrates and lignin. Since then, a large array of lignocellulose-acting enzymes has been characterized and genetic analyses have enabled the understanding of P. anserina metabolism and development on plant biomass. Overall, these research efforts shed light on P. anserina strategy to unlock recalcitrant lignocellulose deconstruction. PMID:27263000

  4. Peroxisome dynamics during development of the fungus Podospora anserina.

    PubMed

    Takano-Rojas, Harumi; Zickler, Denise; Peraza-Reyes, Leonardo

    2016-01-01

    Peroxisomes are versatile and dynamic organelles that are required for the development of diverse eukaryotic organisms. We demonstrated previously that in the fungus Podospora anserina different peroxisomal functions are required at distinct stages of sexual development, including the initiation and progression of meiocyte (ascus) development and the differentiation and germination of sexual spores (ascospores). Peroxisome assembly during these processes relies on the differential activity of the protein machinery that drives the import of proteins into the organelle, indicating a complex developmental regulation of peroxisome formation and activity. Here we demonstrate that peroxisome dynamics is also highly regulated during development. We show that peroxisomes in P. anserina are highly dynamic and respond to metabolic and environmental cues by undergoing changes in size, morphology and number. In addition, peroxisomes of vegetative and sexual cell types are structurally different. During sexual development peroxisome number increases at two stages: at early ascus differentiation and during ascospore formation. These processes are accompanied by changes in peroxisome structure and distribution, which include a cell-polarized concentration of peroxisomes at the beginning of ascus development, as well as a morphological transition from predominantly spherical to elongated shapes at the end of the first meiotic division. Further, the mostly tubular peroxisomes present from second meiotic division to early ascospore formation again become rounded during ascospore differentiation. Ultimately the number of peroxisomes dramatically decreases upon ascospore maturation. Our results reveal a precise regulation of peroxisome dynamics during sexual development and suggest that peroxisome constitution and function during development is defined by the coordinated regulation of the proteins that control peroxisome assembly and dynamics. PMID:26908647

  5. Overlapping Podospora anserina Transcriptional Responses to Bacterial and Fungal Non Self Indicate a Multilayered Innate Immune Response

    PubMed Central

    Lamacchia, Marina; Dyrka, Witold; Breton, Annick; Saupe, Sven J.; Paoletti, Mathieu

    2016-01-01

    Recognition and response to non self is essential to development and survival of all organisms. It can occur between individuals of the same species or between different organisms. Fungi are established models for conspecific non self recognition in the form of vegetative incompatibility (VI), a genetically controlled process initiating a programmed cell death (PCD) leading to the rejection of a fusion cell between genetically different isolates of the same species. In Podospora anserina VI is controlled by members of the hnwd gene family encoding for proteins analogous to NOD Like Receptors (NLR) immune receptors in eukaryotes. It was hypothesized that the hnwd controlled VI reaction was derived from the fungal innate immune response. Here we analyze the P. anserina transcriptional responses to two bacterial species, Serratia fonticola to which P. anserina survives and S. marcescens to which P. anserina succumbs, and compare these to the transcriptional response induced under VI conditions. Transcriptional responses to both bacteria largely overlap, however the number of genes regulated and magnitude of regulation is more important when P. anserina survives. Transcriptional responses to bacteria also overlap with the VI reaction for both up or down regulated gene sets. Genes up regulated tend to be clustered in the genome, and display limited phylogenetic distribution. In all three responses we observed genes related to autophagy to be up-regulated. Autophagy contributes to the fungal survival in all three conditions. Genes encoding for secondary metabolites and histidine kinase signaling are also up regulated in all three conditions. Transcriptional responses also display differences. Genes involved in response to oxidative stress, or encoding small secreted proteins are essentially expressed in response to bacteria, while genes encoding NLR proteins are expressed during VI. Most functions encoded in response to bacteria favor survival of the fungus while most

  6. Insights into Exo- and Endoglucanase Activities of Family 6 Glycoside Hydrolases from Podospora anserina

    PubMed Central

    Poidevin, Laetitia; Feliu, Julia; Doan, Annick; Berrin, Jean-Guy; Bey, Mathieu; Coutinho, Pedro M.; Henrissat, Bernard; Record, Eric

    2013-01-01

    The ascomycete Podospora anserina is a coprophilous fungus that grows at late stages on droppings of herbivores. Its genome encodes a large diversity of carbohydrate-active enzymes. Among them, four genes encode glycoside hydrolases from family 6 (GH6), the members of which comprise putative endoglucanases and exoglucanases, some of them exerting important functions for biomass degradation in fungi. Therefore, this family was selected for functional analysis. Three of the enzymes, P. anserina Cel6A (PaCel6A), PaCel6B, and PaCel6C, were functionally expressed in the yeast Pichia pastoris. All three GH6 enzymes hydrolyzed crystalline and amorphous cellulose but were inactive on hydroxyethyl cellulose, mannan, galactomannan, xyloglucan, arabinoxylan, arabinan, xylan, and pectin. PaCel6A had a catalytic efficiency on cellotetraose comparable to that of Trichoderma reesei Cel6A (TrCel6A), but PaCel6B and PaCel6C were clearly less efficient. PaCel6A was the enzyme with the highest stability at 45°C, while PaCel6C was the least stable enzyme, losing more than 50% of its activity after incubation at temperatures above 30°C for 24 h. In contrast to TrCel6A, all three studied P. anserina GH6 cellulases were stable over a wide range of pHs and conserved high activity at pH values of up to 9. Each enzyme displayed a distinct substrate and product profile, highlighting different modes of action, with PaCel6A being the enzyme most similar to TrCel6A. PaCel6B was the only enzyme with higher specific activity on carboxymethylcellulose (CMC) than on Avicel and showed lower processivity than the others. Structural modeling predicts an open catalytic cleft, suggesting that PaCel6B is an endoglucanase. PMID:23645193

  7. Mitochondrial intronic open reading frames in Podospora: Mobility and consecutive exonic sequence variations

    SciTech Connect

    Sellem, C.H.; Rossignol, M.; Belcour, L.

    1996-06-01

    The mitochondrial genome of 23 wild-type strains belonging to three different species of the filamentous fungus Podospora was examined. Among the 15 optical sequences identified are two intronic reading frames, nad1-i4-orf1 and cox1-i7-orf2. We show that the presence of these sequences was strictly correlated with tightly clustered nucleotide substitutions in the adjacent exon. This correlation applies to the presence or absence of closely related open reading frames (ORFs), found at the same genetic locations, in all the Pyrenomycete genera examined. The recent gain of these optional ORFs in the evolution of the genus Podospora probably account for such sequence differences. In the homoplasmic progeny from heteroplasmons constructed between Podospora strains differing by the presence of these optional ORFs, nad1-i4-orf1 and cox1-i7-orf2 appeared highly invasive. Sequence comparisons in the nad1-i4 intron of various strains of the Pyrenomycete family led us to propose a scenario of its evolution that includes several events of loss and gain of intronic ORFs. These results strongly reinforce the idea that group I intronic ORFs are mobile elements and that their transfer, and comcomitant modification of the adjacent exon, could participate in the modular evolution of mitochondrial genomes. 46 refs., 5 figs., 2 tabs.

  8. Cytosolic Ribosomal Mutations That Abolish Accumulation of Circular Intron in the Mitochondria without Preventing Senescence of Podospora Anserina

    PubMed Central

    Silar, P.; Koll, F.; Rossignol, M.

    1997-01-01

    The filamentous fungus Podospora anserina presents a degeneration syndrome called Senescence associated with mitochondrial DNA modifications. We show that mutations affecting the two different and interacting cytosolic ribosomal proteins (S7 and S19) systematically and specifically prevent the accumulation of senDNAα (a circular double-stranded DNA plasmid derived from the first intron of the mitochondrial cox1 gene or intron α) without abolishing Senescence nor affecting the accumulation of other usually observed mitochondrial DNA rearrangements. One of the mutant proteins is homologous to the Escherichia coli S4 and Saccharomyces cerevisiae S13 ribosomal proteins, known to be involved in accuracy control of cytosolic translation. The lack of accumulation of senDNAα seems to result from a nontrivial ribosomal alteration unrelated to accuracy control, indicating that S7 and S19 proteins have an additional function. The results strongly suggest that modified expression of nucleus-encoded proteins contributes to Senescence in P. anserina. These data do not fit well with some current models, which propose that intron α plays the role of the cytoplasmic and infectious Determinant of Senescence that was defined in early studies. PMID:9055079

  9. Genetic and functional investigation of Zn(2)Cys(6) transcription factors RSE2 and RSE3 in Podospora anserina.

    PubMed

    Bovier, Elodie; Sellem, Carole H; Humbert, Adeline; Sainsard-Chanet, Annie

    2014-01-01

    In Podospora anserina, the two zinc cluster proteins RSE2 and RSE3 are essential for the expression of the gene encoding the alternative oxidase (aox) when the mitochondrial electron transport chain is impaired. In parallel, they activated the expression of gluconeogenic genes encoding phosphoenolpyruvate carboxykinase (pck) and fructose-1,6-biphosphatase (fbp). Orthologues of these transcription factors are present in a wide range of filamentous fungi, and no other role than the regulation of these three genes has been evidenced so far. In order to better understand the function and the organization of RSE2 and RSE3, we conducted a saturated genetic screen based on the constitutive expression of the aox gene. We identified 10 independent mutations in 9 positions in rse2 and 11 mutations in 5 positions in rse3. Deletions were generated at some of these positions and the effects analyzed. This analysis suggests the presence of central regulatory domains and a C-terminal activation domain in both proteins. Microarray analysis revealed 598 genes that were differentially expressed in the strains containing gain- or loss-of-function mutations in rse2 or rse3. It showed that in addition to aox, fbp, and pck, RSE2 and RSE3 regulate the expression of genes encoding the alternative NADH dehydrogenase, a Zn2Cys6 transcription factor, a flavohemoglobin, and various hydrolases. As a complement to expression data, a metabolome profiling approach revealed that both an rse2 gain-of-function mutation and growth on antimycin result in similar metabolic alterations in amino acids, fatty acids, and α-ketoglutarate pools. PMID:24186951

  10. Evaluating Service Organization Models

    PubMed Central

    TOUATI, NASSERA; PINEAULT, RAYNALD; CHAMPAGNE, FRANÇOIS; DENIS, JEAN-LOUIS; BROUSSELLE, ASTRID; CONTANDRIOPOULOS, ANDRÉ-PIERRE; GENEAU, ROBERT

    2016-01-01

    Based on the example of the evaluation of service organization models, this article shows how a configurational approach overcomes the limits of traditional methods which for the most part have studied the individual components of various models considered independently of one another. These traditional methods have led to results (observed effects) that are difficult to interpret. The configurational approach, in contrast, is based on the hypothesis that effects are associated with a set of internally coherent model features that form various configurations. These configurations, like their effects, are context-dependent. We explore the theoretical basis of the configuration approach in order to emphasize its relevance, and discuss the methodological challenges inherent in the application of this approach through an in-depth analysis of the scientific literature. We also propose methodological solutions to these challenges. We illustrate from an example how a configurational approach has been used to evaluate primary care models. Finally, we begin a discussion on the implications of this new evaluation approach for the scientific and decision-making communities.

  11. Incomplete penetrance and variable expressivity of a growth defect as a consequence of knocking out two K(+) transporters in the euascomycete fungus Podospora anserina.

    PubMed Central

    Lalucque, Hervé; Silar, Philippe

    2004-01-01

    We describe an example of incomplete penetrance and variable expressivity in the filamentous fungus Podospora anserina, two genetic properties classically associated with mutations in more complex organisms, such as green plants and animals. We show that the knockouts of two TRK-related K(+) transporters of this ascomycete present variability in their phenotype that cannot be attributed to fluctuations of the genetic background or the environment. Thalli of the knockout strains derived from independent monokaryotic ascospores or from a single monokaryotic ascospore and cultivated under standard growth conditions may or may not present impaired growth. When impaired, thalli exhibit a range of phenotypes. Environmental conditions control expressivity to a large extent and penetrance to a low extent. Restoration of functional potassium transport by heterologous expression of K(+) transporters from Neurospora crassa abolishes or strongly diminishes the growth impairment. These data show that incomplete penetrance and variable expressivity can be an intrinsic property of a single Mendelian loss-of-function mutation. They also show that such variability in the expression of a mutant phenotype can be promoted by a phenomenon not obviously related to the well-known chromatin structure modifications, i.e., potassium transport. They provide a framework to understand human channelopathies with similar properties. PMID:15020412

  12. A homologue of the yeast SHE4 gene is essential for the transition between the syncytial and cellular stages during sexual reproduction of the fungus Podospora anserina.

    PubMed Central

    Berteaux-Lecellier, V; Zickler, D; Debuchy, R; Panvier-Adoutte, A; Thompson-Coffe, C; Picard, M

    1998-01-01

    The Podospora anserina cro1 gene was identified as a gene required for sexual sporulation. Crosses homozygous for the cro1-1 mutation yield fruiting bodies which produce few asci due to the formation of giant plurinucleate cells instead of dikaryotic cells after fertilization. This defect does not impair karyogamy, but meioses of the resultant polyploid nuclei are most often abortive. Cytological studies suggest that the primary defect of the mutant is its inability to form septa between the daughter nuclei after each mitosis, a step specific for normal dikaryotic cell divisions. The cro1-1 mutant would thus be unable to leave the syncytial vegetative state while abiding by the meiotic programme. cro1-1 also shows defects in ascospore germination and growth rate. GFP-tagging of the CRO1 protein reveals that it is a cytosolic protein mainly expressed at the beginning of the dikaryotic stage and at the time of ascospore maturation. The CRO1 protein exhibits significant similarity to the SHE4 protein, which is required for asymmetric mating-type switching in budding yeast cells. Thus, a gene involved in asymmetric cell divisions in a unicellular organism plays a key role at the transition between the syncytial (vegetative) state and the cellular (sexual) state in a filamentous fungus. PMID:9482722

  13. Deletion of the MED13 and CDK8 subunits of the Mediator improves the phenotype of a long-lived respiratory deficient mutant of Podospora anserina.

    PubMed

    Humbert, Adeline; Bovier, Elodie; Sellem, Carole H; Sainsard-Chanet, Annie

    2015-09-01

    In Podospora anserina, the loss of function of the cytochrome segment of the mitochondrial respiratory chain is viable. This is due to the presence in this organism, as in most filamentous fungi, of an alternative respiratory oxidase (AOX) that provides a bypass to the cytochrome pathway. However mutants lacking a functional cytochrome pathway present multiple phenotypes including poorly colored thin mycelium and slow growth. In a large genetic screen based on the improvement of these phenotypes, we isolated a large number of independent suppressor mutations. Most of them led to the constitutive overexpression of the aox gene. In this study, we characterize a new suppressor mutation that does not affect the production of AOX. It is a loss-of-function mutation in the gene encoding the MED13 subunit of the kinase module of the Mediator complex. Inactivation of the cdk8 gene encoding another subunit of the same module also results in partial suppression of a cytochrome-deficient mutant. Analysis of strains lacking the MED13 or CDK8 subunits points to the importance of these subunits as regulators involved in diverse physiological processes such as growth, longevity and sexual development. Interestingly, transcriptional analyses indicate that in P. anserina, loss of the respiratory cytochrome pathway results in the up-regulation of glycolysis-related genes revealing a new type of retrograde regulation. The loss of MED13 augments the up-regulation of some of these genes. PMID:26231682

  14. Structural and Biochemical Analyses of Glycoside Hydrolase Families 5 and 26 β-(1,4)-Mannanases from Podospora anserina Reveal Differences upon Manno-oligosaccharide Catalysis*

    PubMed Central

    Couturier, Marie; Roussel, Alain; Rosengren, Anna; Leone, Philippe; Stålbrand, Henrik; Berrin, Jean-Guy

    2013-01-01

    The microbial deconstruction of the plant cell wall is a key biological process that is of increasing importance with the development of a sustainable biofuel industry. The glycoside hydrolase families GH5 (PaMan5A) and GH26 (PaMan26A) endo-β-1,4-mannanases from the coprophilic ascomycete Podospora anserina contribute to the enzymatic degradation of lignocellulosic biomass. In this study, P. anserina mannanases were further subjected to detailed comparative analysis of their substrate specificities, active site organization, and transglycosylation capacity. Although PaMan5A displays a classical mode of action, PaMan26A revealed an atypical hydrolysis pattern with the release of mannotetraose and mannose from mannopentaose resulting from a predominant binding mode involving the −4 subsite. The crystal structures of PaMan5A and PaMan26A were solved at 1.4 and 2.85 Å resolution, respectively. Analysis of the PaMan26A structure supported strong interaction with substrate at the −4 subsite mediated by two aromatic residues Trp-244 and Trp-245. The PaMan26A structure appended to its family 35 carbohydrate binding module revealed a short and proline-rich rigid linker that anchored together the catalytic and the binding modules. PMID:23558681

  15. Comparative analyses of Podospora anserina secretomes reveal a large array of lignocellulose-active enzymes.

    PubMed

    Poidevin, Laetitia; Berrin, Jean-Guy; Bennati-Granier, Chloé; Levasseur, Anthony; Herpoël-Gimbert, Isabelle; Chevret, Didier; Coutinho, Pedro M; Henrissat, Bernard; Heiss-Blanquet, Senta; Record, Eric

    2014-09-01

    The genome of the coprophilous fungus Podospora anserina harbors a large and highly diverse set of putative lignocellulose-acting enzymes. In this study, we investigated the enzymatic diversity of a broad range of P. anserina secretomes induced by various carbon sources (dextrin, glucose, xylose, arabinose, lactose, cellobiose, saccharose, Avicel, Solka-floc, birchwood xylan, wheat straw, maize bran, and sugar beet pulp (SBP)). Compared with the Trichoderma reesei enzymatic cocktail, P. anserina secretomes displayed similar cellulase, xylanase, and pectinase activities and greater arabinofuranosidase, arabinanase, and galactanase activities. The secretomes were further tested for their capacity to supplement a T. reesei cocktail. Four of them improved significantly the saccharification yield of steam-exploded wheat straw up to 48 %. Fine analysis of the P. anserina secretomes produced with Avicel and SBP using proteomics revealed a large array of CAZymes with a high number of GH6 and GH7 cellulases, CE1 esterases, GH43 arabinofuranosidases, and AA1 laccase-like multicopper oxidases. Moreover, a preponderance of AA9 (formerly GH61) was exclusively produced in the SBP condition. This study brings additional insights into the P. anserina enzymatic machinery and will facilitate the selection of promising targets for the development of future biorefineries. PMID:24695830

  16. Identification of a hypothetical protein from Podospora anserina as a nitroalkane oxidase.

    PubMed

    Tormos, José R; Taylor, Alexander B; Daubner, S Colette; Hart, P John; Fitzpatrick, Paul F

    2010-06-22

    The flavoprotein nitroalkane oxidase (NAO) from Fusarium oxysporum catalyzes the oxidation of primary and secondary nitroalkanes to their respective aldehydes and ketones. Structurally, the enzyme is a member of the acyl-CoA dehydrogenase superfamily. To date no enzymes other than that from F. oxysporum have been annotated as NAOs. To identify additional potential NAOs, the available database was searched for enzymes in which the active site residues Asp402, Arg409, and Ser276 were conserved. Of the several fungal enzymes identified in this fashion, PODANSg2158 from Podospora anserina was selected for expression and characterization. The recombinant enzyme is a flavoprotein with activity on nitroalkanes comparable to the F. oxysporum NAO, although the substrate specificity is somewhat different. Asp399, Arg406, and Ser273 in PODANSg2158 correspond to the active site triad in F. oxysporum NAO. The k(cat)/K(M)-pH profile with nitroethane shows a pK(a) of 5.9 that is assigned to Asp399 as the active site base. Mutation of Asp399 to asparagine decreases the k(cat)/K(M) value for nitroethane over 2 orders of magnitude. The R406K and S373A mutations decrease this kinetic parameter by 64- and 3-fold, respectively. The structure of PODANSg2158 has been determined at a resolution of 2.0 A, confirming its identification as an NAO. PMID:20481475

  17. Genetic and Molecular Analysis of a Long-Lived Strain of Podospora Anserina

    PubMed Central

    Silliker, M. E.; Cummings, D. J.

    1990-01-01

    A genetic and molecular analysis of a long-lived strain of Podospora anserina, Mn19, was undertaken to detect mutations in genes responsible for senescence. In crosses between Mn19 and wild type about 15% of the progeny were long-lived, regardless of the female parent. Molecular analysis of the long-lived progeny showed that none of the strains inherited a mtDNA rearrangement characteristic of the Mn19 parent. Instead, all long-lived strains initially inherited wild-type mtDNA. Over time the mtDNA of most long-lived strains underwent rearrangements, deletions and amplifications. The change over time in the presence of two previously characterized plasmids associated with either senescence or longevity was monitored. Crosses between Mn19 and its long-lived progeny also yielded only a small percent of individuals recovering from senescence. Analysis of mtDNA from crosses suggests that wild-type mtDNA from the paternal parent can be selected over mtDNA from the maternal parent. The life span phenotypes of progeny were not consistent with the hypothesis that mutations in a few nuclear genes were responsible for longevity. PMID:2397883

  18. Teaching biology with model organisms

    NASA Astrophysics Data System (ADS)

    Keeley, Dolores A.

    The purpose of this study is to identify and use model organisms that represent each of the kingdoms biologists use to classify organisms, while experiencing the process of science through guided inquiry. The model organisms will be the basis for studying the four high school life science core ideas as identified by the Next Generation Science Standards (NGSS): LS1-From molecules to organisms, LS2-Ecosystems, LS3- Heredity, and LS4- Biological Evolution. NGSS also have identified four categories of science and engineering practices which include developing and using models and planning and carrying out investigations. The living organisms will be utilized to increase student interest and knowledge within the discipline of Biology. Pre-test and posttest analysis utilizing student t-test analysis supported the hypothesis. This study shows increased student learning as a result of using living organisms as models for classification and working in an inquiry-based learning environment.

  19. Podospora anserina Hemicellulases Potentiate the Trichoderma reesei Secretome for Saccharification of Lignocellulosic Biomass▿

    PubMed Central

    Couturier, Marie; Haon, Mireille; Coutinho, Pedro M.; Henrissat, Bernard; Lesage-Meessen, Laurence; Berrin, Jean-Guy

    2011-01-01

    To improve the enzymatic hydrolysis (saccharification) of lignocellulosic biomass by Trichoderma reesei, a set of genes encoding putative polysaccharide-degrading enzymes were selected from the coprophilic fungus Podospora anserina using comparative genomics. Five hemicellulase-encoding genes were successfully cloned and expressed as secreted functional proteins in the yeast Pichia pastoris. These novel fungal CAZymes belonging to different glycoside hydrolase families (PaMan5A and PaMan26A mannanases, PaXyn11A xylanase, and PaAbf51A and PaAbf62A arabinofuranosidases) were able to break down their predicted cognate substrates. Although PaMan5A and PaMan26A displayed similar specificities toward a range of mannan substrates, they differed in their end products, suggesting differences in substrate binding. The N-terminal CBM35 module of PaMan26A displayed dual binding specificity toward xylan and mannan. PaXyn11A harboring a C-terminal CBM1 module efficiently degraded wheat arabinoxylan, releasing mainly xylobiose as end product. PaAbf51A and PaAbf62A arabinose-debranching enzymes exhibited differences in activity toward arabinose-containing substrates. Further investigation of the contribution made by each P. anserina auxiliary enzyme to the saccharification of wheat straw and spruce demonstrated that the endo-acting hemicellulases (PaXyn11A, PaMan5A, and PaMan26A) individually supplemented the secretome of the industrial T. reesei CL847 strain. The most striking effect was obtained with PaMan5A that improved the release of total sugars by 28% and of glucose by 18%, using spruce as lignocellulosic substrate. PMID:21037302

  20. Natural Variation of Heterokaryon Incompatibility Gene het-c in Podospora anserina Reveals Diversifying Selection

    PubMed Central

    Bastiaans, Eric; Debets, Alfons J.M.; Aanen, Duur K.; van Diepeningen, Anne D.; Saupe, Sven J.; Paoletti, Mathieu

    2014-01-01

    In filamentous fungi, allorecognition takes the form of heterokaryon incompatibility, a cell death reaction triggered when genetically distinct hyphae fuse. Heterokaryon incompatibility is controlled by specific loci termed het-loci. In this article, we analyzed the natural variation in one such fungal allorecognition determinant, the het-c heterokaryon incompatibility locus of the filamentous ascomycete Podospora anserina. The het-c locus determines an allogenic incompatibility reaction together with two unlinked loci termed het-d and het-e. Each het-c allele is incompatible with a specific subset of the het-d and het-e alleles. We analyzed variability at the het-c locus in a population of 110 individuals, and in additional isolates from various localities. We identified a total of 11 het-c alleles, which define 7 distinct incompatibility specificity classes in combination with the known het-d and het-e alleles. We found that the het-c allorecognition gene of P. anserina is under diversifying selection. We find a highly unequal allele distribution of het-c in the population, which contrasts with the more balanced distribution of functional groups of het-c based on their allorecognition function. One explanation for the observed het-c diversity in the population is its function in allorecognition. However, alleles that are most efficient in allorecognition are rare. An alternative and not exclusive explanation for the observed diversity is that het-c is involved in pathogen recognition. In Arabidopsis thaliana, a homolog of het-c is a pathogen effector target, supporting this hypothesis. We hypothesize that the het-c diversity in P. anserina results from both its functions in pathogen-defense, and allorecognition. PMID:24448643

  1. Natural variation of heterokaryon incompatibility gene het-c in Podospora anserina reveals diversifying selection.

    PubMed

    Bastiaans, Eric; Debets, Alfons J M; Aanen, Duur K; van Diepeningen, Anne D; Saupe, Sven J; Paoletti, Mathieu

    2014-04-01

    In filamentous fungi, allorecognition takes the form of heterokaryon incompatibility, a cell death reaction triggered when genetically distinct hyphae fuse. Heterokaryon incompatibility is controlled by specific loci termed het-loci. In this article, we analyzed the natural variation in one such fungal allorecognition determinant, the het-c heterokaryon incompatibility locus of the filamentous ascomycete Podospora anserina. The het-c locus determines an allogenic incompatibility reaction together with two unlinked loci termed het-d and het-e. Each het-c allele is incompatible with a specific subset of the het-d and het-e alleles. We analyzed variability at the het-c locus in a population of 110 individuals, and in additional isolates from various localities. We identified a total of 11 het-c alleles, which define 7 distinct incompatibility specificity classes in combination with the known het-d and het-e alleles. We found that the het-c allorecognition gene of P. anserina is under diversifying selection. We find a highly unequal allele distribution of het-c in the population, which contrasts with the more balanced distribution of functional groups of het-c based on their allorecognition function. One explanation for the observed het-c diversity in the population is its function in allorecognition. However, alleles that are most efficient in allorecognition are rare. An alternative and not exclusive explanation for the observed diversity is that het-c is involved in pathogen recognition. In Arabidopsis thaliana, a homolog of het-c is a pathogen effector target, supporting this hypothesis. We hypothesize that the het-c diversity in P. anserina results from both its functions in pathogen-defense, and allorecognition. PMID:24448643

  2. The PaPsr1 and PaWhi2 genes are members of the regulatory network that connect stationary phase to mycelium differentiation and reproduction in Podospora anserina.

    PubMed

    Timpano, Hélène; Chan Ho Tong, Laetitia; Gautier, Valérie; Lalucque, Hervé; Silar, Philippe

    2016-09-01

    In filamentous fungi, entrance into stationary phase is complex as it is accompanied by several differentiation and developmental processes, including the synthesis of pigments, aerial hyphae, anastomoses and sporophores. The regulatory networks that control these processes are still incompletely known. The analysis of the "Impaired in the development of Crippled Growth (IDC)" mutants of the model filamentous ascomycete Podospora anserina has already yielded important information regarding the pathway regulating entrance into stationary phase. Here, the genes affected in two additional IDC mutants are identified as orthologues of the Saccharomyces cerevisiae WHI2 and PSR1 genes, known to regulate stationary phase in this yeast, arguing for a conserved role of these proteins throughout the evolution of ascomycetes. PMID:27353975

  3. A future of the model organism model

    PubMed Central

    Rine, Jasper

    2014-01-01

    Changes in technology are fundamentally reframing our concept of what constitutes a model organism. Nevertheless, research advances in the more traditional model organisms have enabled fresh and exciting opportunities for young scientists to establish new careers and offer the hope of comprehensive understanding of fundamental processes in life. New advances in translational research can be expected to heighten the importance of basic research in model organisms and expand opportunities. However, researchers must take special care and implement new resources to enable the newest members of the community to engage fully with the remarkable legacy of information in these fields. PMID:24577733

  4. Structure and Biophysical Characterization of the S-Adenosylmethionine-dependent O-Methyltransferase PaMTH1, a Putative Enzyme Accumulating during Senescence of Podospora anserina.

    PubMed

    Chatterjee, Deep; Kudlinzki, Denis; Linhard, Verena; Saxena, Krishna; Schieborr, Ulrich; Gande, Santosh L; Wurm, Jan Philip; Wöhnert, Jens; Abele, Rupert; Rogov, Vladimir V; Dötsch, Volker; Osiewacz, Heinz D; Sreeramulu, Sridhar; Schwalbe, Harald

    2015-06-26

    Low levels of reactive oxygen species (ROS) act as important signaling molecules, but in excess they can damage biomolecules. ROS regulation is therefore of key importance. Several polyphenols in general and flavonoids in particular have the potential to generate hydroxyl radicals, the most hazardous among all ROS. However, the generation of a hydroxyl radical and subsequent ROS formation can be prevented by methylation of the hydroxyl group of the flavonoids. O-Methylation is performed by O-methyltransferases, members of the S-adenosyl-l-methionine (SAM)-dependent O-methyltransferase superfamily involved in the secondary metabolism of many species across all kingdoms. In the filamentous fungus Podospora anserina, a well established aging model, the O-methyltransferase (PaMTH1) was reported to accumulate in total and mitochondrial protein extracts during aging. In vitro functional studies revealed flavonoids and in particular myricetin as its potential substrate. The molecular architecture of PaMTH1 and the mechanism of the methyl transfer reaction remain unknown. Here, we report the crystal structures of PaMTH1 apoenzyme, PaMTH1-SAM (co-factor), and PaMTH1-S-adenosyl homocysteine (by-product) co-complexes refined to 2.0, 1.9, and 1.9 Å, respectively. PaMTH1 forms a tight dimer through swapping of the N termini. Each monomer adopts the Rossmann fold typical for many SAM-binding methyltransferases. Structural comparisons between different O-methyltransferases reveal a strikingly similar co-factor binding pocket but differences in the substrate binding pocket, indicating specific molecular determinants required for substrate selection. Furthermore, using NMR, mass spectrometry, and site-directed active site mutagenesis, we show that PaMTH1 catalyzes the transfer of the methyl group from SAM to one hydroxyl group of the myricetin in a cation-dependent manner. PMID:25979334

  5. Structure and Biophysical Characterization of the S-Adenosylmethionine-dependent O-Methyltransferase PaMTH1, a Putative Enzyme Accumulating during Senescence of Podospora anserina *

    PubMed Central

    Chatterjee, Deep; Kudlinzki, Denis; Linhard, Verena; Saxena, Krishna; Schieborr, Ulrich; Gande, Santosh L.; Wurm, Jan Philip; Wöhnert, Jens; Abele, Rupert; Rogov, Vladimir V.; Dötsch, Volker; Osiewacz, Heinz D.; Sreeramulu, Sridhar; Schwalbe, Harald

    2015-01-01

    Low levels of reactive oxygen species (ROS) act as important signaling molecules, but in excess they can damage biomolecules. ROS regulation is therefore of key importance. Several polyphenols in general and flavonoids in particular have the potential to generate hydroxyl radicals, the most hazardous among all ROS. However, the generation of a hydroxyl radical and subsequent ROS formation can be prevented by methylation of the hydroxyl group of the flavonoids. O-Methylation is performed by O-methyltransferases, members of the S-adenosyl-l-methionine (SAM)-dependent O-methyltransferase superfamily involved in the secondary metabolism of many species across all kingdoms. In the filamentous fungus Podospora anserina, a well established aging model, the O-methyltransferase (PaMTH1) was reported to accumulate in total and mitochondrial protein extracts during aging. In vitro functional studies revealed flavonoids and in particular myricetin as its potential substrate. The molecular architecture of PaMTH1 and the mechanism of the methyl transfer reaction remain unknown. Here, we report the crystal structures of PaMTH1 apoenzyme, PaMTH1-SAM (co-factor), and PaMTH1-S-adenosyl homocysteine (by-product) co-complexes refined to 2.0, 1.9, and 1.9 Å, respectively. PaMTH1 forms a tight dimer through swapping of the N termini. Each monomer adopts the Rossmann fold typical for many SAM-binding methyltransferases. Structural comparisons between different O-methyltransferases reveal a strikingly similar co-factor binding pocket but differences in the substrate binding pocket, indicating specific molecular determinants required for substrate selection. Furthermore, using NMR, mass spectrometry, and site-directed active site mutagenesis, we show that PaMTH1 catalyzes the transfer of the methyl group from SAM to one hydroxyl group of the myricetin in a cation-dependent manner. PMID:25979334

  6. Heterologous production of cellobiose dehydrogenases from the basidiomycete Coprinopsis cinerea and the ascomycete Podospora anserina and their effect on saccharification of wheat straw.

    PubMed

    Turbe-Doan, Annick; Arfi, Yonathan; Record, Eric; Estrada-Alvarado, Isabel; Levasseur, Anthony

    2013-06-01

    Cellobiose dehydrogenases (CDHs) are extracellular glycosylated haemoflavoenzymes produced by many different wood-degrading and phytopathogenic fungi. Putative cellobiose dehydrogenase genes are recurrently discovered by genome sequencing projects in various phylogenetically distinct fungi. The genomes from the basidiomycete Coprinopsis cinerea and the ascomycete Podospora anserina were screened for candidate cdh genes, and one and three putative gene models were evidenced, respectively. Two putative cdh genes were selected and successfully expressed for the first time in Aspergillus niger. CDH activity was measured for both constructions (CDHcc and CDHpa), and both recombinant CDHs were purified to homogeneity and subsequently characterised. Kinetic constants were determined for several carbohydrates including β-1,4-linked di- and oligosaccharides. Optimal temperature and pH were 60 °C and 5 for CDHcc and 65-70 °C and 6 for CDHpa. Both CDHs showed a broad range of pH stability between 4 and 8. The effect of both CDHs on saccharification of micronized wheat straw by an industrial Trichoderma reesei secretome was determined. The addition of each CDH systematically decreased the release of total reducing sugars, but to different extents and according to the CDH concentration. Analytical methods were carried out to quantify the release of glucose, xylose and gluconic acid. An increase of glucose and xylose was measured at a low CDHcc concentration. At moderated and high CDHcc and CDHpa concentrations, glucose was severely reduced with a concomitant increase of gluconic acid. In conclusion, these results give new insights into the physical and chemical parameters and diversity of basidiomycetous and ascomycetous CDHs. These findings also demonstrated that CDH drastically influenced the saccharification on a natural substrate, and thus, CDH origin, concentration and potential enzymatic partners should be carefully considered in future artificial secretomes for

  7. Virtual Organizations: Trends and Models

    NASA Astrophysics Data System (ADS)

    Nami, Mohammad Reza; Malekpour, Abbaas

    The Use of ICT in business has changed views about traditional business. With VO, organizations with out physical, geographical, or structural constraint can collaborate with together in order to fulfill customer requests in a networked environment. This idea improves resource utilization, reduces development process and costs, and saves time. Virtual Organization (VO) is always a form of partnership and managing partners and handling partnerships are crucial. Virtual organizations are defined as a temporary collection of enterprises that cooperate and share resources, knowledge, and competencies to better respond to business opportunities. This paper presents an overview of virtual organizations and main issues in collaboration such as security and management. It also presents a number of different model approaches according to their purpose and applications.

  8. Modeling of heavy organic deposition

    SciTech Connect

    Chung, F.T.H.

    1992-01-01

    Organic deposition is often a major problem in petroleum production and processing. This problem is manifested by current activities in gas flooding and heavy oil production. The need for understanding the nature of asphaltenes and asphaltics and developing solutions to the deposition problem is well recognized. Prediction technique is crucial to solution development. In the past 5 years, some progress in modeling organic deposition has been made. A state-of-the-art review of methods for modeling organic deposition is presented in this report. Two new models were developed in this work; one based on a thermodynamic equilibrium principle and the other on the colloidal stability theory. These two models are more general and realistic than others previously reported. Because experimental results on the characteristics of asphaltene are inconclusive, it is still not well known whether the asphaltenes is crude oil exist as a true solution or as a colloidal suspension. Further laboratory work which is designed to study the solubility properties of asphaltenes and to provide additional information for model development is proposed. Some experimental tests have been conducted to study the mechanisms of CO{sub 2}-induced asphaltene precipitation. Coreflooding experiments show that asphaltene precipitation occurs after gas breakthrough. The mechanism of CO{sub 2}-induced asphaltene precipitation is believed to occur by hydrocarbon extraction which causes change in oil composition. Oil swelling due to CO{sub 2} solubilization does not induce asphaltene precipitation.

  9. The Podospora rmp1 gene implicated in nucleus-mitochondria cross-talk encodes an essential protein whose subcellular location is developmentally regulated.

    PubMed Central

    Contamine, Véronique; Zickler, Denise; Picard, Marguerite

    2004-01-01

    It has been previously reported that, at the time of death, the Podospora anserina AS1-4 mutant strains accumulate specific deleted forms of the mitochondrial genome and that their life spans depend on two natural alleles (variants) of the rmp1 gene: AS1-4 rmp1-2 strains exhibit life spans strikingly longer than those of AS1-4 rmp1-1. Here, we show that rmp1 is an essential gene. In silico analyses of eight rmp1 natural alleles present in Podospora isolates and of the putative homologs of this orphan gene in other filamentous fungi suggest that rmp1 evolves rapidly. The RMP1 protein is localized in the mitochondrial and/or the cytosolic compartment, depending on cell type and developmental stage. Strains producing RMP1 without its mitochondrial targeting peptide are viable but exhibit vegetative and sexual defects. PMID:15020413

  10. Organic Model of Interstellar Grains

    NASA Astrophysics Data System (ADS)

    Yabushita, S.; Inagaki, T.; Kawabe, T.; Wada, K.

    1987-04-01

    Extinction efficiency of grains is calculated from the Mie formula on the premise that the grains are of organic composition. The optical constants adopted for the calculations are those of E. coli, polystyrene and bovine albumin. The grain radius a is assumed to obey a distribution of the form N(a) ∝ a-α and the value of α is chosen so as to make the calculated extinction curve match the observed interstellar extinction curve. Although the calculated curve gives a reasonably good fit to the observed extinction curve for wavelengths less than 2100 Å, at longer wavelength regions, agreement is poor. It is concluded that another component is required for the organic model to be viable.

  11. Altered Mating-Type Identity in the Fungus Podospora Anserina Leads to Selfish Nuclei, Uniparental Progeny, and Haploid Meiosis

    PubMed Central

    Zickler, D.; Arnaise, S.; Coppin, E.; Debuchy, R.; Picard, M.

    1995-01-01

    In wild-type crosses of the filamentous ascomycete Podospora anserina, after fertilization, only nuclei of opposite mating type can form dikaryons that undergo karyogamy and meiosis, producing biparental progeny. To determine the role played by the mating type in these steps, the four mat genes were mutagenized in vitro and introduced into a strain deleted for its mat locus. Genetic and cytological analyses of these mutant strains, crossed to each other and to wild type, showed that mating-type information is required for recognition of nuclear identity during the early steps of sexual reproduction. In crosses with strains carrying a mating-type mutation, two unusual developmental patterns were observed: monokaryotic cells, resulting in haploid meiosis, and uniparental dikaryotic cells providing, after karyogamy and meiosis, a uniparental progeny. Altered mating-type identity leads to selfish behavior of the mutant nucleus: it migrates alone or paired, ignoring its wild-type partner in all mutant X wild-type crosses. This behavior is nucleus-autonomous because, in the same cytoplasm, the wild-type nuclei form only biparental dikaryons. In P. anserina, mat genes are thus required to ensure a biparental dikaryotic state but appear dispensable for later stages, such as meiosis and sporulation. PMID:7498731

  12. Cello-oligosaccharide oxidation reveals differences between two lytic polysaccharide monooxygenases (family GH61) from Podospora anserina.

    PubMed

    Bey, Mathieu; Zhou, Simeng; Poidevin, Laetitia; Henrissat, Bernard; Coutinho, Pedro M; Berrin, Jean-Guy; Sigoillot, Jean-Claude

    2013-01-01

    The genome of the coprophilic ascomycete Podospora anserina encodes 33 different genes encoding copper-dependent lytic polysaccharide monooxygenases (LPMOs) from glycoside hydrolase family 61 (GH61). In this study, two of these enzymes (P. anserina GH61A [PaGH61A] and PaGH61B), which both harbored a family 1 carbohydrate binding module, were successfully produced in Pichia pastoris. Synergistic cooperation between PaGH61A or PaGH61B with the cellobiose dehydrogenase (CDH) of Pycnoporus cinnabarinus on cellulose resulted in the formation of oxidized and nonoxidized cello-oligosaccharides. A striking difference between PaGH61A and PaGH61B was observed through the identification of the products, among which were doubly and triply oxidized cellodextrins, which were released only by the combination of PaGH61B with CDH. The mass spectrometry fragmentation patterns of these oxidized products could be consistent with oxidation at the C-6 position with a geminal diol group. The different properties of PaGH61A and PaGH61B and their effect on the interaction with CDH are discussed in regard to the proposed in vivo function of the CDH/GH61 enzyme system in oxidative cellulose hydrolysis. PMID:23124232

  13. Altering a gene involved in nuclear distribution increases the repeat-induced point mutation process in the fungus Podospora anserina.

    PubMed Central

    Bouhouche, Khaled; Zickler, Denise; Debuchy, Robert; Arnaise, Sylvie

    2004-01-01

    Repeat-induced point mutation (RIP) is a homology-dependent gene-silencing mechanism that introduces C:G-to-T:A transitions in duplicated DNA segments. Cis-duplicated sequences can also be affected by another mechanism called premeiotic recombination (PR). Both are active over the sexual cycle of some filamentous fungi, e.g., Neurospora crassa and Podospora anserina. During the sexual cycle, several developmental steps require precise nuclear movement and positioning, but connections between RIP, PR, and nuclear distributions have not yet been established. Previous work has led to the isolation of ami1, the P. anserina ortholog of the Aspergillus nidulans apsA gene, which is required for nuclear positioning. We show here that ami1 is involved in nuclear distribution during the sexual cycle and that alteration of ami1 delays the fruiting-body development. We also demonstrate that ami1 alteration affects loss of transgene functions during the sexual cycle. Genetically linked multiple copies of transgenes are affected by RIP and PR much more frequently in an ami1 mutant cross than in a wild-type cross. Our results suggest that the developmental slowdown of the ami1 mutant during the period of RIP and PR increases time exposure to the duplication detection system and thus increases the frequency of RIP and PR. PMID:15166143

  14. Co-expression of the mating-type genes involved in internuclear recognition is lethal in Podospora anserina.

    PubMed Central

    Coppin, E; Debuchy, R

    2000-01-01

    In the heterothallic filamentous fungus Podospora anserina, four mating-type genes encoding transcriptional factors have been characterized: FPR1 in the mat+ sequence and FMR1, SMR1, and SMR2 in the alternative mat- sequence. Fertilization is controlled by FPR1 and FMR1. After fertilization, male and female nuclei, which have divided in the same cell, form mat+/mat- pairs during migration into the ascogenous hyphae. Previous data indicate that the formation of mat+/mat- pairs is controlled by FPR1, FMR1, and SMR2. SMR1 was postulated to be necessary for initial development of ascogenous hyphae. In this study, we investigated the transcriptional control of the mat genes by seeking mat transcripts during the vegetative and sexual phase and fusing their promoter to a reporter gene. The data indicate that FMR1 and FPR1 are expressed in both mycelia and perithecia, whereas SMR1 and SMR2 are transcribed in perithecia. Increased or induced vegetative expression of the four mat genes has no effect when the recombined gene is solely in the wild-type strain. However, the combination of resident FPR1 with deregulated SMR2 and overexpressed FMR1 in the same nucleus is lethal. This lethality is suppressed by the expression of SMR1, confirming that SMR1 operates downstream of the other mat genes. PMID:10835389

  15. Regulation of gene expression during the vegetative incompatibility reaction in Podospora anserina. Characterization of three induced genes.

    PubMed Central

    Bourges, N; Groppi, A; Barreau, C; Clavé, C; Bégueret, J

    1998-01-01

    Vegetative incompatibility in fungi limits the formation of viable heterokaryons. It results from the coexpression of incompatible genes in the heterokaryotic cells and leads to a cell death reaction. In Podospora anserina, a modification of gene expression takes place during this reaction, including a strong decrease of total RNA synthesis and the appearance of a new set of proteins. Using in vitro translation of mRNA and separation of protein products by two-dimensional gel electrophoresis, we have shown that the mRNA content of cells is qualitatively modified during the progress of the incompatibility reaction. Thus, gene expression during vegetative incompatibility is regulated, at least in part, by variation of the mRNA content of specific genes. A subtractive cDNA library enriched in sequences preferentially expressed during incompatibility was constructed. This library was used to identify genomic loci corresponding to genes whose mRNA is induced during incompatibility. Three such genes were characterized and named idi genes for genes induced during incompatibility. Their expression profiles suggest that they may be involved in different steps of the incompatibility reaction. The putative IDI proteins encoded by these genes are small proteins with signal peptides. IDI-2 protein is a cysteine-rich protein. IDI-2 and IDI-3 proteins display some similarity in a tryptophan-rich region. PMID:9755195

  16. Production of sordarin and related metabolites by the coprophilous fungus Podospora pleiospora in submerged culture and in its natural substrate.

    PubMed

    Weber, Roland W S; Meffert, Anja; Anke, Heidrun; Sterner, Olov

    2005-05-01

    Rabbit pellets collected from the field were colonized by Podospora pleiospora at the exclusion of other coprophilous fungi, suggesting antibiosis. In liquid culture, P. pleiospora produced sordarin (1); sordarin B (2), a new compound in which sordarose is replaced by rhamnose; hydroxysordarin (3); and sordaricin (4). The major compounds 1 and 2 exhibited minimum inhibitory concentrations of 0.5-2.5 microg ml(-1) against the yeasts Nematospora coryli and Sporobolomyces roseus, but showed little or no activity against bacteria or coprophilous filamentous fungi. In liquid culture, the production of 1 and 2 together amounted to 2.7 microg ml(-1), whereas in rabbit dung only 1 was produced at a similar concentration (2.3 microg g(-1) fresh weight). The biosynthesis of these substances was unaffected by the presence of inoculum of other fungi tested (Sporobolomyces roseus or Penicillium claviforme) in liquid culture or on dung. Sordarin-type natural products are therefore synthesized by P. pleiospora at sufficiently high concentrations to account for antibiosis against yeasts, but not against filamentous fungi. PMID:16018317

  17. Cello-Oligosaccharide Oxidation Reveals Differences between Two Lytic Polysaccharide Monooxygenases (Family GH61) from Podospora anserina

    PubMed Central

    Bey, Mathieu; Zhou, Simeng; Poidevin, Laetitia; Henrissat, Bernard; Coutinho, Pedro M.; Sigoillot, Jean-Claude

    2013-01-01

    The genome of the coprophilic ascomycete Podospora anserina encodes 33 different genes encoding copper-dependent lytic polysaccharide monooxygenases (LPMOs) from glycoside hydrolase family 61 (GH61). In this study, two of these enzymes (P. anserina GH61A [PaGH61A] and PaGH61B), which both harbored a family 1 carbohydrate binding module, were successfully produced in Pichia pastoris. Synergistic cooperation between PaGH61A or PaGH61B with the cellobiose dehydrogenase (CDH) of Pycnoporus cinnabarinus on cellulose resulted in the formation of oxidized and nonoxidized cello-oligosaccharides. A striking difference between PaGH61A and PaGH61B was observed through the identification of the products, among which were doubly and triply oxidized cellodextrins, which were released only by the combination of PaGH61B with CDH. The mass spectrometry fragmentation patterns of these oxidized products could be consistent with oxidation at the C-6 position with a geminal diol group. The different properties of PaGH61A and PaGH61B and their effect on the interaction with CDH are discussed in regard to the proposed in vivo function of the CDH/GH61 enzyme system in oxidative cellulose hydrolysis. PMID:23124232

  18. Publication Trends in Model Organism Research

    PubMed Central

    Dietrich, Michael R.; Ankeny, Rachel A.; Chen, Patrick M.

    2014-01-01

    In 1990, the National Institutes of Health (NIH) gave some organisms special status as designated model organisms. This article documents publication trends for these NIH-designated model organisms over the past 40 years. We find that being designated a model organism by the NIH does not guarantee an increasing publication trend. An analysis of model and nonmodel organisms included in GENETICS since 1960 does reveal a sharp decline in the number of publications using nonmodel organisms yet no decline in the overall species diversity. We suggest that organisms with successful publication records tend to share critical characteristics, such as being well developed as standardized, experimental systems and being used by well-organized communities with good networks of exchange and methods of communication. PMID:25381363

  19. Modeling and Measuring Organization Capital

    ERIC Educational Resources Information Center

    Atkeson, Andrew; Kehoe, Patrick J.

    2005-01-01

    Manufacturing plants have a clear life cycle: they are born small, grow substantially with age, and eventually die. Economists have long thought that this life cycle is driven by organization capital, the accumulation of plant-specific knowledge. The location of plants in the life cycle determines the size of the payments, or organization rents,…

  20. Organization Development: Strategies and Models.

    ERIC Educational Resources Information Center

    Beckhard, Richard

    This book, written for managers, specialists, and students of management, is based largely on the author's experience in helping organization leaders with planned-change efforts, and on related experience of colleagues in the field. Chapter 1 presents the background and causes for the increased concern with organization development and planned…

  1. Maintaining Two Mating Types: Structure of the Mating Type Locus and Its Role in Heterokaryosis in Podospora anserina

    PubMed Central

    Grognet, Pierre; Bidard, Frédérique; Kuchly, Claire; Tong, Laetitia Chan Ho; Coppin, Evelyne; Benkhali, Jinane Ait; Couloux, Arnaud; Wincker, Patrick; Debuchy, Robert; Silar, Philippe

    2014-01-01

    Pseudo-homothallism is a reproductive strategy elected by some fungi producing heterokaryotic sexual spores containing genetically different but sexually compatible nuclei. This lifestyle appears as a compromise between true homothallism (self-fertility with predominant inbreeding) and complete heterothallism (with exclusive outcrossing). However, pseudohomothallic species face the problem of maintaining heterokaryotic mycelia to fully benefit from this lifestyle, as homokaryons are self-sterile. Here, we report on the structure of chromosome 1 in mat+ and mat− isolates of strain S of the pseudohomothallic fungus Podospora anserina. Chromosome 1 contains either one of the mat+ and mat− mating types of P. anserina, which is mostly found in nature as a mat+/mat− heterokaryotic mycelium harboring sexually compatible nuclei. We identified a “mat” region ∼0.8 Mb long, devoid of meiotic recombination and containing the mating-type idiomorphs, which is a candidate to be involved in the maintenance of the heterokaryotic state, since the S mat+ and S mat− strains have different physiology that may enable hybrid-vigor-like phenomena in the heterokaryons. The mat region contains 229 coding sequences. A total of 687 polymorphisms were detected between the S mat+ and S mat− chromosomes. Importantly, the mat region is colinear between both chromosomes, which calls for an original mechanism of recombination inhibition. Microarray analyses revealed that 10% of the P. anserina genes have different transcriptional profiles in S mat+ and S mat−, in line with their different phenotypes. Finally, we show that the heterokaryotic state is faithfully maintained during mycelium growth of P. anserina, yet mat+/mat+ and mat−/mat− heterokaryons are as stable as mat+/mat− ones, evidencing a maintenance of heterokaryosis that does not rely on fitness-enhancing complementation between the S mat+ and S mat− strains. PMID:24558260

  2. Biological Roles of the Podospora anserina Mitochondrial Lon Protease and the Importance of Its N-Domain

    PubMed Central

    Adam, Céline; Picard, Marguerite; Déquard-Chablat, Michelle; Sellem, Carole H.; Denmat, Sylvie Hermann-Le; Contamine, Véronique

    2012-01-01

    Mitochondria have their own ATP-dependent proteases that maintain the functional state of the organelle. All multicellular eukaryotes, including filamentous fungi, possess the same set of mitochondrial proteases, unlike in unicellular yeasts, where ClpXP, one of the two matricial proteases, is absent. Despite the presence of ClpXP in the filamentous fungus Podospora anserina, deletion of the gene encoding the other matricial protease, PaLon1, leads to lethality at high and low temperatures, indicating that PaLON1 plays a main role in protein quality control. Under normal physiological conditions, the PaLon1 deletion is viable but decreases life span. PaLon1 deletion also leads to defects in two steps during development, ascospore germination and sexual reproduction, which suggests that PaLON1 ensures important regulatory functions during fungal development. Mitochondrial Lon proteases are composed of a central ATPase domain flanked by a large non-catalytic N-domain and a C-terminal protease domain. We found that three mutations in the N-domain of PaLON1 affected fungal life cycle, PaLON1 protein expression and mitochondrial proteolytic activity, which reveals the functional importance of the N-domain of the mitochondrial Lon protease. All PaLon1 mutations affected the C-terminal part of the N-domain. Considering that the C-terminal part is predicted to have an α helical arrangement in which the number, length and position of the helices are conserved with the solved structure of its bacterial homologs, we propose that this all-helical structure participates in Lon substrate interaction. PMID:22693589

  3. Tree-Structured Digital Organisms Model

    NASA Astrophysics Data System (ADS)

    Suzuki, Teruhiko; Nobesawa, Shiho; Tahara, Ikuo

    Tierra and Avida are well-known models of digital organisms. They describe a life process as a sequence of computation codes. A linear sequence model may not be the only way to describe a digital organism, though it is very simple for a computer-based model. Thus we propose a new digital organism model based on a tree structure, which is rather similar to the generic programming. With our model, a life process is a combination of various functions, as if life in the real world is. This implies that our model can easily describe the hierarchical structure of life, and it can simulate evolutionary computation through mutual interaction of functions. We verified our model by simulations that our model can be regarded as a digital organism model according to its definitions. Our model even succeeded in creating species such as viruses and parasites.

  4. DNA-dependent RNA polymerase III from the fungus Podospora comata. Purification, subunit structure and comparison with the homologous enzyme of a related species.

    PubMed

    Barreau, C; Begueret, J

    1982-12-15

    DNA-dependent RNA polymerase III has been purified to homogeneity from the filamentous fungus Podospora comata. The enzyme was extracted at low ionic strength, separated from the polymerases I and II by DEAE-Sephadex chromatography and purified by heparin-Sepharose and phosphocellulose chromatography; 0.1-0.2 mg highly purified homogeneous enzyme with a specific activity of 220 units/mg could be obtained from 2 kg wet mycelium. The subunit composition of the enzyme was determined after sodium dodecyl sulphate/polyacrylamide gel electrophoresis; thirteen putative subunits of molecular weight 174000 (a), 129000 b), 87000 (c), 50000 (d), 39000 (e), 23500 (f), 21000 (g), 19000 (h), 17000 (i), 16500 (j), 13500 (k), 11000 (l) and 10000 (m) were identified. All of the polypeptide components of the enzyme are present in about integral stoichiometric amounts as judged by dye binding. The presence of subunit Mr = 87000 in a molar ratio 1:1 is necessary to obtain very active enzyme. Thirteen homologous subunits were observed in a preparation of RNA polymerase III from Podospora anserina, which is a related species. Only subunit i is different in the two species. PMID:7151805

  5. The CORE Model to Student Organization Development.

    ERIC Educational Resources Information Center

    Conyne, Robert K.

    Student organization development (SOD) is an emerging technology for conducting intentional student development through positive alteration of student organizations. One model (CORE) for conceptualizing SOD is in use at the Student Development Center of the University of Cincinnati. The CORE model to SOD is comprised of three concentric rings, the…

  6. Primate models in organ transplantation.

    PubMed

    Anderson, Douglas J; Kirk, Allan D

    2013-09-01

    Large animal models have long served as the proving grounds for advances in transplantation, bridging the gap between inbred mouse experimentation and human clinical trials. Although a variety of species have been and continue to be used, the emergence of highly targeted biologic- and antibody-based therapies has required models to have a high degree of homology with humans. Thus, the nonhuman primate has become the model of choice in many settings. This article will provide an overview of nonhuman primate models of transplantation. Issues of primate genetics and care will be introduced, and a brief overview of technical aspects for various transplant models will be discussed. Finally, several prominent immunosuppressive and tolerance strategies used in primates will be reviewed. PMID:24003248

  7. Chromism of Model Organic Aerosol

    NASA Astrophysics Data System (ADS)

    Rincon, Angela; Guzman, Marcelo; Hoffmann, Michael; Colussi, Agustin

    2008-03-01

    The optical properties of the atmospheric aerosol play a fundamental role in the Earth's radiative balance. Since more than half of the aerosol mass consists of complex organic matter that absorbs in the ultraviolet and visible regions of the spectrum, it is important to establish the identity of the organic chromophores. Here we report studies on the chromism vs. chemical composition of photolyzed (lambda longer than 305 nm) solutions of pyruvic acid, a widespread aerosol component, under a variety of experimental conditions that include substrate concentration, temperature and the presence of relevant spectator solutes, such ammonium sulfate. We use high resolution mass- and 13C NMR-spectrometries to track chemical speciation in photolyzed solutions as they undergo thermochromic and photobleaching cycles. Since the chemical identity of the components of these mixtures does not change in these cycles, in which photobleached solutions gradually recover their yellow color in the dark with non-conventional kinetics typical of aggregation processes, we infer that visible absorptions likely involve the intermolecular coupling of carbonyl chromophores in supramolecular assemblies made possible by the polyfunctional nature of the products of pyruvic acid photolysis.

  8. Photochemistry of Model Organic Aerosol Systems

    NASA Astrophysics Data System (ADS)

    Mang, S. A.; Bateman, A. P.; Dailo, M.; Do, T.; Nizkorodov, S. A.; Pan, X.; Underwood, J. S.; Walser, M. L.

    2007-05-01

    Up to 90 percent of urban aerosol particles have been shown to contain organic molecules. Reactions of these particles with atmospheric oxidants and/or sunlight result in large changes in their composition, toxicity, and ability to act as cloud condensation nuclei. For this reason, chemistry of model organic aerosol particles initiated by oxidation and direct photolysis is of great interest to atmospheric, climate, and health scientists. Most studies in this area have focused on identifying the products of oxidation of the organic aerosols, while the products of direct photolysis of the resulting molecules remaining in the aerosol particle have been left mostly unexplored. We have explored direct photolytic processes occurring in selected organic aerosol systems using infrared cavity ringdown spectroscopy to identify small gas phase products of photolysis, and mass-spectrometric and photometric techniques to study the condensed phase products. The first model system was secondary organic aerosol formed from the oxidation of several monoterpenes by ozone in the presence and absence of NOx, under different humidities. The second system modeled after oxidatively aged primary organic aerosol particles was a thin film of either alkanes or saturated fatty acids oxidized in several different ways, with the oxidation initiated by ozone, chlorine atom, or OH. In every case, the general conclusion was that the photochemical processing of model organic aerosols is significant. Such direct photolysis processes are believed to age organic aerosol particles on time scales that are short compared to the particles' atmospheric lifetimes.

  9. Modeling personnel turnover in the parametric organization

    NASA Technical Reports Server (NTRS)

    Dean, Edwin B.

    1991-01-01

    A model is developed for simulating the dynamics of a newly formed organization, credible during all phases of organizational development. The model development process is broken down into the activities of determining the tasks required for parametric cost analysis (PCA), determining the skills required for each PCA task, determining the skills available in the applicant marketplace, determining the structure of the model, implementing the model, and testing it. The model, parameterized by the likelihood of job function transition, has demonstrated by the capability to represent the transition of personnel across functional boundaries within a parametric organization using a linear dynamical system, and the ability to predict required staffing profiles to meet functional needs at the desired time. The model can be extended by revisions of the state and transition structure to provide refinements in functional definition for the parametric and extended organization.

  10. Modeling Virtual Organization Architecture with the Virtual Organization Breeding Methodology

    NASA Astrophysics Data System (ADS)

    Paszkiewicz, Zbigniew; Picard, Willy

    While Enterprise Architecture Modeling (EAM) methodologies become more and more popular, an EAM methodology tailored to the needs of virtual organizations (VO) is still to be developed. Among the most popular EAM methodologies, TOGAF has been chosen as the basis for a new EAM methodology taking into account characteristics of VOs presented in this paper. In this new methodology, referred as Virtual Organization Breeding Methodology (VOBM), concepts developed within the ECOLEAD project, e.g. the concept of Virtual Breeding Environment (VBE) or the VO creation schema, serve as fundamental elements for development of VOBM. VOBM is a generic methodology that should be adapted to a given VBE. VOBM defines the structure of VBE and VO architectures in a service-oriented environment, as well as an architecture development method for virtual organizations (ADM4VO). Finally, a preliminary set of tools and methods for VOBM is given in this paper.

  11. Modeling Personnel Turnover in the Parametric Organization

    NASA Technical Reports Server (NTRS)

    Dean, Edwin B.

    1991-01-01

    A primary issue in organizing a new parametric cost analysis function is to determine the skill mix and number of personnel required. The skill mix can be obtained by a functional decomposition of the tasks required within the organization and a matrixed correlation with educational or experience backgrounds. The number of personnel is a function of the skills required to cover all tasks, personnel skill background and cross training, the intensity of the workload for each task, migration through various tasks by personnel along a career path, personnel hiring limitations imposed by management and the applicant marketplace, personnel training limitations imposed by management and personnel capability, and the rate at which personnel leave the organization for whatever reason. Faced with the task of relating all of these organizational facets in order to grow a parametric cost analysis (PCA) organization from scratch, it was decided that a dynamic model was required in order to account for the obvious dynamics of the forming organization. The challenge was to create such a simple model which would be credible during all phases of organizational development. The model development process was broken down into the activities of determining the tasks required for PCA, determining the skills required for each PCA task, determining the skills available in the applicant marketplace, determining the structure of the dynamic model, implementing the dynamic model, and testing the dynamic model.

  12. The origin and evolution of model organisms

    NASA Technical Reports Server (NTRS)

    Hedges, S. Blair

    2002-01-01

    The phylogeny and timescale of life are becoming better understood as the analysis of genomic data from model organisms continues to grow. As a result, discoveries are being made about the early history of life and the origin and development of complex multicellular life. This emerging comparative framework and the emphasis on historical patterns is helping to bridge barriers among organism-based research communities.

  13. Putting "Organizations" into an Organization Theory Course: A Hybrid CAO Model for Teaching Organization Theory

    ERIC Educational Resources Information Center

    Hannah, David R.; Venkatachary, Ranga

    2010-01-01

    In this article, the authors present a retrospective analysis of an instructor's multiyear redesign of a course on organization theory into what is called a hybrid Classroom-as-Organization model. It is suggested that this new course design served to apprentice students to function in quasi-real organizational structures. The authors further argue…

  14. Research proceedings on amphibian model organisms

    PubMed Central

    LIU, Lu-Sha; ZHAO, Lan-Ying; WANG, Shou-Hong; JIANG, Jian-Ping

    2016-01-01

    Model organisms have long been important in biology and medicine due to their specific characteristics. Amphibians, especially Xenopus, play key roles in answering fundamental questions on developmental biology, regeneration, genetics, and toxicology due to their large and abundant eggs, as well as their versatile embryos, which can be readily manipulated and developed in vivo. Furthermore, amphibians have also proven to be of considerable benefit in human disease research due to their conserved cellular developmental and genomic organization. This review gives a brief introduction on the progress and limitations of these animal models in biology and human disease research, and discusses the potential and challenge of Microhyla fissipes as a new model organism. PMID:27469255

  15. Web resources for model organism studies.

    PubMed

    Tang, Bixia; Wang, Yanqing; Zhu, Junwei; Zhao, Wenming

    2015-02-01

    An ever-growing number of resources on model organisms have emerged with the continued development of sequencing technologies. In this paper, we review 13 databases of model organisms, most of which are reported by the National Institutes of Health of the United States (NIH; http://www.nih.gov/science/models/). We provide a brief description for each database, as well as detail its data source and types, functions, tools, and availability of access. In addition, we also provide a quality assessment about these databases. Significantly, the organism databases instituted in the early 1990s--such as the Mouse Genome Database (MGD), Saccharomyces Genome Database (SGD), and FlyBase--have developed into what are now comprehensive, core authority resources. Furthermore, all of the databases mentioned here update continually according to user feedback and with advancing technologies. PMID:25707592

  16. Research proceedings on amphibian model organisms.

    PubMed

    Liu, Lu-Sha; Zhao, Lan-Ying; Wang, Shou-Hong; Jiang, Jian-Ping

    2016-07-18

    Model organisms have long been important in biology and medicine due to their specific characteristics. Amphibians, especially Xenopus, play key roles in answering fundamental questions on developmental biology, regeneration, genetics, and toxicology due to their large and abundant eggs, as well as their versatile embryos, which can be readily manipulated and developed in vivo. Furthermore, amphibians have also proven to be of considerable benefit in human disease research due to their conserved cellular developmental and genomic organization. This review gives a brief introduction on the progress and limitations of these animal models in biology and human disease research, and discusses the potential and challenge of Microhyla fissipes as a new model organism. PMID:27469255

  17. Using chemical organization theory for model checking

    PubMed Central

    Kaleta, Christoph; Richter, Stephan; Dittrich, Peter

    2009-01-01

    Motivation: The increasing number and complexity of biomodels makes automatic procedures for checking the models' properties and quality necessary. Approaches like elementary mode analysis, flux balance analysis, deficiency analysis and chemical organization theory (OT) require only the stoichiometric structure of the reaction network for derivation of valuable information. In formalisms like Systems Biology Markup Language (SBML), however, information about the stoichiometric coefficients required for an analysis of chemical organizations can be hidden in kinetic laws. Results: First, we introduce an algorithm that uncovers stoichiometric information that might be hidden in the kinetic laws of a reaction network. This allows us to apply OT to SBML models using modifiers. Second, using the new algorithm, we performed a large-scale analysis of the 185 models contained in the manually curated BioModels Database. We found that for 41 models (22%) the set of organizations changes when modifiers are considered correctly. We discuss one of these models in detail (BIOMD149, a combined model of the ERK- and Wnt-signaling pathways), whose set of organizations drastically changes when modifiers are considered. Third, we found inconsistencies in 5 models (3%) and identified their characteristics. Compared with flux-based methods, OT is able to identify those species and reactions more accurately [in 26 cases (14%)] that can be present in a long-term simulation of the model. We conclude that our approach is a valuable tool that helps to improve the consistency of biomodels and their repositories. Availability: All data and a JAVA applet to check SBML-models is available from http://www.minet.uni-jena.de/csb/prj/ot/tools Contact: dittrich@minet.uni-jena.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19468053

  18. Thermodynamic modeling for organic solid precipitation

    SciTech Connect

    Chung, T.H.

    1992-12-01

    A generalized predictive model which is based on thermodynamic principle for solid-liquid phase equilibrium has been developed for organic solid precipitation. The model takes into account the effects of temperature, composition, and activity coefficient on the solubility of wax and asphaltenes in organic solutions. The solid-liquid equilibrium K-value is expressed as a function of the heat of melting, melting point temperature, solubility parameter, and the molar volume of each component in the solution. All these parameters have been correlated with molecular weight. Thus, the model can be applied to crude oil systems. The model has been tested with experimental data for wax formation and asphaltene precipitation. The predicted wax appearance temperature is very close to the measured temperature. The model not only can match the measured asphaltene solubility data but also can be used to predict the solubility of asphaltene in organic solvents or crude oils. The model assumes that asphaltenes are dissolved in oil in a true liquid state, not in colloidal suspension, and the precipitation-dissolution process is reversible by changing thermodynamic conditions. The model is thermodynamically consistent and has no ambiguous assumptions.

  19. Modeling organic solvents permeation through protective gloves.

    PubMed

    Chao, Keh-Ping; Wang, Ven-Shing; Lee, Pak-Hing

    2004-02-01

    Several researchers have studied the diffusion of organic solvents through chemical protective gloves and have estimated the diffusion coefficients by using various models. In this study, permeation experiments of benzene, toluene, and styrene through nitrile and Neoprene gloves were conducted using the ASTM F-739 standard test method. The diffusion coefficients were estimated using several models from the literature. Using a one-dimensional diffusion equation based on Fick's second law and the estimated diffusion coefficients, the permeation concentrations were simulated and compared with the experimental results. The modeling results indicated that the solubility of the solvent in the glove materials obtained by immersion tests was not an appropriate boundary condition for organic solvent permeation through the polymer gloves. The modeling work of this study will assist industrial hygienists to assess exposure of chemicals to workers through the chemical protective gloves. PMID:15204879

  20. Biophysical Modeling of Respiratory Organ Motion

    NASA Astrophysics Data System (ADS)

    Werner, René

    Methods to estimate respiratory organ motion can be divided into two groups: biophysical modeling and image registration. In image registration, motion fields are directly extracted from 4D ({D}+{t}) image sequences, often without concerning knowledge about anatomy and physiology in detail. In contrast, biophysical approaches aim at identification of anatomical and physiological aspects of breathing dynamics that are to be modeled. In the context of radiation therapy, biophysical modeling of respiratory organ motion commonly refers to the framework of continuum mechanics and elasticity theory, respectively. Underlying ideas and corresponding boundary value problems of those approaches are described in this chapter, along with a brief comparison to image registration-based motion field estimation.

  1. JAKs and STATs in invertebrate model organisms.

    PubMed

    Dearolf, C R

    1999-09-01

    Invertebrate organisms provide systems to elucidate the developmental roles of Janus kinase (JAK)/signal transducers and activators of transcription (STAT) signaling pathways, thereby complementing research conducted with mammalian cells and animals. Components of the JAK/STAT protein pathway have been identified and characterized in the fruit fly Drosophila melanogaster and the cellular slime mold Dictyostelium discoideum. This review summarizes the molecular and genetic data obtained from these model organisms. In particular, a Drosophila JAK/STAT pathway regulates normal segmentation, cell proliferation, and differentiation, and hyperactivation of the pathway leads to tumor formation and leukemia-like defects. A Dictyostelium STAT regulates the development of stalk cells during the multicellular part of the life cycle. Future research utilizing these organisms should continue to provide insights into the roles and regulation of these proteins and their signaling pathways. PMID:10526575

  2. Model Organisms and Traditional Chinese Medicine Syndrome Models

    PubMed Central

    Xu, Jin-Wen

    2013-01-01

    Traditional Chinese medicine (TCM) is an ancient medical system with a unique cultural background. Nowadays, more and more Western countries due to its therapeutic efficacy are accepting it. However, safety and clear pharmacological action mechanisms of TCM are still uncertain. Due to the potential application of TCM in healthcare, it is necessary to construct a scientific evaluation system with TCM characteristics and benchmark the difference from the standard of Western medicine. Model organisms have played an important role in the understanding of basic biological processes. It is easier to be studied in certain research aspects and to obtain the information of other species. Despite the controversy over suitable syndrome animal model under TCM theoretical guide, it is unquestionable that many model organisms should be used in the studies of TCM modernization, which will bring modern scientific standards into mysterious ancient Chinese medicine. In this review, we aim to summarize the utilization of model organisms in the construction of TCM syndrome model and highlight the relevance of modern medicine with TCM syndrome animal model. It will serve as the foundation for further research of model organisms and for its application in TCM syndrome model. PMID:24381636

  3. Modeling plasmonic efficiency enhancement in organic photovoltaics.

    PubMed

    Taff, Y; Apter, B; Katz, E A; Efron, U

    2015-09-10

    Efficiency enhancement of bulk heterojunction (BHJ) organic solar cells by means of the plasmonic effect is investigated by using finite-difference time-domain (FDTD) optical simulations combined with analytical modeling of exciton dissociation and charge transport efficiencies. The proposed method provides an improved analysis of the cell performance compared to previous FDTD studies. The results of the simulations predict an 11.8% increase in the cell's short circuit current with the use of Ag nano-hexagons. PMID:26368970

  4. Modeling the topological organization of cellular processes.

    PubMed

    Giavitto, Jean-Louis; Michel, Olivier

    2003-07-01

    The cell as a dynamical system presents the characteristics of having a dynamical structure. That is, the exact phase space of the system cannot be fixed before the evolution and integrative cell models must state the evolution of the structure jointly with the evolution of the cell state. This kind of dynamical systems is very challenging to model and simulate. New programming concepts must be developed to ease their modeling and simulation. In this context, the goal of the MGS project is to develop an experimental programming language dedicated to the simulation of this kind of systems. MGS proposes a unified view on several computational mechanisms (CHAM, Lindenmayer systems, Paun systems, cellular automata) enabling the specification of spatially localized computations on heterogeneous entities. The evolution of a dynamical structure is handled through the concept of transformation which relies on the topological organization of the system components. An example based on the modeling of spatially distributed biochemical networks is used to illustrate how these notions can be used to model the spatial and temporal organization of intracellular processes. PMID:12915272

  5. Global Exposure Modelling of Semivolatile Organic Compounds

    NASA Astrophysics Data System (ADS)

    Guglielmo, F.; Lammel, G.; Maier-Reimer, E.

    2008-12-01

    Organic compounds which are persistent and toxic as the agrochemicals γ-hexachlorocyclohexane (γ-HCH, lindane) and dichlorodiphenyltrichloroethane (DDT) pose a hazard for the ecosystems. These compounds are semivolatile, hence multicompartmental substances and subject to long-range transport (LRT) in atmosphere and ocean. Being lipophilic, they accumulate in exposed organism tissues and biomagnify along food chains. The multicompartmental global fate and LRT of DDT and lindane in the atmosphere and ocean have been studied using application data for 1980, on a decadal scale using a model based on the coupling of atmosphere and (for the first time for these compounds) ocean General Circulation Models (ECHAM5 and MPI-OM). The model system encompasses furthermore 2D terrestrial compartments (soil and vegetation) and sea ice, a fully dynamic atmospheric aerosol (HAM) module and an ocean biogeochemistry module (HAMOCC5). Large mass fractions of the compounds are found in soil. Lindane is also found in comparable amount in ocean. DDT has the longest residence time in almost all compartments. The sea ice compartment locally almost inhibits volatilization from the sea. The air/sea exchange is also affected , up to a reduction of 35 % for DDT by partitioning to the organic phases (suspended and dissolved particulate matter) in the global oceans. Partitioning enhances vertical transport in the sea. Ocean dynamics are found to be more significant for vertical transport than sinking associated with particulate matter. LRT in the global environment is determined by the fast atmospheric circulation. Net meridional transport taking place in the ocean is locally effective mostly via western boundary currents, upon applications at mid- latitudes. The pathways of the long-lived semivolatile organic compounds studied include a sequence of several cycles of volatilisation, transport in the atmosphere, deposition and transport in the ocean (multihopping substances). Multihopping is

  6. Modelling motions within the organ of Corti

    NASA Astrophysics Data System (ADS)

    Ni, Guangjian; Baumgart, Johannes; Elliott, Stephen

    2015-12-01

    Most cochlear models used to describe the basilar membrane vibration along the cochlea are concerned with macromechanics, and often assume that the organ of Corti moves as a single unit, ignoring the individual motion of different components. New experimental technologies provide the opportunity to measure the dynamic behaviour of different components within the organ of Corti, but only for certain types of excitation. It is thus still difficult to directly measure every aspect of cochlear dynamics, particularly for acoustic excitation of the fully active cochlea. The present work studies the dynamic response of a model of the cross-section of the cochlea, at the microscopic level, using the finite element method. The elastic components are modelled with plate elements and the perilymph and endolymph are modelled with inviscid fluid elements. The individual motion of each component within the organ of Corti is calculated with dynamic pressure loading on the basilar membrane and the motions of the experimentally accessible parts are compared with measurements. The reticular lamina moves as a stiff plate, without much bending, and is pivoting around a point close to the region of the inner hair cells, as observed experimentally. The basilar membrane shows a slightly asymmetric mode shape, with maximum displacement occurring between the second-row and the third-row of the outer hair cells. The dynamics responses is also calculated, and compared with experiments, when driven by the outer hair cells. The receptance of the basilar membrane motion and of the deflection of the hair bundles of the outer hair cells is thus obtained, when driven either acoustically or electrically. In this way, the fully active linear response of the basilar membrane to acoustic excitation can be predicted by using a linear superposition of the calculated receptances and a defined gain function for the outer hair cell feedback.

  7. eEF1A Controls ascospore differentiation through elevated accuracy, but controls longevity and fruiting body formation through another mechanism in Podospora anserina.

    PubMed Central

    Silar, P; Lalucque, H; Haedens, V; Zickler, D; Picard, M

    2001-01-01

    Antisuppressor mutations in the eEF1A gene of Podospora anserina were previously shown to impair ascospore formation, to drastically increase life span, and to permit the development of the Crippled Growth degenerative process. Here, we show that eEF1A controls ascospore formation through accuracy level maintenance. Examination of antisuppressor mutant perithecia reveals two main cytological defects, mislocalization of spindle and nuclei and nuclear death. Antisuppression levels are shown to be highly dependent upon both the mutation site and the suppressor used, precluding any correlation between antisuppression efficiency and severity of the sporulation impairment. Nevertheless, severity of ascospore differentiation defect is correlated with resistance to paromomycin. We also show that eEF1A controls fruiting body formation and longevity through a mechanism(s) different from accuracy control. In vivo, GFP tagging of the protein in a way that partly retains its function confirmed earlier cytological observation; i.e., this factor is mainly diffuse within the cytosol, but may transiently accumulate within nuclei or in defined regions of the cytoplasm. These data emphasize the fact that the translation apparatus exerts a global regulatory control over cell physiology and that eEF1A is one of the key factors involved in this monitoring. PMID:11514440

  8. ami1, an orthologue of the Aspergillus nidulans apsA gene, is involved in nuclear migration events throughout the life cycle of Podospora anserina.

    PubMed Central

    Graïa, F; Berteaux-Lecellier, V; Zickler, D; Picard, M

    2000-01-01

    The Podospora anserina ami1-1 mutant was identified as a male-sterile strain. Microconidia (which act as male gametes) form, but are anucleate. Paraphysae from the perithecium beaks are also anucleate when ami1-1 is used as the female partner in a cross. Furthermore, in crosses heterozygous for ami1-1, some crozier cells are uninucleate rather than binucleate. In addition to these nuclear migration defects, which occur at the transition between syncytial and cellular states, ami1-1 causes abnormal distribution of the nuclei in both mycelial filaments and asci. Finally, an ami1-1 strain bearing information for both mating types is unable to self-fertilize. The ami1 gene is an orthologue of the Aspergillus nidulans apsA gene, which controls nuclear positioning in filaments and during conidiogenesis (at the syncytial/cellular transition). The ApsA and AMI1 proteins display 42% identity and share structural features. The apsA gene complements some ami1-1 defects: it increases the percentage of nucleate microconidia and restores self-fertility in an ami1-1 mat+ (mat-) strain. The latter effect is puzzling, since in apsA null mutants sexual reproduction is quite normal. The functional differences between the two genes are discussed with respect to their possible history in these two fungi, which are very distant in terms of evolution. PMID:10835387

  9. Identification of six loci in which mutations partially restore peroxisome biogenesis and/or alleviate the metabolic defect of pex2 mutants in podospora.

    PubMed Central

    Ruprich-Robert, Gwenaël; Berteaux-Lecellier, Véronique; Zickler, Denise; Panvier-Adoutte, Arlette; Picard, Marguerite

    2002-01-01

    Peroxins (PEX) are proteins required for peroxisome biogenesis. Mutations in PEX genes cause lethal diseases in humans, metabolic defects in yeasts, and developmental disfunctions in plants and filamentous fungi. Here we describe the first large-scale screening for suppressors of a pex mutation. In Podospora anserina, pex2 mutants exhibit a metabolic defect [inability to grow on medium containing oleic acid (OA medium) as sole carbon source] and a developmental defect (inability to differentiate asci in homozygous crosses). Sixty-three mutations able to restore growth of pex2 mutants on OA medium have been analyzed. They fall in six loci (suo1 to suo6) and act as dominant, allele-nonspecific suppressors. Most suo mutations have pleiotropic effects in a pex2(+) background: formation of unripe ascospores (all loci except suo5 and suo6), impaired growth on OA medium (all loci except suo4 and suo6), or sexual defects (suo4). Using immunofluorescence and GFP staining, we show that peroxisome biogenesis is partially restored along with a low level of ascus differentiation in pex2 mutant strains carrying either the suo5 or the suo6 mutations. The data are discussed with respect to beta-oxidation of fatty acids, peroxisome biogenesis, and cell differentiation. PMID:12136013

  10. Identification of the het-r vegetative incompatibility gene of Podospora anserina as a member of the fast evolving HNWD gene family.

    PubMed

    Chevanne, Damien; Bastiaans, Eric; Debets, Alfons; Saupe, Sven J; Clavé, Corinne; Paoletti, Mathieu

    2009-02-01

    In fungi, vegetative incompatibility is a conspecific non-self recognition mechanism that restricts formation of viable heterokaryons when incompatible alleles of specific het loci interact. In Podospora anserina, three non-allelic incompatibility systems have been genetically defined involving interactions between het-c and het-d, het-c and het-e, het-r and het-v. het-d and het-e are paralogues belonging to the HNWD gene family that encode proteins of the STAND class. HET-D and HET-E proteins comprise an N-terminal HET effector domain, a central GTP binding site and a C-terminal WD repeat domain constituted of tandem repeats of highly conserved WD40 repeat units that define the specificity of alleles during incompatibility. The WD40 repeat units of the members of this HNWD family are undergoing concerted evolution. By combining genetic analysis and gain of function experiments, we demonstrate that an additional member of this family, HNWD2, corresponds to the het-r non-allelic incompatibility gene. As for het-d and het-e, allele specificity at the het-r locus is determined by the WD repeat domain. Natural isolates show allelic variation for het-r. PMID:19137300

  11. Organic acid modeling and model validation: Workshop summary. Final report

    SciTech Connect

    Sullivan, T.J.; Eilers, J.M.

    1992-08-14

    A workshop was held in Corvallis, Oregon on April 9--10, 1992 at the offices of E&S Environmental Chemistry, Inc. The purpose of this workshop was to initiate research efforts on the entitled ``Incorporation of an organic acid representation into MAGIC (Model of Acidification of Groundwater in Catchments) and testing of the revised model using Independent data sources.`` The workshop was attended by a team of internationally-recognized experts in the fields of surface water acid-bass chemistry, organic acids, and watershed modeling. The rationale for the proposed research is based on the recent comparison between MAGIC model hindcasts and paleolimnological inferences of historical acidification for a set of 33 statistically-selected Adirondack lakes. Agreement between diatom-inferred and MAGIC-hindcast lakewater chemistry in the earlier research had been less than satisfactory. Based on preliminary analyses, it was concluded that incorporation of a reasonable organic acid representation into the version of MAGIC used for hindcasting was the logical next step toward improving model agreement.

  12. Organic acid modeling and model validation: Workshop summary

    SciTech Connect

    Sullivan, T.J.; Eilers, J.M.

    1992-08-14

    A workshop was held in Corvallis, Oregon on April 9--10, 1992 at the offices of E S Environmental Chemistry, Inc. The purpose of this workshop was to initiate research efforts on the entitled Incorporation of an organic acid representation into MAGIC (Model of Acidification of Groundwater in Catchments) and testing of the revised model using Independent data sources.'' The workshop was attended by a team of internationally-recognized experts in the fields of surface water acid-bass chemistry, organic acids, and watershed modeling. The rationale for the proposed research is based on the recent comparison between MAGIC model hindcasts and paleolimnological inferences of historical acidification for a set of 33 statistically-selected Adirondack lakes. Agreement between diatom-inferred and MAGIC-hindcast lakewater chemistry in the earlier research had been less than satisfactory. Based on preliminary analyses, it was concluded that incorporation of a reasonable organic acid representation into the version of MAGIC used for hindcasting was the logical next step toward improving model agreement.

  13. Making designer mutants in model organisms

    PubMed Central

    Peng, Ying; Clark, Karl J.; Campbell, Jarryd M.; Panetta, Magdalena R.; Guo, Yi; Ekker, Stephen C.

    2014-01-01

    Recent advances in the targeted modification of complex eukaryotic genomes have unlocked a new era of genome engineering. From the pioneering work using zinc-finger nucleases (ZFNs), to the advent of the versatile and specific TALEN systems, and most recently the highly accessible CRISPR/Cas9 systems, we now possess an unprecedented ability to analyze developmental processes using sophisticated designer genetic tools. In this Review, we summarize the common approaches and applications of these still-evolving tools as they are being used in the most popular model developmental systems. Excitingly, these robust and simple genomic engineering tools also promise to revolutionize developmental studies using less well established experimental organisms. PMID:25336735

  14. Regulation of Aerobic Energy Metabolism in Podospora anserina by Two Paralogous Genes Encoding Structurally Different c-Subunits of ATP Synthase

    PubMed Central

    Sellem, Carole H.; di Rago, Jean-Paul; Lasserre, Jean-Paul; Ackerman, Sharon H.; Sainsard-Chanet, Annie

    2016-01-01

    Most of the ATP in living cells is produced by an F-type ATP synthase. This enzyme uses the energy of a transmembrane electrochemical proton gradient to synthesize ATP from ADP and inorganic phosphate. Proton movements across the membrane domain (FO) of the ATP synthase drive the rotation of a ring of 8–15 c-subunits, which induces conformational changes in the catalytic part (F1) of the enzyme that ultimately promote ATP synthesis. Two paralogous nuclear genes, called Atp9-5 and Atp9-7, encode structurally different c-subunits in the filamentous fungus Podospora anserina. We have in this study identified differences in the expression pattern for the two genes that correlate with the mitotic activity of cells in vegetative mycelia: Atp9-7 is transcriptionally active in non-proliferating (stationary) cells while Atp9-5 is expressed in the cells at the extremity (apex) of filaments that divide and are responsible for mycelium growth. When active, the Atp9-5 gene sustains a much higher rate of c-subunit synthesis than Atp9-7. We further show that the ATP9-7 and ATP9-5 proteins have antagonist effects on the longevity of P. anserina. Finally, we provide evidence that the ATP9-5 protein sustains a higher rate of mitochondrial ATP synthesis and yield in ATP molecules per electron transferred to oxygen than the c-subunit encoded by Atp9-7. These findings reveal that the c-subunit genes play a key role in the modulation of ATP synthase production and activity along the life cycle of P. anserina. Such a degree of sophistication for regulating aerobic energy metabolism has not been described before. PMID:27442014

  15. The Time Is Right to Focus on Model Organism Metabolomes.

    PubMed

    Edison, Arthur S; Hall, Robert D; Junot, Christophe; Karp, Peter D; Kurland, Irwin J; Mistrik, Robert; Reed, Laura K; Saito, Kazuki; Salek, Reza M; Steinbeck, Christoph; Sumner, Lloyd W; Viant, Mark R

    2016-01-01

    Model organisms are an essential component of biological and biomedical research that can be used to study specific biological processes. These organisms are in part selected for facile experimental study. However, just as importantly, intensive study of a small number of model organisms yields important synergies as discoveries in one area of science for a given organism shed light on biological processes in other areas, even for other organisms. Furthermore, the extensive knowledge bases compiled for each model organism enable systems-level understandings of these species, which enhance the overall biological and biomedical knowledge for all organisms, including humans. Building upon extensive genomics research, we argue that the time is now right to focus intensively on model organism metabolomes. We propose a grand challenge for metabolomics studies of model organisms: to identify and map all metabolites onto metabolic pathways, to develop quantitative metabolic models for model organisms, and to relate organism metabolic pathways within the context of evolutionary metabolomics, i.e., phylometabolomics. These efforts should focus on a series of established model organisms in microbial, animal and plant research. PMID:26891337

  16. The Time Is Right to Focus on Model Organism Metabolomes

    PubMed Central

    Edison, Arthur S.; Hall, Robert D.; Junot, Christophe; Karp, Peter D.; Kurland, Irwin J.; Mistrik, Robert; Reed, Laura K.; Saito, Kazuki; Salek, Reza M.; Steinbeck, Christoph; Sumner, Lloyd W.; Viant, Mark R.

    2016-01-01

    Model organisms are an essential component of biological and biomedical research that can be used to study specific biological processes. These organisms are in part selected for facile experimental study. However, just as importantly, intensive study of a small number of model organisms yields important synergies as discoveries in one area of science for a given organism shed light on biological processes in other areas, even for other organisms. Furthermore, the extensive knowledge bases compiled for each model organism enable systems-level understandings of these species, which enhance the overall biological and biomedical knowledge for all organisms, including humans. Building upon extensive genomics research, we argue that the time is now right to focus intensively on model organism metabolomes. We propose a grand challenge for metabolomics studies of model organisms: to identify and map all metabolites onto metabolic pathways, to develop quantitative metabolic models for model organisms, and to relate organism metabolic pathways within the context of evolutionary metabolomics, i.e., phylometabolomics. These efforts should focus on a series of established model organisms in microbial, animal and plant research. PMID:26891337

  17. Organizations, Environments, and Models of Public Relations.

    ERIC Educational Resources Information Center

    Grunig, James E.

    Noting that little theory has been developed to explain how and why organizations choose to manage public relations, this paper argues that theorists cannot improve the practice of public relations until they can explain what public relations is and what it contributes to the functions of an organization. The paper addresses that issue by…

  18. 3D Bioprinting of Tissue/Organ Models.

    PubMed

    Pati, Falguni; Gantelius, Jesper; Svahn, Helene Andersson

    2016-04-01

    In vitro tissue/organ models are useful platforms that can facilitate systematic, repetitive, and quantitative investigations of drugs/chemicals. The primary objective when developing tissue/organ models is to reproduce physiologically relevant functions that typically require complex culture systems. Bioprinting offers exciting prospects for constructing 3D tissue/organ models, as it enables the reproducible, automated production of complex living tissues. Bioprinted tissues/organs may prove useful for screening novel compounds or predicting toxicity, as the spatial and chemical complexity inherent to native tissues/organs can be recreated. In this Review, we highlight the importance of developing 3D in vitro tissue/organ models by 3D bioprinting techniques, characterization of these models for evaluating their resemblance to native tissue, and their application in the prioritization of lead candidates, toxicity testing, and as disease/tumor models. PMID:26895542

  19. A Modeling Exercise for the Organic Classroom

    ERIC Educational Resources Information Center

    Whitlock, Christine R.

    2010-01-01

    An in-class molecular modeling exercise is described. Groups of students are given molecular models to investigate and questions about the models to answer. This exercise is a quick and effective way to review nomenclature, stereochemistry, and conformational analysis.

  20. A model of willingness to become a potential organ donor.

    PubMed

    Horton, R L; Horton, P J

    1991-01-01

    This article presents two models of the decision to become a potential organ donor. In the first model the act of carrying or requesting an organ donor card is related to values and factual knowledge regarding organ donation, through intervening attitude and willingness constructs. A sample of 286 students is used to test this model via the LISREL computer program for modeling latent variables. All hypothesized relationships had the predicted sign and were significant. This model is extended by adding the variables attitude towards death, prior blood donation, and age of subject to the model. A second sample of 365 adults from the local community is used to test the second model via LISREL. With two exceptions in the adult sample, all hypothesized relationships had the predicted sign and were significant. Where the two models overlap the results are generally similar. Implications of the models for marketing the act of becoming a potential organ donor are discussed. PMID:1771431

  1. In praise of other model organisms

    PubMed Central

    2015-01-01

    The early cell biological literature is the resting place of false starts and lost opportunities. Though replete with multiple studies of diverse organisms, a few of which served as foundations for several fields, most were not pursued, abandoned largely for technical reasons that are no longer limiting. The time has come to revisit the old literature and to resurrect the organisms that are buried there, both to uncover new mechanisms and to marvel at the richness of the cellular world. PMID:25688132

  2. Evaluating Organic Aerosol Model Performance: Impact of two Embedded Assumptions

    NASA Astrophysics Data System (ADS)

    Jiang, W.; Giroux, E.; Roth, H.; Yin, D.

    2004-05-01

    Organic aerosols are important due to their abundance in the polluted lower atmosphere and their impact on human health and vegetation. However, modeling organic aerosols is a very challenging task because of the complexity of aerosol composition, structure, and formation processes. Assumptions and their associated uncertainties in both models and measurement data make model performance evaluation a truly demanding job. Although some assumptions are obvious, others are hidden and embedded, and can significantly impact modeling results, possibly even changing conclusions about model performance. This paper focuses on analyzing the impact of two embedded assumptions on evaluation of organic aerosol model performance. One assumption is about the enthalpy of vaporization widely used in various secondary organic aerosol (SOA) algorithms. The other is about the conversion factor used to obtain ambient organic aerosol concentrations from measured organic carbon. These two assumptions reflect uncertainties in the model and in the ambient measurement data, respectively. For illustration purposes, various choices of the assumed values are implemented in the evaluation process for an air quality model based on CMAQ (the Community Multiscale Air Quality Model). Model simulations are conducted for the Lower Fraser Valley covering Southwest British Columbia, Canada, and Northwest Washington, United States, for a historical pollution episode in 1993. To understand the impact of the assumed enthalpy of vaporization on modeling results, its impact on instantaneous organic aerosol yields (IAY) through partitioning coefficients is analysed first. The analysis shows that utilizing different enthalpy of vaporization values causes changes in the shapes of IAY curves and in the response of SOA formation capability of reactive organic gases to temperature variations. These changes are then carried into the air quality model and cause substantial changes in the organic aerosol modeling

  3. A Model for Implementing E-Learning in Iranian Organizations

    ERIC Educational Resources Information Center

    Ghaeni, Emad; Abdehagh, Babak

    2010-01-01

    This article reviews the current status of information and communications technology (ICT) usage and provides a comprehensive outlook on e-learning in both virtual universities and organizations in Iran. A model for e-learning implementation is presented. This model tries to address specific issues in Iranian organizations. (Contains 1 table and 2…

  4. Modeling the Explicit Chemistry of Anthropogenic and Biogenic Organic Aerosols

    SciTech Connect

    Madronich, Sasha

    2015-12-09

    The atmospheric burden of Secondary Organic Aerosols (SOA) remains one of the most important yet uncertain aspects of the radiative forcing of climate. This grant focused on improving our quantitative understanding of SOA formation and evolution, by developing, applying, and improving a highly detailed model of atmospheric organic chemistry, the Generation of Explicit Chemistry and Kinetics of Organics in the Atmosphere (GECKO-A) model. Eleven (11) publications have resulted from this grant.

  5. Exploring Organic Mechanistic Puzzles with Molecular Modeling

    ERIC Educational Resources Information Center

    Horowitz, Gail; Schwartz, Gary

    2004-01-01

    The molecular modeling was used to reinforce more general skills such as deducing and drawing reaction mechanisms, analyzing reaction kinetics and thermodynamics and drawing reaction coordinate energy diagrams. This modeling was done through the design of mechanistic puzzles, involving reactions not familiar to the students.

  6. NERVE AS MODEL TEMPERATURE END ORGAN

    PubMed Central

    Bernhard, C. G.; Granit, Ragnar

    1946-01-01

    Rapid local cooling of mammalian nerve sets up a discharge which is preceded by a local temperature potential, the cooled region being electronegative relative to a normal portion of the nerve. Heating the nerve locally above its normal temperature similarly makes the heated region electronegative relative to a region at normal temperature, and again a discharge is set up from the heated region. These local temperature potentials, set up by the nerve itself, are held to serve as "generator potentials" and the mechanism found is regarded as the prototype for temperature end organs. PMID:19873460

  7. Modeling the influence of organic acids on soil weathering

    USGS Publications Warehouse

    Lawrence, Corey R.; Harden, Jennifer W.; Maher, Kate

    2014-01-01

    Biological inputs and organic matter cycling have long been regarded as important factors in the physical and chemical development of soils. In particular, the extent to which low molecular weight organic acids, such as oxalate, influence geochemical reactions has been widely studied. Although the effects of organic acids are diverse, there is strong evidence that organic acids accelerate the dissolution of some minerals. However, the influence of organic acids at the field-scale and over the timescales of soil development has not been evaluated in detail. In this study, a reactive-transport model of soil chemical weathering and pedogenic development was used to quantify the extent to which organic acid cycling controls mineral dissolution rates and long-term patterns of chemical weathering. Specifically, oxalic acid was added to simulations of soil development to investigate a well-studied chronosequence of soils near Santa Cruz, CA. The model formulation includes organic acid input, transport, decomposition, organic-metal aqueous complexation and mineral surface complexation in various combinations. Results suggest that although organic acid reactions accelerate mineral dissolution rates near the soil surface, the net response is an overall decrease in chemical weathering. Model results demonstrate the importance of organic acid input concentrations, fluid flow, decomposition and secondary mineral precipitation rates on the evolution of mineral weathering fronts. In particular, model soil profile evolution is sensitive to kaolinite precipitation and oxalate decomposition rates. The soil profile-scale modeling presented here provides insights into the influence of organic carbon cycling on soil weathering and pedogenesis and supports the need for further field-scale measurements of the flux and speciation of reactive organic compounds.

  8. An Organic Model for Detecting Cyber Events

    SciTech Connect

    Oehmen, Christopher S.; Peterson, Elena S.; Dowson, Scott T.

    2010-04-21

    Cyber entities in many ways mimic the behavior of organic systems. Individuals or groups compete for limited resources using a variety of strategies and effective strategies are re-used and refined in later ‘generations’. Traditionally this drift has made detection of malicious entities very difficult because 1) recognition systems are often built on exact matching to a pattern that can only be ‘learned’ after a malicious entity reveals itself and 2) the enormous volume and variation in benign entities is an overwhelming source of previously unseen entities that often confound detectors. To turn the tables of complexity on the would-be attackers, we have developed a method for mapping the sequence of behaviors in which cyber entities engage to strings of text and analyze these strings using modified bioinformatics algorithms. Bioinformatics algorithms optimize the alignment between text strings even in the presence of mismatches, insertions or deletions and do not require an a priori definition of the patterns one is seeking. Nor does it require any type of exact matching. This allows the data itself to suggest meaningful patterns that are conserved between cyber entities. We demonstrate this method on data generated from network traffic. The impact of this approach is that it can rapidly calculate similarity measures of previously unseen cyber entities in terms of well-characterized entities. These measures may also be used to organize large collections of data into families, making it possible to identify motifs indicative of each family.

  9. Collaborative multi organ segmentation by integrating deformable and graphical models.

    PubMed

    Uzunbaş, Mustafa Gökhan; Chen, Chao; Zhang, Shaoting; Poh, Kilian M; Li, Kang; Metaxas, Dimitris

    2013-01-01

    Organ segmentation is a challenging problem on which significant progress has been made. Deformable models (DM) and graphical models (GM) are two important categories of optimization based image segmentation methods. Efforts have been made on integrating two types of models into one framework. However, previous methods are not designed for segmenting multiple organs simultaneously and accurately. In this paper, we propose a hybrid multi organ segmentation approach by integrating DM and GM in a coupled optimization framework. Specifically, we show that region-based deformable models can be integrated with Markov Random Fields (MRF), such that multiple models' evolutions are driven by a maximum a posteriori (MAP) inference. It brings global and local deformation constraints into a unified framework for simultaneous segmentation of multiple objects in an image. We validate this proposed method on two challenging problems of multi organ segmentation, and the results are promising. PMID:24579136

  10. Elimination kinetic model for organic chemicals in earthworms.

    PubMed

    Dimitrova, N; Dimitrov, S; Georgieva, D; Van Gestel, C A M; Hankard, P; Spurgeon, D; Li, H; Mekenyan, O

    2010-08-15

    Mechanistic understanding of bioaccumulation in different organisms and environments should take into account the influence of organism and chemical depending factors on the uptake and elimination kinetics of chemicals. Lipophilicity, metabolism, sorption (bioavailability) and biodegradation of chemicals are among the important factors that may significantly affect the bioaccumulation process in soil organisms. This study attempts to model elimination kinetics of organic chemicals in earthworms by accounting for the effects of both chemical and biological properties, including metabolism. The modeling approach that has been developed is based on the concept for simulating metabolism used in the BCF base-line model developed for predicting bioaccumulation in fish. Metabolism was explicitly accounted for by making use of the TIMES engine for simulation of metabolism and a set of principal transformations. Kinetic characteristics of transformations were estimated on the basis of observed kinetics data for the elimination of organic chemicals from earthworms. PMID:20185163

  11. Personality organization, five-factor model, and mental health.

    PubMed

    Laverdière, Olivier; Gamache, Dominick; Diguer, Louis; Hébert, Etienne; Larochelle, Sébastien; Descôteaux, Jean

    2007-10-01

    Otto Kernberg has developed a model of personality and psychological functioning centered on the concept of personality organization. The purpose of this study is to empirically examine the relationships between this model, the five-factor model, and mental health. The Personality Organization Diagnostic Form (Diguer et al., The Personality Organization Diagnostic Form-II (PODF-II), 2001), the NEO Five-Factor Inventory (Costa and McCrae, Revised NEO Personality Inventory (NEO-PI-R) and NEO Five-Factor Inventory (NEO-FFI) Professional Manual. 1992a), and the Health-Sickness Rating Scale (Luborsky, Arch Gen Psychiatry. 1962;7:407-417) were used to assess these constructs. Results show that personality organization and personality factors are distinct but interrelated constructs and that both contribute in similar proportion to mental health. Results also suggest that the integration of personality organization and factors can provide clinicians and researchers with an enriched understanding of psychological functioning. PMID:18043522

  12. Lattice animal model of chromosome organization

    NASA Astrophysics Data System (ADS)

    Iyer, Balaji V. S.; Arya, Gaurav

    2012-07-01

    Polymer models tied together by constraints of looping and confinement have been used to explain many of the observed organizational characteristics of interphase chromosomes. Here we introduce a simple lattice animal representation of interphase chromosomes that combines the features of looping and confinement constraints into a single framework. We show through Monte Carlo simulations that this model qualitatively captures both the leveling off in the spatial distance between genomic markers observed in fluorescent in situ hybridization experiments and the inverse decay in the looping probability as a function of genomic separation observed in chromosome conformation capture experiments. The model also suggests that the collapsed state of chromosomes and their segregation into territories with distinct looping activities might be a natural consequence of confinement.

  13. Acoustic modeling of the speech organ

    NASA Astrophysics Data System (ADS)

    Kacprowski, J.

    The state of research on acoustic modeling of phonational and articulatory speech producing elements is reviewed. Consistent with the physical interpretation of the speech production process, the acoustic theory of speech production is expressed as the product of three factors: laryngeal involvement, sound transmission, and emanations from the mouth and/or nose. Each of these factors is presented in the form of a simplified mathematical description which provides the theoretical basis for the formation of physical models of the appropriate functional members of this complex bicybernetic system. Vocal tract wall impedance, vocal tract synthesizers, laryngeal dysfunction, vowel nasalization, resonance circuits, and sound wave propagation are discussed.

  14. Nematodes: Model Organisms in High School Biology

    ERIC Educational Resources Information Center

    Bliss, TJ; Anderson, Margery; Dillman, Adler; Yourick, Debra; Jett, Marti; Adams, Byron J.; Russell, RevaBeth

    2007-01-01

    In a collaborative effort between university researchers and high school science teachers, an inquiry-based laboratory module was designed using two species of insecticidal nematodes to help students apply scientific inquiry and elements of thoughtful experimental design. The learning experience and model are described in this article. (Contains 4…

  15. Expatriate Training in International Nongovernmental Organizations: A Model for Research

    ERIC Educational Resources Information Center

    Chang, Wei-Wen

    2005-01-01

    In light of the massive tsunami relief efforts that were still being carried out by humanitarian organizations around the world when this article went to press, this article points out a lack of human resources development research in international nongovernmental organizations (INGOs) and proposes a conceptual model for future empirical research.…

  16. Resilient organizations: matrix model and service line management.

    PubMed

    Westphal, Judith A

    2005-09-01

    Resilient organizations modify structures to meet the demands of the marketplace. The author describes a structure that enables multihospital organizations to innovate and rapidly adapt to changes. Service line management within a matrix model is an evolving organizational structure for complex systems in which nurses are pivotal members. PMID:16200010

  17. Representational Translation with Concrete Models in Organic Chemistry

    ERIC Educational Resources Information Center

    Stull, Andrew T.; Hegarty, Mary; Dixon, Bonnie; Stieff, Mike

    2012-01-01

    In representation-rich domains such as organic chemistry, students must be facile and accurate when translating between different 2D representations, such as diagrams. We hypothesized that translating between organic chemistry diagrams would be more accurate when concrete models were used because difficult mental processes could be augmented by…

  18. A Model Linking the Learning Organization and Performance Job Satisfaction

    ERIC Educational Resources Information Center

    Dirani, Khalil M.

    2006-01-01

    The underlying theories of learning and performance are quite complex. This paper proposes a model that links the learning organization theory as a process with job satisfaction as a performance theory outcome. The literature reviewed considered three process levels of learning within the learning organization and three outcome levels of job…

  19. VERIFICATION OF A TOXIC ORGANIC SUBSTANCE TRANSPORT AND BIOACCUMULATION MODEL

    EPA Science Inventory

    A field verification of the Toxic Organic Substance Transport and Bioaccumulation Model (TOXIC) was conducted using the insecticide dieldrin and the herbicides alachlor and atrazine as the test compounds. The test sites were two Iowa reservoirs. The verification procedure include...

  20. A REVIEW OF BIOACCUMULATION MODELING APPROACHES FOR PERSISTENT ORGANIC POLLUTANTS

    EPA Science Inventory

    Persistent organic pollutants and mercury are likely to bioaccumulate in biological components of the environment, including fish and wildlife. The complex and long-term dynamics involved with bioaccumulation are often represented with models. Current scientific developments in t...

  1. RCF1-dependent respiratory supercomplexes are integral for lifespan-maintenance in a fungal ageing model

    PubMed Central

    Fischer, Fabian; Filippis, Christodoulos; Osiewacz, Heinz D.

    2015-01-01

    Mitochondrial respiratory supercomplexes (mtRSCs) are stoichiometric assemblies of electron transport chain (ETC) complexes in the inner mitochondrial membrane. They are hypothesized to regulate electron flow, the generation of reactive oxygen species (ROS) and to stabilize ETC complexes. Using the fungal ageing model Podospora anserina, we investigated the impact of homologues of the Saccharomyces cerevisiae respiratory supercomplex factors 1 and 2 (termed PaRCF1 and PaRCF2) on mtRSC formation, fitness and lifespan. Whereas PaRCF2’s role seems negligible, ablation of PaRCF1 alters size of monomeric complex IV, reduces the abundance of complex IV-containing supercomplexes, negatively affects vital functions and shortens lifespan. PaRcf1 overexpression slightly prolongs lifespan, though without appreciably influencing ETC organization. Overall, our results identify PaRCF1 as necessary yet not sufficient for mtRSC formation and demonstrate that PaRCF1-dependent stability of complex IV and associated supercomplexes is highly relevant for maintenance of the healthy lifespan in a eukaryotic model organism. PMID:26220011

  2. Dietary Uptake Models Used for Modeling the Bioaccumulation of Organic Contaminants in Fish

    EPA Science Inventory

    Numerous models have been developed to predict the bioaccumulation of organic chemicals in fish. Although chemical dietary uptake can be modeled using assimilation efficiencies, bioaccumulation models fall into two distinct groups. The first group implicitly assumes that assimila...

  3. Spatial Arrangment of Organic Compounds on a Model Mineral Surface: Implications for Soil Organic Matter Stabilization

    SciTech Connect

    Petridis, Loukas; Ambaye, Haile Arena; Jagadamma, Sindhu; Kilbey, S. Michael; Lokitz, Bradley S; Lauter, Valeria; Mayes, Melanie

    2014-01-01

    The complexity of the mineral organic carbon interface may influence the extent of stabilization of organic carbon compounds in soils, which is important for global climate futures. The nanoscale structure of a model interface was examined here by depositing films of organic carbon compounds of contrasting chemical character, hydrophilic glucose and amphiphilic stearic acid, onto a soil mineral analogue (Al2O3). Neutron reflectometry, a technique which provides depth-sensitive insight into the organization of the thin films, indicates that glucose molecules reside in a layer between Al2O3 and stearic acid, a result that was verified by water contact angle measurements. Molecular dynamics simulations reveal the thermodynamic driving force behind glucose partitioning on the mineral interface: The entropic penalty of confining the less mobile glucose on the mineral surface is lower than for stearic acid. The fundamental information obtained here helps rationalize how complex arrangements of organic carbon on soil mineral surfaces may arise

  4. Principles of chromatin organization in yeast: relevance of polymer models to describe nuclear organization and dynamics.

    PubMed

    Wang, Renjie; Mozziconacci, Julien; Bancaud, Aurélien; Gadal, Olivier

    2015-06-01

    Nuclear organization can impact on all aspects of the genome life cycle. This organization is thoroughly investigated by advanced imaging and chromosome conformation capture techniques, providing considerable amount of datasets describing the spatial organization of chromosomes. In this review, we will focus on polymer models to describe chromosome statics and dynamics in the yeast Saccharomyces cerevisiae. We suggest that the equilibrium configuration of a polymer chain tethered at both ends and placed in a confined volume is consistent with the current literature, implying that local chromatin interactions play a secondary role in yeast nuclear organization. Future challenges are to reach an integrated multi-scale description of yeast chromosome organization, which is crucially needed to improve our understanding of the regulation of genomic transaction. PMID:25956973

  5. Organism-level models: When mechanisms and statistics fail us

    NASA Astrophysics Data System (ADS)

    Phillips, M. H.; Meyer, J.; Smith, W. P.; Rockhill, J. K.

    2014-03-01

    Purpose: To describe the unique characteristics of models that represent the entire course of radiation therapy at the organism level and to highlight the uses to which such models can be put. Methods: At the level of an organism, traditional model-building runs into severe difficulties. We do not have sufficient knowledge to devise a complete biochemistry-based model. Statistical model-building fails due to the vast number of variables and the inability to control many of them in any meaningful way. Finally, building surrogate models, such as animal-based models, can result in excluding some of the most critical variables. Bayesian probabilistic models (Bayesian networks) provide a useful alternative that have the advantages of being mathematically rigorous, incorporating the knowledge that we do have, and being practical. Results: Bayesian networks representing radiation therapy pathways for prostate cancer and head & neck cancer were used to highlight the important aspects of such models and some techniques of model-building. A more specific model representing the treatment of occult lymph nodes in head & neck cancer were provided as an example of how such a model can inform clinical decisions. A model of the possible role of PET imaging in brain cancer was used to illustrate the means by which clinical trials can be modelled in order to come up with a trial design that will have meaningful outcomes. Conclusions: Probabilistic models are currently the most useful approach to representing the entire therapy outcome process.

  6. Mutant mice: experimental organisms as materialised models in biomedicine.

    PubMed

    Huber, Lara; Keuck, Lara K

    2013-09-01

    Animal models have received particular attention as key examples of material models. In this paper, we argue that the specificities of establishing animal models-acknowledging their status as living beings and as epistemological tools-necessitate a more complex account of animal models as materialised models. This becomes particularly evident in animal-based models of diseases that only occur in humans: in these cases, the representational relation between animal model and human patient needs to be generated and validated. The first part of this paper presents an account of how disease-specific animal models are established by drawing on the example of transgenic mice models for Alzheimer's disease. We will introduce an account of validation that involves a three-fold process including (1) from human being to experimental organism; (2) from experimental organism to animal model; and (3) from animal model to human patient. This process draws upon clinical relevance as much as scientific practices and results in disease-specific, yet incomplete, animal models. The second part of this paper argues that the incompleteness of models can be described in terms of multi-level abstractions. We qualify this notion by pointing to different experimental techniques and targets of modelling, which give rise to a plurality of models for a specific disease. PMID:23545252

  7. A Workforce Design Model: Providing Energy to Organizations in Transition

    ERIC Educational Resources Information Center

    Halm, Barry J.

    2011-01-01

    The purpose of this qualitative study was to examine the change in performance realized by a professional services organization, which resulted in the Life Giving Workforce Design (LGWD) model through a grounded theory research design. This study produced a workforce design model characterized as an organizational blueprint that provides virtuous…

  8. Institutionalizing Innovation in an Organization: A Model and Case Study.

    ERIC Educational Resources Information Center

    Slawski, Carl

    A policy systems theoretical analysis of the problem of institutionalizing innovation in an organization is summarized in a flow diagram. The model is presented in terms of specific hypotheses, and then illustrated with a case of frustrated innovation, the 1968-69 crisis and strike at San Francisco State College. The model is set up (1) to help…

  9. Simple model of self-organized biological evolution

    SciTech Connect

    de Boer, J.; Derrida, B.; Flyvbjerg, H.; Jackson, A.D.; Wettig, T. The Isaac Newton Institute for Mathematical Sciences, 20 Clarkson Road, Cambridge, CB4 0EH Laboratoire de Physique Statistique, Ecole Normale Superieure, 24 rue Lhomond, F-75005 Paris Service de Physique Theorique, Centre de Etudes Nucleaires de Saclay, F-91191, Gif-Sur-Yvette CONNECT, The Niels Bohr Institute, Blegdamsvej 17, DK-2100 Copenhagen )

    1994-08-08

    We give an exact solution of a recently proposed self-organized critical model of biological evolution. We show that the model has a power law distribution of durations of coevolutionary avalanches'' with a mean field exponent 3/2. We also calculate analytically the finite size effects which cut off this power law at times of the order of the system size.

  10. Mechanism for production of secondary organic aerosols and their representation in atmospheric models. Final report

    SciTech Connect

    Seinfeld, J.H.; Flagan, R.C.

    1999-06-07

    This document contains the following: organic aerosol formation from the oxidation of biogenic hydrocarbons; gas/particle partitioning of semivolatile organic compounds to model inorganic, organic, and ambient smog aerosols; and representation of secondary organic aerosol formation in atmospheric models.

  11. BeetleBase: the model organism database for Tribolium castaneum.

    PubMed

    Wang, Liangjiang; Wang, Suzhi; Li, Yonghua; Paradesi, Martin S R; Brown, Susan J

    2007-01-01

    BeetleBase (http://www.bioinformatics.ksu.edu/BeetleBase/) is an integrated resource for the Tribolium research community. The red flour beetle (Tribolium castaneum) is an important model organism for genetics, developmental biology, toxicology and comparative genomics, the genome of which has recently been sequenced. BeetleBase is constructed to integrate the genomic sequence data with information about genes, mutants, genetic markers, expressed sequence tags and publications. BeetleBase uses the Chado data model and software components developed by the Generic Model Organism Database (GMOD) project. This strategy not only reduces the time required to develop the database query tools but also makes the data structure of BeetleBase compatible with that of other model organism databases. BeetleBase will be useful to the Tribolium research community for genome annotation as well as comparative genomics. PMID:17090595

  12. The expanding epigenetic landscape of non-model organisms

    PubMed Central

    Bonasio, Roberto

    2015-01-01

    Epigenetics studies the emergence of different phenotypes from a single genotype. Although these processes are essential to cellular differentiation and transcriptional memory, they are also widely used in all branches of the tree of life by organisms that require plastic but stable adaptation to their physical and social environment. Because of the inherent flexibility of epigenetic regulation, a variety of biological phenomena can be traced back to evolutionary adaptations of few conserved molecular pathways that converge on chromatin. For these reasons chromatin biology and epigenetic research have a rich history of chasing discoveries in a variety of model organisms, including yeast, flies, plants and humans. Many more fascinating examples of epigenetic plasticity lie outside the realm of model organisms and have so far been only sporadically investigated at a molecular level; however, recent progress on sequencing technology and genome editing tools have begun to blur the lines between model and non-model organisms, opening numerous new avenues for investigation. Here, I review examples of epigenetic phenomena in non-model organisms that have emerged as potential experimental systems, including social insects, fish and flatworms, and are becoming accessible to molecular approaches. PMID:25568458

  13. Making Organisms Model Human Behavior: Situated Models in North-American Alcohol Research, 1950-onwards

    PubMed Central

    Leonelli, Sabina; Ankeny, Rachel A.; Nelson, Nicole C.; Ramsden, Edmund

    2014-01-01

    Argument We examine the criteria used to validate the use of nonhuman organisms in North-American alcohol addiction research from the 1950s to the present day. We argue that this field, where the similarities between behaviors in humans and non-humans are particularly difficult to assess, has addressed questions of model validity by transforming the situatedness of non-human organisms into an experimental tool. We demonstrate that model validity does not hinge on the standardization of one type of organism in isolation, as often the case with genetic model organisms. Rather, organisms are viewed as necessarily situated: they cannot be understood as a model for human behavior in isolation from their environmental conditions. Hence the environment itself is standardized as part of the modeling process; and model validity is assessed with reference to the environmental conditions under which organisms are studied. PMID:25233743

  14. Model Organisms Fact Sheet: Using Model Organisms to Study Health and Disease

    MedlinePlus

    ... for the related ones, as well. What about computer models? Computers serve as virtual laboratories where scientists ... scientists have more confidence in the predictions. Can computer models replace animal models in research? Even though ...

  15. Modelling of organic matter dynamics during the composting process.

    PubMed

    Zhang, Y; Lashermes, G; Houot, S; Doublet, J; Steyer, J P; Zhu, Y G; Barriuso, E; Garnier, P

    2012-01-01

    Composting urban organic wastes enables the recycling of their organic fraction in agriculture. The objective of this new composting model was to gain a clearer understanding of the dynamics of organic fractions during composting and to predict the final quality of composts. Organic matter was split into different compartments according to its degradability. The nature and size of these compartments were studied using a biochemical fractionation method. The evolution of each compartment and the microbial biomass were simulated, as was the total organic carbon loss corresponding to organic carbon mineralisation into CO(2). Twelve composting experiments from different feedstocks were used to calibrate and validate our model. We obtained a unique set of estimated parameters. Good agreement was achieved between the simulated and experimental results that described the evolution of different organic fractions, with the exception of some compost because of a poor simulation of the cellulosic and soluble pools. The degradation rate of the cellulosic fraction appeared to be highly variable and dependent on the origin of the feedstocks. The initial soluble fraction could contain some degradable and recalcitrant elements that are not easily accessible experimentally. PMID:21978424

  16. Precisely parameterized experimental and computational models of tissue organization.

    PubMed

    Molitoris, Jared M; Paliwal, Saurabh; Sekar, Rajesh B; Blake, Robert; Park, JinSeok; Trayanova, Natalia A; Tung, Leslie; Levchenko, Andre

    2016-02-01

    Patterns of cellular organization in diverse tissues frequently display a complex geometry and topology tightly related to the tissue function. Progressive disorganization of tissue morphology can lead to pathologic remodeling, necessitating the development of experimental and theoretical methods of analysis of the tolerance of normal tissue function to structural alterations. A systematic way to investigate the relationship of diverse cell organization to tissue function is to engineer two-dimensional cell monolayers replicating key aspects of the in vivo tissue architecture. However, it is still not clear how this can be accomplished on a tissue level scale in a parameterized fashion, allowing for a mathematically precise definition of the model tissue organization and properties down to a cellular scale with a parameter dependent gradual change in model tissue organization. Here, we describe and use a method of designing precisely parameterized, geometrically complex patterns that are then used to control cell alignment and communication of model tissues. We demonstrate direct application of this method to guiding the growth of cardiac cell cultures and developing mathematical models of cell function that correspond to the underlying experimental patterns. Several anisotropic patterned cultures spanning a broad range of multicellular organization, mimicking the cardiac tissue organization of different regions of the heart, were found to be similar to each other and to isotropic cell monolayers in terms of local cell-cell interactions, reflected in similar confluency, morphology and connexin-43 expression. However, in agreement with the model predictions, different anisotropic patterns of cell organization, paralleling in vivo alterations of cardiac tissue morphology, resulted in variable and novel functional responses with important implications for the initiation and maintenance of cardiac arrhythmias. We conclude that variations of tissue geometry and topology

  17. Electrochemical model of the polyaniline based organic memristive device

    NASA Astrophysics Data System (ADS)

    Demin, V. A.; Erokhin, V. V.; Kashkarov, P. K.; Kovalchuk, M. V.

    2014-08-01

    The electrochemical organic memristive device with polyaniline active layer is a stand-alone device designed and realized for reproduction of some synapse properties in the innovative electronic circuits, including the neuromorphic networks capable for learning. In this work, a new theoretical model of the polyaniline memristive is presented. The developed model of organic memristive functioning was based on the detailed consideration of possible electrochemical processes occuring in the active zone of this device. Results of the calculation have demonstrated not only the qualitative explanation of the characteristics observed in the experiment but also the quantitative similarities of the resultant current values. It is shown how the memristive could behave at zero potential difference relative to the reference electrode. This improved model can establish a basis for the design and prediction of properties of more complicated circuits and systems (including stochastic ones) based on the organic memristive devices.

  18. Electrochemical model of the polyaniline based organic memristive device

    SciTech Connect

    Demin, V. A. E-mail: victor.erokhin@fis.unipr.it; Erokhin, V. V. E-mail: victor.erokhin@fis.unipr.it; Kashkarov, P. K.; Kovalchuk, M. V.

    2014-08-14

    The electrochemical organic memristive device with polyaniline active layer is a stand-alone device designed and realized for reproduction of some synapse properties in the innovative electronic circuits, including the neuromorphic networks capable for learning. In this work, a new theoretical model of the polyaniline memristive is presented. The developed model of organic memristive functioning was based on the detailed consideration of possible electrochemical processes occuring in the active zone of this device. Results of the calculation have demonstrated not only the qualitative explanation of the characteristics observed in the experiment but also the quantitative similarities of the resultant current values. It is shown how the memristive could behave at zero potential difference relative to the reference electrode. This improved model can establish a basis for the design and prediction of properties of more complicated circuits and systems (including stochastic ones) based on the organic memristive devices.

  19. A Conceptual Model of the Information Requirements of Nursing Organizations

    PubMed Central

    Miller, Emmy

    1989-01-01

    Three related issues play a role in the identification of the information requirements of nursing organizations. These issues are the current state of computer systems in health care organizations, the lack of a well-defined data set for nursing, and the absence of models representing data and information relevant to clinical and administrative nursing practice. This paper will examine current methods of data collection, processing, and storage in clinical and administrative nursing practice for the purpose of identifying the information requirements of nursing organizations. To satisfy these information requirements, database technology can be used; however, a model for database design is needed that reflects the conceptual framework of nursing and the professional concerns of nurses. A conceptual model of the types of data necessary to produce the desired information will be presented and the relationships among data will be delineated.

  20. The models for assessment of chemopreventive agents: single organ models.

    PubMed

    Das, Sukta; Banerjee, Sarmistha; Saha, Prosenjit

    2004-01-01

    Research in cancer chemoprevention involves a number of activities, the first and foremost of which is acquisition of detailed knowledge concerning the process of carcinogenesis and identification of points of intervention whereby the process can be reversed or stalled. Parallel to this is the search for ideal chemopreventive agents--natural or synthetic--and screening for their activity and efficacy in vitro and in vivo. For ethical reasons it is not possible to test new agents on humans, so preclinical studies are dependent on results first being obtained with suitable animal models. Since it is not possible for a single model to reflect the diversity and heterogeneity of human cancers, it is necessary to have as many different models as possible, depending on the requirement of the studies on different aspects of cancer biology. Advances in research on carcinogenesis and chemoprevention therefore have to be accompanied by development of appropriate laboratory animal models using a variety of carcinogens that produce tumours at different sites. Animal models have contributed significantly to our understanding of carcinogenesis and ways to intervene in the underlying processes. Many animal carcinogenesis and tumour models have been found to mirror corresponding human cancers with respect to cell of origin, morphogenesis, phenotype markers and genetic alteration. In spite of the fact that interpolation of data from animal studies to humans is difficult for various reasons, animal models are widely used for assessment of new compounds with cancer chemopreventive potential and for preclinical trials. So despite the movements of animal rights activists, animal models will continue to be used for biomedical research for saving human lives. In doing so, care should be taken to treat and handle the animals with minimal discomfort to them and ensuring that alternatives are used whenever possible. PMID:15074999

  1. Organic carbon cycling in landfills: Model for a continuum approach

    SciTech Connect

    Bogner, J.; Lagerkvist, A.

    1997-09-01

    Organic carbon cycling in landfills can be addressed through a continuum model where the end-points are conventional anaerobic digestion of organic waste (short-term analogue) and geologic burial of organic material (long-term analogue). Major variables influencing status include moisture state, temperature, organic carbon loading, nutrient status, and isolation from the surrounding environment. Bioreactor landfills which are engineered for rapid decomposition approach (but cannot fully attain) the anaerobic digester end-point and incur higher unit costs because of their high degree of environmental isolation and control. At the other extreme, uncontrolled land disposal of organic waste materials is similar to geologic burial where organic carbon may be aerobically recycled to atmospheric CO{sub 2}, anaerobically converted to CH{sub 4} and CO{sub 2} during early diagenesis, or maintained as intermediate or recalcitrant forms into geologic time (> 1,000 years) for transformations via kerogen pathways. A family of improved landfill models are needed at several scales (molecular to landscape) which realistically address landfill processes and can be validated with field data.

  2. Implementing marine organic aerosols into the GEOS-Chem model

    DOE PAGESBeta

    Gantt, B.; Johnson, M. S.; Crippa, M.; Prévôt, A. S. H.; Meskhidze, N.

    2014-09-09

    Marine organic aerosols (MOA) have been shown to play an important role in tropospheric chemistry by impacting surface mass, cloud condensation nuclei, and ice nuclei concentrations over remote marine and coastal regions. In this work, an online marine primary organic aerosol emission parameterization, designed to be used for both global and regional models, was implemented into the GEOS-Chem model. The implemented emission scheme improved the large underprediction of organic aerosol concentrations in clean marine regions (normalized mean bias decreases from -79% when using the default settings to -12% when marine organic aerosols are added). Model predictions were also in goodmore » agreement (correlation coefficient of 0.62 and normalized mean bias of -36%) with hourly surface concentrations of MOA observed during the summertime at an inland site near Paris, France. Our study shows that MOA have weaker coastal-to-inland concentration gradients than sea-salt aerosols, leading to several inland European cities having > 10% of their surface submicron organic aerosol mass concentration with a marine source. The addition of MOA tracers to GEOS-Chem enabled us to identify the regions with large contributions of freshly-emitted or aged aerosol having distinct physicochemical properties, potentially indicating optimal locations for future field studies.« less

  3. Stochastic models for plant microtubule self-organization and structure.

    PubMed

    Eren, Ezgi C; Dixit, Ram; Gautam, Natarajan

    2015-12-01

    One of the key enablers of shape and growth in plant cells is the cortical microtubule (CMT) system, which is a polymer array that forms an appropriately-structured scaffolding in each cell. Plant biologists have shown that stochastic dynamics and simple rules of interactions between CMTs can lead to a coaligned CMT array structure. However, the mechanisms and conditions that cause CMT arrays to become organized are not well understood. It is prohibitively time-consuming to use actual plants to study the effect of various genetic mutations and environmental conditions on CMT self-organization. In fact, even computer simulations with multiple replications are not fast enough due to the spatio-temporal complexity of the system. To redress this shortcoming, we develop analytical models and methods for expeditiously computing CMT system metrics that are related to self-organization and array structure. In particular, we formulate a mean-field model to derive sufficient conditions for the organization to occur. We show that growth-prone dynamics itself is sufficient to lead to organization in presence of interactions in the system. In addition, for such systems, we develop predictive methods for estimation of system metrics such as expected average length and number of CMTs over time, using a stochastic fluid-flow model, transient analysis, and approximation algorithms tailored to our problem. We illustrate the effectiveness of our approach through numerical test instances and discuss biological insights. PMID:25700800

  4. Compartmental model for organic matter digestion in facultative ponds.

    PubMed

    Giraldo, E; Garzón, A

    2002-01-01

    A model has been developed for the digestion of organic matter in facultative ponds in tropical regions. Complete mixing has been assumed for the aerobic and anaerobic compartments. Settling, aerobic layer oxidation, and anaerobic layer methanogenesis are the main processes for organic matter removal in the water column. Exchange processes between layers are dispersive or soluble exchange, solubilization and transport of organic matter from sediments to water column are also taken into account. Degradation of organic matter in the sediments produces gaseous emissions to the water column. The exchange between bubbles ascending and the water column was measured. The model was calibrated with data obtained from a pilot facultative pond built in Muña Reservoir in Bogotá. The pond was sampled during 4 months to compare data between its water hyacinth covered section and uncovered section. The results clearly show the relative importance of different BOD removal processes in facultative ponds and suggest modifications to further improve performance. The results from the model suggest that internal loadings to facultative ponds due to solubilization and return of organic matter from the sediments to the aerobic layer greatly influence the soluble BOD effluent concentration. Aerobic degradation activity in the facultative pond does not affect significantly the effluent concentration. Anaerobic degradation activity in the facultative pond can more easily achieve increases in the removal efficiencies of BOD. PMID:11833730

  5. Implementing marine organic aerosols into the GEOS-Chem model

    NASA Astrophysics Data System (ADS)

    Gantt, B.; Johnson, M. S.; Crippa, M.; Prévôt, A. S. H.; Meskhidze, N.

    2014-09-01

    Marine organic aerosols (MOA) have been shown to play an important role in tropospheric chemistry by impacting surface mass, cloud condensation nuclei, and ice nuclei concentrations over remote marine and coastal regions. In this work, an online marine primary organic aerosol emission parameterization, designed to be used for both global and regional models, was implemented into the GEOS-Chem model. The implemented emission scheme improved the large underprediction of organic aerosol concentrations in clean marine regions (normalized mean bias decreases from -79% when using the default settings to -12% when marine organic aerosols are added). Model predictions were also in good agreement (correlation coefficient of 0.62 and normalized mean bias of -36%) with hourly surface concentrations of MOA observed during the summertime at an inland site near Paris, France. Our study shows that MOA have weaker coastal-to-inland concentration gradients than sea-salt aerosols, leading to several inland European cities having > 10% of their surface submicron organic aerosol mass concentration with a marine source. The addition of MOA tracers to GEOS-Chem enabled us to identify the regions with large contributions of freshly-emitted or aged aerosol having distinct physicochemical properties, potentially indicating optimal locations for future field studies.

  6. Implementing marine organic aerosols into the GEOS-Chem model

    NASA Astrophysics Data System (ADS)

    Gantt, B.; Johnson, M. S.; Crippa, M.; Prévôt, A. S. H.; Meskhidze, N.

    2015-03-01

    Marine-sourced organic aerosols (MOAs) have been shown to play an important role in tropospheric chemistry by impacting surface mass, cloud condensation nuclei, and ice nuclei concentrations over remote marine and coastal regions. In this work, an online marine primary organic aerosol emission parameterization, designed to be used for both global and regional models, was implemented into the GEOS-Chem (Global Earth Observing System Chemistry) model. The implemented emission scheme improved the large underprediction of organic aerosol concentrations in clean marine regions (normalized mean bias decreases from -79% when using the default settings to -12% when marine organic aerosols are added). Model predictions were also in good agreement (correlation coefficient of 0.62 and normalized mean bias of -36%) with hourly surface concentrations of MOAs observed during the summertime at an inland site near Paris, France. Our study shows that MOAs have weaker coastal-to-inland concentration gradients than sea-salt aerosols, leading to several inland European cities having >10% of their surface submicron organic aerosol mass concentration with a marine source. The addition of MOA tracers to GEOS-Chem enabled us to identify the regions with large contributions of freshly emitted or aged aerosol having distinct physicochemical properties, potentially indicating optimal locations for future field studies.

  7. Model of electrodialysis process associated with organic adsorption

    SciTech Connect

    Chatchupong, T.; Murphy, R.J.

    1996-02-01

    A convective-diffusion model was developed to predict the performance of both electrodialysis (ED) and adsorption on species in an aqueous solution. The quasi-steady-state model was solved by finite difference to assess the effects of a packed bed of graphite on separation of an univalent electrolyte and an organic compound in an ED cell. A sensitivity analysis of parameters in the model was also performed. Comparison of simulation results with experimental data of 2-Naphthol (2-C{sub 10}H{sub 7}OH) in sodium chloride solution was used for this case study. The model satisfactorily predicts 2-Naphthol removal at the 95% confidence level.

  8. Financial incentives: alternatives to the altruistic model of organ donation.

    PubMed

    Siminoff, L A; Leonard, M D

    1999-12-01

    Improvements in transplantation techniques have resulted in a demand for transplantable organs that far outpaces supply. Present efforts to secure organs use an altruistic system designed to appeal to a public that will donate organs because they are needed. Efforts to secure organs under this system have not been as successful as hoped. Many refinements to the altruistic model have been or are currently being proposed, such as "required request," "mandated choice," "routine notification," and "presumed consent." Recent calls for market approaches to organ procurement reflect growing doubts about the efficacy of these refinements. Market approaches generally use a "futures market," with benefits payable either periodically or when or if organs are procured. Lump-sum arrangements could include donations to surviving family or contributions to charities or to funeral costs. Possibilities for a periodic system of payments include reduced premiums for health or life insurance, or a reciprocity system whereby individuals who periodically reaffirm their willingness to donate are given preference if they require a transplant. Market approaches do raise serious ethical issues, including potential exploitation of the poor. Such approaches may also be effectively proscribed by the 1984 National Organ Transplant Act. PMID:10889698

  9. Regeneration across metazoan phylogeny: lessons from model organisms.

    PubMed

    Li, Qiao; Yang, Hao; Zhong, Tao P

    2015-02-20

    Comprehending the diversity of the regenerative potential across metazoan phylogeny represents a fundamental challenge in biology. Invertebrates like Hydra and planarians exhibit amazing feats of regeneration, in which an entire organism can be restored from minute body segments. Vertebrates like teleost fish and amphibians can also regrow large sections of the body. While this regenerative capacity is greatly attenuated in mammals, there are portions of major organs that remain regenerative. Regardless of the extent, there are common basic strategies to regeneration, including activation of adult stem cells and proliferation of differentiated cells. Here, we discuss the cellular features and molecular mechanisms that are involved in regeneration in different model organisms, including Hydra, planarians, zebrafish and newts as well as in several mammalian organs. PMID:25697100

  10. Green Algae as Model Organisms for Biological Fluid Dynamics

    NASA Astrophysics Data System (ADS)

    Goldstein, Raymond E.

    2015-01-01

    In the past decade, the volvocine green algae, spanning from the unicellular Chlamydomonas to multicellular Volvox, have emerged as model organisms for a number of problems in biological fluid dynamics. These include flagellar propulsion, nutrient uptake by swimming organisms, hydrodynamic interactions mediated by walls, collective dynamics and transport within suspensions of microswimmers, the mechanism of phototaxis, and the stochastic dynamics of flagellar synchronization. Green algae are well suited to the study of such problems because of their range of sizes (from 10 μm to several millimeters), their geometric regularity, the ease with which they can be cultured, and the availability of many mutants that allow for connections between molecular details and organism-level behavior. This review summarizes these recent developments and highlights promising future directions in the study of biological fluid dynamics, especially in the context of evolutionary biology, that can take advantage of these remarkable organisms.

  11. Green Algae as Model Organisms for Biological Fluid Dynamics*

    PubMed Central

    Goldstein, Raymond E.

    2015-01-01

    In the past decade the volvocine green algae, spanning from the unicellular Chlamydomonas to multicellular Volvox, have emerged as model organisms for a number of problems in biological fluid dynamics. These include flagellar propulsion, nutrient uptake by swimming organisms, hydrodynamic interactions mediated by walls, collective dynamics and transport within suspensions of microswimmers, the mechanism of phototaxis, and the stochastic dynamics of flagellar synchronization. Green algae are well suited to the study of such problems because of their range of sizes (from 10 μm to several millimetres), their geometric regularity, the ease with which they can be cultured and the availability of many mutants that allow for connections between molecular details and organism-level behavior. This review summarizes these recent developments and highlights promising future directions in the study of biological fluid dynamics, especially in the context of evolutionary biology, that can take advantage of these remarkable organisms. PMID:26594068

  12. Review of existing terrestrial bioaccumulation models and terrestrial bioaccumulation modeling needs for organic chemicals

    EPA Science Inventory

    Protocols for terrestrial bioaccumulation assessments are far less-developed than for aquatic systems. This manuscript reviews modeling approaches that can be used to assess the terrestrial bioaccumulation potential of commercial organic chemicals. Models exist for plant, inver...

  13. A dynamical phyllotaxis model to determine floral organ number.

    PubMed

    Kitazawa, Miho S; Fujimoto, Koichi

    2015-05-01

    How organisms determine particular organ numbers is a fundamental key to the development of precise body structures; however, the developmental mechanisms underlying organ-number determination are unclear. In many eudicot plants, the primordia of sepals and petals (the floral organs) first arise sequentially at the edge of a circular, undifferentiated region called the floral meristem, and later transition into a concentric arrangement called a whorl, which includes four or five organs. The properties controlling the transition to whorls comprising particular numbers of organs is little explored. We propose a development-based model of floral organ-number determination, improving upon earlier models of plant phyllotaxis that assumed two developmental processes: the sequential initiation of primordia in the least crowded space around the meristem and the constant growth of the tip of the stem. By introducing mutual repulsion among primordia into the growth process, we numerically and analytically show that the whorled arrangement emerges spontaneously from the sequential initiation of primordia. Moreover, by allowing the strength of the inhibition exerted by each primordium to decrease as the primordium ages, we show that pentamerous whorls, in which the angular and radial positions of the primordia are consistent with those observed in sepal and petal primordia in Silene coeli-rosa, Caryophyllaceae, become the dominant arrangement. The organ number within the outmost whorl, corresponding to the sepals, takes a value of four or five in a much wider parameter space than that in which it takes a value of six or seven. These results suggest that mutual repulsion among primordia during growth and a temporal decrease in the strength of the inhibition during initiation are required for the development of the tetramerous and pentamerous whorls common in eudicots. PMID:25950739

  14. A Dynamical Phyllotaxis Model to Determine Floral Organ Number

    PubMed Central

    Kitazawa, Miho S.; Fujimoto, Koichi

    2015-01-01

    How organisms determine particular organ numbers is a fundamental key to the development of precise body structures; however, the developmental mechanisms underlying organ-number determination are unclear. In many eudicot plants, the primordia of sepals and petals (the floral organs) first arise sequentially at the edge of a circular, undifferentiated region called the floral meristem, and later transition into a concentric arrangement called a whorl, which includes four or five organs. The properties controlling the transition to whorls comprising particular numbers of organs is little explored. We propose a development-based model of floral organ-number determination, improving upon earlier models of plant phyllotaxis that assumed two developmental processes: the sequential initiation of primordia in the least crowded space around the meristem and the constant growth of the tip of the stem. By introducing mutual repulsion among primordia into the growth process, we numerically and analytically show that the whorled arrangement emerges spontaneously from the sequential initiation of primordia. Moreover, by allowing the strength of the inhibition exerted by each primordium to decrease as the primordium ages, we show that pentamerous whorls, in which the angular and radial positions of the primordia are consistent with those observed in sepal and petal primordia in Silene coeli-rosa, Caryophyllaceae, become the dominant arrangement. The organ number within the outmost whorl, corresponding to the sepals, takes a value of four or five in a much wider parameter space than that in which it takes a value of six or seven. These results suggest that mutual repulsion among primordia during growth and a temporal decrease in the strength of the inhibition during initiation are required for the development of the tetramerous and pentamerous whorls common in eudicots. PMID:25950739

  15. Incorporating organic soil into a global climate model

    NASA Astrophysics Data System (ADS)

    Lawrence, David M.; Slater, Andrew G.

    2008-02-01

    Organic matter significantly alters a soil’s thermal and hydraulic properties but is not typically included in land-surface schemes used in global climate models. This omission has consequences for ground thermal and moisture regimes, particularly in the high-latitudes where soil carbon content is generally high. Global soil carbon data is used to build a geographically distributed, profiled soil carbon density dataset for the Community Land Model (CLM). CLM parameterizations for soil thermal and hydraulic properties are modified to accommodate both mineral and organic soil matter. Offline simulations including organic soil are characterized by cooler annual mean soil temperatures (up to ˜2.5°C cooler for regions of high soil carbon content). Cooling is strong in summer due to modulation of early and mid-summer soil heat flux. Winter temperatures are slightly warmer as organic soils do not cool as efficiently during fall and winter. High porosity and hydraulic conductivity of organic soil leads to a wetter soil column but with comparatively low surface layer saturation levels and correspondingly low soil evaporation. When CLM is coupled to the Community Atmosphere Model, the reduced latent heat flux drives deeper boundary layers, associated reductions in low cloud fraction, and warmer summer air temperatures in the Arctic. Lastly, the insulative properties of organic soil reduce interannual soil temperature variability, but only marginally. This result suggests that, although the mean soil temperature cooling will delay the simulated date at which frozen soil begins to thaw, organic matter may provide only limited insulation from surface warming.

  16. Modeling organic matter stabilization during windrow composting of livestock effluents.

    PubMed

    Oudart, D; Paul, E; Robin, P; Paillat, J M

    2012-01-01

    Composting is a complex bioprocess, requiring a lot of empirical experiments to optimize the process. A dynamical mathematical model for the biodegradation of the organic matter during the composting process has been developed. The initial organic matter expressed by chemical oxygen demand (COD) is decomposed into rapidly and slowly degraded compartments and an inert one. The biodegradable COD is hydrolysed and consumed by microorganisms and produces metabolic water and carbon dioxide. This model links a biochemical characterization of the organic matter by Van Soest fractionating with COD. The comparison of experimental and simulation results for carbon dioxide emission, dry matter and carbon content balance showed good correlation. The initial sizes of the biodegradable COD compartments are explained by the soluble, hemicellulose-like and lignin fraction. Their sizes influence the amplitude of the carbon dioxide emission peak. The initial biomass is a sensitive variable too, influencing the time at which the emission peak occurs. PMID:23393964

  17. An Ontology for Modeling Complex Inter-relational Organizations

    NASA Astrophysics Data System (ADS)

    Wautelet, Yves; Neysen, Nicolas; Kolp, Manuel

    This paper presents an ontology for organizational modeling through multiple complementary aspects. The primary goal of the ontology is to dispose of an adequate set of related concepts for studying complex organizations involved in a lot of relationships at the same time. In this paper, we define complex organizations as networked organizations involved in a market eco-system that are playing several roles simultaneously. In such a context, traditional approaches focus on the macro analytic level of transactions; this is supplemented here with a micro analytic study of the actors' rationale. At first, the paper overviews enterprise ontologies literature to position our proposal and exposes its contributions and limitations. The ontology is then brought to an advanced level of formalization: a meta-model in the form of a UML class diagram allows to overview the ontology concepts and their relationships which are formally defined. Finally, the paper presents the case study on which the ontology has been validated.

  18. Unified electronic charge transport model for organic solar cells

    NASA Astrophysics Data System (ADS)

    Mottaghian, Seyyed Sadegh; Biesecker, Matt; Bayat, Khadijeh; Farrokh Baroughi, Mahdi

    2013-07-01

    This paper provides a comprehensive modeling approach for simulation of electronic charge transport in excitonic solar cells with organic and organic/inorganic structures. Interaction of energy carrying particles (electrons, holes, singlet excitons, and triplet excitons) with each other and their transformation in the bulk of the donor and acceptor media as well as the donor/acceptor interfaces are incorporated in form of coupling matrices into the continuity equations and interface boundary conditions. As a case study, the model is applied to simulate an organic bilayer photovoltaic (PV) device to quantify the effects of photo generation, recombination coefficient, carrier mobility, and electrode work function on its PV characteristics. The study proves that electron-hole recombination at the donor/acceptor interface is the dominant mechanism that limits open circuit voltage of the device.

  19. Modelling the fate of organic micropollutants in stormwater ponds.

    PubMed

    Vezzaro, Luca; Eriksson, Eva; Ledin, Anna; Mikkelsen, Peter S

    2011-06-01

    Urban water managers need to estimate the potential removal of organic micropollutants (MP) in stormwater treatment systems to support MP pollution control strategies. This study documents how the potential removal of organic MP in stormwater treatment systems can be quantified by using multimedia models. The fate of four different MP in a stormwater retention pond was simulated by applying two steady-state multimedia fate models (EPI Suite and SimpleBox) commonly applied in chemical risk assessment and a dynamic multimedia fate model (Stormwater Treatment Unit Model for Micro Pollutants--STUMP). The four simulated organic stormwater MP (iodopropynyl butylcarbamate--IPBC, benzene, glyphosate and pyrene) were selected according to their different urban sources and environmental fate. This ensures that the results can be extended to other relevant stormwater pollutants. All three models use substance inherent properties to calculate MP fate but differ in their ability to represent the small physical scale and high temporal variability of stormwater treatment systems. Therefore the three models generate different results. A Global Sensitivity Analysis (GSA) highlighted that settling/resuspension of particulate matter was the most sensitive process for the dynamic model. The uncertainty of the estimated MP fluxes can be reduced by calibrating the dynamic model against total suspended solids data. This reduction in uncertainty was more significant for the substances with strong tendency to sorb, i.e. glyphosate and pyrene and less significant for substances with a smaller tendency to sorb, i.e. IPBC and benzene. The results provide support to the elaboration of MP pollution control strategies by limiting the need for extensive and complex monitoring campaigns targeting the wide range of specific organic MP found in stormwater runoff. PMID:21496881

  20. MODELING THE FATE OF TOXIC ORGANIC MATERIALS IN AQUATIC ENVIRONMENTS

    EPA Science Inventory

    Documentation is given for PEST, a dynamic simulation model for evaluating the fate of toxic organic materials (TOM) in freshwater environments. PEST represents the time-varying concentration (in ppm) of a given TOM in each of as many as 16 carrier compartments; it also computes ...

  1. Modeling emissions of volatile organic compounds from silage

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Volatile organic compounds (VOCs), necessary reactants for photochemical smog formation, are emitted from numerous sources. Limited available data suggest that dairy farms emit VOCs with cattle feed, primarily silage, being the primary source. Process-based models of VOC transfer within and from si...

  2. An Integrated Model for Effective Knowledge Management in Chinese Organizations

    ERIC Educational Resources Information Center

    An, Xiaomi; Deng, Hepu; Wang, Yiwen; Chao, Lemen

    2013-01-01

    Purpose: The purpose of this paper is to provide organizations in the Chinese cultural context with a conceptual model for an integrated adoption of existing knowledge management (KM) methods and to improve the effectiveness of their KM activities. Design/methodology/approaches: A comparative analysis is conducted between China and the western…

  3. VOC (VOLATILE ORGANIC COMPOUND) FUGITIVE EMISSION PREDICTIVE MODEL - USER'S GUIDE

    EPA Science Inventory

    The report discusses a mathematical model that can be used to evaluate the effectiveness of various leak detection and repair (LDAR) programs on controlling volatile organic compound (VOC) fugitive emissions from chemical, petroleum, and other process units. The report also descr...

  4. Functional genomics of the chicken - a model organism

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The chicken has reached model organism status after genome sequencing and development of high-throughput tools for the exploration of functional elements of the genome. Functional genomics focuses on understanding the function and regulation of genes and gene products on a global or genome-wide scal...

  5. MODELING MULTIPHASE ORGANIC CHEMICAL TRANSPORT IN SOILS AND GROUND WATER

    EPA Science Inventory

    Subsurface contamination due to immiscible organic liquids is a widespread problem which poses a serious threat to ground-water resources. n order to understand the movement of such materials in the subsurface, a mathematical model was developed for multiphase flow and multicompo...

  6. A Process Model for the Comprehension of Organic Chemistry Notation

    ERIC Educational Resources Information Center

    Havanki, Katherine L.

    2012-01-01

    This dissertation examines the cognitive processes individuals use when reading organic chemistry equations and factors that affect these processes, namely, visual complexity of chemical equations and participant characteristics (expertise, spatial ability, and working memory capacity). A six stage process model for the comprehension of organic…

  7. Supramolecular organization of functional organic materials in the bulk and at organic/organic interfaces: a modeling and computer simulation approach.

    PubMed

    Muccioli, Luca; D'Avino, Gabriele; Berardi, Roberto; Orlandi, Silvia; Pizzirusso, Antonio; Ricci, Matteo; Roscioni, Otello Maria; Zannoni, Claudio

    2014-01-01

    The molecular organization of functional organic materials is one of the research areas where the combination of theoretical modeling and experimental determinations is most fruitful. Here we present a brief summary of the simulation approaches used to investigate the inner structure of organic materials with semiconducting behavior, paying special attention to applications in organic photovoltaics and clarifying the often obscure jargon hindering the access of newcomers to the literature of the field. Special attention is paid to the choice of the computational "engine" (Monte Carlo or Molecular Dynamics) used to generate equilibrium configurations of the molecular system under investigation and, more importantly, to the choice of the chemical details in describing the molecular interactions. Recent literature dealing with the simulation of organic semiconductors is critically reviewed in order of increasing complexity of the system studied, from low molecular weight molecules to semiflexible polymers, including the challenging problem of determining the morphology of heterojunctions between two different materials. PMID:24322782

  8. Unexpected capacity for organic carbon assimilation by Thermosynechococcus elongatus, a crucial photosynthetic model organism.

    PubMed

    Zilliges, Yvonne; Dau, Holger

    2016-04-01

    Genetic modification of key residues of photosystems is essential to identify functionally crucial processes by spectroscopic and crystallographic investigation; the required protein stability favours use of thermophilic species. The currently unique thermophilic photosynthetic model organism is the cyanobacterial genus Thermosynechococcus. We report the ability of Thermosynechococcus elongatus to assimilate organic carbon, specifically D-fructose. Growth in the presence of a photosynthesis inhibitor opens the door towards crucial amino acid substitutions in photosystems by the rescue of otherwise lethal mutations. Yet depression of batch-culture growth after 7 days implies that additional developments are needed. PMID:26935247

  9. Lamination of organic solar cells and organic light emitting devices: Models and experiments

    SciTech Connect

    Oyewole, O. K.; Yu, D.; Du, J.; Asare, J.; Fashina, A.; Anye, V. C.; Zebaze Kana, M. G.; Soboyejo, W. O.

    2015-08-21

    In this paper, a combined experimental, computational, and analytical approach is used to provide new insights into the lamination of organic solar cells and light emitting devices at macro- and micro-scales. First, the effects of applied lamination force (on contact between the laminated layers) are studied. The crack driving forces associated with the interfacial cracks (at the bi-material interfaces) are estimated along with the critical interfacial crack driving forces associated with the separation of thin films, after layer transfer. The conditions for successful lamination are predicted using a combination of experiments and computational models. Guidelines are developed for the lamination of low-cost organic electronic structures.

  10. A general framework for modelling the vertical organic matter profile in mineral and organic soils

    NASA Astrophysics Data System (ADS)

    Braakhekke, Maarten; Ahrens, Bernhard

    2016-04-01

    The vertical distribution of soil organic matter (SOM) within the mineral soil and surface organic layer is an important property of terrestrial ecosystems that affects carbon and nutrient cycling and soil heat and moisture transport. The overwhelming majority of models of SOM dynamics are zero-dimensional, i.e. they do not resolve heterogeneity of SOM concentration along the vertical profile. In recent years, however, a number of new vertically explicit SOM models or vertically explicit versions of existing models have been published. These models describe SOM in units of concentration (mass per unit volume) by means of a reactive-transport model that includes diffusion and/or advection terms for SOM transport, and vertically resolves SOM inputs and factors that influence decomposition. An important assumption behind these models is that the volume of soil elements is constant over time, i.e. not affected by SOM dynamics. This assumption only holds if the SOM content is negligible compared to the mineral content. When this is not the case, SOM input or loss in a soil element may cause a change in volume of the element rather than a change in SOM concentration. Furthermore, these volume changes can cause vertical shifts of material relative to the surface. This generally causes material in an organic layer to gradually move downward, even in absence of mixing processes. Since the classical reactive-transport model of the SOM profile can only be applied to the mineral soil, the surface organic layer is usually either treated separately or not explicitly considered. We present a new and elegant framework that treats the surface organic layer and mineral soil as one continuous whole. It explicitly accounts for volume changes due to SOM dynamics and changes in bulk density. The vertical shifts resulting from these volume changes are included in an Eulerian representation as an additional advective transport flux. Our approach offers a more elegant and realistic

  11. Implementing marine organic aerosols into the GEOS-Chem model

    DOE PAGESBeta

    Gantt, B.; Johnson, M. S.; Crippa, M.; Prévôt, A. S. H.; Meskhidze, N.

    2015-03-17

    Marine-sourced organic aerosols (MOAs) have been shown to play an important role in tropospheric chemistry by impacting surface mass, cloud condensation nuclei, and ice nuclei concentrations over remote marine and coastal regions. In this work, an online marine primary organic aerosol emission parameterization, designed to be used for both global and regional models, was implemented into the GEOS-Chem (Global Earth Observing System Chemistry) model. The implemented emission scheme improved the large underprediction of organic aerosol concentrations in clean marine regions (normalized mean bias decreases from -79% when using the default settings to -12% when marine organic aerosols are added). Modelmore » predictions were also in good agreement (correlation coefficient of 0.62 and normalized mean bias of -36%) with hourly surface concentrations of MOAs observed during the summertime at an inland site near Paris, France. Our study shows that MOAs have weaker coastal-to-inland concentration gradients than sea-salt aerosols, leading to several inland European cities having >10% of their surface submicron organic aerosol mass concentration with a marine source. The addition of MOA tracers to GEOS-Chem enabled us to identify the regions with large contributions of freshly emitted or aged aerosol having distinct physicochemical properties, potentially indicating optimal locations for future field studies.« less

  12. Kinetic model of DNA replication in eukaryotic organisms

    NASA Astrophysics Data System (ADS)

    Bechhoefer, John; Herrick, John; Bensimon, Aaron

    2001-03-01

    We introduce an analogy between DNA replication in eukaryotic organisms and crystal growth in one dimension. Drawing on models of crystallization kinetics developed in the 1930s to describe the freezing of metals, we formulate a kinetic model of DNA replication that quantitatively describes recent results on DNA replication in the in vitro system of Xenopus laevis prior to the mid-blastula transition. It allows one, for the first time, to determine the parameters governing the DNA replication program in a eukaryote on a genome-wide basis. In particular, we have determined the frequency of origin activation in time and space during the cell cycle. Although we focus on a specific stage of development, this model can easily be adapted to describe replication in many other organisms, including budding yeast.

  13. Finite-element model of the active organ of Corti.

    PubMed

    Ni, Guangjian; Elliott, Stephen J; Baumgart, Johannes

    2016-02-01

    The cochlear amplifier that provides our hearing with its extraordinary sensitivity and selectivity is thought to be the result of an active biomechanical process within the sensory auditory organ, the organ of Corti. Although imaging techniques are developing rapidly, it is not currently possible, in a fully active cochlea, to obtain detailed measurements of the motion of individual elements within a cross section of the organ of Corti. This motion is predicted using a two-dimensional finite-element model. The various solid components are modelled using elastic elements, the outer hair cells (OHCs) as piezoelectric elements and the perilymph and endolymph as viscous and nearly incompressible fluid elements. The model is validated by comparison with existing measurements of the motions within the passive organ of Corti, calculated when it is driven either acoustically, by the fluid pressure or electrically, by excitation of the OHCs. The transverse basilar membrane (BM) motion and the shearing motion between the tectorial membrane and the reticular lamina are calculated for these two excitation modes. The fully active response of the BM to acoustic excitation is predicted using a linear superposition of the calculated responses and an assumed frequency response for the OHC feedback. PMID:26888950

  14. Numerical model for organic light-emitting diodes

    NASA Astrophysics Data System (ADS)

    Tutiš, E.; Bussac, M. N.; Masenelli, B.; Carrard, M.; Zuppiroli, L.

    2001-01-01

    An extensive numerical model recently developed for the multilayer organic light-emitting diode is described and applied to a set of real devices. The model contains a detailed description of electrical contacts including dipolar layer formation, thermionic and tunneling injection, space charge effects, field dependent mobilities and recombination processes. The model is applied to simulate several single layer devices and the family of bilayer devices made in our group. It provides insight into the energy level shifts, internal electric fields and charge distribution (and consequently recombination) throughout the device. Finally, the analysis is extended to the optimization of bilayer device.

  15. Modeling stable isotope and organic carbon in hillslope stormflow

    NASA Astrophysics Data System (ADS)

    Dusek, Jaromir; Vogel, Tomas; Dohnal, Michal; Marx, Anne; Jankovec, Jakub; Sanda, Martin; Votrubova, Jana; Barth, Johannes A. C.; Cislerova, Milena

    2016-04-01

    Reliable prediction of water movement and fluxes of dissolved substances (such as stable isotopes and organic carbon) at both the hillslope and the catchment scales remains a challenge due to complex boundary conditions and soil spatial heterogeneity. In addition, microbially mediated transformations of dissolved organic carbon (DOC) are known to affect balance of DOC in soils, hence the transformations need to be included in a conceptual model of a DOC transport. So far, only few studies utilized stable isotope information in modeling and even fewer linked dissolved carbon fluxes to mixing and/or transport models. In this study, stormflow dynamics of oxygen-18 isotope and dissolved organic carbon was analyzed using a physically based modeling approach. One-dimensional dual-continuum vertical flow and transport model, based on Richards and advection-dispersion equations, was used to simulate the subsurface transport processes in a forest soil during several observed rainfall-runoff episodes. The transport of heat in the soil profile was described by conduction-advection equation. Water flow and transport of solutes and heat were assumed to take place in two mutually communicating porous domains, the soil matrix and the network of preferential pathways. The rate of microbial transformations of DOC was assumed to depend on soil water content and soil temperature. Oxygen-18 and dissolved organic carbon concentrations were observed in soil pore water, hillslope stormflow (collected in the experimental hillslope trench), and stream discharge (at the catchment outlet). The modeling was used to analyze the transformation of input solute signals into output hillslope signals observed in the trench stormflow. Signatures of oxygen-18 isotope in hillslope stormflow as well as isotope concentration in soil pore water were predicted reasonably well. Due to complex nature of microbial transformations, prediction of DOC rate and transport was associated with a high uncertainty.

  16. Solid Solution Model for Interstellar Dust Grains and Their Organics

    NASA Astrophysics Data System (ADS)

    Freund, Minoru M.; Freund, Friedemann T.

    2006-03-01

    We present a dust grain model based on the fundamental principle of solid solutions. The model is applicable to the mineral (silicate) component of the dust in the interstellar medium (ISM). We show that nanometer-sized mineral grains, which condense in the gas-rich outflow of late-stage stars or expanding gas shells of supernova explosions, do not consist of just high melting point oxides or silicates. Instead they form solid solutions with gas-phase components H2O, CO, and CO2 that are omnipresent in environments where the grains condense. Through a series of thermodynamically well-understood solid-state processes, these solid solutions become ``parents'' of organic matter that precipitates inside the grains. Thus, the mineral dust grains and their organics become part of the same thermodynamically defined solid phase and, hence, physically inseparable. This model can account for many astronomical observations, which no prior model can adequately address, specifically: (1) Organics in the diffuse ISM are identified by a 3.4 μm IR band, characteristic of aliphatic hydrocarbons composed of CH2 and of CH3 groups. (2) The methylene-to-methyl ratio is nearly constant, implying a CH2:CH3 ratio of ~5:2. (3) The intensity ratio between the 9.7 and the 3.4 μm band is nearly constant, implying a silicate-to-organics ratio of ~10:1. (4) In dense clouds the complex 3.4 μm band is replaced by a weak, featureless 3.47 μm band. (5) Whereas silicate grains identified by their 9.7 μm band tend to align in magnetic fields, grains with a strong 3.4 μm organic signature do not tend to align.

  17. Conservative Self-Organized Extremal Model for Wealth Distribution

    NASA Astrophysics Data System (ADS)

    Chakraborty, Abhijit; Mukherjee, G.; Manna, S. S.

    2012-06-01

    We present an extensive numerical study of the modified version of a conservative self-organized extremal model introduced by Pianegonda et al. (Physica A322 (2003) 667-675) in the context of wealth distribution of the people in a society. Here the trading process has been modified by the stochastic bipartite trading rule. More specifically in a trade one of the agents is necessarily the one with the globally minimal value of wealth, the other one being selected randomly from the neighbors of the first agent. The pair of agents then randomly re-shuffle their entire amount of wealth without saving. This model has most of the characteristics similar to the self-organized critical Bak-Sneppen model of evolutionary dynamics. Numerical estimates of a number of critical exponents indicate this model is likely to belong to a new universality class different from the well known models in the literature. In addition the persistence time, which is the time interval between two successive updates of wealth of an agent has been observed to have a non-trivial power law distribution. An opposite version of the model has also been studied where the agent with maximal wealth is selected instead of the one with minimal wealth, which however, exhibits similar behavior as the Minimal Wealth model.

  18. Stacked Multilayer Self-Organizing Map for Background Modeling.

    PubMed

    Zhao, Zhenjie; Zhang, Xuebo; Fang, Yongchun

    2015-09-01

    In this paper, a new background modeling method called stacked multilayer self-organizing map background model (SMSOM-BM) is proposed, which presents several merits such as strong representative ability for complex scenarios, easy to use, and so on. In order to enhance the representative ability of the background model and make the parameters learned automatically, the recently developed idea of representative learning (or deep learning) is elegantly employed to extend the existing single-layer self-organizing map background model to a multilayer one (namely, the proposed SMSOM-BM). As a consequence, the SMSOM-BM gains several merits including strong representative ability to learn background model of challenging scenarios, and automatic determination for most network parameters. More specifically, every pixel is modeled by a SMSOM, and spatial consistency is considered at each layer. By introducing a novel over-layer filtering process, we can train the background model layer by layer in an efficient manner. Furthermore, for real-time performance consideration, we have implemented the proposed method using NVIDIA CUDA platform. Comparative experimental results show superior performance of the proposed approach. PMID:25935034

  19. Invertebrates as model organisms for research on aging biology

    PubMed Central

    Murthy, Mahadev; Ram, Jeffrey L.

    2015-01-01

    Invertebrate model systems, such as nematodes and fruit flies, have provided valuable information about the genetics and cellular biology involved in aging. However, limitations of these simple, genetically tractable organisms suggest the need for other model systems, some of them invertebrate, to facilitate further advances in the understanding of mechanisms of aging and longevity in mammals, including humans. This paper introduces 10 review articles about the use of invertebrate model systems for the study of aging by authors who participated in an ‘NIA-NIH symposium on aging in invertebrate model systems’ at the 2013 International Congress for Invertebrate Reproduction and Development. In contrast to the highly derived characteristics of nematodes and fruit flies as members of the superphylum Ecdysozoa, cnidarians, such as Hydra, are more ‘basal’ organisms that have a greater number of genetic orthologs in common with humans. Moreover, some other new model systems, such as the urochordate Botryllus schlosseri, the tunicate Ciona, and the sea urchins (Echinodermata) are members of the Deuterostomia, the same superphylum that includes all vertebrates, and thus have mechanisms that are likely to be more closely related to those occurring in humans. Additional characteristics of these new model systems, such as the recent development of new molecular and genetic tools and a more similar pattern to humans of regeneration and stem cell function suggest that these new model systems may have unique advantages for the study of mechanisms of aging and longevity. PMID:26241448

  20. Modeling Secondary Organic Aerosol Formation From Emissions of Combustion Sources

    NASA Astrophysics Data System (ADS)

    Jathar, Shantanu Hemant

    Atmospheric aerosols exert a large influence on the Earth's climate and cause adverse public health effects, reduced visibility and material degradation. Secondary organic aerosol (SOA), defined as the aerosol mass arising from the oxidation products of gas-phase organic species, accounts for a significant fraction of the submicron atmospheric aerosol mass. Yet, there are large uncertainties surrounding the sources, atmospheric evolution and properties of SOA. This thesis combines laboratory experiments, extensive data analysis and global modeling to investigate the contribution of semi-volatile and intermediate volatility organic compounds (SVOC and IVOC) from combustion sources to SOA formation. The goals are to quantify the contribution of these emissions to ambient PM and to evaluate and improve models to simulate its formation. To create a database for model development and evaluation, a series of smog chamber experiments were conducted on evaporated fuel, which served as surrogates for real-world combustion emissions. Diesel formed the most SOA followed by conventional jet fuel / jet fuel derived from natural gas, gasoline and jet fuel derived from coal. The variability in SOA formation from actual combustion emissions can be partially explained by the composition of the fuel. Several models were developed and tested along with existing models using SOA data from smog chamber experiments conducted using evaporated fuel (this work, gasoline, fischertropschs, jet fuel, diesels) and published data on dilute combustion emissions (aircraft, on- and off-road gasoline, on- and off-road diesel, wood burning, biomass burning). For all of the SOA data, existing models under-predicted SOA formation if SVOC/IVOC were not included. For the evaporated fuel experiments, when SVOC/IVOC were included predictions using the existing SOA model were brought to within a factor of two of measurements with minor adjustments to model parameterizations. Further, a volatility

  1. Lateral organization of complex lipid mixtures from multiscale modeling

    NASA Astrophysics Data System (ADS)

    Tumaneng, Paul W.; Pandit, Sagar A.; Zhao, Guijun; Scott, H. L.

    2010-02-01

    The organizational properties of complex lipid mixtures can give rise to functionally important structures in cell membranes. In model membranes, ternary lipid-cholesterol (CHOL) mixtures are often used as representative systems to investigate the formation and stabilization of localized structural domains ("rafts"). In this work, we describe a self-consistent mean-field model that builds on molecular dynamics simulations to incorporate multiple lipid components and to investigate the lateral organization of such mixtures. The model predictions reveal regions of bimodal order on ternary plots that are in good agreement with experiment. Specifically, we have applied the model to ternary mixtures composed of dioleoylphosphatidylcholine:18:0 sphingomyelin:CHOL. This work provides insight into the specific intermolecular interactions that drive the formation of localized domains in these mixtures. The model makes use of molecular dynamics simulations to extract interaction parameters and to provide chain configuration order parameter libraries.

  2. Nonequilibrium drift-diffusion model for organic semiconductor devices

    NASA Astrophysics Data System (ADS)

    Felekidis, Nikolaos; Melianas, Armantas; Kemerink, Martijn

    2016-07-01

    Two prevailing formalisms are currently used to model charge transport in organic semiconductor devices. Drift-diffusion calculations, on the one hand, are time effective but assume local thermodynamic equilibrium, which is not always realistic. Kinetic Monte Carlo models, on the other hand, do not require this assumption but are computationally expensive. Here, we present a nonequilibrium drift-diffusion model that bridges this gap by fusing the established multiple trap and release formalism with the drift-diffusion transport equation. For a prototypical photovoltaic system the model is shown to quantitatively describe, with a single set of parameters, experiments probing (1) temperature-dependent steady-state charge transport—space-charge limited currents, and (2) time-resolved charge transport and relaxation of nonequilibrated photocreated charges. Moreover, the outputs of the developed kinetic drift-diffusion model are an order of magnitude, or more, faster to compute and in good agreement with kinetic Monte Carlo calculations.

  3. Modeling regional secondary organic aerosol using the Master Chemical Mechanism

    NASA Astrophysics Data System (ADS)

    Li, Jingyi; Cleveland, Meredith; Ziemba, Luke D.; Griffin, Robert J.; Barsanti, Kelley C.; Pankow, James F.; Ying, Qi

    2015-02-01

    A modified near-explicit Master Chemical Mechanism (MCM, version 3.2) with 5727 species and 16,930 reactions and an equilibrium partitioning module was incorporated into the Community Air Quality Model (CMAQ) to predict the regional concentrations of secondary organic aerosol (SOA) from volatile organic compounds (VOCs) in the eastern United States (US). In addition to the semi-volatile SOA from equilibrium partitioning, reactive surface uptake processes were used to simulate SOA formation due to isoprene epoxydiol, glyoxal and methylglyoxal. The CMAQ-MCM-SOA model was applied to simulate SOA formation during a two-week episode from August 28 to September 7, 2006. The southeastern US has the highest SOA, with a maximum episode-averaged concentration of ∼12 μg m-3. Primary organic aerosol (POA) and SOA concentrations predicted by CMAQ-MCM-SOA agree well with AMS-derived hydrocarbon-like organic aerosol (HOA) and oxygenated organic aerosol (OOA) urban concentrations at the Moody Tower at the University of Houston. Predicted molecular properties of SOA (O/C, H/C, N/C and OM/OC ratios) at the site are similar to those reported in other urban areas, and O/C values agree with measured O/C at the same site. Isoprene epoxydiol is predicted to be the largest contributor to total SOA concentration in the southeast US, followed by methylglyoxal and glyoxal. The semi-volatile SOA components are dominated by products from β-caryophyllene oxidation, but the major species and their concentrations are sensitive to errors in saturation vapor pressure estimation. A uniform decrease of saturation vapor pressure by a factor of 100 for all condensable compounds can lead to a 150% increase in total SOA. A sensitivity simulation with UNIFAC-calculated activity coefficients (ignoring phase separation and water molecule partitioning into the organic phase) led to a 10% change in the predicted semi-volatile SOA concentrations.

  4. Efficient control of population structure in model organism association mapping.

    PubMed

    Kang, Hyun Min; Zaitlen, Noah A; Wade, Claire M; Kirby, Andrew; Heckerman, David; Daly, Mark J; Eskin, Eleazar

    2008-03-01

    Genomewide association mapping in model organisms such as inbred mouse strains is a promising approach for the identification of risk factors related to human diseases. However, genetic association studies in inbred model organisms are confronted by the problem of complex population structure among strains. This induces inflated false positive rates, which cannot be corrected using standard approaches applied in human association studies such as genomic control or structured association. Recent studies demonstrated that mixed models successfully correct for the genetic relatedness in association mapping in maize and Arabidopsis panel data sets. However, the currently available mixed-model methods suffer from computational inefficiency. In this article, we propose a new method, efficient mixed-model association (EMMA), which corrects for population structure and genetic relatedness in model organism association mapping. Our method takes advantage of the specific nature of the optimization problem in applying mixed models for association mapping, which allows us to substantially increase the computational speed and reliability of the results. We applied EMMA to in silico whole-genome association mapping of inbred mouse strains involving hundreds of thousands of SNPs, in addition to Arabidopsis and maize data sets. We also performed extensive simulation studies to estimate the statistical power of EMMA under various SNP effects, varying degrees of population structure, and differing numbers of multiple measurements per strain. Despite the limited power of inbred mouse association mapping due to the limited number of available inbred strains, we are able to identify significantly associated SNPs, which fall into known QTL or genes identified through previous studies while avoiding an inflation of false positives. An R package implementation and webserver of our EMMA method are publicly available. PMID:18385116

  5. Modelling the metabolic shift of polyphosphate-accumulating organisms.

    PubMed

    Acevedo, B; Borrás, L; Oehmen, A; Barat, R

    2014-11-15

    Enhanced biological phosphorus removal (EBPR) is one of the most important methods of phosphorus removal in municipal wastewater treatment plants, having been described by different modelling approaches. In this process, the PAOs (polyphosphate accumulating organisms) and GAOs (glycogen accumulating organisms) compete for volatile fatty acids uptake under anaerobic conditions. Recent studies have revealed that the metabolic pathways used by PAOs in order to obtain the energy and the reducing power needed for polyhydroxyalkanoates synthesis could change depending on the amount of polyphosphate stored in the cells. The model presented in this paper extends beyond previously developed metabolic models by including the ability of PAO to change their metabolic pathways according to the content of poly-P available. The processes of the PAO metabolic model were adapted to new formulations enabling the change from P-driven VFA uptake to glycogen-driven VFA uptake using the same process equations. The stoichiometric parameters were changed from a typical PAO coefficient to a typical GAO coefficient depending on the internal poly-P with Monod-type expressions. The model was calibrated and validated with seven experiments under different internal poly-P concentrations, showing the ability to correctly represent the PAO metabolic shift at low poly-P concentrations. The sensitivity and error analysis showed that the model is robust and has the ability to describe satisfactorily the change from one metabolic pathway to the other one, thereby encompassing a wider range of process conditions found in EBPR plants. PMID:25123437

  6. Global modeling of organic aerosol: the importance of reactive nitrogen

    NASA Astrophysics Data System (ADS)

    Pye, H. O. T.; Chan, A. W. H.; Barkley, M. P.; Seinfeld, J. H.

    2010-09-01

    Reactive nitrogen compounds, specifically NOx and NO3, likely influence global organic aerosol levels. To assess these interactions, GEOS-Chem, a chemical transport model, is updated to include improved biogenic emissions (following MEGAN v2.1/2.04), a new organic aerosol tracer lumping scheme, aerosol from nitrate radical (NO3) oxidation of isoprene, and NOx-dependent terpene aerosol yields. As a result of significant nighttime terpene emissions, fast reaction of monoterpenes with the nitrate radical, and relatively high aerosol yields from NO3 oxidation, biogenic hydrocarbon-NO3 reactions are expected to be a major contributor to surface level aerosol concentrations in anthropogenically influenced areas such as the United States. By including aerosol from nitrate radical oxidation in GEOS-Chem, terpene aerosol approximately doubles and isoprene aerosol is enhanced by 30 to 40% in the Southeast United States. In terms of the global budget of organic aerosol, however, aerosol from nitrate radical oxidation is somewhat minor (slightly more than 3 Tg/yr) due to the relatively high volatility of organic-NO3 oxidation products. Globally, 69 to 88 Tg/yr of organic aerosol is predicted to be produced annually, of which 14-15 Tg/yr is from oxidation of monoterpenes and sesquiterpenes and 8-9 Tg/yr from isoprene.

  7. Dissecting genetic and environmental mutation signatures with model organisms.

    PubMed

    Segovia, Romulo; Tam, Annie S; Stirling, Peter C

    2015-08-01

    Deep sequencing has impacted on cancer research by enabling routine sequencing of genomes and exomes to identify genetic changes associated with carcinogenesis. Researchers can now use the frequency, type, and context of all mutations in tumor genomes to extract mutation signatures that reflect the driving mutational processes. Identifying mutation signatures, however, may not immediately suggest a mechanism. Consequently, several recent studies have employed deep sequencing of model organisms exposed to discrete genetic or environmental perturbations. These studies exploit the simpler genomes and availability of powerful genetic tools in model organisms to analyze mutation signatures under controlled conditions, forging mechanistic links between mutational processes and signatures. We discuss the power of this approach and suggest that many such studies may be on the horizon. PMID:25940384

  8. An analytical model for in situ extraction of organic vapors

    USGS Publications Warehouse

    Roy, W.R.; Griffin, R.A.

    1991-01-01

    This paper introduces a simple convective-flow model that can be used as a screening tool and for conducting sensitivity analyses for in situ vapor extraction of organic compounds from porous media. An assumption basic to this model was that the total mass of volatile organic chemicals (VOC) exists in three forms: as vapors, in the soil solution, and adsorbed to soil particles. The equilibrium partitioning between the vapor-liquid phase was described by Henry's law constants (K(H)) and between the liquid-soil phase by soil adsorption constants (K(d)) derived from soil organic carbon-water partition coefficients (K(oc)). The model was used to assess the extractability of 36 VOCs from a hypothetical site. Most of the VOCs appeared to be removable from soil by this technology, although modeling results suggested that rates for the alcohols and ketones may be very slow. In general, rates for weakly adsorbed compounds (K(oc) < 100 mL/g) were significantly higher when K(H) was greater than 10-4 atm??m3??mol-1. When K(oc) was greater than about 100 mL/g, the rates of extraction were sensitive to the amount of organic carbon present in the soil. The air permeability of the soil material (k) was a critical factor. In situ extraction needs careful evaluation when k is less than 10 millidarcies to determine its applicability. An increase in the vacuum applied to an extraction well accelerated removal rates but the diameter of the well had little effect. However, an increase in the length of the well screen open to the contaminated zone significantly affected removal rates, especially in low-permeability materials.This paper introduces a simple convective-flow model that can be used as a screening tool and for conducting sensitivity analyses for in situ vapor extraction of organic compounds from porous media. An assumption basic to this model was that the total mass of volatile organic chemicals (VOC) exists in three forms: as vapors, in the soil solution, and adsorbed to soil

  9. Cube Kohonen self-organizing map (CKSOM) model with new equations in organizing unstructured data.

    PubMed

    Lim, Seng Poh; Haron, Habibollah

    2013-09-01

    Surface reconstruction by using 3-D data is used to represent the surface of an object and perform important tasks. The type of data used is important and can be described as either structured or unstructured. For unstructured data, there is no connectivity information between data points. As a result, incorrect shapes will be obtained during the imaging process. Therefore, the data should be reorganized by finding the correct topology so that the correct shape can be obtained. Previous studies have shown that the Kohonen self-organizing map (KSOM) could be used to solve data organizing problems. However, 2-D Kohonen maps are limited because they are unable to cover the whole surface of closed 3-D surface data. Furthermore, the neurons inside the 3-D KSOM structure should be removed in order to create a correct wireframe model. This is because only the outside neurons are used to represent the surface of an object. The aim of this paper is to use KSOM to organize unstructured data for closed surfaces. KSOM isused in this paper by testing its ability to organize medical image data because KSOM is mostly used in constructing engineering field data. Enhancements are added to the model by introducing class number and the index vector, and new equations are created. Various grid sizes and maximum iterations are tested in the experiments. Based on the results, the number of redundancies is found to be directly proportional to the grid size. When we increase the maximum iterations, the surface of the image becomes smoother. An area formula is used and manual calculations are performed to validate the results. This model is implemented and images are created using Dev C++ and GNUPlot. PMID:24808578

  10. Mechanical models for the self-organization of tubular patterns

    PubMed Central

    2013-01-01

    Organogenesis, such as long tubule self-organization, requires long-range coordination of cell mechanics to arrange cell positions and to remodel the extracellular matrix. While the current mainstream in the field of tissue morphogenesis focuses primarily on genetics and chemical signaling, the influence of cell mechanics on the programming of patterning cues in tissue morphogenesis has not been adequately addressed. Here, we review experimental evidence and propose quantitative mechanical models by which cells can create tubular patterns. PMID:23719257

  11. Combining Traits and Density to Model Recruitment of Sessile Organisms

    PubMed Central

    Giménez, Luis; Jenkins, Stuart R.

    2013-01-01

    We propose an integrative approach that explains patterns of recruitment to adult populations in sessile organisms by considering the numbers of individuals and their body size. A recruitment model, based on a small number of parameters, was developed for sessile organisms and tested using the barnacle Semibalanus balanoides, a marine invertebrate inhabiting North Atlantic intertidal shores. Incorporating barnacle body size improved model fit beyond that based on density alone, showing that growth played an important role in how resource limitation affected survival. Our approach uncovered the following: First, changes in the shape of the recruitment curve resulted from the balance between individual growth and mortality. Second, recruitment was limited by the least plastic trait used to characterise body size, operculum area. Basal area, a trait that responded to increases in barnacle density, did not contribute significantly to explain patterns of recruitment. Third, some temporal variation is explained by changes in the amount of space occupied by shells of dead barnacles: at high cover barnacles are densely packed and these shells remain long after death. Fourth, seasonal variation and spatial variation in survival can be separated from that resulting from resource limitation; survival was predicted for two different shores and four sampling times using a single recruitment model. We conclude that applying this integrative approach to recruitment will lead to a considerable advance in understanding patterns of mortality of early stages of sessile organisms. PMID:23469247

  12. Model Organisms in G Protein-Coupled Receptor Research.

    PubMed

    Langenhan, Tobias; Barr, Maureen M; Bruchas, Michael R; Ewer, John; Griffith, Leslie C; Maiellaro, Isabella; Taghert, Paul H; White, Benjamin H; Monk, Kelly R

    2015-09-01

    The study of G protein-coupled receptors (GPCRs) has benefited greatly from experimental approaches that interrogate their functions in controlled, artificial environments. Working in vitro, GPCR receptorologists discovered the basic biologic mechanisms by which GPCRs operate, including their eponymous capacity to couple to G proteins; their molecular makeup, including the famed serpentine transmembrane unit; and ultimately, their three-dimensional structure. Although the insights gained from working outside the native environments of GPCRs have allowed for the collection of low-noise data, such approaches cannot directly address a receptor's native (in vivo) functions. An in vivo approach can complement the rigor of in vitro approaches: as studied in model organisms, it imposes physiologic constraints on receptor action and thus allows investigators to deduce the most salient features of receptor function. Here, we briefly discuss specific examples in which model organisms have successfully contributed to the elucidation of signals controlled through GPCRs and other surface receptor systems. We list recent examples that have served either in the initial discovery of GPCR signaling concepts or in their fuller definition. Furthermore, we selectively highlight experimental advantages, shortcomings, and tools of each model organism. PMID:25979002

  13. Multiscale modeling of metabolism, flows, and exchanges in heterogeneous organs

    PubMed Central

    Bassingthwaighte, James B.; Raymond, Gary M.; Butterworth, Erik; Alessio, Adam; Caldwell, James H.

    2010-01-01

    Large-scale models accounting for the processes supporting metabolism and function in an organ or tissue with a marked heterogeneity of flows and metabolic rates are computationally complex and tedious to compute. Their use in the analysis of data from positron emission tomography (PET) and magnetic resonance imaging (MRI) requires model reduction since the data are composed of concentration–time curves from hundreds of regions of interest (ROI) within the organ. Within each ROI, one must account for blood flow, intracapillary gradients in concentrations, transmembrane transport, and intracellular reactions. Using modular design, we configured a whole organ model, GENTEX, to allow adaptive usage for multiple reacting molecular species while omitting computation of unused components. The temporal and spatial resolution and the number of species are adaptable and the numerical accuracy and computational speed is adjustable during optimization runs, which increases accuracy and spatial resolution as convergence approaches. An application to the interpretation of PET image sequences after intravenous injection of 13NH3 provides functional image maps of regional myocardial blood flows. PMID:20201893

  14. Aging, Neurogenesis, and Caloric Restriction in Different Model Organisms

    PubMed Central

    Arslan-Ergul, Ayca; Ozdemir, A Tugrul; Adams, Michelle M

    2013-01-01

    Brain aging is a multifactorial process that is occurring across multiple cognitive domains. A significant complaint that occurs in the elderly is a decrement in learning and memory ability. Both rodents and zebrafish exhibit a similar problem with memory during aging. The neurobiological changes that underlie this cognitive decline are complex and undoubtedly influenced by many factors. Alterations in the birth of new neurons and neuron turnover may contribute to age-related cognitive problems. Caloric restriction is the only non-genetic intervention that reliably increases life span and healthspan across multiple organisms although the molecular mechanisms are not well-understood. Recently the zebrafish has become a popular model organism for understanding the neurobiological consequences but to date very little work has been performed. Similarly, few studies have examined the effects of dietary restriction in zebrafish. Here we review the literature related to memory decline, neurogenesis, and caloric restriction across model organisms and suggest that zebrafish has the potential to be an important animal model for understanding the complex interactions between age, neurobiological changes in the brain, and dietary regimens or their mimetics as interventions. PMID:23936746

  15. Model Organisms in G Protein–Coupled Receptor Research

    PubMed Central

    Barr, Maureen M.; Bruchas, Michael R.; Ewer, John; Griffith, Leslie C.; Maiellaro, Isabella; Taghert, Paul H.; White, Benjamin H.

    2015-01-01

    The study of G protein–coupled receptors (GPCRs) has benefited greatly from experimental approaches that interrogate their functions in controlled, artificial environments. Working in vitro, GPCR receptorologists discovered the basic biologic mechanisms by which GPCRs operate, including their eponymous capacity to couple to G proteins; their molecular makeup, including the famed serpentine transmembrane unit; and ultimately, their three-dimensional structure. Although the insights gained from working outside the native environments of GPCRs have allowed for the collection of low-noise data, such approaches cannot directly address a receptor’s native (in vivo) functions. An in vivo approach can complement the rigor of in vitro approaches: as studied in model organisms, it imposes physiologic constraints on receptor action and thus allows investigators to deduce the most salient features of receptor function. Here, we briefly discuss specific examples in which model organisms have successfully contributed to the elucidation of signals controlled through GPCRs and other surface receptor systems. We list recent examples that have served either in the initial discovery of GPCR signaling concepts or in their fuller definition. Furthermore, we selectively highlight experimental advantages, shortcomings, and tools of each model organism. PMID:25979002

  16. Resolving detailed molecular structures in complex organic mixtures and modeling their secondary organic aerosol formation

    NASA Astrophysics Data System (ADS)

    Goodman-Rendall, Kevin A. S.; Zhuang, Yang R.; Amirav, Aviv; Chan, Arthur W. H.

    2016-03-01

    Characterization of unresolved complex mixtures (UCMs) remains an ongoing challenge towards developing detailed and accurate inputs for modeling secondary organic aerosol (SOA) formation. Traditional techniques based on gas chromatography/electron impact-mass spectrometry induce excessive fragmentation, making it difficult to speciate and quantify isomers precisely. The goal of this study is to identify individual organic isomers by gas chromatography/mass spectrometry with supersonic molecular beam (SMB-GC/MS, also known as GC/MS with Cold EI) and to incorporate speciated isomers into an SOA model that accounts for the specific structures elucidated. Two samples containing atmospherically relevant UCMs are analyzed. The relative isomer distributions exhibit remarkably consistent trends across a wide range of carbon numbers. Constitutional isomers of different alkanes are speciated and individually quantified as linear, branched - for the first time by position of branching - multiply branched, or unsaturated - by degree of ring substitution and number of rings. Relative amounts of exact molecular structures are used as input parameters in an SOA box model to study the effects of molecular structures on SOA yields and volatility evolution. Highly substituted cyclic, mono-substituted cyclic, and linear species have the highest SOA yields while branched alkanes formed the least SOA. The rate of functionalization of a representative UCM is found to be in agreement with current volatility basis set (VBS) parameterizations based on detailed knowledge of composition and known oxidation mechanisms, confirming the validity of VBS parameters currently used in air quality models.

  17. Conceptual hierarchical modeling to describe wetland plant community organization

    USGS Publications Warehouse

    Little, A.M.; Guntenspergen, G.R.; Allen, T.F.H.

    2010-01-01

    Using multivariate analysis, we created a hierarchical modeling process that describes how differently-scaled environmental factors interact to affect wetland-scale plant community organization in a system of small, isolated wetlands on Mount Desert Island, Maine. We followed the procedure: 1) delineate wetland groups using cluster analysis, 2) identify differently scaled environmental gradients using non-metric multidimensional scaling, 3) order gradient hierarchical levels according to spatiotem-poral scale of fluctuation, and 4) assemble hierarchical model using group relationships with ordination axes and post-hoc tests of environmental differences. Using this process, we determined 1) large wetland size and poor surface water chemistry led to the development of shrub fen wetland vegetation, 2) Sphagnum and water chemistry differences affected fen vs. marsh / sedge meadows status within small wetlands, and 3) small-scale hydrologic differences explained transitions between forested vs. non-forested and marsh vs. sedge meadow vegetation. This hierarchical modeling process can help explain how upper level contextual processes constrain biotic community response to lower-level environmental changes. It creates models with more nuanced spatiotemporal complexity than classification and regression tree procedures. Using this process, wetland scientists will be able to generate more generalizable theories of plant community organization, and useful management models. ?? Society of Wetland Scientists 2009.

  18. Transferable Atomic Multipole Machine Learning Models for Small Organic Molecules.

    PubMed

    Bereau, Tristan; Andrienko, Denis; von Lilienfeld, O Anatole

    2015-07-14

    Accurate representation of the molecular electrostatic potential, which is often expanded in distributed multipole moments, is crucial for an efficient evaluation of intermolecular interactions. Here we introduce a machine learning model for multipole coefficients of atom types H, C, O, N, S, F, and Cl in any molecular conformation. The model is trained on quantum-chemical results for atoms in varying chemical environments drawn from thousands of organic molecules. Multipoles in systems with neutral, cationic, and anionic molecular charge states are treated with individual models. The models' predictive accuracy and applicability are illustrated by evaluating intermolecular interaction energies of nearly 1,000 dimers and the cohesive energy of the benzene crystal. PMID:26575759

  19. Modelling nitrous oxide emissions from organic soils in Europe

    NASA Astrophysics Data System (ADS)

    Leppelt, Thomas; Dechow, Rene; Gebbert, Sören; Freibauer, Annette

    2013-04-01

    The greenhouse gas emission potential of peatland ecosystems are mandatory for a complete annual emission budget in Europe. The GHG-Europe project aims to improve the modelling capabilities for greenhouse gases, e.g., nitrous oxide. The heterogeneous and event driven fluxes of nitrous oxide are challenging to model on European scale, especially regarding the upscaling purpose and certain parameter estimations. Due to these challenges adequate techniques are needed to create a robust empirical model. Therefore a literature study of nitrous oxide fluxes from organic soils has been carried out. This database contains flux data from boreal and temperate climate zones and covers the different land use categories: cropland, grassland, forest, natural and peat extraction sites. Especially managed crop- and grassland sites feature high emission potential. Generally nitrous oxide emissions increases significantly with deep drainage and intensive application of nitrogen fertilisation. Whereas natural peatland sites with a near surface groundwater table can act as nitrous oxide sink. An empirical fuzzy logic model has been applied to predict annual nitrous oxide emissions from organic soils. The calibration results in two separate models with best model performances for bogs and fens, respectively. The derived parameter combinations of these models contain mean groundwater table, nitrogen fertilisation, annual precipitation, air temperature, carbon content and pH value. Influences of the calibrated parameters on nitrous oxide fluxes are verified by several studies in literature. The extrapolation potential has been tested by an implemented cross validation. Furthermore the parameter ranges of the calibrated models are compared to occurring values on European scale. This avoid unknown systematic errors for the regionalisation purpose. Additionally a sensitivity analysis specify the model behaviour for each alternating parameter. The upscaling process for European peatland

  20. Measuring and modeling continuous quality distributions of soil organic matter

    NASA Astrophysics Data System (ADS)

    Bruun, S.; Gren, G. I. Ã.; Christensen, B. T.; Jensen, L. S.

    2010-01-01

    An understanding of the dynamics of soil organic matter (SOM) is important for our ability to develop management practices that preserve soil quality and sequester carbon. Most SOM decomposition models represent the heterogeneity of organic matter by a few discrete compartments with different turnover rates, while other models employ a continuous quality distribution. To make the multi-compartment models more mechanistic in nature, it has been argued that the compartments should be related to soil fractions actually occurring and having a functional role in the soil. In this paper, we make the case that fractionation methods that can measure continuous quality distributions should be developed, and that the temporal development of these distributions should be incorporated into SOM models. The measured continuous SOM quality distributions should hold valuable information not only for model development, but also for direct interpretation. Measuring continuous distributions requires that the measurements along the quality variable are so frequent that the distribution approaches the underlying continuum. Continuous distributions lead to possible simplifications of the model formulations, which considerably reduce the number of parameters needed to describe SOM turnover. A general framework for SOM models representing SOM across measurable quality distributions is presented and simplifications for specific situations are discussed. Finally, methods that have been used or have the potential to be used to measure continuous quality SOM distributions are reviewed. Generally, existing fractionation methods will have to be modified to allow measurement of distributions or new fractionation techniques will have to be developed. Developing the distributional models in concert with the fractionation methods to measure the distributions will be a major task. We hope the current paper will help generate the interest needed to accommodate this.

  1. Measuring and modelling continuous quality distributions of soil organic matter

    NASA Astrophysics Data System (ADS)

    Bruun, S.; Gren, G. I.; Christensen, B. T.; Jensen, L. S.

    2009-09-01

    An understanding of the dynamics of soil organic matter (SOM) is important for our ability to develop management practices that preserve soil quality and sequester carbon. Most SOM decomposition models represent the heterogeneity of organic matter by a few discrete compartments with different turnover rates, while other models employ a continuous quality distribution. To make the multi-compartment models more mechanistic in nature, it has been argued that the compartments should be related to soil fractions actually occurring and having a functional role in the soil. In this paper, we make the case that fractionation methods that can measure continuous quality distributions should be developed, and that the temporal development of these distributions should be incorporated into SOM models. The measured continuous SOM quality distributions should hold valuable information not only for model development, but also for direct interpretation. Measuring continuous distributions requires that the measurements along the quality variable are so frequent that the distribution is approaching the underlying continuum. Continuous distributions leads to possible simplifications of the model formulations, which considerably reduce the number of parameters needed to describe SOM turnover. A general framework for SOM models representing SOM across measurable quality distributions is presented and simplifications for specific situations are discussed. Finally, methods that have been used or have the potential to be used to measure continuous quality SOM distributions are reviewed. Generally, existing fractionation methods have to be modified to allow measurement of distributions or new fractionation techniques will have to be developed. Developing the distributional models in concert with the fractionation methods to measure the distributions will be a major task. We hope the current paper will help spawning the interest needed to accommodate this.

  2. Modeling organic aerosols during MILAGRO: importance of biogenic secondary organic aerosols

    NASA Astrophysics Data System (ADS)

    Hodzic, A.; Jimenez, J. L.; Madronich, S.; Aiken, A. C.; Bessagnet, B.; Curci, G.; Fast, J.; Lamarque, J.-F.; Onasch, T. B.; Roux, G.; Schauer, J. J.; Stone, E. A.; Ulbrich, I. M.

    2009-09-01

    The meso-scale chemistry-transport model CHIMERE is used to assess our understanding of major sources and formation processes leading to a fairly large amount of organic aerosols - OA, including primary OA (POA) and secondary OA (SOA) - observed in Mexico City during the MILAGRO field project (March 2006). Chemical analyses of submicron aerosols from aerosol mass spectrometers (AMS) indicate that organic particles found in the Mexico City basin contain a large fraction of oxygenated organic species (OOA) which have strong correspondence with SOA, and that their production actively continues downwind of the city. The SOA formation is modeled here by the one-step oxidation of anthropogenic (i.e. aromatics, alkanes), biogenic (i.e. monoterpenes and isoprene), and biomass-burning SOA precursors and their partitioning into both organic and aqueous phases. Conservative assumptions are made for uncertain parameters to maximize the amount of SOA produced by the model. The near-surface model evaluation shows that predicted OA correlates reasonably well with measurements during the campaign, however it remains a factor of 2 lower than the measured total OA. Fairly good agreement is found between predicted and observed POA within the city suggesting that anthropogenic and biomass burning emissions are reasonably captured. Consistent with previous studies in Mexico City, large discrepancies are encountered for SOA, with a factor of 2-10 model underestimate. When only anthropogenic SOA precursors were considered, the model was able to reproduce within a factor of two the sharp increase in OOA concentrations during the late morning at both urban and near-urban locations but the discrepancy increases rapidly later in the day, consistent with previous results, and is especially obvious when the column-integrated SOA mass is considered instead of the surface concentration. The increase in the missing SOA mass in the afternoon coincides with the sharp drop in POA suggesting a

  3. Model simulation of atrazine exposure to aquatic nontarget organisms

    SciTech Connect

    Williams, W.M.; Cheplick, J.M.; Balu, K.

    1996-10-01

    Pesticide fate and transport models have been identified by a number of regulatory work groups, including the Aquatic Risk Assessment and Mitigation Dialogue Group (ARAMDG) and the FIFRA Exposure Modeling Work Group (EMWG), as potential valuable tools in improving regulatory decisions for pesticide registration. To date, models uses have been limited to preliminary screening evaluations because the predictive capabilities of candidate models have not been adequately characterized and because procedures for scenario identification have not been tested. This paper presents an overview of a comprehensive modeling study that was conducted to evaluate exposure concentrations of atrazine to nontarget organisms and their ecosystems that may result from usage patterns of the herbicide throughout the United States. Simulations were conducted using the Pesticide Root Zone Model (PRZM-2.3) and the Riverine Environments Water Quality Model (RIVWQ-2.0). Included are procedures used for scenario identification, model comparisons to field runoff and aquatic monitoring studies, and the statistical compilation of results for risk assessment use.

  4. Spatiotemporal Organization of Spin-Coated Supported Model Membranes

    NASA Astrophysics Data System (ADS)

    Simonsen, Adam Cohen

    All cells of living organisms are separated from their surroundings and organized internally by means of flexible lipid membranes. In fact, there is consensus that the minimal requirements for self-replicating life processes include the following three features: (1) information carriers (DNA, RNA), (2) a metabolic system, and (3) encapsulation in a container structure [1]. Therefore, encapsulation can be regarded as an essential part of life itself. In nature, membranes are highly diverse interfacial structures that compartmentalize cells [2]. While prokaryotic cells only have an outer plasma membrane and a less-well-developed internal membrane structure, eukaryotic cells have a number of internal membranes associated with the organelles and the nucleus. Many of these membrane structures, including the plasma membrane, are complex layered systems, but with the basic structure of a lipid bilayer. Biomembranes contain hundreds of different lipid species in addition to embedded or peripherally associated membrane proteins and connections to scaffolds such as the cytoskeleton. In vitro, lipid bilayers are spontaneously self-organized structures formed by a large group of amphiphilic lipid molecules in aqueous suspensions. Bilayer formation is driven by the entropic properties of the hydrogen bond network in water in combination with the amphiphilic nature of the lipids. The molecular shapes of the lipid constituents play a crucial role in bilayer formation, and only lipids with approximately cylindrical shapes are able to form extended bilayers. The bilayer structure of biomembranes was discovered by Gorter and Grendel in 1925 [3] using monolayer studies of lipid extracts from red blood cells. Later, a number of conceptual models were developed to rationalize the organization of lipids and proteins in biological membranes. One of the most celebrated is the fluid-mosaic model by Singer and Nicolson (1972) [4]. According to this model, the lipid bilayer component of

  5. Multimedia transport of organic contaminants and exposure modeling

    SciTech Connect

    Layton, D.W.; McKone, T.E.

    1988-01-01

    Human exposures to organic contaminants in the environment are a complex function of human factors, physicochemical properties of the contaminants, and characteristics of the environmental media in which the contaminants reside. One subject of interest in the screening of organic chemicals for the purpose of identifying exposure pathways of potential concern is the relationship between exposures and contaminant properties. To study such relationships, a multimedia environmental model termed GEOTOX is used to predict the equilibrium partitioning and transport of ''reference'' organic chemicals between compartments representing different media (i.e., soil layers, ground water, air, biota, etc.) of a contaminated landscape. Reference chemicals, which are added to the surface soil of a landscape, are defined by properties consisting of the Henry's law constant, soil water-soil organic carbon partition coefficient, and bioconcentration factors. The steady-state concentrations of the chemical in the GEOTOX compartments are then used to estimate lifetime exposures (in mg/kg-d) to the compartments for individuals living in the contaminated landscape. Exposure pathways addressed include ingestion, inhalation, and dermal absorption. Local sensitivity analyses are performed to determine which chemical and landscape properties have the greatest effect on the exposure estimates. 9 refs., 4 figs., 3 tabs.

  6. Can the Equivalent Sphere Model Approximate Organ Doses in Space?

    NASA Technical Reports Server (NTRS)

    Lin, Zi-Wei

    2007-01-01

    For space radiation protection it is often useful to calculate dose or dose,equivalent in blood forming organs (BFO). It has been customary to use a 5cm equivalent sphere to. simulate the BFO dose. However, many previous studies have concluded that a 5cm sphere gives very different dose values from the exact BFO values. One study [1] . concludes that a 9 cm sphere is a reasonable approximation for BFO'doses in solar particle event environments. In this study we use a deterministic radiation transport [2] to investigate the reason behind these observations and to extend earlier studies. We take different space radiation environments, including seven galactic cosmic ray environments and six large solar particle events, and calculate the dose and dose equivalent in the skin, eyes and BFO using their thickness distribution functions from the CAM (Computerized Anatomical Man) model [3] The organ doses have been evaluated with a water or aluminum shielding of an areal density from 0 to 20 g/sq cm. We then compare with results from the equivalent sphere model and determine in which cases and at what radius parameters the equivalent sphere model is a reasonable approximation. Furthermore, we address why the equivalent sphere model is not a good approximation in some cases. For solar particle events, we find that the radius parameters for the organ dose equivalent increase significantly with the shielding thickness, and the model works marginally for BFO but is unacceptable for the eye or the skin. For galactic cosmic rays environments, the equivalent sphere model with an organ-specific constant radius parameter works well for the BFO dose equivalent, marginally well for the BFO dose and the dose equivalent of the eye or the skin, but is unacceptable for the dose of the eye or the skin. The ranges of the radius parameters are also being investigated, and the BFO radius parameters are found to be significantly, larger than 5 cm in all cases, consistent with the conclusion of

  7. Modeling uptake of hydrophobic organic contaminants into polyethylene passive samplers.

    PubMed

    Thompson, Jay M; Hsieh, Ching-Hong; Luthy, Richard G

    2015-02-17

    Single-phase passive samplers are gaining acceptance as a method to measure hydrophobic organic contaminant (HOC) concentration in water. Although the relationship between the HOC concentration in water and passive sampler is linear at equilibrium, mass transfer models are needed for nonequilibrium conditions. We report measurements of organochlorine pesticide diffusion and partition coefficients with respect to polyethylene (PE), and present a Fickian approach to modeling HOC uptake by PE in aqueous systems. The model is an analytic solution to Fick's second law applied through an aqueous diffusive boundary layer and a polyethylene layer. Comparisons of the model with existing methods indicate agreement at appropriate boundary conditions. Laboratory release experiments on the organochlorine pesticides DDT, DDE, DDD, and chlordane in well-mixed slurries support the model's applicability to aqueous systems. In general, the advantage of the model is its application in the cases of well-agitated systems, low values of polyethylene-water partioning coefficients, thick polyethylene relative to the boundary layer thickness, and/or short exposure times. Another significant advantage is the ability to estimate, or at least bound, the needed exposure time to reach a desired CPE without empirical model inputs. A further finding of this work is that polyethylene diffusivity does not vary by transport direction through the sampler thickness. PMID:25607420

  8. Self-Organized Criticality Model for Brain Plasticity

    NASA Astrophysics Data System (ADS)

    de Arcangelis, Lucilla; Perrone-Capano, Carla; Herrmann, Hans J.

    2006-01-01

    Networks of living neurons exhibit an avalanche mode of activity, experimentally found in organotypic cultures. Here we present a model that is based on self-organized criticality and takes into account brain plasticity, which is able to reproduce the spectrum of electroencephalograms (EEG). The model consists of an electrical network with threshold firing and activity-dependent synapse strengths. The system exhibits an avalanche activity in a power-law distribution. The analysis of the power spectra of the electrical signal reproduces very robustly the power-law behavior with the exponent 0.8, experimentally measured in EEG spectra. The same value of the exponent is found on small-world lattices and for leaky neurons, indicating that universality holds for a wide class of brain models.

  9. Modeling Evolution of Regulatory Networks in Artificial Organisms

    NASA Astrophysics Data System (ADS)

    Sánchez-Dehesa, Yolanda; Beslon, Guillaume; Peña, José-María

    2007-09-01

    Regulatory networks are not randomly connected. They are modular, scale-free networks and some motifs distribution is clearly different from random distribution. However, the evolutionary causes and consequences of this specific connectivity are mainly unknown. In this paper we propose Raevol, an integrative model to study the evolution of regulatory networks. While most existing models consider direct evolution of the regulatory network, Raevol integrates a realistic genotype-phenotype mapping where the genome undergo mutations that indirectly modify the genetic network. Moreover, the organisms are selected at the phenotype level (which is produced by the genome via the regulation network). Thus, in Raevol, the network only indirectly evolve and it can only be selected if its activity influences the phenotype. We plan to use this model to better understand the network evolution and to study the influence of networks topology on evolution.

  10. Genome Editing and Its Applications in Model Organisms

    PubMed Central

    Ma, Dongyuan; Liu, Feng

    2016-01-01

    Technological advances are important for innovative biological research. Development of molecular tools for DNA manipulation, such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and the clustered regularly-interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas), has revolutionized genome editing. These approaches can be used to develop potential therapeutic strategies to effectively treat heritable diseases. In the last few years, substantial progress has been made in CRISPR/Cas technology, including technical improvements and wide application in many model systems. This review describes recent advancements in genome editing with a particular focus on CRISPR/Cas, covering the underlying principles, technological optimization, and its application in zebrafish and other model organisms, disease modeling, and gene therapy used for personalized medicine. PMID:26762955

  11. ZFIN: enhancements and updates to the zebrafish model organism database

    PubMed Central

    Bradford, Yvonne; Conlin, Tom; Dunn, Nathan; Fashena, David; Frazer, Ken; Howe, Douglas G.; Knight, Jonathan; Mani, Prita; Martin, Ryan; Moxon, Sierra A. T.; Paddock, Holly; Pich, Christian; Ramachandran, Sridhar; Ruef, Barbara J.; Ruzicka, Leyla; Bauer Schaper, Holle; Schaper, Kevin; Shao, Xiang; Singer, Amy; Sprague, Judy; Sprunger, Brock; Van Slyke, Ceri; Westerfield, Monte

    2011-01-01

    ZFIN, the Zebrafish Model Organism Database, http://zfin.org, serves as the central repository and web-based resource for zebrafish genetic, genomic, phenotypic and developmental data. ZFIN manually curates comprehensive data for zebrafish genes, phenotypes, genotypes, gene expression, antibodies, anatomical structures and publications. A wide-ranging collection of web-based search forms and tools facilitates access to integrated views of these data promoting analysis and scientific discovery. Data represented in ZFIN are derived from three primary sources: curation of zebrafish publications, individual research laboratories and collaborations with bioinformatics organizations. Data formats include text, images and graphical representations. ZFIN is a dynamic resource with data added daily as part of our ongoing curation process. Software updates are frequent. Here, we describe recent additions to ZFIN including (i) enhanced access to images, (ii) genomic features, (iii) genome browser, (iv) transcripts, (v) antibodies and (vi) a community wiki for protocols and antibodies. PMID:21036866

  12. ZFIN, the Zebrafish Model Organism Database: updates and new directions

    PubMed Central

    Ruzicka, Leyla; Bradford, Yvonne M.; Frazer, Ken; Howe, Douglas G.; Paddock, Holly; Ramachandran, Sridhar; Singer, Amy; Toro, Sabrina; Van Slyke, Ceri E.; Eagle, Anne E.; Fashena, David; Kalita, Patrick; Knight, Jonathan; Mani, Prita; Martin, Ryan; Moxon, Sierra A. T.; Pich, Christian; Schaper, Kevin; Shao, Xiang; Westerfield, Monte

    2015-01-01

    The Zebrafish Model Organism Database (ZFIN; http://zfin.org) is the central resource for genetic and genomic data from zebrafish (Danio rerio) research. ZFIN staff curate detailed information about genes, mutants, genotypes, reporter lines, sequences, constructs, antibodies, knockdown reagents, expression patterns, phenotypes, gene product function, and orthology from publications. Researchers can submit mutant, transgenic, expression, and phenotype data directly to ZFIN and use the ZFIN Community Wiki to share antibody and protocol information. Data can be accessed through topic-specific searches, a new site-wide search, and the data-mining resource ZebrafishMine (http://zebrafishmine.org). Data download and web service options are also available. ZFIN collaborates with major bioinformatics organizations to verify and integrate genomic sequence data, provide nomenclature support, establish reciprocal links and participate in the development of standardized structured vocabularies (ontologies) used for data annotation and searching. ZFIN-curated gene, function, expression, and phenotype data are available for comparative exploration at several multi-species resources. The use of zebrafish as a model for human disease is increasing. ZFIN is supporting this growing area with three major projects: adding easy access to computed orthology data from gene pages, curating details of the gene expression pattern changes in mutant fish, and curating zebrafish models of human diseases. PMID:26097180

  13. ZFIN, The zebrafish model organism database: Updates and new directions.

    PubMed

    Ruzicka, Leyla; Bradford, Yvonne M; Frazer, Ken; Howe, Douglas G; Paddock, Holly; Ramachandran, Sridhar; Singer, Amy; Toro, Sabrina; Van Slyke, Ceri E; Eagle, Anne E; Fashena, David; Kalita, Patrick; Knight, Jonathan; Mani, Prita; Martin, Ryan; Moxon, Sierra A T; Pich, Christian; Schaper, Kevin; Shao, Xiang; Westerfield, Monte

    2015-08-01

    The Zebrafish Model Organism Database (ZFIN; http://zfin.org) is the central resource for genetic and genomic data from zebrafish (Danio rerio) research. ZFIN staff curate detailed information about genes, mutants, genotypes, reporter lines, sequences, constructs, antibodies, knockdown reagents, expression patterns, phenotypes, gene product function, and orthology from publications. Researchers can submit mutant, transgenic, expression, and phenotype data directly to ZFIN and use the ZFIN Community Wiki to share antibody and protocol information. Data can be accessed through topic-specific searches, a new site-wide search, and the data-mining resource ZebrafishMine (http://zebrafishmine.org). Data download and web service options are also available. ZFIN collaborates with major bioinformatics organizations to verify and integrate genomic sequence data, provide nomenclature support, establish reciprocal links, and participate in the development of standardized structured vocabularies (ontologies) used for data annotation and searching. ZFIN-curated gene, function, expression, and phenotype data are available for comparative exploration at several multi-species resources. The use of zebrafish as a model for human disease is increasing. ZFIN is supporting this growing area with three major projects: adding easy access to computed orthology data from gene pages, curating details of the gene expression pattern changes in mutant fish, and curating zebrafish models of human diseases. PMID:26097180

  14. Contemporary model of language organization: an overview for neurosurgeons.

    PubMed

    Chang, Edward F; Raygor, Kunal P; Berger, Mitchel S

    2015-02-01

    Classic models of language organization posited that separate motor and sensory language foci existed in the inferior frontal gyrus (Broca's area) and superior temporal gyrus (Wernicke's area), respectively, and that connections between these sites (arcuate fasciculus) allowed for auditory-motor interaction. These theories have predominated for more than a century, but advances in neuroimaging and stimulation mapping have provided a more detailed description of the functional neuroanatomy of language. New insights have shaped modern network-based models of speech processing composed of parallel and interconnected streams involving both cortical and subcortical areas. Recent models emphasize processing in "dorsal" and "ventral" pathways, mediating phonological and semantic processing, respectively. Phonological processing occurs along a dorsal pathway, from the posterosuperior temporal to the inferior frontal cortices. On the other hand, semantic information is carried in a ventral pathway that runs from the temporal pole to the basal occipitotemporal cortex, with anterior connections. Functional MRI has poor positive predictive value in determining critical language sites and should only be used as an adjunct for preoperative planning. Cortical and subcortical mapping should be used to define functional resection boundaries in eloquent areas and remains the clinical gold standard. In tracing the historical advancements in our understanding of speech processing, the authors hope to not only provide practicing neurosurgeons with additional information that will aid in surgical planning and prevent postoperative morbidity, but also underscore the fact that neurosurgeons are in a unique position to further advance our understanding of the anatomy and functional organization of language. PMID:25423277

  15. Molecular simulation of a model of dissolved organic matter

    SciTech Connect

    Sutton, Rebecca; Sposito, Garrison; Diallo, Mamadou S.; Schulten,Hans-Rolf

    2004-11-08

    A series of atomistic simulations was performed to assess the ability of the Schulten dissolved organic matter (DOM) molecule, a well-established model humic molecule, to reproduce the physical and chemical behavior of natural humic substances. The unhydrated DOM molecule had a bulk density value appropriate to humic matter, but its Hildebrand solubility parameter was lower than the range of current experimental estimates. Under hydrated conditions, the DOM molecule went through conformational adjustments that resulted in disruption of intramolecular hydrogen bonds (H-bonds), although few water molecules penetrated the organic interior. The radius of gyration of the hydrated DOM molecule was similar to those measured for aquatic humic substances. To simulate humic materials under aqueous conditions with varying pH levels, carboxyl groups were deprotonated, and hydrated Na{sup +} or Ca{sup 2+} were added to balance the resulting negative charge. Because of intrusion of the cation hydrates, the model metal- humic structures were more porous, had greater solvent-accessible surface areas, and formed more H-bonds with water than the protonated, hydrated DOM molecule. Relative to Na{sup +}, Ca{sup 2+} was both more strongly bound to carboxylate groups and more fully hydrated. This difference was attributed to the higher charge of the divalent cation. The Ca-DOM hydrate, however, featured fewer H-bonds than the Na-DOM hydrate, perhaps because of the reduced orientational freedom of organic moieties and water molecules imposed by Ca{sup 2+}. The present work is, to our knowledge, the first rigorous computational exploration regarding the behavior of a model humic molecule under a range of physical conditions typical of soil and water systems.

  16. A Revised Iranian Model of Organ Donation as an Answer to the Current Organ Shortage Crisis.

    PubMed

    Hamidian Jahromi, Alireza; Fry-Revere, Sigrid; Bastani, Bahar

    2015-09-01

    Kidney transplantation has become the treatment of choice for patients with end-stage renal disease. Six decades of success in the field of transplantation have made it possible to save thousands of lives every year. Unfortunately, in recent years success has been overshadowed by an ever-growing shortage of organs. In the United States, there are currently more than 100 000 patients waiting for kidneys. However, the supply of kidneys (combined cadaveric and live donations) has stagnated around 17 000 per year. The ever-widening gap between demand and supply has resulted in an illegal black market and unethical transplant tourism of global proportions. While we believe there is much room to improve the Iranian model of regulated incentivized live kidney donation, with some significant revisions, the Iranian Model could serve as an example for how other countries could make significant strides to lessening their own organ shortage crises. PMID:26338158

  17. Chemotaxis of a model organism: progress with Dictyostelium.

    PubMed

    Nichols, John Me; Veltman, Douwe; Kay, Robert R

    2015-10-01

    Model organisms have been key to understanding many core biological processes. Dictyostelium amoebae have the attributes required to perform this role for chemotaxis, and by providing an evolutionary distant reference point to mammalian cells, they allow the central features of chemotaxis to be discerned. Here we highlight progress with Dictyostelium in understanding: pseudopod and bleb driven movement; the role of the actin cytoskeleton; chemotactic signal processing, including how cells adapt to background stimulation, and the controversial role of PIP3. Macropinocytosis and the axenic mutations are raised as potential confounding factors, while the identification of new players through proteomics holds great promise. PMID:26183444

  18. Transmission electron microscopy of a model crystalline organic, theophylline

    NASA Astrophysics Data System (ADS)

    Cattle, J.; S'ari, M.; Hondow, N.; Abellán, P.; Brown, A. P.; Brydson, R. M. D.

    2015-10-01

    We report on the use of transmission electron microscopy (TEM) to analyse the diffraction patterns of the model crystalline organic theophylline to investigate beam damage in relation to changing accelerating voltage, sample temperature and TEM grid support films. We find that samples deposited on graphene film grids have the longest lifetimes when also held at -190 °C and imaged at 200 kV accelerating voltage. Finally, atomic lattice images are obtained in bright field STEM by working close to the estimated critical electron dose for theophylline.

  19. Flow simulations on an organ pipe foot model.

    PubMed

    Vaik, István; Paál, György

    2013-02-01

    The present paper shows numerical simulations of the flow responsible for the sound generation in an organ pipe. Only the foot model of the organ pipe (i.e., with the resonator detached) is investigated by two-dimensional incompressible CFD simulations. It is shown that in spite of the moderately high Reynolds number (Re≈2350) no turbulence modeling is necessary. Free jet simulation (foot model without the upper lip) showed that the jet oscillates due to its natural instability. The velocity profile, the centerline and the width of the jet is determined at different heights above the flue. Edge tone simulations (foot model with the upper lip) were carried out having the upper lip at a constant height but at different x positions. It was found that the strongest and most stable edge tone oscillation occurs if the lower left corner of the upper lip is in the centerline of the jet (optimum position). When the upper lip is far from its optimum position the oscillation of the jet is rather due to the natural instability of the jet than the edge tone phenomenon. The results agree well with the experimental results of Außerlechner et al. [J. Acoust. Soc. Am. 126, 878-886 (2009)] and Außerlechner (Ph.D. thesis, Universität Stuttgart, Stuttgart, Germany) and with former results of the authors [Paál and Vaik, Int. J. Heat Fluid Flow 28, 575-586 (2007); Paál and Vaik, in Conference on Modelling Fluid Flow (CMFF'09), Budapest, Hungary]. PMID:23363125

  20. Modeling the economics of landfilling organic processing waste streams

    NASA Astrophysics Data System (ADS)

    Rosentrater, Kurt A.

    2005-11-01

    As manufacturing industries become more cognizant of the ecological effects that their firms have on the surrounding environment, their waste streams are increasingly becoming viewed not only as materials in need of disposal, but also as resources that can be reused, recycled, or reprocessed into valuable products. Within the food processing sector are many examples of various liquid, sludge, and solid biological and organic waste streams that require remediation. Alternative disposal methods for food and other bio-organic manufacturing waste streams are increasingly being investigated. Direct shipping, blending, extrusion, pelleting, and drying are commonly used to produce finished human food, animal feed, industrial products, and components ready for further manufacture. Landfilling, the traditional approach to waste remediation, however, should not be dismissed entirely. It does provide a baseline to which all other recycling and reprocessing options should be compared. This paper discusses the implementation of a computer model designed to examine the economics of landfilling bio-organic processing waste streams. Not only are these results applicable to food processing operations, but any industrial or manufacturing firm would benefit from examining the trends discussed here.

  1. A Multiagent Modeling Environment for Simulating Work Practice in Organizations

    NASA Technical Reports Server (NTRS)

    Sierhuis, Maarten; Clancey, William J.; vanHoof, Ron

    2004-01-01

    In this paper we position Brahms as a tool for simulating organizational processes. Brahms is a modeling and simulation environment for analyzing human work practice, and for using such models to develop intelligent software agents to support the work practice in organizations. Brahms is the result of more than ten years of research at the Institute for Research on Learning (IRL), NYNEX Science & Technology (the former R&D institute of the Baby Bell telephone company in New York, now Verizon), and for the last six years at NASA Ames Research Center, in the Work Systems Design and Evaluation group, part of the Computational Sciences Division (Code IC). Brahms has been used on more than ten modeling and simulation research projects, and recently has been used as a distributed multiagent development environment for developing work practice support tools for human in-situ science exploration on planetary surfaces, in particular a human mission to Mars. Brahms was originally conceived of as a business process modeling and simulation tool that incorporates the social systems of work, by illuminating how formal process flow descriptions relate to people s actual located activities in the workplace. Our research started in the early nineties as a reaction to experiences with work process modeling and simulation . Although an effective tool for convincing management of the potential cost-savings of the newly designed work processes, the modeling and simulation environment was only able to describe work as a normative workflow. However, the social systems, uncovered in work practices studied by the design team played a significant role in how work actually got done-actual lived work. Multi- tasking, informal assistance and circumstantial work interactions could not easily be represented in a tool with a strict workflow modeling paradigm. In response, we began to develop a tool that would have the benefits of work process modeling and simulation, but be distinctively able to

  2. Modeling financial markets by self-organized criticality

    NASA Astrophysics Data System (ADS)

    Biondo, Alessio Emanuele; Pluchino, Alessandro; Rapisarda, Andrea

    2015-10-01

    We present a financial market model, characterized by self-organized criticality, that is able to generate endogenously a realistic price dynamics and to reproduce well-known stylized facts. We consider a community of heterogeneous traders, composed by chartists and fundamentalists, and focus on the role of informative pressure on market participants, showing how the spreading of information, based on a realistic imitative behavior, drives contagion and causes market fragility. In this model imitation is not intended as a change in the agent's group of origin, but is referred only to the price formation process. We introduce in the community also a variable number of random traders in order to study their possible beneficial role in stabilizing the market, as found in other studies. Finally, we also suggest some counterintuitive policy strategies able to dampen fluctuations by means of a partial reduction of information.

  3. Models of charge pair generation in organic solar cells.

    PubMed

    Few, Sheridan; Frost, Jarvist M; Nelson, Jenny

    2015-01-28

    Efficient charge pair generation is observed in many organic photovoltaic (OPV) heterojunctions, despite nominal electron-hole binding energies which greatly exceed the average thermal energy. Empirically, the efficiency of this process appears to be related to the choice of donor and acceptor materials, the resulting sequence of excited state energy levels and the structure of the interface. In order to establish a suitable physical model for the process, a range of different theoretical studies have addressed the nature and energies of the interfacial states, the energetic profile close to the heterojunction and the dynamics of excited state transitions. In this paper, we review recent developments underpinning the theory of charge pair generation and phenomena, focussing on electronic structure calculations, electrostatic models and approaches to excited state dynamics. We discuss the remaining challenges in achieving a predictive approach to charge generation efficiency. PMID:25462189

  4. Self-organization in a simple brain model

    SciTech Connect

    Stassinopoulos, D.; Bak, P.; Alstroem, P.

    1994-03-10

    Simulations on a simple model of the brain are presented. The model consists of a set of randomly connected neurons. Inputs and outputs are also connected randomly to a subset of neurons. For each input there is a set of output neurons which must fire in order to achieve success. A signal giving information as to whether or not the action was successful is fed back to the brain from the environment. The connections between firing neurons are strengthened or weakened according to whether or not the action was successful. The system learns, through a self-organization process, to react intelligently to input signals, i.e. it learns to quickly select the correct output for each input. If part of the network is damaged, the system relearns the correct response after a training period.

  5. [Volvox (Chlorophyta, Volvocales) as a model organism in developmental biology].

    PubMed

    Desnitskiĭ, A G

    2009-01-01

    Model systems based on two or more related species with different types of development are finding increasing use in current comparative embryology. Green algae of the genus Volvox offer an interesting opportunity to study sex pheromones, morphogenesis as well as the formation of a somatic cell line undergoing terminal differentiation, senescence, and death as well as a line of reproductive cells, which at first grow and then undergo a series of consecutive divisions that give rise to new organisms. However, almost all studies of the recent years were conducted on a single species, Volvox carteri f. nagariensis. The goal of this publication was to advertise the cosmopolitan alga V. aureus as a model species in developmental biology. Published data on V. aureus are briefly reviewed in comparison with the development of V. carteri and outlooks of further studies are specified. In particular, the expediency of collecting new V. aureus strains from nature to study their development in clonal culture is outlined. PMID:19705761

  6. Partitioning of Nanoparticles into Organic Phases and Model Cells

    SciTech Connect

    Posner, J.D.; Westerhoff, P.; Hou, W-C.

    2011-08-25

    There is a recognized need to understand and predict the fate, transport and bioavailability of engineered nanoparticles (ENPs) in aquatic and soil ecosystems. Recent research focuses on either collection of empirical data (e.g., removal of a specific NP through water or soil matrices under variable experimental conditions) or precise NP characterization (e.g. size, degree of aggregation, morphology, zeta potential, purity, surface chemistry, and stability). However, it is almost impossible to transition from these precise measurements to models suitable to assess the NP behavior in the environment with complex and heterogeneous matrices. For decades, the USEPA has developed and applies basic partitioning parameters (e.g., octanol-water partition coefficients) and models (e.g., EPI Suite, ECOSAR) to predict the environmental fate, bioavailability, and toxicity of organic pollutants (e.g., pesticides, hydrocarbons, etc.). In this project we have investigated the hypothesis that NP partition coefficients between water and organic phases (octanol or lipid bilayer) is highly dependent on their physiochemical properties, aggregation, and presence of natural constituents in aquatic environments (salts, natural organic matter), which may impact their partitioning into biological matrices (bioaccumulation) and human exposure (bioavailability) as well as the eventual usage in modeling the fate and bioavailability of ENPs. In this report, we use the terminology "partitioning" to operationally define the fraction of ENPs distributed among different phases. The mechanisms leading to this partitioning probably involve both chemical force interactions (hydrophobic association, hydrogen bonding, ligand exchange, etc.) and physical forces that bring the ENPs in close contact with the phase interfaces (diffusion, electrostatic interactions, mixing turbulence, etc.). Our work focuses on partitioning, but also provides insight into the relative behavior of ENPs as either "more like

  7. A MULTISCALE MODEL OF THE ORGAN OF CORTI

    PubMed Central

    Steele, Charles R.; Boutet de Monvel, Jacques; Puria, Sunil

    2010-01-01

    The organ of Corti is the sensory epithelium in the cochlea of the inner ear. It is modeled as a shell-of-revolution structure with continuous and discrete components. Our recent work has been on the inclusion of the viscous fluid. Measurements from various laboratories provide the opportunity to refocus on the elastic properties. The current detailed model for the organ of Corti is reasonably consistent with diverse measurements. Most components have little stiffness in the propagation direction. However, the isotropic stiffness of the pillar heads is found to offer an explanation for the difference in point load and pressure measurements. The individual rows of inner hair cell stereocilia with tip links and the Hensen stripe are included, since these details are important for the determination of the neural excitation. The results for low frequency show a phase of tip link tension similar to auditory nerve measurements. The nonlinearity of fluid in the small gaps is considered. A result is that as amplitude increases, because of the near contact with the Hensen stripe, the excitation changes polarity, similar to the peak-splitting neural behavior sometimes observed. PMID:20485573

  8. Adaptive self-organization in a realistic neural network model

    NASA Astrophysics Data System (ADS)

    Meisel, Christian; Gross, Thilo

    2009-12-01

    Information processing in complex systems is often found to be maximally efficient close to critical states associated with phase transitions. It is therefore conceivable that also neural information processing operates close to criticality. This is further supported by the observation of power-law distributions, which are a hallmark of phase transitions. An important open question is how neural networks could remain close to a critical point while undergoing a continual change in the course of development, adaptation, learning, and more. An influential contribution was made by Bornholdt and Rohlf, introducing a generic mechanism of robust self-organized criticality in adaptive networks. Here, we address the question whether this mechanism is relevant for real neural networks. We show in a realistic model that spike-time-dependent synaptic plasticity can self-organize neural networks robustly toward criticality. Our model reproduces several empirical observations and makes testable predictions on the distribution of synaptic strength, relating them to the critical state of the network. These results suggest that the interplay between dynamics and topology may be essential for neural information processing.

  9. Self-Organizing Hidden Markov Model Map (SOHMMM).

    PubMed

    Ferles, Christos; Stafylopatis, Andreas

    2013-12-01

    A hybrid approach combining the Self-Organizing Map (SOM) and the Hidden Markov Model (HMM) is presented. The Self-Organizing Hidden Markov Model Map (SOHMMM) establishes a cross-section between the theoretic foundations and algorithmic realizations of its constituents. The respective architectures and learning methodologies are fused in an attempt to meet the increasing requirements imposed by the properties of deoxyribonucleic acid (DNA), ribonucleic acid (RNA), and protein chain molecules. The fusion and synergy of the SOM unsupervised training and the HMM dynamic programming algorithms bring forth a novel on-line gradient descent unsupervised learning algorithm, which is fully integrated into the SOHMMM. Since the SOHMMM carries out probabilistic sequence analysis with little or no prior knowledge, it can have a variety of applications in clustering, dimensionality reduction and visualization of large-scale sequence spaces, and also, in sequence discrimination, search and classification. Two series of experiments based on artificial sequence data and splice junction gene sequences demonstrate the SOHMMM's characteristics and capabilities. PMID:24001407

  10. Terrestrial and marine perspectives on modeling organic matter degradation pathways.

    PubMed

    Burd, Adrian B; Frey, Serita; Cabre, Anna; Ito, Takamitsu; Levine, Naomi M; Lønborg, Christian; Long, Matthew; Mauritz, Marguerite; Thomas, R Quinn; Stephens, Brandon M; Vanwalleghem, Tom; Zeng, Ning

    2016-01-01

    Organic matter (OM) plays a major role in both terrestrial and oceanic biogeochemical cycles. The amount of carbon stored in these systems is far greater than that of carbon dioxide (CO2 ) in the atmosphere, and annual fluxes of CO2 from these pools to the atmosphere exceed those from fossil fuel combustion. Understanding the processes that determine the fate of detrital material is important for predicting the effects that climate change will have on feedbacks to the global carbon cycle. However, Earth System Models (ESMs) typically utilize very simple formulations of processes affecting the mineralization and storage of detrital OM. Recent changes in our view of the nature of this material and the factors controlling its transformation have yet to find their way into models. In this review, we highlight the current understanding of the role and cycling of detrital OM in terrestrial and marine systems and examine how this pool of material is represented in ESMs. We include a discussion of the different mineralization pathways available as organic matter moves from soils, through inland waters to coastal systems and ultimately into open ocean environments. We argue that there is strong commonality between aspects of OM transformation in both terrestrial and marine systems and that our respective scientific communities would benefit from closer collaboration. PMID:26015089

  11. The hamster flank organ model: Is it relevant to man

    SciTech Connect

    Franz, T.J.; Lehman, P.A.; Pochi, P.; Odland, G.F.; Olerud, J. )

    1989-10-01

    The critical role that androgens play in the etiology of acne has led to a search for topically active antiandrogens and the frequent use of the flank organ of the golden Syrian hamster as an animal model. 17-alpha-propyltestosterone (17-PT) has been identified as having potent antiandrogenic activity in the hamster model, and this report describes its clinical evaluation. Two double-blind placebo controlled studies comparing 4% 17-PT in 80% alcohol versus vehicle alone were conducted. One study examined 17-PT sebosuppressive activity in 20 subjects. The second study examined its efficacy in 44 subjects having mild to moderate acne. A third study measured in vitro percutaneous absorption of 17-PT through hamster flank and monkey skin, and human face skin in-vivo, using radioactive drug. 17-PT was found to be ineffective in reducing either the sebum excretion rate or the number of inflammatory acne lesions. Failure of 17-PT to show clinical activity was not a result of poor percutaneous absorption. Total absorption in man was 7.7% of the dose and only 1.0% in the hamster. The sebaceous gland of hamster flank organ is apparently more sensitive to antiandrogens than the human sebaceous gland.

  12. Xenbase: expansion and updates of the Xenopus model organism database

    PubMed Central

    James-Zorn, Christina; Ponferrada, Virgilio G.; Jarabek, Chris J.; Burns, Kevin A.; Segerdell, Erik J.; Lee, Jacqueline; Snyder, Kevin; Bhattacharyya, Bishnu; Karpinka, J. Brad; Fortriede, Joshua; Bowes, Jeff B.; Zorn, Aaron M.; Vize, Peter D.

    2013-01-01

    Xenbase (http://www.xenbase.org) is a model organism database that provides genomic, molecular, cellular and developmental biology content to biomedical researchers working with the frog, Xenopus and Xenopus data to workers using other model organisms. As an amphibian Xenopus serves as a useful evolutionary bridge between invertebrates and more complex vertebrates such as birds and mammals. Xenbase content is collated from a variety of external sources using automated and semi-automated pipelines then processed via a combination of automated and manual annotation. A link-matching system allows for the wide variety of synonyms used to describe biological data on unique features, such as a gene or an anatomical entity, to be used by the database in an equivalent manner. Recent updates to the database include the Xenopus laevis genome, a new Xenopus tropicalis genome build, epigenomic data, collections of RNA and protein sequences associated with genes, more powerful gene expression searches, a community and curated wiki, an extensive set of manually annotated gene expression patterns and a new database module that contains data on over 700 antibodies that are useful for exploring Xenopus cell and developmental biology. PMID:23125366

  13. Modeling of the accumulation of organic lipophilic chemicals in earthworms

    SciTech Connect

    Belfroid, A.; Seinen, W.; Leeuwen, K. van; Hermens, J.; Gestel, K. van

    1994-12-31

    For aquatic and terrestrial species living in contaminated sediments and soils it is assumed that the major route of uptake of organic lipophilic compounds is by passive diffusion of the compound dissolved in the interstitial water. Dietary uptake will only be important for extremely lipophilic compounds with log K{sub ow} larger than 5--6. An accumulation study with earthworms in OECD artificial soil confirmed this hypothesis. However, the authors also observed dietary uptake in earthworms after feeding them with food contaminated with three chlorobenzenes, PCB153 and octachloronaphthalene. Still, the question remained whether dietary uptake is an important route of exposure. Therefore, a model was developed that, unlike for example the equilibrium partition theory, incorporates two routes of uptake. The model can be used to estimate the accumulation of inert organic chemicals with log Kow 2--7 in earthworms, but also to determine the relative contribution of the two routes of uptake to the total body burden. It will be shown that the relative contribution depends on the lipophilicity of the compound and also on the type of soil.

  14. Digital gene expression for non-model organisms.

    PubMed

    Hong, Lewis Z; Li, Jun; Schmidt-Küntzel, Anne; Warren, Wesley C; Barsh, Gregory S

    2011-11-01

    Next-generation sequencing technologies offer new approaches for global measurements of gene expression but are mostly limited to organisms for which a high-quality assembled reference genome sequence is available. We present a method for gene expression profiling called EDGE, or EcoP15I-tagged Digital Gene Expression, based on ultra-high-throughput sequencing of 27-bp cDNA fragments that uniquely tag the corresponding gene, thereby allowing direct quantification of transcript abundance. We show that EDGE is capable of assaying for expression in >99% of genes in the genome and achieves saturation after 6-8 million reads. EDGE exhibits very little technical noise, reveals a large (10(6)) dynamic range of gene expression, and is particularly suited for quantification of transcript abundance in non-model organisms where a high-quality annotated genome is not available. In a direct comparison with RNA-seq, both methods provide similar assessments of relative transcript abundance, but EDGE does better at detecting gene expression differences for poorly expressed genes and does not exhibit transcript length bias. Applying EDGE to laboratory mice, we show that a loss-of-function mutation in the melanocortin 1 receptor (Mc1r), recognized as a Mendelian determinant of yellow hair color in many different mammals, also causes reduced expression of genes involved in the interferon response. To illustrate the application of EDGE to a non-model organism, we examine skin biopsy samples from a cheetah (Acinonyx jubatus) and identify genes likely to control differences in the color of spotted versus non-spotted regions. PMID:21844123

  15. Modeling organic aerosols during MILAGRO: application of the CHIMERE model and importance of biogenic secondary organic aerosols

    NASA Astrophysics Data System (ADS)

    Hodzic, A.; Jimenez, J. L.; Madronich, S.; Aiken, A. C.; Bessagnet, B.; Curci, G.; Fast, J.; Lamarque, J. F.; Onasch, T. B.; Roux, G.; Ulbrich, I. M.

    2009-05-01

    The meso-scale chemistry-transport model CHIMERE is used to assess our understanding of major sources and formation processes leading to a fairly large amount of organic aerosols (OA, including primary OA (POA) and secondary OA (SOA)) observed in Mexico City during the MILAGRO field project (March 2006). Chemical analyses of submicron aerosols from aerosol mass spectrometers (AMS) indicate that organic particles found in the Mexico City basin contain a large fraction of oxygenated organic species (OOA) which have strong correspondence with SOA, and that their production actively continues downwind of the city. The SOA formation is modeled here by the one-step oxidation of anthropogenic (i.e. aromatics, alkanes), biogenic (i.e. monoterpenes and isoprene), and biomass-burning SOA precursors and their partitioning into both organic and aqueous phases. The near-surface model evaluation shows that predicted OA correlates reasonably well with measurements during the campaign, however it remains a factor of 2 lower than the measured total OA. Fairly good agreement is found between predicted and observed POA within the city suggesting that anthropogenic and biomass burning emissions are reasonably captured. Consistent with previous studies in Mexico City, large discrepancies are encountered for SOA, with a factor of 2-10 model underestimate. When only anthropogenic SOA precursors were considered, the model was able to reproduce within a factor of two the sharp increase in SOA concentrations during the late morning at both urban and near-urban locations but the discrepancy increases rapidly later in the day, consistent with previous results, and is especially obvious when the column-integrated SOA mass is considered instead of the surface concentration. The increase in the missing SOA mass in the afternoon coincides with the sharp drop in POA suggesting a tendency of the model to excessively evaporate the freshly formed SOA. Predicted SOA concentrations in our base case

  16. Modeling emissions of volatile organic compounds from new carpets

    NASA Astrophysics Data System (ADS)

    Little, John C.; Hodgson, Alfred T.; Gadgil, Ashok J.

    A simple model is proposed to account for observed emissions of volatile organic compounds (VOCs) from new carpets. The model assumes that the VOCs originate predominantly in a uniform slab of polymer backing material. Parameters for the model (the initial concentration of a VOC in the polymer, a diffusion coefficient and an equilibrium polymer/air partition coefficient) are obtained from experimental data produced by a previous chamber study. The diffusion coefficients generally decrease as the molecular weight of the VOCs increase, while the partition coefficients generally increase as the vapor pressure of the compounds decreases. In addition, for two of the study carpets that have a styrene-butadiene rubber (SBR) backing, the diffusion and partition coefficients are similar to independently reported values for SBR. The results suggest that prediction of VOC emissions from new carpets may be possible based solely on a knowledge of the physical properties of the relevant compounds and the carpet backing material. However, a more rigorous validation of the model is desirable.

  17. Modeling Emissions of Volatile Organic Compounds from New Carpets

    SciTech Connect

    Little, J.C.; Hodgson, A.T.; Gadgil, A.J.

    1993-02-01

    A simple model is proposed to account for observed emissions of volatile organic compounds (VOCs) from new carpets. The model assumes that the VOCs originate predominantly in a uniform slab of polymer backing material. Parameters for the model (the initial concentration of a VOC in the polymer, a diffusion coefficient and an equilibrium polymer/air partition coefficient) are obtained from experimental data produced by a previous chamber study. The diffusion coefficients generally decrease as the molecular weight of the VOCs increase, while the polymer/air partition coefficients generally increase as the vapor pressure of the compounds decrease. In addition, for two of the study carpets that have a styrene-butadiene rubber (SBR) backing, the diffusion and partition coefficients are similar to independently reported values for SBR. The results suggest that predictions of VOCs emissions from new carpets may be possible based solely on a knowledge of the physical properties of the relevant compounds and the carpet backing material. However, a more rigorous validation of the model is desirable.

  18. Mathematical modeling of wastewater-derived biodegradable dissolved organic nitrogen.

    PubMed

    Simsek, Halis

    2016-11-01

    Wastewater-derived dissolved organic nitrogen (DON) typically constitutes the majority of total dissolved nitrogen (TDN) discharged to surface waters from advanced wastewater treatment plants (WWTPs). When considering the stringent regulations on nitrogen discharge limits in sensitive receiving waters, DON becomes problematic and needs to be reduced. Biodegradable DON (BDON) is a portion of DON that is biologically degradable by bacteria when the optimum environmental conditions are met. BDON in a two-stage trickling filter WWTP was estimated using artificial intelligence techniques, such as adaptive neuro-fuzzy inference systems, multilayer perceptron, radial basis neural networks (RBNN), and generalized regression neural networks. Nitrite, nitrate, ammonium, TDN, and DON data were used as input neurons. Wastewater samples were collected from four different locations in the plant. Model performances were evaluated using root mean square error, mean absolute error, mean bias error, and coefficient of determination statistics. Modeling results showed that the R(2) values were higher than 0.85 in all four models for all wastewater samples, except only R(2) in the final effluent sample for RBNN modeling was low (0.52). Overall, it was found that all four computing techniques could be employed successfully to predict BDON. PMID:27019968

  19. Dynamical Models of Task Organization in Social Insect Colonies.

    PubMed

    Kang, Yun; Theraulaz, Guy

    2016-05-01

    The organizations of insect societies, such as division of labor, task allocation, collective regulation, mass action responses, have been considered as main reasons for the ecological success. In this article, we propose and study a general modeling framework that includes the following three features: (a) the average internal response threshold for each task (the internal factor); (b) social network communications that could lead to task switching (the environmental factor); and (c) dynamical changes of task demands (the external factor). Since workers in many social insect species exhibit age polyethism, we also extend our model to incorporate age polyethism in which worker task preferences change with age. We apply our general modeling framework to the cases of two task groups: the inside colony task versus the outside colony task. Our analytical study of the models provides important insights and predictions on the effects of colony size, social communication, and age-related task preferences on task allocation and division of labor in the adaptive dynamical environment. Our study implies that the smaller size colony invests its resource for the colony growth and allocates more workers in the risky tasks such as foraging while the larger colony shifts more workers to perform the safer tasks inside the colony. Social interactions among different task groups play an important role in shaping task allocation depending on the relative cost and demands of the tasks. PMID:27125656

  20. Modelling cometabolic biotransformation of organic micropollutants in nitrifying reactors.

    PubMed

    Fernandez-Fontaina, E; Carballa, M; Omil, F; Lema, J M

    2014-11-15

    Cometabolism is the ability of microorganisms to degrade non-growth substrates in the presence of primary substrates, being the main removal mechanism behind the biotransformation of organic micropollutants in wastewater treatment plants. In this paper, a cometabolic Monod-type kinetics, linking biotransformation of micropollutants with primary substrate degradation, was applied to a highly enriched nitrifying activated sludge (NAS) reactor operated under different operational conditions (hydraulic retention time (HRT) and nitrifying activity). A dynamic model of the bioreactor was built taking into account biotransformation, sorption and volatilization. The micropollutant transformation capacity (Tc), the half-saturation constant (Ksc) and the solid-liquid partitioning coefficient (Kd) of several organic micropollutants were estimated at 25 °C using an optimization algorithm to fit experimental data to the proposed model with the cometabolic Monod-type biotransformation kinetics. The cometabolic Monod-type kinetic model was validated under different HRTs (1.0-3.7 d) and nitrification rates (0.12-0.45 g N/g VSS d), describing more accurately the fate of those compounds affected by the biological activity of nitrifiers (ibuprofen, naproxen, erythromycin and roxithromycin) compared to the commonly applied pseudo-first order micropollutant biotransformation kinetics, which does not link biotransformation of micropollutants to consumption of primary substrate. Furthermore, in contrast to the pseudo-first order biotransformation constant (k(biol)), the proposed cometabolic kinetic coefficients are independent of operational conditions such as the nitrogen loading rate applied. Also, the influence of the kinetic parameters on the biotransformation efficiency of NAS reactors, defined as the relative amount of the total inlet micropollutant load being biotransformed, was assessed considering different HRTs and nitrification rates. PMID:25150522

  1. Isotope-based Fluvial Organic Carbon (ISOFLOC) Model: Model formulation, sensitivity, and evaluation

    NASA Astrophysics Data System (ADS)

    Ford, William I.; Fox, James F.

    2015-06-01

    Watershed-scale carbon budgets remain poorly understood, in part due to inadequate simulation tools to assess in-stream carbon fate and transport. A new numerical model termed ISOtope-based FLuvial Organic Carbon (ISOFLOC) is formulated to simulate the fluvial organic carbon budget in watersheds where hydrologic, sediment transport, and biogeochemical processes are coupled to control benthic and transported carbon composition and flux. One ISOFLOC innovation is the formulation of new stable carbon isotope model subroutines that include isotope fractionation processes in order to estimate carbon isotope source, fate, and transport. A second innovation is the coupling of transfers between carbon pools, including algal particulate organic carbon, fine particulate and dissolved organic carbon, and particulate and dissolved inorganic carbon, to simulate the carbon cycle in a comprehensive manner beyond that of existing watershed water quality models. ISOFLOC was tested and verified in a low-gradient, agriculturally impacted stream. Results of a global sensitivity analysis suggested the isotope response variable had unique sensitivity to the coupled interaction between fluvial shear resistance of algal biomass and the concentration of dissolved inorganic carbon. Model calibration and validation suggested good agreement at event, seasonal, and annual timescales. Multiobjective uncertainty analysis suggested inclusion of the carbon stable isotope routine reduced uncertainty by 80% for algal particulate organic carbon flux estimates.

  2. Nephrology around Europe: organization models and management strategies: Spain.

    PubMed

    de Francisco, Angel L M; Piñera, Celestino

    2011-01-01

    The main aim of this report is to present a picture of the current organization of nephrology in Spain. The Spanish health system offers almost universal coverage, a wide variety of services and a high-quality network of hospitals and primary care centers. Spain has a specialized health care training system that is highly developed, highly regulated, with the capacity to provide high-quality training in 54 different specialties. Nephrology is basically a hospital-based specialty. There are no private dialysis patients in Spain. Hemodialysis centers are 40% public, 15% private and 45% run by companies. The National Health System covers 95% of the population, and there is no cost to patients for treatment of renal disease (dialysis and transplant). We observed a clear decrease of nephrology in residents' election rankings, with position 29 out of 47 specialties in 2007. Some of the reasons for this are the complexity of the subject, no clear information at the university, reduction of professional posts and a very good public service with minimal private practice. In Spain, a model of organization for transplantation was adopted based on a decentralized transplant coordinating network. For cadaveric donors, it compares favorably with rates in other Western countries. Living donor transplantation is very low in Spain--just 10% of total renal transplantation activity. New programs due to financial constraints need to include reduced dialysis costs, greater cost-effectiveness of prescriptions, better handling of ethical issues related to the need for using a clinical score of chronic kidney disease patients to make decisions about conservative or renal replacement therapy and an action plan for improvement of organ donation and transplantation. Recovery of skills (acute kidney injury, biopsies, vascular access, etc.), research and advances in autonomous activities (imaging, surgical and medical vascular training, etc.) are some of the future educational paths needed in

  3. Spectrophotometry and organic matter on Iapetus. 1: Composition models

    NASA Technical Reports Server (NTRS)

    Wilson, Peter D.; Sagan, Carl

    1995-01-01

    Iapetus shows a greater hemispheric albedo asymmetry than any other body in the solar system. Hapke scattering theory and optical constants measured in the laboratory are used to identify possible compositions for the dark material on the leading hemisphere of Iapetus. The materials considered are poly-HCN, kerogen, Murchison organic residue, Titan tholin, ice tholin, and water ice. Three-component mixtures of these materials are modeled in intraparticle mixture of 25% poly-HCN, 10% Murchison residue, and 65% water ice is found to best fit the spectrum, albedo, and phase behavior of the dark material. The Murchison residue and/or water ice can be replaced by kerogen and ice tholin, respectively, and still produce very good fits. Areal and particle mixtures of poly-HCN, Titan tholin, and either ice tholin or Murchison residue are also possible models. Poly-HCN is a necessary component in almost all good models. The presence of poly-HCN can be further tested by high-resolution observations near 4.5 micrometers.

  4. In Vivo RNAi-Based Screens: Studies in Model Organisms

    PubMed Central

    Yamamoto-Hino, Miki; Goto, Satoshi

    2013-01-01

    RNA interference (RNAi) is a technique widely used for gene silencing in organisms and cultured cells, and depends on sequence homology between double-stranded RNA (dsRNA) and target mRNA molecules. Numerous cell-based genome-wide screens have successfully identified novel genes involved in various biological processes, including signal transduction, cell viability/death, and cell morphology. However, cell-based screens cannot address cellular processes such as development, behavior, and immunity. Drosophila and Caenorhabditis elegans are two model organisms whose whole bodies and individual body parts have been subjected to RNAi-based genome-wide screening. Moreover, Drosophila RNAi allows the manipulation of gene function in a spatiotemporal manner when it is implemented using the Gal4/UAS system. Using this inducible RNAi technique, various large-scale screens have been performed in Drosophila, demonstrating that the method is straightforward and valuable. However, accumulated results reveal that the results of RNAi-based screens have relatively high levels of error, such as false positives and negatives. Here, we review in vivo RNAi screens in Drosophila and the methods that could be used to remove ambiguity from screening results. PMID:24705267

  5. Modeling of natural organic matter transport processes in groundwater.

    PubMed Central

    Yeh, T C; Mas-Pla, J; McCarthy, J F; Williams, T M

    1995-01-01

    A forced-gradient tracer test was conducted at the Georgetown site to study the transport of natural organic matter (NOM) in groundwater. In particular, the goal of this experiment was to investigate the interactions between NOM and the aquifer matrix. A detailed three-dimensional characterization of the hydrologic conductivity heterogeneity of the site was obtained using slug tests. The transport of a conservative tracer (chloride) was successfully reproduced using these conductivity data. Despite the good simulation of the flow field, NOM breakthrough curves could not be reproduced using a two-site sorption model with spatially constant parameters. Preliminary results suggest that different mechanisms for the adsorption/desorption processes, as well as their spatial variability, may significantly affect the transport and fate of NOM. PMID:7621798

  6. A Fast Technology Infusion Model for Aerospace Organizations

    NASA Technical Reports Server (NTRS)

    Shapiro, Andrew A.; Schone, Harald; Brinza, David E.; Garrett, Henry B.; Feather, Martin S.

    2006-01-01

    A multi-year Fast Technology Infusion initiative proposes a model for aerospace organizations to improve the cost-effectiveness by which they mature new, in-house developed software and hardware technologies for space mission use. The first year task under the umbrella of this initiative will provide the framework to demonstrate and document the fast infusion process. The viability of this approach will be demonstrated on two technologies developed in prior years with internal Jet Propulsion Laboratory (JPL) funding. One hardware technology and one software technology were selected for maturation within one calendar year or less. The overall objective is to achieve cost and time savings in the qualification of technologies. At the end of the recommended three-year effort, we will have demonstrated for six or more in-house developed technologies a clear path to insertion using a documented process that permits adaptation to a broad range of hardware and software projects.

  7. Comparing and modelling land use organization in cities

    PubMed Central

    Lenormand, Maxime; Picornell, Miguel; Cantú-Ros, Oliva G.; Louail, Thomas; Herranz, Ricardo; Barthelemy, Marc; Frías-Martínez, Enrique; San Miguel, Maxi; Ramasco, José J.

    2015-01-01

    The advent of geolocated information and communication technologies opens the possibility of exploring how people use space in cities, bringing an important new tool for urban scientists and planners, especially for regions where data are scarce or not available. Here we apply a functional network approach to determine land use patterns from mobile phone records. The versatility of the method allows us to run a systematic comparison between Spanish cities of various sizes. The method detects four major land use types that correspond to different temporal patterns. The proportion of these types, their spatial organization and scaling show a strong similarity between all cities that breaks down at a very local scale, where land use mixing is specific to each urban area. Finally, we introduce a model inspired by Schelling's segregation, able to explain and reproduce these results with simple interaction rules between different land uses. PMID:27019730

  8. A self-organized critical model for evolution

    SciTech Connect

    Flyvbjerg, H.; Bak, P.; Jensen, M.H.; Sneppen, K.

    1996-01-01

    A simple mathematical model of biological macroevolution is presented. It describes an ecology of adapting, interacting species. Species evolve to maximize their individual fitness in their environment. The environment of any given species is affected by other evolving species; hence it is not constant in time. The ecology evolves to a ``self-organized critical`` state where periods of stasis alternate with avalanches of causally connected evolutionary changes. This characteristic intermittent behaviour of natural history, known as ``punctuated equilibrium,`` thus finds a theoretical explanation as a selforganized critical phenomenon. In particular, large bursts of apparently simultaneous evolutionary activity require no external cause. They occur as the less frequent result of the very same dynamics that governs the more frequent small-scale evolutionary activity. Our results are compared with data from the fossil record collected by J. Sepkoski, Jr., and others.

  9. Organizations.

    ERIC Educational Resources Information Center

    Aviation/Space, 1980

    1980-01-01

    This is a list of aerospace organizations and other groups that provides educators with assistance and information in specific areas. Both government and nongovernment organizations are included. (Author/SA)

  10. A global model of natural volatile organic compound emissions

    NASA Astrophysics Data System (ADS)

    Guenther, Alex; Hewitt, C. Nicholas; Erickson, David; Fall, Ray; Geron, Chris; Graedel, Tom; Harley, Peter; Klinger, Lee; Lerdau, Manuel; McKay, W. A.; Pierce, Tom; Scholes, Bob; Steinbrecher, Rainer; Tallamraju, Raja; Taylor, John; Zimmerman, Pat

    1995-05-01

    Numerical assessments of global air quality and potential changes in atmospheric chemical constituents require estimates of the surface fluxes of a variety of trace gas species. We have developed a global model to estimate emissions of volatile organic compounds from natural sources (NVOC). Methane is not considered here and has been reviewed in detail elsewhere. The model has a highly resolved spatial grid (0.5°×0.5° latitude/longitude) and generates hourly average emission estimates. Chemical species are grouped into four categories: isoprene, monoterpenes, other reactive VOC (ORVOC), and other VOC (OVOC). NVOC emissions from oceans are estimated as a function of geophysical variables from a general circulation model and ocean color satellite data. Emissions from plant foliage are estimated from ecosystem specific biomass and emission factors and algorithms describing light and temperature dependence of NVOC emissions. Foliar density estimates are based on climatic variables and satellite data. Temporal variations in the model are driven by monthly estimates of biomass and temperature and hourly light estimates. The annual global VOC flux is estimated to be 1150 Tg C, composed of 44% isoprene, 11% monoterpenes, 22.5% other reactive VOC, and 22.5% other VOC. Large uncertainties exist for each of these estimates and particularly for compounds other than isoprene and monoterpenes. Tropical woodlands (rain forest, seasonal, drought-deciduous, and savanna) contribute about half of all global natural VOC emissions. Croplands, shrublands and other woodlands contribute 10-20% apiece. Isoprene emissions calculated for temperate regions are as much as a factor of 5 higher than previous estimates.

  11. FROM ORGANISMS TO POPULATIONS: MODELING AQUATIC TOXICITY DATA ACROSS TWO LEVELS OF BIOLOGICAL ORGANIZATION.

    EPA Science Inventory

    A critical step in estimating the ecological effects of a toxicant is extrapolating organism-level response data across higher levels of biological organization. In the present study, the organism-to-population link is made for the mysid, Americamysis bahia, exposed to a range of...

  12. Perceptions of organ donors and willingness to donate organs upon death: a test of the prototype/willingness model.

    PubMed

    Hyde, Melissa K; White, Katherine M

    2014-01-01

    Understanding people's organ donation decisions may narrow the gap between organ supply and demand. In two studies, participants who had not recorded their posthumous organ donation decision (Study 1, N = 210; Study 2, N = 307) completed items assessing prototype/willingness model (PWM; attitude, subjective norm, donor prototype favorability and similarity, willingness) constructs. Attitude, subjective norm, and prototype similarity predicted willingness to donate. Prototype favorability and a Prototype Favorability × Similarity interaction predicted willingness (Study 2). These findings provide support for the PWM in altruistic health contexts, highlighting the importance of people's perceptions about organ donors in their donation decisions. PMID:24758216

  13. Perceptions of Organ Donors and Willingness to Donate Organs Upon Death: A Test of the Prototype/Willingness Model.

    PubMed

    Hyde, Melissa K; White, Katherine M

    2014-06-01

    Understanding people's organ donation decisions may narrow the gap between organ supply and demand. In two studies, participants who had not recorded their posthumous organ donation decision (Study 1 N = 210; Study 2 N = 307) completed items assessing Prototype/Willingness Model (PWM) (attitude, subjective norm, donor prototype favorability and similarity, willingness) constructs. Attitude, subjective norm, and prototype similarity predicted willingness to donate. Prototype favorability and a prototype favorability x similarity interaction predicted willingness (Study 2). These findings provide support for the PWM in altruistic health contexts, highlighting the importance of people's perceptions about organ donors in their donation decisions. PMID:24910896

  14. AggModel: A soil organic matter model with measurable pools for use in incubation studies

    SciTech Connect

    Segoli, Moran; De Gryze, S.; Dou, Fugen; Lee, J.; Post, Wilfred M; Denef, K.; Six, Johan W U A

    2013-01-01

    Current soil organic matter (SOM) models are empirical in nature by employing few conceptual SOM pools that have a specific turnover time, but that are not measurable and have no direct relationship with soil structural properties. Most soil particles are held together in aggregates and the number, size and stability of these aggregates significantly affect the size and amount of organic matter contained in these aggregates, and its susceptibility to decomposition. While it has been shown that soil aggregates and their dynamics can be measured directly in the laboratory and in the field, the impact of soil aggregate dynamics on SOM decomposition has not been explicitly incorporated in ecosystem models. Here, we present AggModel, a conceptual and simulation model that integrates soil aggregate and SOM dynamics. In AggModel, we consider unaggregated and microaggregated soil that can exist within or external to macroaggregated soil. Each of the four aggregate size classes contains particulate organic matter and mineral-associated organic matter fractions. We used published data from laboratory incubations to calibrate and validate the biological and environmental effects on the rate of formation and breakdown of macroaggregates and microaggregates, and the organic matter dynamics within these different aggregate fractions. After calibration, AggModel explained more than 70% of the variation in aggregate masses and over 90% of the variation in aggregate-associated carbon. The model estimated the turnover time of macroaggregates as 32 days and 166 days for microaggregates. Sensitivity analysis of AggModel parameterization supported the notion that macroaggregate turnover rate has a strong control over microaggregate masses and, hence, carbon sequestration. In addition to AggModel being a proof-of-concept, the advantage of a model that is based on measurable SOM fractions is that its internal structure and dynamics can be directly calibrated and validated by using

  15. Development of an analytical model for organic-fluid fouling

    SciTech Connect

    Panchal, C.B.; Watkinson, A.P.

    1994-10-01

    The research goal of this project is to determine ways to effectively mitigate fouling in organic fluids: hydrocarbons and derived fluids. The fouling research focuses on the development of methodology for determining threshold conditions for fouling. Initially, fluid containing chemicals known to produce foulant is analyzed; subsequently, fouling of industrial fluids is investigated. The fouling model developed for determining the effects of physical parameters is the subject of this report. The fouling model is developed on the premise that the chemical reaction for generation of precursor can take place in the bulk fluid, in the thermal-boundary layer, or at the fluid/wall interface, depending upon the interactive effects of fluid dynamics, heat and mass transfer, and the controlling chemical reaction. In the analysis, the experimental data are examined for fouling deposition of polyperoxide produced by autoxidation of indene in kerosene. The effects of fluid and wall temperatures for two flow geometries are analyzed. The results show that the relative effects of physical parameters on the fouling rate differ for the three fouling mechanisms. Therefore, to apply the closed-flow-loop data to industrial conditions, the controlling mechanism must be identified.

  16. A Pelvic Phantom for Modeling Internal Organ Motions

    SciTech Connect

    Kovacs, Peter; Sebestyen, Zsolt; Farkas, Robert; Bellyei, Szabolcs; Szigeti, Andras; Liposits, Gabor; Hideghety, Katalin; Derczy, Katalin; Mangel, Laszlo

    2011-10-01

    A pelvic phantom was developed for use in testing image-guided radiation therapy (IGRT) and adaptive applications in radiation therapy (ART) with simulating the anterior-posterior internal organ motions during prostate radiotherapy. Measurements could be done with an ionization chamber (IC) in the simulated prostate. The rectum was simulated by air-equivalent material (AEM). The volume superior to the IC placement was considered as the bladder. The extension of AEM volume could be varied. The vertical position of the IC placement could be shifted by {+-}1 cm to simulate the prostate motion parallel to the changes in bladder volume. The reality of the simulation was inspected. Three-millimeter-slice-increment computed tomography (CT) scans were taken for irradiation planning. The structure set was adapted to the phantom from a treated patient. Planning target volume was delineated according to the RTOG 0126 study. IMRT and 3D conformal radiation therapy (3D-CRT) plans were made. Prostate motion and rectum volume changes were simulated in the phantom. IC displacement was corrected by phantom shifting. The delivered dose was measured with IC in 7 cases using intensity-modulated radiation therapy (IMRT) and 3D-CRT fractions, and single square-shaped beams: anteroposterior (AP), posteroanterior (PA), and lateral (LAT). Variations from the calculated doses were slightly below 1% at IMRT and around 1% at 3D-CRT; below 4.5% at square AP beam; up to 9% at square PA beam; and around 0.5% at square LAT beam. Other authors have already shown that by using planning systems and ultrasonic and cone beam CT guidance, correction of organ motions in a real patient during prostate cancer IGRT does not have a significant dosimetric effect. The inspection of our phantom-as described here-ended with similar results. Our team suggested that our model is sufficiently realistic and can be used for IGRT and ART testing.

  17. A pelvic phantom for modeling internal organ motions.

    PubMed

    Kovács, Péter; Sebestyén, Zsolt; Farkas, Róbert; Bellyei, Szabolcs; Szigeti, András; Liposits, Gábor; Hideghéty, Katalin; Dérczy, Katalin; Mangel, László

    2011-01-01

    A pelvic phantom was developed for use in testing image-guided radiation therapy (IGRT) and adaptive applications in radiation therapy (ART) with simulating the anterior-posterior internal organ motions during prostate radiotherapy. Measurements could be done with an ionization chamber (IC) in the simulated prostate. The rectum was simulated by air-equivalent material (AEM). The volume superior to the IC placement was considered as the bladder. The extension of AEM volume could be varied. The vertical position of the IC placement could be shifted by ± 1 cm to simulate the prostate motion parallel to the changes in bladder volume. The reality of the simulation was inspected. Three-millimeter-slice-increment computed tomography (CT) scans were taken for irradiation planning. The structure set was adapted to the phantom from a treated patient. Planning target volume was delineated according to the RTOG 0126 study. IMRT and 3D conformal radiation therapy (3D-CRT) plans were made. Prostate motion and rectum volume changes were simulated in the phantom. IC displacement was corrected by phantom shifting. The delivered dose was measured with IC in 7 cases using intensity-modulated radiation therapy (IMRT) and 3D-CRT fractions, and single square-shaped beams: anteroposterior (AP), posteroanterior (PA), and lateral (LAT). Variations from the calculated doses were slightly below 1% at IMRT and around 1% at 3D-CRT; below 4.5% at square AP beam; up to 9% at square PA beam; and around 0.5% at square LAT beam. Other authors have already shown that by using planning systems and ultrasonic and cone beam CT guidance, correction of organ motions in a real patient during prostate cancer IGRT does not have a significant dosimetric effect. The inspection of our phantom--as described here-ended with similar results. Our team suggested that our model is sufficiently realistic and can be used for IGRT and ART testing. PMID:20561777

  18. Review of existing terrestrial bioaccumulation models and terrestrial bioaccumulation modeling needs for organic chemicals.

    PubMed

    Gobas, Frank A P C; Burkhard, Lawrence P; Doucette, William J; Sappington, Keith G; Verbruggen, Eric M J; Hope, Bruce K; Bonnell, Mark A; Arnot, Jon A; Tarazona, Jose V

    2016-01-01

    Protocols for terrestrial bioaccumulation assessments are far less-developed than for aquatic systems. This article reviews modeling approaches that can be used to assess the terrestrial bioaccumulation potential of commercial organic chemicals. Models exist for plant, invertebrate, mammal, and avian species and for entire terrestrial food webs, including some that consider spatial factors. Limitations and gaps in terrestrial bioaccumulation modeling include the lack of QSARs for biotransformation and dietary assimilation efficiencies for terrestrial species; the lack of models and QSARs for important terrestrial species such as insects, amphibians and reptiles; the lack of standardized testing protocols for plants with limited development of plant models; and the limited chemical domain of existing bioaccumulation models and QSARs (e.g., primarily applicable to nonionic organic chemicals). There is an urgent need for high-quality field data sets for validating models and assessing their performance. There is a need to improve coordination among laboratory, field, and modeling efforts on bioaccumulative substances in order to improve the state of the science for challenging substances. PMID:26272325

  19. Towards Increased Relevance: Context-Adapted Models of the Learning Organization

    ERIC Educational Resources Information Center

    Örtenblad, Anders

    2015-01-01

    Purpose: The purposes of this paper are to take a closer look at the relevance of the idea of the learning organization for organizations in different generalized organizational contexts; to open up for the existence of multiple, context-adapted models of the learning organization; and to suggest a number of such models.…

  20. Modelling the volatile and organic content of Enceladus' ocean

    NASA Astrophysics Data System (ADS)

    Sotin, Christophe; Lunine, Jonathan

    2015-04-01

    A variety of Cassini data on Enceladus suggest that the jets of material spraying out of the south polar region of this Saturnian moon are connected to a regional or global ocean below an icy crust -- an ocean in contact with a rocky core [1, 2, 3]. In this study we construct models of the mineralogical and elemental composition of Enceladus' rocky core so as to predict the abundance of species that may provide more detail on the extent of hydrothermal evolution of the ocean and its interaction with the rocky core. Using equations of state of the relevant material, the models are made consistent with the values of the gravity coefficients [1]. We investigate the amount of organic molecules (amino acids and fatty acids) as well as the amount of 40Ar that could be present in Enceladus' deep ocean and, therefore, in the icy grains expelled into space. Some models show that the conditions in Enceladus rocky core can be very similar to those existing in the Earth's oceanic crust, suggesting that all of Enceladus rocky core would have been leached over the age of the solar system. The amount of 40Ar dissolved in the ocean provides constraints on the amount of K in the building blocks of Enceladus, the amount of leaching of the silicate fraction, and the extent of the ocean. Based on chondritic abundances for K, we have calculated that the total potential of 40Ar is about 5.6x1012 kg. We also investigate the amount of organic material that would have been concentrated in the ocean. The Murchison meteorite contains about 60 ppm of amino acids, mainly glycine [4]. Assuming that all the rocky core has been leached by water, the modelled concentration of amino acids exceeds 150 ppm. Carboxylic acids were detected in the Asuka carbonaceous chondrites in Antarctica with values, for example, of 90 nmol/g of benzoic acid. Assuming this value, about 35 ppm of benzoic acid would be present in Enceladus' ocean. The concentrations are larger if the ocean is not global, but rather

  1. Modeling adsorption and reactions of organic molecules at metal surfaces.

    PubMed

    Liu, Wei; Tkatchenko, Alexandre; Scheffler, Matthias

    2014-11-18

    CONSPECTUS: The understanding of adsorption and reactions of (large) organic molecules at metal surfaces plays an increasingly important role in modern surface science and technology. Such hybrid inorganic/organic systems (HIOS) are relevant for many applications in catalysis, light-emitting diodes, single-molecule junctions, molecular sensors and switches, and photovoltaics. Obviously, the predictive modeling and understanding of the structure and stability of such hybrid systems is an essential prerequisite for tuning their electronic properties and functions. At present, density-functional theory (DFT) is the most promising approach to study the structure, stability, and electronic properties of complex systems, because it can be applied to both molecules and solids comprising thousands of atoms. However, state-of-the-art approximations to DFT do not provide a consistent and reliable description for HIOS, which is largely due to two issues: (i) the self-interaction of the electrons with themselves arising from the Hartree term of the total energy that is not fully compensated in approximate exchange-correlation functionals, and (ii) the lack of long-range part of the ubiquitous van der Waals (vdW) interactions. The self-interaction errors sometimes lead to incorrect description of charge transfer and electronic level alignment in HIOS, although for molecules adsorbed on metals these effects will often cancel out in total energy differences. Regarding vdW interactions, several promising vdW-inclusive DFT-based methods have been recently demonstrated to yield remarkable accuracy for intermolecular interactions in the gas phase. However, the majority of these approaches neglect the nonlocal collective electron response in the vdW energy tail, an effect that is particularly strong in condensed phases and at interfaces between different materials. Here we show that the recently developed DFT+vdW(surf) method that accurately accounts for the collective electronic

  2. The prisoner as model organism: malaria research at Stateville Penitentiary.

    PubMed

    Comfort, Nathaniel

    2009-09-01

    In a military-sponsored research project begun during the Second World War, inmates of the Stateville Penitentiary in Illinois were infected with malaria and treated with experimental drugs that sometimes had vicious side effects. They were made into reservoirs for the disease and they provided a food supply for the mosquito cultures. They acted as secretaries and technicians, recording data on one another, administering malarious mosquito bites and experimental drugs to one another, and helping decide who was admitted to the project and who became eligible for early parole as a result of his participation. Thus, the prisoners were not simply research subjects; they were deeply constitutive of the research project. Because a prisoner's time on the project was counted as part of his sentence, and because serving on the project could shorten one's sentence, the project must be seen as simultaneously serving the functions of research and punishment. Michel Foucault wrote about such 'mixed mechanisms' in his Discipline and punish. His shining example of such a 'transparent' and subtle style of punishment was the panopticon, Jeremy Bentham's architectural invention of prison cellblocks arrayed around a central guard tower. Stateville prison was designed on Bentham's model; Foucault featured it in his own discussion. This paper, then, explores the power relations in this highly idiosyncratic experimental system, in which the various roles of model organism, reagent, and technician are all occupied by sentient beings who move among them fluidly. This, I argue, created an environment in the Stateville hospital wing more panoptic than that in the cellblocks. Research and punishment were completely interpenetrating, and mutually reinforcing. PMID:19720327

  3. The prisoner as model organism: malaria research at Stateville Penitentiary

    PubMed Central

    Comfort, Nathaniel

    2009-01-01

    In a military-sponsored research project begun during the Second World War, inmates of the Stateville Penitentiary in Illinois were infected with malaria and treated with experimental drugs that sometimes had vicious side effects. They were made into reservoirs for the disease and they provided a food supply for the mosquito cultures. They acted as secretaries and technicians, recording data on one another, administering malarious mosquito bites and experimental drugs to one another, and helping decide who was admitted to the project and who became eligible for early parole as a result of his participation. Thus, the prisoners were not simply research subjects; they were deeply constitutive of the research project. Because a prisoner’s time on the project was counted as part of his sentence, and because serving on the project could shorten one’s sentence, the project must be seen as simultaneously serving the functions of research and punishment. Michel Foucault wrote about such ‘mixed mechanisms’ in his Discipline and punish. His shining example of such a ‘transparent’ and subtle style of punishment was the panopticon, Jeremy Bentham’s architectural invention of prison cellblocks arrayed around a central guard tower. Stateville prison was designed on Bentham’s model; Foucault featured it in his own discussion. This paper, then, explores the power relations in this highly idiosyncratic experimental system, in which the various roles of model organism, reagent, and technician are all occupied by sentient beings who move among them fluidly. This, I argue, created an environment in the Stateville hospital wing more panoptic than that in the cellblocks. Research and punishment were completely interpenetrating, and mutually reinforcing. PMID:19720327

  4. AgBase: supporting functional modeling in agricultural organisms.

    PubMed

    McCarthy, Fiona M; Gresham, Cathy R; Buza, Teresia J; Chouvarine, Philippe; Pillai, Lakshmi R; Kumar, Ranjit; Ozkan, Seval; Wang, Hui; Manda, Prashanti; Arick, Tony; Bridges, Susan M; Burgess, Shane C

    2011-01-01

    AgBase (http://www.agbase.msstate.edu/) provides resources to facilitate modeling of functional genomics data and structural and functional annotation of agriculturally important animal, plant, microbe and parasite genomes. The website is redesigned to improve accessibility and ease of use, including improved search capabilities. Expanded capabilities include new dedicated pages for horse, cat, dog, cotton, rice and soybean. We currently provide 590 240 Gene Ontology (GO) annotations to 105 454 gene products in 64 different species, including GO annotations linked to transcripts represented on agricultural microarrays. For many of these arrays, this provides the only functional annotation available. GO annotations are available for download and we provide comprehensive, species-specific GO annotation files for 18 different organisms. The tools available at AgBase have been expanded and several existing tools improved based upon user feedback. One of seven new tools available at AgBase, GOModeler, supports hypothesis testing from functional genomics data. We host several associated databases and provide genome browsers for three agricultural pathogens. Moreover, we provide comprehensive training resources (including worked examples and tutorials) via links to Educational Resources at the AgBase website. PMID:21075795

  5. AgBase: supporting functional modeling in agricultural organisms

    PubMed Central

    McCarthy, Fiona M.; Gresham, Cathy R.; Buza, Teresia J.; Chouvarine, Philippe; Pillai, Lakshmi R.; Kumar, Ranjit; Ozkan, Seval; Wang, Hui; Manda, Prashanti; Arick, Tony; Bridges, Susan M.; Burgess, Shane C.

    2011-01-01

    AgBase (http://www.agbase.msstate.edu/) provides resources to facilitate modeling of functional genomics data and structural and functional annotation of agriculturally important animal, plant, microbe and parasite genomes. The website is redesigned to improve accessibility and ease of use, including improved search capabilities. Expanded capabilities include new dedicated pages for horse, cat, dog, cotton, rice and soybean. We currently provide 590 240 Gene Ontology (GO) annotations to 105 454 gene products in 64 different species, including GO annotations linked to transcripts represented on agricultural microarrays. For many of these arrays, this provides the only functional annotation available. GO annotations are available for download and we provide comprehensive, species-specific GO annotation files for 18 different organisms. The tools available at AgBase have been expanded and several existing tools improved based upon user feedback. One of seven new tools available at AgBase, GOModeler, supports hypothesis testing from functional genomics data. We host several associated databases and provide genome browsers for three agricultural pathogens. Moreover, we provide comprehensive training resources (including worked examples and tutorials) via links to Educational Resources at the AgBase website. PMID:21075795

  6. Myasthenia gravis, a model of organ-specific autoimmune disease.

    PubMed

    Berrih-Aknin, S

    1995-04-01

    Myasthenia gravis (MG) is a neuromuscular disorder of autoimmune origin. Most patients have antibodies directed against the acetylcholine receptor (AChR) that interfere with neuromuscular transmission. MG is a model of organ-specific autoimmune disease in which the autoantigen, AChR, is well characterized. However, several questions remain unanswered. Why is AChR, which is present in the thymus, not tolerized? Why does the anti-AChR antibody titre not correlate with clinical manifestations, and why do some patients not have such antibodies? What genetic elements are involved in disease susceptibility? How is the expression of AChR regulated after its attack by autoantibodies? Could MG patients benefit from new immunomodulatory treatments? At the IVth EuroMyasthenia meeting, held in Versailles in April 1994, almost 200 researchers and physicians met to discuss the pathophysiology and treatment of myasthenia gravis and to provide answers to some of these questions. The sessions covered immunological, genetic and clinical aspects of MG. PMID:7612144

  7. MATHEMATICAL MODEL OF PLANT UPTAKE AND TRANSLOCATION OF ORGANIC CHEMICALS: APPLICATION TO EXPERIMENTS

    EPA Science Inventory

    Uptake, transport, and accumulation of organic chemicals by plants are influenced by characteristics of the plant and properties of the chemical, soil, and environmental conditions. athematical model for uptake of organic chemicals by plants was calibrated by application to data ...

  8. Modeling the current and future role of particulate organic nitrates in the southeastern United States

    EPA Science Inventory

    Organic nitrates are an important aerosol constituent in locations where biogenic hydrocarbon emissions mix with anthropogenic NOx sources. While regional and global chemical transport models may include a representation of organic aerosol from monoterpene reactions with nitrate ...

  9. Organics.

    ERIC Educational Resources Information Center

    Chian, Edward S. K.; DeWalle, Foppe B.

    1978-01-01

    Presents water analysis literature for 1978. This review is concerned with organics, and it covers: (1) detergents and surfactants; (2) aliphatic and aromatic hydrocarbons; (3) pesticides and chlorinated hydrocarbons; and (4) naturally occurring organics. A list of 208 references is also presented. (HM)

  10. Organizers.

    ERIC Educational Resources Information Center

    Callison, Daniel

    2000-01-01

    Focuses on "organizers," tools or techniques that provide identification and classification along with possible relationships or connections among ideas, concepts, and issues. Discusses David Ausubel's research and ideas concerning advance organizers; the implications of Ausubel's theory to curriculum and teaching; "webbing," a specific…

  11. Punctuated-equilibrium model of biological evolution is also a self-organized-criticality model of earthquakes

    NASA Astrophysics Data System (ADS)

    Ito, Keisuke

    1995-09-01

    Bak and Sneppen proposed a self-organized-criticality model to explain the punctuated equilibrium of biological evolution. The model, as it is, is a good self-organized-criticality model of earthquakes. Real earthquakes satisfy the required conditions of criticality; that is, power laws in (1) the size distribution of earthquakes, and (2) both the spatial and the temporal correlation functions.

  12. Managing professional work: three models of control for health organizations.

    PubMed Central

    Scott, W R

    1982-01-01

    Three arrangements for structuring the work of professional participants in professional organizations are described, contrasted and evaluated. Arguments are illustrated by application to the organization of physicians within hospitals. The primary rationale, the support structures that have fostered its development, the key structural features and the advantages and disadvantages of each arrangement are described. The effect on these arrangements of structures and forces external to any particular professional organization is emphasized. PMID:6749761

  13. THERMODYNAMIC MODELING OF LIQUID AEROSOLS CONTAINING DISSOLVED ORGANICS AND ELECTROLYTES

    EPA Science Inventory

    Many tropospheric aerosols contain large fractions of soluble organic material, believed to derive from the oxidation of precursors such alpha-pinene. The chemical composition of aerosol organic matter is complex and not yet fully understood.

    The key properties of solu...

  14. Community Organizing Practices in Academia: A Model, and Stories of Partnerships

    ERIC Educational Resources Information Center

    Avila, Maria

    2010-01-01

    This article describes a model of civic engagement based on four key community organizing practices, created at Occidental College and implemented since 2001. The foundations of this model do not include confrontation, mass mobilization, or demonstrations--tactics commonly associated with the term community organizing. This model, instead,…

  15. A Framework of Operating Models for Interdisciplinary Research Programs in Clinical Service Organizations

    ERIC Educational Resources Information Center

    King, Gillian; Currie, Melissa; Smith, Linda; Servais, Michelle; McDougall, Janette

    2008-01-01

    A framework of operating models for interdisciplinary research programs in clinical service organizations is presented, consisting of a "clinician-researcher" skill development model, a program evaluation model, a researcher-led knowledge generation model, and a knowledge conduit model. Together, these models comprise a tailored, collaborative…

  16. Studies on sensitivity of zebrafish as a model organism for Parkinson's disease: Comparison with rat model

    PubMed Central

    Makhija, Dinesh T.; Jagtap, Aarti G.

    2014-01-01

    Objective: To determine the utility of zebra fish as an animal model for Parkinson's disease (PD) in comparison with rat model. Materials and Methods: MTT assay was performed on rat and zebrafish brain synaptosomal fractions using rotenone as a neurotoxic agent. Quercetin and resveratrol were used as standards to compare anti-apoptotic activity in both organisms. Catalepsy was induced in zebrafish by exposing them to haloperidol (9 μM) solution. Drug-treated groups were exposed to bromocriptine and pramipexole, 30 min prior to haloperidol exposure at the dose of 2, 5, and 10 μg/mL. Swimming speed, time spent in the bottom of the tank, and complete cataleptic time were evaluated to assess behavioral changes. In rats, catalepsy was induced using haloperidol (1.25 mg/kg i.p.). Drug-treated groups received bromocriptine (2.5 mg/kg.) and pramipexole (1 mg/kg) orally. Bar test, block test, and locomotor activity were carried out to assess behavioral changes. Results: Resveratrol and quercetin showed comparable inhibition of apoptosis in rats and zebrafish. In anti-cataleptic study, bromocriptine and pramipexole-treated groups showed significant difference (P < 0.05) in behavioral parameters as compared to haloperidol control group in both the experimental organisms. Results obtained from fish model were in correlation with rat model. Conclusion: Findings of the present study revealed that zebrafish model is highly sensitive and can be used for basic screening of drugs against PD. PMID:24554909

  17. Modeling dissolved organic carbon in temperate forest soils: TRIPLEX-DOC model development and validation

    NASA Astrophysics Data System (ADS)

    Wu, H.; Peng, C.; Moore, T. R.; Hua, D.; Li, C.; Zhu, Q.; Peichl, M.; Arain, M. A.; Guo, Z.

    2014-05-01

    Even though dissolved organic carbon (DOC) is the most active carbon (C) cycling in soil organic carbon (SOC) pools, it receives little attention from the global C budget. DOC fluxes are critical to aquatic ecosystem inputs and contribute to the C balance of terrestrial ecosystems, but few ecosystem models have attempted to integrate DOC dynamics into terrestrial C cycling. This study introduces a new process-based model, TRIPLEX-DOC, that is capable of estimating DOC dynamics in forest soils by incorporating both ecological drivers and biogeochemical processes. TRIPLEX-DOC was developed from Forest-DNDC, a biogeochemical model simulating C and nitrogen (N) dynamics, coupled with a new DOC process module that predicts metabolic transformations, sorption/desorption, and DOC leaching in forest soils. The model was validated against field observations of DOC concentrations and fluxes at white pine forest stands located in southern Ontario, Canada. The model was able to simulate seasonal dynamics of DOC concentrations and the magnitudes observed within different soil layers, as well as DOC leaching in the age sequence of these forests. Additionally, TRIPLEX-DOC estimated the effect of forest harvesting on DOC leaching, with a significant increase following harvesting, illustrating that land use change is of critical importance in regulating DOC leaching in temperate forests as an important source of C input to aquatic ecosystems.

  18. Electromagnetic modeling of organic light-emitting devices

    NASA Astrophysics Data System (ADS)

    Chen, Hung-Chi; Lee, Jiun-Haw; Shiau, Chia-Chiang; Kiang, Yean-Woei; Yang, C. C.; Chang, Chih-Hsiang

    2006-02-01

    In this paper, we demonstrate the numerical simulations of the organic light-emitting device (OLED) based on a rigorous and efficient numerical method. The input parameters of such a program include the layer thickness and complex refractive index of each layer, the locations and density of the oscillating dipoles, and the emission photoluminescence spectrum. In evaluating the device performances, the output spectrum, the intensity distribution, and the viewing-angle characteristics of an OLED are concerned. Since the numerical difficulty arising from the large thickness of the glass layer in the OLED is carefully overcome, the program can simulate the optical performances with different glass substrate thickness ranged from less than one to hundreds of μm. When the glass substrate becomes thinner, multi-peak spectrum of an OLED is observed due to the strong interference effect between the two sides of the glass substrate. When the thickness of the glass substrate is reduced to less than 1 μm, the device is identical to a top-emission OLED with a two-microcavity structure. The simulation results are consistent with the Fabry-Perot cavity equation, which can be used as a guideline for optimizing the optical characteristics of an OLED from the normal direction. We have also demonstrated the procedures to maximize the total flux from an OLED which is more important than the luminance from the normal direction for the lighting application. Since our development of numerical algorithms is based on the general electromagnetic theory, the proposed model is, in principle, applicable to an OLED consisting of any number of layers.

  19. Self-organized behavior of modeled shoreline shapes

    NASA Astrophysics Data System (ADS)

    Ashton, A.; Murray, A. B.

    2003-04-01

    Whenever waves approach a coast and break at oblique angles, they drive a current along the shore. This current, along with wave-induced sediment suspension, transports relatively large amounts of sediment, affecting the shape and evolution of a coastline. Traditionally, researchers have assumed that alongshore sediment transport will diffuse, or smooth, bumps along a shoreline. Recent research, however, shows that when the angle between wave crests in deep water and the shoreline is sufficiently high (greater than approximately 45 degrees), a shoreline is unstable. Linear stability analysis does not predict that this instability will cause a preferred wavelength of shoreline perturbation growth or that organized patterns will emerge. However, a simple numerical model of shoreline change shows those when there is a predominance of high angle waves approaching a shoreline, finite-amplitude features will develop that interact with each other and increase in wavelength over time, translating in the direction of net alongshore sediment transport. Some of these simulated features resemble naturally occurring shoreline features, such as 'alongshore sandwaves', 'ords', 'cuspate spits', and 'cuspate forelands'. By varying two wave climate parameters, one describing the relative dominance of waves approaching at high angles and the other controlling the signs of the approach angle of incoming waves (i.e., the asymmetry of waves approaching from the right vs. the left), we investigate how the attributes of the input wave climate determine the aspect ratio and characteristic form of the simulated features. Varying these two parameters also affects the wavelength of the initially fastest growing perturbation. By tracking the average wavelength of simulated features, which increases over time for all simulations, we show that more complicated phenomena, such as rapid period doubling, can dominate simulated shoreline evolution. These rich behaviors result from large

  20. Current developments in soil organic matter modeling and the expansion of model applications. A review

    DOE PAGESBeta

    Campbell, Eleanor E.; Paustian, Keith

    2015-12-23

    It is important to note that Soil organic matter (SOM) is a great natural resource. It is fundamental to soil and ecosystem functions across a wide range of scales, from site-specific soil fertility and water holding capacity to global biogeochemical cycling. It is also a highly complex material that is sensitive to direct and indirect human impacts. In our SOM research, simulation models play an important role by providing a mathematical framework to integrate, examine, and test the understanding of SOM dynamics. Simulation models of SOM are also increasingly used in more ‘applied’ settings to evaluate human impacts on ecosystemmore » function, and to manage SOM for greenhouse gas mitigation, improved soil health, and sustainable use as a natural resource. Within this context, there is a need to maintain a robust connection between scientific developments in SOM modeling approaches and SOM model applications. This need forms the basis of this review. In this review we first provide an overview of SOM modeling, focusing on SOM theory, data-model integration, and model development as evidenced by a quantitative review of SOM literature. Second, we present the landscape of SOM model applications, focusing on examples in climate change policy. Finally, we conclude by discussing five areas of recent developments in SOM modeling including: (1) microbial roles in SOM stabilization; (2) modeling SOM saturation kinetics; (3) temperature controls on decomposition; (4)SOM dynamics in deep soil layers; and (5)SOM representation in earth system models. Our aim is to comprehensively connect SOM model development to its applications, revealing knowledge gaps in need of focused interdisciplinary attention and exposing pitfalls that, if avoided, can lead to best use of SOM models to support policy initiatives and sustainable land management solutions.« less

  1. Current developments in soil organic matter modeling and the expansion of model applications. A review

    SciTech Connect

    Campbell, Eleanor E.; Paustian, Keith

    2015-12-23

    It is important to note that Soil organic matter (SOM) is a great natural resource. It is fundamental to soil and ecosystem functions across a wide range of scales, from site-specific soil fertility and water holding capacity to global biogeochemical cycling. It is also a highly complex material that is sensitive to direct and indirect human impacts. In our SOM research, simulation models play an important role by providing a mathematical framework to integrate, examine, and test the understanding of SOM dynamics. Simulation models of SOM are also increasingly used in more ‘applied’ settings to evaluate human impacts on ecosystem function, and to manage SOM for greenhouse gas mitigation, improved soil health, and sustainable use as a natural resource. Within this context, there is a need to maintain a robust connection between scientific developments in SOM modeling approaches and SOM model applications. This need forms the basis of this review. In this review we first provide an overview of SOM modeling, focusing on SOM theory, data-model integration, and model development as evidenced by a quantitative review of SOM literature. Second, we present the landscape of SOM model applications, focusing on examples in climate change policy. Finally, we conclude by discussing five areas of recent developments in SOM modeling including: (1) microbial roles in SOM stabilization; (2) modeling SOM saturation kinetics; (3) temperature controls on decomposition; (4)SOM dynamics in deep soil layers; and (5)SOM representation in earth system models. Our aim is to comprehensively connect SOM model development to its applications, revealing knowledge gaps in need of focused interdisciplinary attention and exposing pitfalls that, if avoided, can lead to best use of SOM models to support policy initiatives and sustainable land management solutions.

  2. Current developments in soil organic matter modeling and the expansion of model applications: a review

    NASA Astrophysics Data System (ADS)

    Campbell, Eleanor E.; Paustian, Keith

    2015-12-01

    Soil organic matter (SOM) is an important natural resource. It is fundamental to soil and ecosystem functions across a wide range of scales, from site-specific soil fertility and water holding capacity to global biogeochemical cycling. It is also a highly complex material that is sensitive to direct and indirect human impacts. In SOM research, simulation models play an important role by providing a mathematical framework to integrate, examine, and test the understanding of SOM dynamics. Simulation models of SOM are also increasingly used in more ‘applied’ settings to evaluate human impacts on ecosystem function, and to manage SOM for greenhouse gas mitigation, improved soil health, and sustainable use as a natural resource. Within this context, there is a need to maintain a robust connection between scientific developments in SOM modeling approaches and SOM model applications. This need forms the basis of this review. In this review we first provide an overview of SOM modeling, focusing on SOM theory, data-model integration, and model development as evidenced by a quantitative review of SOM literature. Second, we present the landscape of SOM model applications, focusing on examples in climate change policy. We conclude by discussing five areas of recent developments in SOM modeling including: (1) microbial roles in SOM stabilization; (2) modeling SOM saturation kinetics; (3) temperature controls on decomposition; (4) SOM dynamics in deep soil layers; and (5) SOM representation in earth system models. Our aim is to comprehensively connect SOM model development to its applications, revealing knowledge gaps in need of focused interdisciplinary attention and exposing pitfalls that, if avoided, can lead to best use of SOM models to support policy initiatives and sustainable land management solutions.

  3. A 360° Vision for Virtual Organizations Characterization and Modelling: Two Intentional Level Aspects

    NASA Astrophysics Data System (ADS)

    Priego-Roche, Luz-María; Rieu, Dominique; Front, Agnès

    Nowadays, organizations aiming to be successful in an increasingly competitive market tend to group together into virtual organizations. Designing the information system (IS) of such virtual organizations on the basis of the IS of those participating is a real challenge. The IS of a virtual organization plays an important role in the collaboration and cooperation of the participants organizations and in reaching the common goal. This article proposes criteria allowing virtual organizations to be identified and classified at an intentional level, as well as the information necessary for designing the organizations’ IS. Instantiation of criteria for a specific virtual organization and its participants, will allow simple graphical models to be generated in a modelling tool. The models will be used as bases for the IS design at organizational and operational levels. The approach is illustrated by the example of the virtual organization UGRT (a regional stockbreeders union in Tabasco, Mexico).

  4. Organic chemistry in the atmosphere. [laboratory modeling of Titan atmosphere

    NASA Technical Reports Server (NTRS)

    Sagan, C.

    1974-01-01

    The existence of an at least moderately complex organic chemistry on Titan is stipulated based on clear evidence of methane, and at least presumptive evidence of hydrogen in its atmosphere. The ratio of methane to hydrogen is the highest of any atmosphere in the solar system. Irradiation of hydrogen/methane mixtures produces aromatic and aliphatic hydrocarbons. A very reasonable hypothesis assumes that the red cloud cover of Titan is made of organic chemicals. Two-carbon hydrocarbons experimentally produced from irradiated mixtures of methane, ammonia, water, and hydrogen bear out the possible organic chemistry of the Titanian environment.

  5. PROCESS DOCUMENTATION: A MODEL FOR KNOWLEDGE MANAGEMENT IN ORGANIZATIONS

    PubMed Central

    Haddadpoor, Asefeh; Taheri, Behjat; Nasri, Mehran; Heydari, Kamal; Bahrami, Gholamreza

    2015-01-01

    Background: Continuous and interconnected processes are a chain of activities that turn the inputs of an organization to its outputs and help achieve partial and overall goals of the organization. These activates are carried out by two types of knowledge in the organization called explicit and implicit knowledge. Among these, implicit knowledge is the knowledge that controls a major part of the activities of an organization, controls these activities internally and will not be transferred to the process owners unless they are present during the organization’s work. Therefore the goal of this study is identification of implicit knowledge and its integration with explicit knowledge in order to improve human resources management, physical resource management, information resource management, training of new employees and other activities of Isfahan University of Medical Science. Methods: The project for documentation of activities in department of health of Isfahan University of Medical Science was carried out in several stages. First the main processes and related sub processes were identified and categorized with the help of planning expert. The categorization was carried out from smaller processes to larger ones. In this stage the experts of each process wrote down all their daily activities and organized them into general categories based on logical and physical relations between different activities. Then each activity was assigned a specific code. The computer software was designed after understanding the different parts of the processes, including main and sup processes, and categorization, which will be explained in the following sections. Results: The findings of this study showed that documentation of activities can help expose implicit knowledge because all of inputs and outputs of a process along with the length, location, tools and different stages of the process, exchanged information, storage location of the information and information flow can be

  6. Modelling and mapping the topsoil organic carbon content for Tanzania

    NASA Astrophysics Data System (ADS)

    Kempen, Bas; Kaaya, Abel; Ngonyani Mhaiki, Consolatha; Kiluvia, Shani; Ruiperez-Gonzalez, Maria; Batjes, Niels; Dalsgaard, Soren

    2014-05-01

    Soil organic carbon (SOC), held in soil organic matter, is a key indicator of soil health and plays an important role in the global carbon cycle. The soil can act as a net source or sink of carbon depending on land use and management. Deforestation and forest degradation lead to the release of vast amounts of carbon from the soil in the form of greenhouse gasses, especially in tropical countries. Tanzania has a high deforestation rate: it is estimated that the country loses 1.1% of its total forested area annually. During 2010-2013 Tanzania has been a pilot country under the UN-REDD programme. This programme has supported Tanzania in its initial efforts towards reducing greenhouse gas emission from forest degradation and deforestation and towards preserving soil carbon stocks. Formulation and implementation of the national REDD strategy requires detailed information on the five carbon pools among these the SOC pool. The spatial distribution of SOC contents and stocks was not available for Tanzania. The initial aim of this research, was therefore to develop high-resolution maps of the SOC content for the country. The mapping exercise was carried out in a collaborative effort with four Tanzanian institutes and data from the Africa Soil Information Service initiative (AfSIS). The mapping exercise was provided with over 3200 field observations on SOC from four sources; this is the most comprehensive soil dataset collected in Tanzania so far. The main source of soil samples was the National Forest Monitoring and Assessment (NAFORMA). The carbon maps were generated by means of digital soil mapping using regression-kriging. Maps at 250 m spatial resolution were developed for four depth layers: 0-10 cm, 10-20 cm, 20-30 cm, and 0-30 cm. A total of 37 environmental GIS data layers were prepared for use as covariates in the regression model. These included vegetation indices, terrain parameters, surface temperature, spectral reflectances, a land cover map and a small

  7. Modeling the neurodynamic organizations and interactions of teams.

    PubMed

    Stevens, Ronald H; Galloway, Trysha L

    2016-01-01

    Across-brain neurodynamic organizations arise when teams perform coordinated tasks. We describe a symbolic electroencephalographic (EEG) approach that identifies when team neurodynamic organizations occur and demonstrate its utility with scientific problem solving and submarine navigation tasks. Each second, neurodynamic symbols (NS) were created showing the 1-40 Hz EEG power spectral densities for each team member. These data streams contained a performance history of the team's across-brain neurodynamic organizations. The degree of neurodynamic organization was calculated each second from a moving window average of the Shannon entropy over the task. Decreased NS entropy (i.e., greater neurodynamic organization) was prominent in the ~16 Hz EEG bins during problem solving, while during submarine navigation, the maximum NS entropy decreases were ~10 Hz and were associated with establishing the ship's location. Decreased NS entropy also occurred in the 20-40 Hz bins of both teams and was associated with uncertainty or stress. The highest mutual information levels, calculated from the EEG values of team dyads, were associated with decreased NS entropy, suggesting a link between these two measures. These studies show entropy and mutual information mapping of symbolic EEG data streams from teams can be useful for identifying organized across-brain team activation patterns. PMID:26079050

  8. Source apportionment modeling of volatile organic compounds in streams

    USGS Publications Warehouse

    Pankow, J.F.; Asher, W.E.; Zogorski, J.S.

    2006-01-01

    It often is of interest to understand the relative importance of the different sources contributing to the concentration cw of a contaminant in a stream; the portions related to sources 1, 2, 3, etc. are denoted cw,1, cw,2, cw,3, etc. Like c w, 'he fractions ??1, = cw,1/c w, ??2 = cw,2/cw, ??3 = cw,3/cw, etc. depend on location and time. Volatile organic compounds (VOCs) can undergo absorption from the atmosphere into stream water or loss from stream water to the atmosphere, causing complexities affecting the source apportionment (SA) of VOCs in streams. Two SA rules are elaborated. Rule 1: VOC entering a stream across the air/water interface exclusively is assigned to the atmospheric portion of cw. Rule 2: VOC loss by volatilization, flow loss to groundwater, in-stream degradation, etc. is distributed over cw,1 cw,2, c w,3, etc. in proportion to their corresponding ?? values. How the two SA rules are applied, as well as the nature of the SA output for a given case, will depend on whether transport across the air/water interface is handled using the net flux F convention or using the individual fluxes J convention. Four hypothetical stream cases involving acetone, methyl-tert-butyl ether (MTBE), benzene, chloroform, and perchloroethylene (PCE) are considered. Acetone and MTBE are sufficiently water soluble from air for a domestic atmospheric source to be capable of yielding cw values approaching the common water quality guideline range of 1 to 10 ??g/L. For most other VOCs, such levels cause net outgassing (F > 0). When F > 0 in a given section of stream, in the net flux convention, all of the ??j, for the compound remain unchanged over that section while cw decreases. A characteristic time ??d can be calculated to predict when there will be differences between SA results obtained by the net flux convention versus the individual fluxes convention. Source apportionment modeling provides the framework necessary for comparing different strategies for mitigating

  9. Modelling the fate of persistent organic pollutants in europe: parameterization of a gridded distribution model

    SciTech Connect

    Prevedouros, Konstantinos; MacLeod, Matthew; Jones, Kevin C.; Sweetman Andrew J.

    2003-12-01

    A regionally segmented multimedia fate model for the European continent is described together with an illustrative steady-state case study examining the fate of small gamma, Greek-HCH (lindane) based on 1998 emission data. The study builds on the regionally segmented BETR North America model structure and describes the regional segmentation and parameterization for Europe. The European continent is described by a 5 degree x 5 degree grid, leading to 50 regions together with four perimetric boxes representing regions buffering the European environment. Each zone comprises seven compartments including; upper and lower atmosphere, soil, vegetation, fresh water and sediment and coastal water. Inter-regions flows of air and water are described, exploiting information originating from GIS databases and other georeferenced data. The model is primarily designed to describe the fate of Persistent Organic Pollutants (POPs) within the European environment by examining chemical partitioning and de gradation in each region, and inter-region transport either under steady-state conditions or fully dynamically. A test case scenario is presented which examines the fate of estimated spatially resolved atmospheric emissions of lindane throughout Europe within the lower atmosphere and surface soil compartments. In accordance with the predominant wind direction in Europe, the model predicts high concentrations close to the major sources as well as towards Central and Northeast regions. Elevated soil concentrations in Scandinavian soils provide further evidence of the potential of increased scavenging by forests and subsequent accumulation by organic-rich terrestrial surfaces. Initial model predictions have revealed a factor of 5 10 underestimation of lindane concentrations in the atmosphere. This is explained by an underestimation of source strength and/or an underestimation of European background levels. The model presented can further be used to predict deposition fluxes and chemical

  10. Models of Micro-Organisms: Children's Knowledge and Understanding of Micro-Organisms from 7 to 14 Years Old

    ERIC Educational Resources Information Center

    Byrne, Jenny

    2011-01-01

    This paper describes the expressed models that children aged 7, 11, and 14 years have about micro-organisms and microbial activity. These were elicited using a variety of data collection techniques that complemented each other, resulting in a rich dataset, and provided information about the level of knowledge and progression of ideas across the…

  11. Double-stranded DNA organization in bacteriophage heads: An alternative toroid-based model

    SciTech Connect

    Hud, N.V.

    1995-10-01

    Studies of the organization of double-stranded DNA within bacteriophage heads during the past four decades have produced a wealth of data. However, despite the presentation of numerous models, the true organization of DNA within phage heads remains unresolved. The observations of toroidal DNA structures in electron micrographs of phage lysates have long been cited as support for the organization of DNA in a spool-like fashion. This particular model, like all other models, has not been found to be consistent with all available data. Recently, the authors proposed that DNA within toroidal condensates produced in vitro is organized in a manner significantly different from that suggested by the spool model. This new toroid model has allowed the development of an alternative model for DNA organization within bacteriophage heads that is consistent with a wide range of biophysical data. Here the authors propose that bacteriophage DNA is packaged in a toroid that is folded into a highly compact structure.

  12. A computational model predicts Xenopus meiotic spindle organization

    PubMed Central

    Loughlin, Rose

    2010-01-01

    The metaphase spindle is a dynamic bipolar structure crucial for proper chromosome segregation, but how microtubules (MTs) are organized within the bipolar architecture remains controversial. To explore MT organization along the pole-to-pole axis, we simulated meiotic spindle assembly in two dimensions using dynamic MTs, a MT cross-linking force, and a kinesin-5–like motor. The bipolar structures that form consist of antiparallel fluxing MTs, but spindle pole formation requires the addition of a NuMA-like minus-end cross-linker and directed transport of MT depolymerization activity toward minus ends. Dynamic instability and minus-end depolymerization generate realistic MT lifetimes and a truncated exponential MT length distribution. Keeping the number of MTs in the simulation constant, we explored the influence of two different MT nucleation pathways on spindle organization. When nucleation occurs throughout the spindle, the simulation quantitatively reproduces features of meiotic spindles assembled in Xenopus egg extracts. PMID:21173114

  13. Microfluidic tools for developmental studies of small model organisms--nematodes, fruit flies, and zebrafish.

    PubMed

    Hwang, Hyundoo; Lu, Hang

    2013-02-01

    Studying the genetics of development with small model organisms such as the zebrafish (Danio Rerio), the fruit fly (Drosophila melanogaster), and the soil-dwelling nematode (Caenorhabditis elegans), provide unique opportunities for understanding related processes and diseases in humans. These model organisms also have potential for use in drug discovery and toxicity-screening applications. There have been sweeping developments in microfabrication and microfluidic technologies for manipulating and imaging small objects, including small model organisms, which allow high-throughput quantitative biological studies. Here, we review recent progress in microfluidic tools able to manipulate small organisms and project future directions and applications of these techniques and technologies. PMID:23161817

  14. Keeping the Faith: A Model of Cultural Transmission in Formal Organizations.

    ERIC Educational Resources Information Center

    Harrison, J. Richard; Carroll, Glenn R.

    1991-01-01

    Develops a cultural transmission model with the following variables: worker entry and exit rate, organization growth rate, recruiting selectivity, socialization intensity, and the rate that socialization decays if not reinforced. A computer simulation of the model found that cultural systems in organizations are highly robust and reach equilibrium…

  15. Alinsky's Reveille: A Community-Organizing Model for Neighborhood-Based Literacy Project

    ERIC Educational Resources Information Center

    Goldblatt, Eli

    2005-01-01

    A community-organizing model for neighborhood-based literacy project is presented, which is based on the works of Saul Alinsky, who was an influential community organizer during the period from 1930s to the 1960s. The model shows that it is possible to reframe the sites and texts of literacy instruction by having satisfying and reciprocating…

  16. The Family FIRO Model: A Modest Proposal for Organizing Family Treatment.

    ERIC Educational Resources Information Center

    Doherty, William J.; Colangelo, Nicholas

    1984-01-01

    Presents a model for organizing family issues and family treatment. Schutz's Fundamental Interpersonal Relations Orientation (FIRO) model is offered as a framework for organizing family issues into inclusion, control, and affection categories, constituting a logical hierarchy of core issues to be dealt with in treating multiproblem families. (JAC)

  17. From Learning Object to Learning Cell: A Resource Organization Model for Ubiquitous Learning

    ERIC Educational Resources Information Center

    Yu, Shengquan; Yang, Xianmin; Cheng, Gang; Wang, Minjuan

    2015-01-01

    This paper presents a new model for organizing learning resources: Learning Cell. This model is open, evolving, cohesive, social, and context-aware. By introducing a time dimension into the organization of learning resources, Learning Cell supports the dynamic evolution of learning resources while they are being used. In addition, by introducing a…

  18. Modeling the Current and Future Roles of Particulate Organic Nitrates in the Southeastern United States.

    PubMed

    Pye, Havala O T; Luecken, Deborah J; Xu, Lu; Boyd, Christopher M; Ng, Nga L; Baker, Kirk R; Ayres, Benjamin R; Bash, Jesse O; Baumann, Karsten; Carter, William P L; Edgerton, Eric; Fry, Juliane L; Hutzell, William T; Schwede, Donna B; Shepson, Paul B

    2015-12-15

    Organic nitrates are an important aerosol constituent in locations where biogenic hydrocarbon emissions mix with anthropogenic NOx sources. While regional and global chemical transport models may include a representation of organic aerosol from monoterpene reactions with nitrate radicals (the primary source of particle-phase organic nitrates in the Southeast United States), secondary organic aerosol (SOA) models can underestimate yields. Furthermore, SOA parametrizations do not explicitly take into account organic nitrate compounds produced in the gas phase. In this work, we developed a coupled gas and aerosol system to describe the formation and subsequent aerosol-phase partitioning of organic nitrates from isoprene and monoterpenes with a focus on the Southeast United States. The concentrations of organic aerosol and gas-phase organic nitrates were improved when particulate organic nitrates were assumed to undergo rapid (τ = 3 h) pseudohydrolysis resulting in nitric acid and nonvolatile secondary organic aerosol. In addition, up to 60% of less oxidized-oxygenated organic aerosol (LO-OOA) could be accounted for via organic nitrate mediated chemistry during the Southern Oxidants and Aerosol Study (SOAS). A 25% reduction in nitrogen oxide (NO + NO2) emissions was predicted to cause a 9% reduction in organic aerosol for June 2013 SOAS conditions at Centreville, Alabama. PMID:26544021

  19. VOLATILE ORGANIC COMPOUND MODEL (VERSION 1.8) (FOR MICROCOMPUTERS)

    EPA Science Inventory

    Future emissions of volatile organic compounds (VOCs) and costs of their control can be estimated by applying growth factors, emission constraints, control cost functions, and capacity retirement rates to the base line estimates of VOC emissions and industrial VOC source capacity...

  20. Modeling emissions of volatile organic compounds from silage

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Photochemical smog is a major air pollution problem and a significant cause of premature death in the U.S. Smog forms in the presence of volatile organic compounds (VOCs), which are emitted primarily from industry and motor vehicles in the U.S. However, dairy farms may be an important source in so...

  1. Investigation of membrane fouling in ultrafiltration using model organic compounds.

    PubMed

    Kweon, J H; Lawler, D F

    2005-01-01

    Natural organic matter (NOM) is known to be the worst foulant in the membrane processes, but the complexities of NOM make it difficult to determine its effects on membrane fouling. Therefore, simple organic compounds (surrogates for NOM) were used in this research to investigate the fouling mechanisms in ultrafiltration. Previous research on NOM components in membrane processes indicated that polysaccharides formed an important part of the fouling cake. Three polysaccharides (dextran, alginic acid, and polygalacturonic acid) and a smaller carbohydrate (tannic acid) were evaluated for their removal in softening (the treatment process in the City of Austin). Two polysaccharides (dextran and alginic acid) were selected and further investigated for their effects on membrane fouling. The two raw organic waters (4 mg/L C) showed quite different patterns of flux decline indicating different fouling mechanisms. Softening pretreatment was effective to reduce flux decline of both waters. The SEM images of the fouled membrane clearly showed the shapes of deposited foulants. The high resolution results of the XPS spectra showed substantially different spectra of carbon, C(1s), in the membrane fouled by two raw organic waters. The XPS was beneficial in determining the relative composition of each fouling material on the membrane surface. PMID:16003967

  2. The Learning Organization: A Model for Educational Change.

    ERIC Educational Resources Information Center

    Brown, Rexford

    1997-01-01

    Analyzes public school bureaucracy and ways to reform institutions into learning communities that value shared knowledge and learning experiences. Describes how a bureaucratic organizational structure impairs learning. Proposes the "learning organization" in which adults learn alongside students, planning is decentralized, families are part of the…

  3. MICROBIAL VOLATILE ORGANIC COMPOUND EMISSION RATES AND EXPOSURE MODEL

    EPA Science Inventory

    This paper presents the results from a study that examined microbial volatile organic compound (MVOC) emissions from six fungi and one bacterial species (Streptomyces spp.) commonly found in indoor environments. Data are presented on peak emission rates from inoculated agar plate...

  4. Explicit modeling of organic chemistry and secondary organic aerosol partitioning for Mexico City and its outflow plume

    SciTech Connect

    Lee-Taylor, J.; Madronich, Sasha; Aumont, B.; Baker, A.; Camredon, M.; Hodzic, Alma; Tyndall, G. S.; Apel, Eric; Zaveri, Rahul A.

    2011-12-21

    The evolution of organic aerosols (OA) in Mexico City and its outflow is investigated with the nearly explicit gas phase photochemistry model GECKO-A (Generator of Explicit Chemistry and Kinetics of Organics in the Atmosphere), wherein precursor hydrocarbons are oxidized to numerous intermediate species for which vapor pressures are computed and used to determine gas/particle partitioning in a chemical box model. Precursor emissions included observed C3-10 alkanes, alkenes, and light aromatics, as well as larger n-alkanes (up to C25) not directly observed but estimated by scaling to particulate emissions according to their volatility. Conditions were selected for comparison with observations made in March 2006 (MILAGRO). The model successfully reproduces the magnitude and diurnal shape for both primary (POA) and secondary (SOA) organic aerosols, with POA peaking in the early morning at 15-20 ug m-3, and SOA peaking at 10-15 μg m-3 during mid-day. The majority (> 75%) of the model SOA stems from the large n-alkanes, with the remainder mostly from the light aromatics. Simulated OA elemental composition reproduces observed H/C and O/C ratios reasonably well, although modeled ratios develop more slowly than observations suggest. SOA chemical composition is initially dominated by *- hydroxy ketones and nitrates from the large alkanes, with contributions from peroxy acyl nitrates and, at later times when NOx is lower, organic hydroperoxides. The simulated plume-integrated OA mass continues to increase for several days downwind despite dilution-induced particle evaporation, since oxidation chemistry leading to SOA formation remains strong. In this model, the plume SOA burden several days downwind exceeds that leaving the city by a factor of >3. These results suggest significant regional radiative impacts of SOA.

  5. Explicit modeling of organic chemistry and secondary organic aerosol partitioning for Mexico City and its outflow plume

    NASA Astrophysics Data System (ADS)

    Lee-Taylor, J.; Madronich, S.; Aumont, B.; Baker, A.; Camredon, M.; Hodzic, A.; Tyndall, G. S.; Apel, E.; Zaveri, R. A.

    2011-12-01

    The evolution of organic aerosols (OA) in Mexico City and its outflow is investigated with the nearly explicit gas phase photochemistry model GECKO-A (Generator of Explicit Chemistry and Kinetics of Organics in the Atmosphere), wherein precursor hydrocarbons are oxidized to numerous intermediate species for which vapor pressures are computed and used to determine gas/particle partitioning in a chemical box model. Precursor emissions included observed C3-10 alkanes, alkenes, and light aromatics, as well as larger n-alkanes (up to C25) not directly observed but estimated by scaling to particulate emissions according to their volatility. Conditions were selected for comparison with observations made in March 2006 (MILAGRO). The model successfully reproduces the magnitude and diurnal shape for both primary (POA) and secondary (SOA) organic aerosols, with POA peaking in the early morning at 15-20 μg m-3, and SOA peaking at 10-15 μg m-3 during mid-day. The majority (≥75%) of the model SOA stems from reaction products of the large n-alkanes, used here as surrogates for all emitted hydrocarbons of similar volatility, with the remaining SOA originating mostly from the light aromatics. Simulated OA elemental composition reproduces observed H/C and O/C ratios reasonably well, although modeled ratios develop more slowly than observations suggest. SOA chemical composition is initially dominated by δ-hydroxy ketones and nitrates from the large alkanes, with contributions from peroxy acyl nitrates and, at later times when NOx is lower, organic hydroperoxides. The simulated plume-integrated OA mass continues to increase for several days downwind despite dilution-induced particle evaporation, since oxidation chemistry leading to SOA formation remains strong. In this model, the plume SOA burden several days downwind exceeds that leaving the city by a factor of >3. These results suggest significant regional radiative impacts of SOA.

  6. Ames Culture Chamber System: Enabling Model Organism Research Aboard the international Space Station

    NASA Technical Reports Server (NTRS)

    Steele, Marianne

    2014-01-01

    Understanding the genetic, physiological, and behavioral effects of spaceflight on living organisms and elucidating the molecular mechanisms that underlie these effects are high priorities for NASA. Certain organisms, known as model organisms, are widely studied to help researchers better understand how all biological systems function. Small model organisms such as nem-atodes, slime mold, bacteria, green algae, yeast, and moss can be used to study the effects of micro- and reduced gravity at both the cellular and systems level over multiple generations. Many model organisms have sequenced genomes and published data sets on their transcriptomes and proteomes that enable scientific investigations of the molecular mechanisms underlying the adaptations of these organisms to space flight.

  7. [Generation of bioartificial organs. The cornea as a model].

    PubMed

    Campos Muñoz, Antonio; Alaminos Mingorance, Miguel

    2011-01-01

    The development of bioartificial organs is a new target in the development of tissue engineering. It consists in the use of stem cells in a decellularized stroma of other organs. In this paper we present our previous experience in the construction of a complete artificial cornea using cell cultures and biomaterials and compare it with the construction of a bioartificial cornea using a decellularized porcine stroma. The results, in building this new type of cornea, showed that 1.5 M NaCl treatment of porcine corneas is able to generate an acellular corneal stroma with adequate histologic and optical properties and that human keratocytes are able to penetrate and spread within this scaffold with proper levels of cell differentiation. In contrast, 0.1% SDS treatment of porcine corneas resulted in high levels of fibril disorganization and poor optical behavior of these corneas. PMID:23350328

  8. CMAQ model performance enhanced when in-cloud secondary organic aerosol is included: comparisons of organic carbon predictions with measurements.

    PubMed

    Carlton, Annmarie G; Turpin, Barbara I; Altieri, Katye E; Seitzinger, Sybil P; Mathur, Rohit; Roselle, Shawn J; Weber, Rodney J

    2008-12-01

    Mounting evidence suggests that low-volatility (particle-phase) organic compounds form in the atmosphere through aqueous phase reactions in clouds and aerosols. Although some models have begun including secondary organic aerosol (SOA) formation through cloud processing, validation studies that compare predictions and measurements are needed. In this work, agreement between modeled organic carbon (OC) and aircraft measurements of water soluble OC improved for all 5 of the compared ICARTT NOAA-P3 flights during August when an in-cloud SOA (SOAcld) formation mechanism was added to CMAQ (a regional-scale atmospheric model). The improvement was most dramatic for the August 14th flight, a flight designed specifically to investigate clouds. During this flight the normalized mean bias for layer-averaged OC was reduced from -64 to -15% and correlation (r) improved from 0.5 to 0.6. Underpredictions of OC aloft by atmospheric models may be explained, in part, by this formation mechanism (SOAcld). OC formation aloft contributes to long-range pollution transport and has implications to radiative forcing, regional air quality and climate. PMID:19192800

  9. Modeling the surface tension of complex, reactive organic-inorganic mixtures

    NASA Astrophysics Data System (ADS)

    Schwier, A. N.; Viglione, G. A.; Li, Z.; McNeill, V. Faye

    2013-11-01

    Atmospheric aerosols can contain thousands of organic compounds which impact aerosol surface tension, affecting aerosol properties such as heterogeneous reactivity, ice nucleation, and cloud droplet formation. We present new experimental data for the surface tension of complex, reactive organic-inorganic aqueous mixtures mimicking tropospheric aerosols. Each solution contained 2-6 organic compounds, including methylglyoxal, glyoxal, formaldehyde, acetaldehyde, oxalic acid, succinic acid, leucine, alanine, glycine, and serine, with and without ammonium sulfate. We test two semi-empirical surface tension models and find that most reactive, complex, aqueous organic mixtures which do not contain salt are well described by a weighted Szyszkowski-Langmuir (S-L) model which was first presented by Henning et al. (2005). Two approaches for modeling the effects of salt were tested: (1) the Tuckermann approach (an extension of the Henning model with an additional explicit salt term), and (2) a new implicit method proposed here which employs experimental surface tension data obtained for each organic species in the presence of salt used with the Henning model. We recommend the use of method (2) for surface tension modeling of aerosol systems because the Henning model (using data obtained from organic-inorganic systems) and Tuckermann approach provide similar modeling results and goodness-of-fit (χ2) values, yet the Henning model is a simpler and more physical approach to modeling the effects of salt, requiring less empirically determined parameters.

  10. Modeling the surface tension of complex, reactive organic-inorganic mixtures

    NASA Astrophysics Data System (ADS)

    Schwier, A. N.; Viglione, G. A.; Li, Z.; McNeill, V. F.

    2013-01-01

    Atmospheric aerosols can contain thousands of organic compounds which impact aerosol surface tension, affecting aerosol properties such as cloud condensation nuclei (CCN) ability. We present new experimental data for the surface tension of complex, reactive organic-inorganic aqueous mixtures mimicking tropospheric aerosols. Each solution contained 2-6 organic compounds, including methylglyoxal, glyoxal, formaldehyde, acetaldehyde, oxalic acid, succinic acid, leucine, alanine, glycine, and serine, with and without ammonium sulfate. We test two surface tension models and find that most reactive, complex, aqueous organic mixtures which do not contain salt are well-described by a weighted Szyszkowski-Langmuir (S-L) model which was first presented by Henning et al. (2005). Two approaches for modeling the effects of salt were tested: (1) the Tuckermann approach (an extension of the Henning model with an additional explicit salt term), and (2) a new implicit method proposed here which employs experimental surface tension data obtained for each organic species in the presence of salt used with the Henning model. We recommend the use of method (2) for surface tension modeling because the Henning model (using data obtained from organic-inorganic systems) and Tuckermann approach provide similar modeling fits and goodness of fit (χ2) values, yet the Henning model is a simpler and more physical approach to modeling the effects of salt, requiring less empirically determined parameters.

  11. What RNAi screens in model organisms revealed about microbicidal response in mammals?

    PubMed Central

    Abnave, Prasad; Conti, Filippo; Torre, Cedric; Ghigo, Eric

    2015-01-01

    The strategies evolved by pathogens to infect hosts and the mechanisms used by the host to eliminate intruders are highly complex. Because several biological pathways and processes are conserved across model organisms, these organisms have been used for many years to elucidate and understand the mechanisms of the host-pathogen relationship and particularly to unravel the molecular processes enacted by the host to kill pathogens. The emergence of RNA interference (RNAi) and the ability to apply it toward studies in model organisms have allowed a breakthrough in the elucidation of host-pathogen interactions. The aim of this mini-review is to highlight and describe recent breakthroughs in the field of host-pathogen interactions using RNAi screens of model organisms. We will focus specifically on the model organisms Drosophila melanogaster, Caenorhabditis elegans, and Danio rerio. Moreover, a recent study examining the immune system of planarian will be discussed. PMID:25629007

  12. Group-enabled DEVS model construction methodology for distributed organizations

    NASA Astrophysics Data System (ADS)

    Sarjoughian, Hessam S.; Vahie, Sankait; Lee, James D.

    1997-06-01

    A USAF project has been initiated to enable groupware that currently supports IDEF activity model capture to be extended to support DEVS model construction. The methodology developed for this purpose enables team participants to enter activity data and then be queried for additional data that support DEVS system decomposition, assigning the activities to components and adding in relevant dynamics.

  13. Politics, Organizations, and Choice: Applications of an Equilibrium Model

    ERIC Educational Resources Information Center

    Roos, Leslie L., Jr.

    1972-01-01

    An economic model of consumer choice is used to link the separate theories that have dealt with comparative politics, job satisfaction, and organizational mobility. The model is used to structure data taken from studies of Turkish and French elites on environmental change, organizational mobility, and satisfaction. (Author/DN)

  14. Drosophila melanogaster as a Model Organism of Brain Diseases

    PubMed Central

    Jeibmann, Astrid; Paulus, Werner

    2009-01-01

    Drosophila melanogaster has been utilized to model human brain diseases. In most of these invertebrate transgenic models, some aspects of human disease are reproduced. Although investigation of rodent models has been of significant impact, invertebrate models offer a wide variety of experimental tools that can potentially address some of the outstanding questions underlying neurological disease. This review considers what has been gleaned from invertebrate models of neurodegenerative diseases, including Alzheimer’s disease, Parkinson’s disease, metabolic diseases such as Leigh disease, Niemann-Pick disease and ceroid lipofuscinoses, tumor syndromes such as neurofibromatosis and tuberous sclerosis, epilepsy as well as CNS injury. It is to be expected that genetic tools in Drosophila will reveal new pathways and interactions, which hopefully will result in molecular based therapy approaches. PMID:19333415

  15. Using semantic data modeling techniques to organize an object-oriented database for extending the mass storage model

    NASA Technical Reports Server (NTRS)

    Campbell, William J.; Short, Nicholas M., Jr.; Roelofs, Larry H.; Dorfman, Erik

    1991-01-01

    A methodology for optimizing organization of data obtained by NASA earth and space missions is discussed. The methodology uses a concept based on semantic data modeling techniques implemented in a hierarchical storage model. The modeling is used to organize objects in mass storage devices, relational database systems, and object-oriented databases. The semantic data modeling at the metadata record level is examined, including the simulation of a knowledge base and semantic metadata storage issues. The semantic data model hierarchy and its application for efficient data storage is addressed, as is the mapping of the application structure to the mass storage.

  16. Pediatric Chest and Abdominopelvic CT: Organ Dose Estimation Based on 42 Patient Models

    PubMed Central

    Tian, Xiaoyu; Li, Xiang; Segars, W. Paul; Paulson, Erik K.; Frush, Donald P.

    2014-01-01

    Purpose To estimate organ dose from pediatric chest and abdominopelvic computed tomography (CT) examinations and evaluate the dependency of organ dose coefficients on patient size and CT scanner models. Materials and Methods The institutional review board approved this HIPAA–compliant study and did not require informed patient consent. A validated Monte Carlo program was used to perform simulations in 42 pediatric patient models (age range, 0–16 years; weight range, 2–80 kg; 24 boys, 18 girls). Multidetector CT scanners were modeled on those from two commercial manufacturers (LightSpeed VCT, GE Healthcare, Waukesha, Wis; SOMATOM Definition Flash, Siemens Healthcare, Forchheim, Germany). Organ doses were estimated for each patient model for routine chest and abdominopelvic examinations and were normalized by volume CT dose index (CTDIvol). The relationships between CTDIvol-normalized organ dose coefficients and average patient diameters were evaluated across scanner models. Results For organs within the image coverage, CTDIvol-normalized organ dose coefficients largely showed a strong exponential relationship with the average patient diameter (R2 > 0.9). The average percentage differences between the two scanner models were generally within 10%. For distributed organs and organs on the periphery of or outside the image coverage, the differences were generally larger (average, 3%–32%) mainly because of the effect of overranging. Conclusion It is feasible to estimate patient-specific organ dose for a given examination with the knowledge of patient size and the CTDIvol. These CTDIvol-normalized organ dose coefficients enable one to readily estimate patient-specific organ dose for pediatric patients in clinical settings. This dose information, and, as appropriate, attendant risk estimations, can provide more substantive information for the individual patient for both clinical and research applications and can yield more expansive information on dose profiles

  17. AEROSOL INORGANICS AND ORGANICS MODEL (AIOM) WITH USER DEFINED PROPERTIES FOR ORGANIC COMPOUNDS

    EPA Science Inventory

    The Aerosol Inorganics Model (AIM) is widely used to calculate gas/liquid/solid phase equilibrium in aerosol systems containing the species H+-NH4+-SO42--NO3--H2O over a range of tropospheric ...

  18. Modeling and predicting competitive sorption of organic compounds in soil

    PubMed Central

    Faria, Isabel R.; Young, Thomas M.

    2011-01-01

    Binary systems consisting of 1,2-dichlorobenzene (12DCB) + competitor were investigated over a range of concentrations of competitor in three natural sorbents with distinct characteristics. Two models, the ideal adsorbed solution theory (IAST) and the Potential theory (Polanyi based multi-solute model), widely used in the prediction of multi-solute sorption equilibrium from single solute data were used to simulate competitive sorption in our systems. The goal was to determine which multi-solute model best represented the experimentally obtained multi-solute data in natural sorbents of varied properties. Results suggested that for the sorbents and sorbates studied the IAST model provided much better results. On average the IAST model provided lower errors (23%) than the Potential model (45%). The effect of competitor structure on the degree of competition was also investigated to identify any relationships between competition and structure using molecular descriptors. The competitors chlorobenzene, naphthalene, 1,4-dichlorobenzene, 1,2,4-trichlorobenzene all showed very similar degrees of competition, while benzene, phenanthrene and pyrene were the least effective competitors towards 12DCB across all sorbents. Different sorption sites or sorption mechanisms might be involved in the sorption of these molecules leading to a lack of competitive behavior. A significant relationship between competitor structure and the degree of competition was observed at environmentally relevant sorbed competitor concentrations for the soil containing the highest fraction of hard carbon (Forbes). PMID:21061392

  19. InterMOD: integrated data and tools for the unification of model organism research.

    PubMed

    Sullivan, Julie; Karra, Kalpana; Moxon, Sierra A T; Vallejos, Andrew; Motenko, Howie; Wong, J D; Aleksic, Jelena; Balakrishnan, Rama; Binkley, Gail; Harris, Todd; Hitz, Benjamin; Jayaraman, Pushkala; Lyne, Rachel; Neuhauser, Steven; Pich, Christian; Smith, Richard N; Trinh, Quang; Cherry, J Michael; Richardson, Joel; Stein, Lincoln; Twigger, Simon; Westerfield, Monte; Worthey, Elizabeth; Micklem, Gos

    2013-01-01

    Model organisms are widely used for understanding basic biology, and have significantly contributed to the study of human disease. In recent years, genomic analysis has provided extensive evidence of widespread conservation of gene sequence and function amongst eukaryotes, allowing insights from model organisms to help decipher gene function in a wider range of species. The InterMOD consortium is developing an infrastructure based around the InterMine data warehouse system to integrate genomic and functional data from a number of key model organisms, leading the way to improved cross-species research. So far including budding yeast, nematode worm, fruit fly, zebrafish, rat and mouse, the project has set up data warehouses, synchronized data models, and created analysis tools and links between data from different species. The project unites a number of major model organism databases, improving both the consistency and accessibility of comparative research, to the benefit of the wider scientific community. PMID:23652793

  20. Use of model organisms for the study of neuronal ceroid lipofuscinosis.

    PubMed

    Bond, Michael; Holthaus, Sophia-Martha Kleine; Tammen, Imke; Tear, Guy; Russell, Claire

    2013-11-01

    Neuronal ceroid lipofuscinoses are a group of fatal progressive neurodegenerative diseases predominantly affecting children. Identification of mutations that cause neuronal ceroid lipofuscinosis, and subsequent functional and pathological studies of the affected genes, underpins efforts to investigate disease mechanisms and identify and test potential therapeutic strategies. These functional studies and pre-clinical trials necessitate the use of model organisms in addition to cell and tissue culture models as they enable the study of protein function within a complex organ such as the brain and the testing of therapies on a whole organism. To this end, a large number of disease models and genetic tools have been identified or created in a variety of model organisms. In this review, we will discuss the ethical issues associated with experiments using model organisms, the factors underlying the choice of model organism, the disease models and genetic tools available, and the contributions of those disease models and tools to neuronal ceroid lipofuscinosis research. This article is part of a Special Issue entitled: The Neuronal Ceroid Lipofuscinoses or Batten Disease. PMID:23338040

  1. A non-equilibrium model for predicting bioaccumulation of organic contaminants in aquatic food-webs

    SciTech Connect

    Morrison, H.; Lazar, R.; Haffner, G.D.; Whittle, D.M.; Gobas, F.A.P.C.

    1995-12-31

    A sub-model describing bioaccumulation and biomagnification in benthic invertebrates was incorporated into a steady-state food-web model (Gobas, 1993) was modified, to estimate concentrations of organic contaminants in aquatic organisms based on chemical concentrations in water and sediments. Model predictions were in good agreement with field data when applied to western Lake Erie. The improved ability of the model to simulate bioaccumulation by benthic invertebrates, makes this model particularly useful for quantifying contaminant transfer in the benthic food-web.

  2. Object-oriented urban 3D spatial data model organization method

    NASA Astrophysics Data System (ADS)

    Li, Jing-wen; Li, Wen-qing; Lv, Nan; Su, Tao

    2015-12-01

    This paper combined the 3d data model with object-oriented organization method, put forward the model of 3d data based on object-oriented method, implemented the city 3d model to quickly build logical semantic expression and model, solved the city 3d spatial information representation problem of the same location with multiple property and the same property with multiple locations, designed the space object structure of point, line, polygon, body for city of 3d spatial database, and provided a new thought and method for the city 3d GIS model and organization management.

  3. Caenorhabditis elegans, a Model Organism for Investigating Immunity

    PubMed Central

    Marsh, Elizabeth K.

    2012-01-01

    The nematode Caenorhabditis elegans has been a powerful experimental organism for almost half a century. Over the past 10 years, researchers have begun to exploit the power of C. elegans to investigate the biology of a number of human pathogens. This work has uncovered mechanisms of host immunity and pathogen virulence that are analogous to those involved during pathogenesis in humans or other animal hosts, as well as novel immunity mechanisms which appear to be unique to the worm. More recently, these investigations have uncovered details of the natural pathogens of C. elegans, including the description of a novel intracellular microsporidian parasite as well as new nodaviruses, the first identification of viral infections of this nematode. In this review, we consider the application of C. elegans to human infectious disease research, as well as consider the nematode response to these natural pathogens. PMID:22286994

  4. Electrophysiological Modeling of Cardiac Ventricular Function: From Cell to Organ

    PubMed Central

    Winslow, R. L.; Scollan, D. F.; Holmes, A.; Yung, C. K.; Zhang, J.; Jafri, M. S.

    2005-01-01

    Three topics of importance to modeling the integrative function of the heart are reviewed. The first is modeling of the ventricular myocyte. Emphasis is placed on excitation-contraction coupling and intracellular Ca2+ handling, and the interpretation of experimental data regarding interval-force relationships. Second, data on use of diffusion tensor magnetic resonance (DTMR) imaging for measuring the anatomical structure of the cardiac ventricles are presented. A method for the semi-automated reconstruction of the ventricles using a combination of gradient recalled acquisition in the steady state (GRASS) and DTMR images is described. Third, we describe how these anatomically and biophysically based models of the cardiac ventricles can be implemented on parallel computers. PMID:11701509

  5. Modeling emissions of volatile organic compounds from silage storages and feed lanes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    An initial volatile organic compound (VOC) emission model for silage sources, developed using experimental data from previous studies, was incorporated into the Integrated Farm System Model (IFSM), a whole-farm simulation model used to assess the performance, environmental impacts, and economics of ...

  6. Teaching International Organization through Model U.N.'s.

    ERIC Educational Resources Information Center

    Karns, Margaret Padelford

    Model United Nations (MUN) conferences are held throughout the United States each year to help college students learn about major international issues and the problems and possibilities for international cooperation. There are many educational aspects of the MUN program in which students play the role of a representative of a particular country to…

  7. Learning Strategies for Police Organization--Modeling Organizational Learning Perquisites.

    ERIC Educational Resources Information Center

    Luoma, Markku; Nokelainen, Petri; Ruohotie, Pekka

    The factors contributing to organizational learning in police units in Finland and elsewhere were examined to find strategies to improve the prerequisites of learning and compare linear and nonlinear methods of modeling organizational learning prerequisites. A questionnaire was used to collect data from the 281 staff members of five police…

  8. Concentric Collaboration: A Model of Leadership Development for Healthcare Organizations

    ERIC Educational Resources Information Center

    Roberts, Cynthia; Coghlan, David

    2011-01-01

    Drawing on their experience in a Midwest healthcare system, the authors propose a model of leadership development through action learning that embraces "concentric collaboration" at its core. The present study suggests that the process of concentric collaboration can serve to strengthen the skills of the individual leader as well as foster…

  9. Changing Organizations by Changing Individuals: A Model of Leadership Training.

    ERIC Educational Resources Information Center

    Bloom, Paula Jorde; Sheerer, Marilyn

    1992-01-01

    Effectiveness of a training model in a leadership training program for Head Start personnel was assessed quantitatively and qualitatively for 31 participants. Results demonstrate positive effects on perceived competence, the quality of teaching practices, and the organizational climate of Head Start centers. Case studies further support these…

  10. Year of Coordinated Observations, Modeling and Forecasting: Addressing the Challenge of Organized Tropical Convection

    NASA Technical Reports Server (NTRS)

    Waliser, Duane E.

    2006-01-01

    The multi-scale organization of tropical convection and scale interaction are grand challenges in the prediction of weather and climate. As part of a international effort UN Year of Planet Earth, this proposed effort to observe, model and forecast the effects of organized tropical convection is reviewed. This viewgraph presentation reviews the proposal.

  11. From Learning Object to Learning Cell: A Resource Organization Model for Ubiquitous Learning

    ERIC Educational Resources Information Center

    Yu, Shengquan; Yang, Xianmin; Cheng, Gang

    2013-01-01

    The key to implementing ubiquitous learning is the construction and organization of learning resources. While current research on ubiquitous learning has primarily focused on concept models, supportive environments and small-scale empirical research, exploring ways to organize learning resources to make them available anywhere on-demand is also…

  12. Teaching Diversified Organic Crop Production Using the Community Supported Agriculture Farming System Model

    ERIC Educational Resources Information Center

    Falk, Constance L.; Pao, Pauline; Cramer, Christopher S.

    2005-01-01

    An organic garden operated as a community supported agriculture (CSA) venture on the New Mexico State University (NMSU) main campus was begun in January 2002. Students enroll in an organic vegetable production class during spring and fall semesters to help manage and work on the project. The CSA model of farming involves the sale of shares to…

  13. VOLATILE ORGANIC COMPOUND MODEL-QUALITY ASSURANCE AND SENSITIVITY TESTING (VERSION 1.8)

    EPA Science Inventory

    The report describes test runs of the Volatile Organic Compound Model (VOCM), Version 1.8. VOCM predicts future emission levels of volatile organic compounds (VOCs) by projecting uncontrolled base year emissions into the future. These projected emissions are then reduced by const...

  14. Indoor Residence Times of Semivolatile Organic Compounds: Model Estimation and Field Evaluation

    EPA Science Inventory

    Indoor residence times of semivolatile organic compounds (SVOCs) are a major and mostly unavailable input for residential exposure assessment. We calculated residence times for a suite of SVOCs using a fugacity model applied to residential environments. Residence times depend on...

  15. Lessons Learned About Organic Aerosol Formation in the Southeast U.S. Using Observations and Modeling

    EPA Science Inventory

    Isoprene emitted by vegetation is an important precursor of secondary organic aerosol (SOA). In this work, modeling of isoprene SOA via heterogeneous uptake is explored and compared to observations from the Southern Oxidant and Aerosol Study (SOAS).

  16. Model Representation of Secondary Organic Aerosol in CMAQ v4.7

    EPA Science Inventory

    Numerous scientific upgrades to the representation of secondary organic aerosol (SOA) are incorporated into the Community Multiscale Air Quality (CMAQ) modeling system. Additions include several recently identified SOA precursors: benzene, isoprene, and sesquiterpenes; and pathwa...

  17. Modeling the Role of Alkanes, Polycyclic Aromatic Hydrocarbons, and Their Oligomers in Secondary Organic Aerosol Formation

    EPA Science Inventory

    A computationally efficient method to treat secondary organic aerosol (SOA) from various length and structure alkanes as well as SOA from polycyclic aromatic hydrocarbons (PAHs) is implemented in the Community Multiscale Air Quality (CMAQ) model to predict aerosol concentrations ...

  18. Sleep and Development in Genetically Tractable Model Organisms.

    PubMed

    Kayser, Matthew S; Biron, David

    2016-05-01

    Sleep is widely recognized as essential, but without a clear singular function. Inadequate sleep impairs cognition, metabolism, immune function, and many other processes. Work in genetic model systems has greatly expanded our understanding of basic sleep neurobiology as well as introduced new concepts for why we sleep. Among these is an idea with its roots in human work nearly 50 years old: sleep in early life is crucial for normal brain maturation. Nearly all known species that sleep do so more while immature, and this increased sleep coincides with a period of exuberant synaptogenesis and massive neural circuit remodeling. Adequate sleep also appears critical for normal neurodevelopmental progression. This article describes recent findings regarding molecular and circuit mechanisms of sleep, with a focus on development and the insights garnered from models amenable to detailed genetic analyses. PMID:27183564

  19. Organization of IGCC processes with reduced order CFD models

    SciTech Connect

    Lang, Y.; Zitney, S.; Biegler, L.

    2011-01-01

    Integrated gasificationcombinedcycle(IGCC)plantshavesignificantadvantagesforefficientpowergen- eration withcarboncapture.Moreover,withthedevelopmentofaccurateCFDmodelsforgasificationand combined cyclecombustion,keyunitsoftheseprocessescannowbemodeledmoreaccurately.However, the integrationofCFDmodelswithinsteady-stateprocesssimulators,andsubsequentoptimizationof the integratedsystem,stillpresentssignificantchallenges.Thisstudydescribesthedevelopmentand demonstration ofareducedordermodeling(ROM)frameworkforthesetasks.Theapproachbuildson the conceptsofco-simulationandROMdevelopmentforprocessunitsdescribedinearlierstudies.Here we showhowtheROMsderivedfrombothgasificationandcombustionunitscanbeintegratedwithin an equation-orientedsimulationenvironmentfortheoveralloptimizationofanIGCCprocess.Inaddi- tion toasystematicapproachtoROMdevelopment,theapproachincludesvalidationtasksfortheCFD model aswellasclosed-looptestsfortheintegratedflowsheet.Thisapproachallowstheapplicationof equation-based nonlinearprogrammingalgorithmsandleadstofastoptimizationofCFD-basedprocess flowsheets. TheapproachisillustratedontwoflowsheetsbasedonIGCCtechnology.

  20. Tardigrades as a Potential Model Organism in Space Research

    NASA Astrophysics Data System (ADS)

    Jönsson, K. Ingemar

    2007-10-01

    Exposure of living organisms to open space requires a high level of tolerance to desiccation, cold, and radiation. Among animals, only anhydrobiotic species can fulfill these requirements. The invertebrate phylum Tardigrada includes many anhydrobiotic species, which are adapted to survive in very dry or cold environmental conditions. As a likely by-product of the adaptations for desiccation and freezing, tardigrades also show a very high tolerance to a number of other, unnatural conditions, including exposure to ionizing radiation. This makes tardigrades an interesting candidate for experimental exposure to open space. This paper reviews the tolerances that make tardigrades suitable for astrobiological studies and the reported radiation tolerance in other anhydrobiotic animals. Several studies have shown that tardigrades can survive γ-irradiation well above 1 kilogray, and desiccated and hydrated (active) tardigrades respond similarly to irradiation. Thus, tolerance is not restricted to the dry anhydrobiotic state, and I discuss the possible involvement of an efficient, but yet undocumented, mechanism for DNA repair. Other anhydrobiotic animals (Artemia, Polypedium), when dessicated, show a higher tolerance to γ-irradiation than hydrated animals, possibly due to the presence of high levels of the protective disaccharide trehalose in the dry state. Tardigrades and other anhydrobiotic animals provide a unique opportunity to study the effects of space exposure on metabolically inactive but vital metazoans.

  1. Modeling the World Health Organization Disability Assessment Schedule II using non-parametric item response models.

    PubMed

    Galindo-Garre, Francisca; Hidalgo, María Dolores; Guilera, Georgina; Pino, Oscar; Rojo, J Emilio; Gómez-Benito, Juana

    2015-03-01

    The World Health Organization Disability Assessment Schedule II (WHO-DAS II) is a multidimensional instrument developed for measuring disability. It comprises six domains (getting around, self-care, getting along with others, life activities and participation in society). The main purpose of this paper is the evaluation of the psychometric properties for each domain of the WHO-DAS II with parametric and non-parametric Item Response Theory (IRT) models. A secondary objective is to assess whether the WHO-DAS II items within each domain form a hierarchy of invariantly ordered severity indicators of disability. A sample of 352 patients with a schizophrenia spectrum disorder is used in this study. The 36 items WHO-DAS II was administered during the consultation. Partial Credit and Mokken scale models are used to study the psychometric properties of the questionnaire. The psychometric properties of the WHO-DAS II scale are satisfactory for all the domains. However, we identify a few items that do not discriminate satisfactorily between different levels of disability and cannot be invariantly ordered in the scale. In conclusion the WHO-DAS II can be used to assess overall disability in patients with schizophrenia, but some domains are too general to assess functionality in these patients because they contain items that are not applicable to this pathology. PMID:25524862

  2. Generalized effective-medium model for the carrier mobility in amorphous organic semiconductors

    NASA Astrophysics Data System (ADS)

    Rodin, Vadim; Symalla, Franz; Meded, Velimir; Friederich, Pascal; Danilov, Denis; Poschlad, Angela; Nelles, Gabriele; von Wrochem, Florian; Wenzel, Wolfgang

    2015-04-01

    Electronic transport through disordered organic materials is relevant in many applications, including organic light-emitting diodes and organic photovoltaics. The charge-carrier mobility is one of the most important material characteristics that must be optimized to make organic devices competitive. Here we introduce a general effective-medium model for the analytic calculation of zero-field mobilities on the basis of material-specific parameters that are obtained from extensive ab initio simulations. By means of kinetic Monte Carlo simulations, we generalize the model to also include the strong disorder limit. As a proof of concept the model is applied to two different disordered organic materials exhibiting medium and strong disorder, respectively. Surprisingly, even at strong disorder the hole mobilities computed with the effective-medium model in its original form are found to agree best with the experimental data. Seeking a possible explanation for this result, we investigate the strong dependence of the mobility on the connectivity of the model topology and show that the distribution of hopping matrix elements in the material is indeed much broader than assumed in simple lattice models. As the input parameters of the model can be computed on the basis of relatively small samples, this model may be used for materials' screening without adjustable parameters.

  3. Modeling Secondary Organic Aerosols over Europe: Impact of Activity Coefficients and Viscosity

    NASA Astrophysics Data System (ADS)

    Kim, Y.; Sartelet, K.; Couvidat, F.

    2014-12-01

    Semi-volatile organic species (SVOC) can condense on suspended particulate materials (PM) in the atmosphere. The modeling of condensation/evaporation of SVOC often assumes that gas-phase and particle-phase concentrations are at equilibrium. However, recent studies show that secondary organic aerosols (SOA) may not be accurately represented by an equilibrium approach between the gas and particle phases, because organic aerosols in the particle phase may be very viscous. The condensation in the viscous liquid phase is limited by the diffusion from the surface of PM to its core. Using a surrogate approach to represent SVOC, depending on the user's choice, the secondary organic aerosol processor (SOAP) may assume equilibrium or model dynamically the condensation/evaporation between the gas and particle phases to take into account the viscosity of organic aerosols. The model is implemented in the three-dimensional chemistry-transport model of POLYPHEMUS. In SOAP, activity coefficients for organic mixtures can be computed using UNIFAC for short-range interactions between molecules and AIOMFAC to also take into account the effect of inorganic species on activity coefficients. Simulations over Europe are performed and POLYPHEMUS/SOAP is compared to POLYPHEMUS/H2O, which was previously used to model SOA using the equilibrium approach with activity coefficients from UNIFAC. Impacts of the dynamic approach on modeling SOA over Europe are evaluated. The concentrations of SOA using the dynamic approach are compared with those using the equilibrium approach. The increase of computational cost is also evaluated.

  4. Mapping and Cracking Sensorimotor Circuits in Genetic Model Organisms

    PubMed Central

    Clark, Damon A.; Freifeld, Limor; Clandinin, Thomas R.

    2013-01-01

    One central goal of systems neuroscience is to understand how neural circuits implement the computations that link sensory inputs to behavior. Work combining electrophysiological and imaging-based approaches to measure neural activity with pharmacological and electrophysiological manipulations has provided fundamental insights. More recently, genetic approaches have been used to monitor and manipulate neural activity, opening up new experimental opportunities and challenges. Here, we discuss issues associated with applying genetic approaches to circuit dissection in sensorimotor transformations, outlining important considerations for experimental design and considering how modeling can complement experimental approaches. PMID:23719159

  5. Salmonella enterica serovars Typhimurium and Typhi as model organisms

    PubMed Central

    Garai, Preeti; Gnanadhas, Divya Prakash; Chakravortty, Dipshikha

    2012-01-01

    The lifestyle of intracellular pathogens has always questioned the skill of a microbiologist in the context of finding the permanent cure to the diseases caused by them. The best tool utilized by these pathogens is their ability to reside inside the host cell, which enables them to easily bypass the humoral immunity of the host, such as the complement system. They further escape from the intracellular immunity, such as lysosome and inflammasome, mostly by forming a protective vacuole-bound niche derived from the host itself. Some of the most dreadful diseases are caused by these vacuolar pathogens, for example, tuberculosis by Mycobacterium or typhoid fever by Salmonella. To deal with such successful pathogens therapeutically, the knowledge of a host-pathogen interaction system becomes primarily essential, which further depends on the use of a model system. A well characterized pathogen, namely Salmonella, suits the role of a model for this purpose, which can infect a wide array of hosts causing a variety of diseases. This review focuses on various such aspects of research on Salmonella which are useful for studying the pathogenesis of other intracellular pathogens. PMID:22722237

  6. [Insects as model organisms to study the pathogenesis of fungal infections and evaluation of potential antimycotics].

    PubMed

    Niedźwiecka, Katarzyna; Dyląg, Mariusz

    2015-01-01

    Systemic fungal infections are becoming an increasingly important problem. Exploring the development of mechanisms of pathogenesis, immune response of the human organism and the search for new potential antifungal agents requires in vivo testing. Mice, rats and rabbits are indispensable model organisms for this type of study. Unfortunately, such a kinds of studies carried out on a large scale are associated with high costs as well as with logistical and ethical problems. This paper reports proposal for the use of insects as model organisms to study the development of systemic fungal infections and analysis of biological activities of antifungal agents. PMID:26591665

  7. Predicting the lifetime of organic vapor cartridges exposed to volatile organic compound mixtures using a partial differential equations model.

    PubMed

    Vuong, François; Chauveau, Romain; Grevillot, Georges; Marsteau, Stéphanie; Silvente, Eric; Vallieres, Cécile

    2016-09-01

    In this study, equilibria, breakthrough curves, and breakthrough times were predicted for three binary mixtures of four volatile organic compounds (VOCs) using a model based on partial differential equations of dynamic adsorption coupling a mass balance, a simple Linear Driving Force (LDF) hypothesis to describe the kinetics, and the well-known Extended-Langmuir (EL) equilibrium model. The model aims to predict with a limited complexity, the BTCs of respirator cartridges exposed to binary vapor mixtures from equilibria and kinetics data obtained from single component. In the model, multicomponent mass transfer was simplified to use only single dynamic adsorption data. The EL expression used in this study predicted equilibria with relatively good accuracy for acetone/ethanol and ethanol/cyclohexane mixtures, but the prediction of cyclohexane uptake when mixed with heptane is less satisfactory. The BTCs given by the model were compared to experimental BTCs to determine the accuracy of the model and the impact of the approximation on mass transfer coefficients. From BTCs, breakthrough times at 10% of the exposure concentration t10% were determined. All t10% were predicted within 20% of the experimental values, and 63% of the breakthrough times were predicted within a 10% error. This study demonstrated that a simple mass balance combined with kinetic approximations is sufficient to predict lifetime for respirator cartridges exposed to VOC mixtures. It also showed that a commonly adopted approach to describe multicomponent adsorption based on volatility of VOC rather than adsorption equilibrium greatly overestimated the breakthrough times. PMID:27028086

  8. Promoting the organ donor card: a causal model of persuasion effects.

    PubMed

    Skumanich, S A; Kintsfather, D P

    1996-08-01

    Due to the present critical shortage of donor organs available for transplantation, effective communication strategies are necessary to heighten public commitment to donation. The promotion of organ donor card-signing may be a successful vehicle in the achievement of this goal. Based on the Elaboration Likelihood Model of persuasion effects, evidence of the motivation for organ donor card-signing, and examination of previous donation message tests, this study proposes and tests a causal model of response to organ donor card appeals. The inter-relationship of values, empathy arousal, and issue involvement was found to be a significant driving force in the persuasive process for the behavioral intention to sign an organ donor card. Implications of these findings for future research are addressed. PMID:8844941

  9. Improved AIOMFAC model parameterisation of the temperature dependence of activity coefficients for aqueous organic mixtures

    NASA Astrophysics Data System (ADS)

    Ganbavale, G.; Zuend, A.; Marcolli, C.; Peter, T.

    2014-06-01

    This study presents a new, improved parameterisation of the temperature dependence of activity coefficients in the AIOMFAC (Aerosol Inorganic-Organic Mixtures Functional groups Activity Coefficients) model applicable for aqueous as well as water-free organic solutions. For electrolyte-free organic and organic-water mixtures the AIOMFAC model uses a group-contribution approach based on UNIFAC (UNIversal quasi-chemical Functional-group Activity Coefficients). This group-contribution approach explicitly accounts for interactions among organic functional groups and between organic functional groups and water. The previous AIOMFAC version uses a simple parameterisation of the temperature dependence of activity coefficients, aimed to be applicable in the temperature range from ~275 to ~400 K. With the goal to improve the description of a wide variety of organic compounds found in atmospheric aerosols, we extend the AIOMFAC parameterisation for the functional groups carboxyl, hydroxyl, ketone, aldehyde, ether, ester, alkyl, aromatic carbon-alcohol, and aromatic hydrocarbon to atmospherically relevant low temperatures with the introduction of a new temperature dependence parameterisation. The improved temperature dependence parameterisation is derived from classical thermodynamic theory by describing effects from changes in molar enthalpy and heat capacity of a multicomponent system. Thermodynamic equilibrium data of aqueous organic and water-free organic mixtures from the literature are carefully assessed and complemented with new measurements to establish a comprehensive database, covering a wide temperature range (~190 to ~440 K) for many of the functional group combinations considered. Different experimental data types and their processing for the estimation of AIOMFAC model parameters are discussed. The new AIOMFAC parameterisation for the temperature dependence of activity coefficients from low to high temperatures shows an overall improvement of 25% in comparison to

  10. From genomes to function: haloarchaea as model organisms.

    PubMed

    Soppa, Jörg

    2006-03-01

    Haloarchaea are adapted to high-salt environments and accumulate equally high salt concentrations in the cytoplasm. The genomes of representatives of six haloarchaeal genera have been fully or partially sequenced, allowing the analysis of haloarchaeal properties in silico. Transcriptome and proteome analyses have been established for Halobacterium salinarum and Haloferax volcanii. Genetic systems are available including methods that allow the fast in-frame deletion or modification of chromosomal genes. The high-efficiency transformation system of Hf. volcanii allows the isolation of genes essential for a biological process by complementation of loss-of-function mutants. For the analysis of haloarchaeal biology many molecular genetic, biochemical, structural and cell biological methods have been adapted to application at high salt concentrations. Recently it has become clear that several different mechanisms allow the adaptation of proteins to the high salt concentration of the cytoplasm. Taken together, the wealth of techniques available make haloarchaea excellent archaeal model species. PMID:16514139

  11. Lampreys as Diverse Model Organisms in the Genomics Era

    PubMed Central

    McCauley, David W.; Docker, Margaret F.; Whyard, Steve; Li, Weiming

    2015-01-01

    Lampreys, one of the two surviving groups of ancient vertebrates, have become important models for study in diverse fields of biology. Lampreys (of which there are approximately 40 species) are being studied, for example, (a) to control pest sea lamprey in the North American Great Lakes and to restore declining populations of native species elsewhere; (b) in biomedical research, focusing particularly on the regenerative capability of lampreys; and (c) by developmental biologists studying the evolution of key vertebrate characters. Although a lack of genetic resources has hindered research on the mechanisms regulating many aspects of lamprey life history and development, formerly intractable questions are now amenable to investigation following the recent publication of the sea lamprey genome. Here, we provide an overview of the ways in which genomic tools are currently being deployed to tackle diverse research questions and suggest several areas that may benefit from the availability of the sea lamprey genome. PMID:26951616

  12. Calorie Restriction in Mammals and Simple Model Organisms

    PubMed Central

    Mirisola, Mario G.

    2014-01-01

    Calorie restriction (CR), which usually refers to a 20–40% reduction in calorie intake, can effectively prolong lifespan preventing most age-associated diseases in several species. However, recent data from both human and nonhumans point to the ratio of macronutrients rather than the caloric intake as a major regulator of both lifespan and health-span. In addition, specific components of the diet have recently been identified as regulators of some age-associated intracellular signaling pathways in simple model systems. The comprehension of the mechanisms underpinning these findings is crucial since it may increase the beneficial effects of calorie restriction making it accessible to a broader population as well. PMID:24883306

  13. Calorie restriction in mammals and simple model organisms.

    PubMed

    Taormina, Giusi; Mirisola, Mario G

    2014-01-01

    Calorie restriction (CR), which usually refers to a 20-40% reduction in calorie intake, can effectively prolong lifespan preventing most age-associated diseases in several species. However, recent data from both human and nonhumans point to the ratio of macronutrients rather than the caloric intake as a major regulator of both lifespan and health-span. In addition, specific components of the diet have recently been identified as regulators of some age-associated intracellular signaling pathways in simple model systems. The comprehension of the mechanisms underpinning these findings is crucial since it may increase the beneficial effects of calorie restriction making it accessible to a broader population as well. PMID:24883306

  14. Multi-generational oxidation model to simulate secondary organic aerosol in a 3-D air quality model

    NASA Astrophysics Data System (ADS)

    Jathar, S. H.; Cappa, C. D.; Wexler, A. S.; Seinfeld, J. H.; Kleeman, M. J.

    2015-08-01

    Multi-generational gas-phase oxidation of organic vapors can influence the abundance, composition and properties of secondary organic aerosol (SOA). Only recently have SOA models been developed that explicitly represent multi-generational SOA formation. In this work, we integrated the statistical oxidation model (SOM) into SAPRC-11 to simulate the multi-generational oxidation and gas/particle partitioning of SOA in the regional UCD/CIT (University of California, Davis/California Institute of Technology) air quality model. In the SOM, evolution of organic vapors by reaction with the hydroxyl radical is defined by (1) the number of oxygen atoms added per reaction, (2) the decrease in volatility upon addition of an oxygen atom and (3) the probability that a given reaction leads to fragmentation of the organic molecule. These SOM parameter values were fit to laboratory smog chamber data for each precursor/compound class. SOM was installed in the UCD/CIT model, which simulated air quality over 2-week periods in the South Coast Air Basin of California and the eastern United States. For the regions and episodes tested, the two-product SOA model and SOM produce similar SOA concentrations but a modestly different SOA chemical composition. Predictions of the oxygen-to-carbon ratio qualitatively agree with those measured globally using aerosol mass spectrometers. Overall, the implementation of the SOM in a 3-D model provides a comprehensive framework to simulate the atmospheric evolution of organic aerosol.

  15. A Unifying Organ Model of Pancreatic Insulin Secretion

    PubMed Central

    De Gaetano, Andrea; Gaz, Claudio; Palumbo, Pasquale; Panunzi, Simona

    2015-01-01

    The secretion of insulin by the pancreas has been the object of much attention over the past several decades. Insulin is known to be secreted by pancreatic β-cells in response to hyperglycemia: its blood concentrations however exhibit both high-frequency (period approx. 10 minutes) and low-frequency oscillations (period approx. 1.5 hours). Furthermore, characteristic insulin secretory response to challenge maneuvers have been described, such as frequency entrainment upon sinusoidal glycemic stimulation; substantial insulin peaks following minimal glucose administration; progressively strengthened insulin secretion response after repeated administration of the same amount of glucose; insulin and glucose characteristic curves after Intra-Venous administration of glucose boli in healthy and pre-diabetic subjects as well as in Type 2 Diabetes Mellitus. Previous modeling of β-cell physiology has been mainly directed to the intracellular chain of events giving rise to single-cell or cell-cluster hormone release oscillations, but the large size, long period and complex morphology of the diverse responses to whole-body glucose stimuli has not yet been coherently explained. Starting with the seminal work of Grodsky it was hypothesized that the population of pancreatic β-cells, possibly functionally aggregated in islets of Langerhans, could be viewed as a set of independent, similar, but not identical controllers (firing units) with distributed functional parameters. The present work shows how a single model based on a population of independent islet controllers can reproduce very closely a diverse array of actually observed experimental results, with the same set of working parameters. The model’s success in reproducing a diverse array of experiments implies that, in order to understand the macroscopic behaviour of the endocrine pancreas in regulating glycemia, there is no need to hypothesize intrapancreatic pacemakers, influences between different islets of Langerhans

  16. Self-organization with equilibration: a model for the intermediate phase in rigidity percolation.

    PubMed

    Chubynsky, M V; Brière, M-A; Mousseau, Normand

    2006-07-01

    Recent experimental results for covalent glasses suggest the existence of an intermediate phase attributed to the self-organization of the glass network resulting from the tendency to minimize its internal stress. However, the exact nature of this experimentally measured phase remains unclear. We modified a previously proposed model of self-organization by generating a uniform sampling of stress-free networks. In our model, studied on a diluted triangular lattice, an unusual intermediate phase appears, in which both rigid and floppy networks have a chance to occur, a result also observed in a related model on a Bethe lattice by Barré et al[Phys. Rev. Lett. 94, 208701 (2005)]. Our results for the bond-configurational entropy of self-organized networks, which turns out to be only about 2% lower than that of random networks, suggest that a self-organized intermediate phase could be common in systems near the rigidity percolation threshold. PMID:16907160

  17. IMPROVING CHEMICAL TRANSPORT MODEL PREDICTIONS OF ORGANIC AEROSOL: MEASUREMENT AND SIMULATION OF SEMIVOLATILE ORGANIC EMISSIONS FROM MOBILE AND NON-MOBILE SOURCES

    EPA Science Inventory

    Organic material contributes a significant fraction of PM2.5 mass across all regions of the United States, but state-of-the-art chemical transport models often substantially underpredict measured organic aerosol concentrations. Recent revisions to these models that...

  18. A thermodynamic model of mixed organic-inorganic aerosols to predict activity coefficients

    NASA Astrophysics Data System (ADS)

    Zuend, A.; Marcolli, C.; Luo, B. P.; Peter, T.

    2008-08-01

    Tropospheric aerosols contain mixtures of inorganic salts, acids, water, and a large variety of organic compounds. Interactions between these substances in liquid mixtures lead to discrepancies from ideal thermodynamic behaviour. By means of activity coefficients, non-ideal behaviour can be taken into account. We present here a thermodynamic model named AIOMFAC (Aerosol Inorganic-Organic Mixtures Functional groups Activity Coefficients) that is able to calculate activity coefficients covering inorganic, organic, and organic-inorganic interactions in aqueous solutions over a wide concentration range. This model is based on the activity coefficient model LIFAC by Yan et al. (1999) that we modified and reparametrised to better describe atmospherically relevant conditions and mixture compositions. Focusing on atmospheric applications we considered H+, Li+, Na+, K+, NH+4, Mg2+, Ca2+, Cl-, Br-, NO-3, HSO-4, and SO2-4 as cations and anions and a wide range of alcohols/polyols composed of the functional groups CHn and OH as organic compounds. With AIOMFAC, the activities of the components within an aqueous electrolyte solution are well represented up to high ionic strength. Most notably, a semi-empirical middle-range parametrisation of direct organic-inorganic interactions in alcohol+water+salt solutions strongly improves the agreement between experimental and modelled activity coefficients. At room temperature, this novel thermodynamic model offers the possibility to compute equilibrium relative humidities, gas/particle partitioning and liquid-liquid phase separations with high accuracy. In further studies, other organic functional groups will be introduced. The model framework is not restricted to specific ions or organic compounds and is therefore also applicable for other research topics.

  19. A thermodynamic model of mixed organic-inorganic aerosols to predict activity coefficients

    NASA Astrophysics Data System (ADS)

    Zuend, A.; Marcolli, C.; Luo, B. P.; Peter, Th.

    2008-03-01

    Tropospheric aerosols contain mixtures of inorganic salts, acids, water, and a large variety of organic compounds. Interactions between these substances in liquid mixtures lead to discrepancies from ideal thermodynamic behaviour. By means of activity coefficients, non-ideal behaviour can be taken into account. We present here a thermodynamic model named AIOMFAC (Aerosol Inorganic-Organic Mixtures Functional groups Activity Coefficients) that is able to calculate activity coefficients covering inorganic, organic, and organic-inorganic interactions in aqueous solutions over a wide concentration range. This model is based on the activity coefficient model LIFAC by Yan et al. (1999) that we modified and reparametrised to better describe atmospherically relevant conditions and mixture compositions. Focusing on atmospheric applications we considered H+, Li+, Na+, K+, NH4+, Mg2+, Ca2+, Cl-, Br-, NO3-, HSO4-, and SO42- as cations and anions and a wide range of alcohols/polyols composed of the functional groups CHn and OH as organic compounds. With AIOMFAC, the activities of the components within an aqueous electrolyte solution are well represented up to high ionic strength. Most notably, a semi-empirical middle-range parametrisation of direct organic-inorganic interactions in alcohol + water + salt solutions strongly improves the agreement between experimental and modelled activity coefficients. At room temperature, this novel thermodynamic model offers the possibility to compute equilibrium relative humidities, gas/particle partitioning and liquid-liquid phase separations with high accuracy. In further studies, other organic functional groups will be introduced. The model framework is not restricted to specific ions or organic compounds and is therefore also applicable for other research topics.

  20. Dimethylarginine Dimethylaminohydrolase1 Is an Organ-Specific Mediator of End Organ Damage in a Murine Model of Hypertension

    PubMed Central

    Sydow, Karsten; Schmitz, Christine; von Leitner, Eike-Christin; von Leitner, Robin; Klinke, Anna; Atzler, Dorothee; Krebs, Christian; Wieboldt, Hartwig; Ehmke, Heimo; Schwedhelm, Edzard; Meinertz, Thomas; Blankenberg, Stefan; Böger, Rainer H.; Magnus, Tim

    2012-01-01

    Background The endogenous nitric oxide synthase inhibitor asymmetric dimethylarginine (ADMA) is an independent predictor of cardiovascular and overall mortality. Moreover, elevated ADMA plasma concentrations are associated with the extent of hypertension. However, data from small-sized clinical trials and experimental approaches using murine transgenic models have revealed conflicting results regarding the impact of ADMA and its metabolizing enzyme dimethylarginine dimethylaminohydrolase (DDAH) in the pathogenesis of hypertension. Methodology/Principal Findings Therefore, we investigated the role of ADMA and DDAH1 in hypertension-induced end organ damage using the uninephrectomized, deoxycorticosterone actetate salt, and angiotensin II-induced hypertension model in human DDAH1 (hDDAH1) overexpressing and wild-type (WT) mice. ADMA plasma concentrations differed significantly between hDDAH1 and WT mice at baseline, but did not significantly change during the induction of hypertension. hDDAH1 overexpression did not protect against hypertension-induced cardiac fibrosis and hypertrophy. In addition, the hypertension-induced impairment of the endothelium-dependent vasorelaxation of aortic segments ex vivo was not significantly attenuated by hDDAH1 overexpression. However, hDDAH1 mice displayed an attenuated hypertensive inflammatory response in renal tissue, resulting in less hypertensive renal injury. Conclusion/Significance Our data reveal that hDDAH1 organ-specifically modulates the inflammatory response in this murine model of hypertension. The lack of protection in cardiac and aortic tissues may be due to DDAH1 tissue selectivity and/or the extent of hypertension by the used combined model. However, our study underlines the potency of hDDAH1 overexpression in modulating inflammatory processes as a crucial step in the pathogenesis of hypertension, which needs further experimental and clinical investigation. PMID:23110194

  1. 3D deformable organ model based liver motion tracking in ultrasound videos

    NASA Astrophysics Data System (ADS)

    Kim, Jung-Bae; Hwang, Youngkyoo; Oh, Young-Taek; Bang, Won-Chul; Lee, Heesae; Kim, James D. K.; Kim, Chang Yeong

    2013-03-01

    This paper presents a novel method of using 2D ultrasound (US) cine images during image-guided therapy to accurately track the 3D position of a tumor even when the organ of interest is in motion due to patient respiration. Tracking is possible thanks to a 3D deformable organ model we have developed. The method consists of three processes in succession. The first process is organ modeling where we generate a personalized 3D organ model from high quality 3D CT or MR data sets captured during three different respiratory phases. The model includes the organ surface, vessel and tumor, which can all deform and move in accord with patient respiration. The second process is registration of the organ model to 3D US images. From 133 respiratory phase candidates generated from the deformable organ model, we resolve the candidate that best matches the 3D US images according to vessel centerline and surface. As a result, we can determine the position of the US probe. The final process is real-time tracking using 2D US cine images captured by the US probe. We determine the respiratory phase by tracking the diaphragm on the image. The 3D model is then deformed according to respiration phase and is fitted to the image by considering the positions of the vessels. The tumor's 3D positions are then inferred based on respiration phase. Testing our method on real patient data, we have found the accuracy of 3D position is within 3.79mm and processing time is 5.4ms during tracking.

  2. Leeches of the genus Helobdella as model organisms for Evo-Devo studies.

    PubMed

    Kutschera, Ulrich; Weisblat, David A

    2015-12-01

    Model organisms are important tools in modern biology and have been used elucidate mechanism underlying processes, such as development, heredity, neuronal signaling, and phototropism, to name but a few. In this context, the use of model organisms is predicated on uncovering evolutionarily conserved features of biological processes in the expectation that the findings will be applicable to organisms that are either inaccessible or intractable for direct experimentation. For the most part, particular species have been adapted as model organisms because they can be easily reared and manipulated in the laboratory. In contrast, a major goal in the field of evolutionary developmental biology (Evo-Devo) is to identify and elucidate the differences in developmental processes among species associated with the dramatic range of body plans among organisms, and how these differences have emerged over time in various branches of phylogeny. At first glance then, it would appear that the concept of model organisms for Evo-Devo is oxymoronic. In fact, however, laboratory-compatible, experimentally tractable species are of great use for Evo-Devo, subject to the condition that the ensemble of models investigated should reflect the range of taxonomic diversity, and for this purpose glossiphoniid leeches are useful. Four decades ago (1975), leeches of the species-rich genus Helobdella (Lophotrochozoa; Annelida; Clitellata; Hirudinida; Glossiphoniidae) were collected in Stow Lake, Golden Gate Park, San Francisco, CA (USA). These and other Helobdella species may be taken as Evo-Devo models of leeches, clitellate annelids, and the super-phylum Lophotrochozoa. Here we depict/discuss the biology/taxonomy of these Evo-Devo systems, and the challenges of identifying species within Helobdella. In addition, we document that H. austinensis has been established as a new model organism that can easily be cultivated in the laboratory. Finally, we provide an updated scheme illustrating the unique

  3. Statistical Thermodynamic Model for Surface Tension of Aqueous Organic Acids with Consideration of Partial Dissociation.

    PubMed

    Boyer, Hallie C; Dutcher, Cari S

    2016-06-30

    With statistical mechanics, an isotherm-based surface tension model for single solute aqueous solutions was derived previously (Wexler et al. J. Phys. Chem. Lett. 2013) for the entire concentration range, from infinite dilution to pure liquid solute, as a function of solute activity. In recent work (Boyer et al. J. Phys. Chem. Lett. 2015), empirical model parameters were reduced through physicochemical interpretations of both electrolyte and organic solutes, enabling surface tension predictions for systems where there is little or no data. The prior binary model is extended in the current work for the first time to treat multicomponent systems to predict surface tensions of partially dissociating organic acids (acetic, butyric, citric, formic, glutaric, maleic, malic, malonic, oxalic, propionic, and succinic acids). These organic acids are especially applicable to the study of atmospheric aqueous aerosols, due to their abundance in the atmosphere. In the model developed here, surface tension depends explicitly on activities of both the neutral organic and deprotonated components of the acid. The relative concentrations of the nondissociated and dissociated mole fractions are found using known dissociation constants. Model parameters strongly depend on molecular size, number of functional groups, O:C ratio, and number of carbons. For all organic acids in this study, fully predictive modeling of surface tensions is demonstrated. PMID:27219322

  4. Exploration of the seasonal variation of organic aerosol composition using an explicit modeling approach

    NASA Astrophysics Data System (ADS)

    Ouzebidour, Farida; Camredon, Marie; Stéphanie La, Yuyi; Madronich, Sasha; Taylor, Julia Lee; Hodzic, Alma; Beekmann, Matthias; Siour, Guillaume; Aumont, Bernard

    2014-05-01

    Organic compounds account for a major fraction of fine aerosols in the atmosphere. This organic fraction is dominated by secondary organic aerosol (SOA). Processes leading to SOA formation are however still uncertain and SOA composition is far from being fully characterized. The goals of this study are to evaluate our current understanding of SOA formation and explore its composition. For this purpose, a box-model that describes explicitly processes involved in SOA formation has been developed. This model includes the emission of 183 gaseous and particulate organic compounds. The oxidation of these emitted organic compounds is described using the Generator of Explicit Chemistry and Kinetics of Organics in the Atmosphere (GECKO-A). Gas/particle partitioning has been implemented considering an ideal homogeneous condensed phase. The generated chemical scheme contains 500,000 species and the gas/particle partitioning is performed for 90,000 of them. Simulations have been performed for summer and winter scenarios representative of continental and urban conditions. NOx and ozone simulated concentrations reproduce the expected winter and summer diurnal evolutions. The predicted organic aerosol composition is a mixture of primary and secondary organic aerosols during the winter and is largely dominated by SOA during the summer.

  5. Frogs as integrative models for understanding digestive organ development and evolution.

    PubMed

    Womble, Mandy; Pickett, Melissa; Nascone-Yoder, Nanette

    2016-03-01

    The digestive system comprises numerous cells, tissues and organs that are essential for the proper assimilation of nutrients and energy. Many aspects of digestive organ function are highly conserved among vertebrates, yet the final anatomical configuration of the gut varies widely between species, especially those with different diets. Improved understanding of the complex molecular and cellular events that orchestrate digestive organ development is pertinent to many areas of biology and medicine, including the regeneration or replacement of diseased organs, the etiology of digestive organ birth defects, and the evolution of specialized features of digestive anatomy. In this review, we highlight specific examples of how investigations using Xenopus laevis frog embryos have revealed insight into the molecular and cellular dynamics of digestive organ patterning and morphogenesis that would have been difficult to obtain in other animal models. Additionally, we discuss recent studies of gut development in non-model frog species with unique feeding strategies, such as Lepidobatrachus laevis and Eleutherodactylous coqui, which are beginning to provide glimpses of the evolutionary mechanisms that may generate morphological variation in the digestive tract. The unparalleled experimental versatility of frog embryos make them excellent, integrative models for studying digestive organ development across multiple disciplines. PMID:26851628

  6. MATRIX-VBS Condensing Organic Aerosols in an Aerosol Microphysics Model

    NASA Technical Reports Server (NTRS)

    Gao, Chloe Y.; Tsigaridis, Konstas; Bauer, Susanne E.

    2015-01-01

    The condensation of organic aerosols is represented in a newly developed box-model scheme, where its effect on the growth and composition of particles are examined. We implemented the volatility-basis set (VBS) framework into the aerosol mixing state resolving microphysical scheme Multiconfiguration Aerosol TRacker of mIXing state (MATRIX). This new scheme is unique and advances the representation of organic aerosols in models in that, contrary to the traditional treatment of organic aerosols as non-volatile in most climate models and in the original version of MATRIX, this new scheme treats them as semi-volatile. Such treatment is important because low-volatility organics contribute significantly to the growth of particles. The new scheme includes several classes of semi-volatile organic compounds from the VBS framework that can partition among aerosol populations in MATRIX, thus representing the growth of particles via condensation of low volatility organic vapors. Results from test cases representing Mexico City and a Finish forrest condistions show good representation of the time evolutions of concentration for VBS species in the gas phase and in the condensed particulate phase. Emitted semi-volatile primary organic aerosols evaporate almost completely in the high volatile range, and they condense more efficiently in the low volatility range.

  7. A Performance Enhanced Interactive Learning Workshop Model as a Supplement for Organic Chemistry Instruction

    ERIC Educational Resources Information Center

    Phillips, Karen E. S.; Grose-Fifer, Jilliam

    2011-01-01

    In this study, the authors describe a Performance Enhanced Interactive Learning (PEIL) workshop model as a supplement for organic chemistry instruction. This workshop model differs from many others in that it includes public presentations by students and other whole-class-discussion components that have not been thoroughly investigated in the…

  8. A Cross-Cultural Analysis of the Effectiveness of the Learning Organization Model in School Contexts

    ERIC Educational Resources Information Center

    Alavi, Seyyed Babak; McCormick, John

    2004-01-01

    It has been argued that some management theories and models may not be universal and are based on some cultural assumptions. It is argued in this paper that the effectiveness of applying the Learning Organization (LO) model in school contexts across different countries may be associated with cultural differences such as individualism,…

  9. An Information Processing Model of Organizations: A Focus on Environmental Uncertainty and Communication Network Structuring.

    ERIC Educational Resources Information Center

    Danowski, James A.

    In this paper, an information processing model of social systems is developed with particular concern for large complex organizations. In explicating the sixteen assumptions and propositions of the model, the literature on environmental uncertainty, interorganizational communication, technology, and their effects on internal organizational…

  10. Self-organization in a model of economic system with scale invariant interactions

    NASA Astrophysics Data System (ADS)

    Pis`mak, Yu. M.

    2001-10-01

    The method of constructing the local scale invariant stochastic models is proposed. The possible extension of minimal scale-invariant interaction principle for stochastic systems is formulated. A simple scale invariant model that possesses an economical interpretation is considered. Essential characteristics of its self-organization mechanisms are discussed.

  11. 76 FR 29249 - Medicare Program; Pioneer Accountable Care Organization Model: Request for Applications

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-20

    ... HUMAN SERVICES Centers for Medicare & Medicaid Services Medicare Program; Pioneer Accountable Care... participate in the Pioneer Accountable Care Organization Model for a period beginning in 2011 and ending...://innovations.cms.gov/areas-of-focus/seamless-and-coordinated-care-models/pioneer-aco . Application...

  12. PHYSIOLOGICALLY BASED TOXICOKINETIC MODEL FOR THE UPTAKE AND DISPOSITION OF WATERBORNE ORGANIC CHEMICALS IN FISH

    EPA Science Inventory

    A physiologically based toxicokinetic model was developed to predict the uptake and disposition of waterborne organic chemicals in fish, he model consists of a set of mass-balance differential equations which describe the time course of chemical concentration within each of five ...

  13. MODELLING BIOACCUMULATION OF ORGANIC POLLUTANTS IN FISH WITH AN APPLICATION TO PCBS IN LAKE ONTARIO SALMONIDS

    EPA Science Inventory

    A model describing passive accumulatiOn of organic chemicals from the aqueous environment and contaminated food in fish is developed. This model considers both biological attributes of the fish and physicochemical properties of the chemical that determine diffusive exchange acros...

  14. Modeling multiphase migration of organic chemicals in groundwater systems--a review and assessment.

    PubMed Central

    Abriola, L M

    1989-01-01

    Over the past two decades, a number of models have been developed to describe the multiphase migration of organic chemicals in the subsurface. This paper presents the state-of-the-art with regard to such modeling efforts. The mathematical foundations of these models are explored and individual models are presented and discussed. Models are divided into three groups: a) those that assume a sharp interface between the migrating fluids; b) those that incorporate capillarity; and c) those that consider interphase transport of mass. Strengths and weaknesses of each approach are considered along with supporting data for model validation. Future research directions are also highlighted. PMID:2695322

  15. Multi-generational oxidation model to simulate secondary organic aerosol in a 3-D air quality model

    NASA Astrophysics Data System (ADS)

    Jathar, S. H.; Cappa, C. D.; Wexler, A. S.; Seinfeld, J. H.; Kleeman, M. J.

    2015-02-01

    Multi-generational gas-phase oxidation of organic vapors can influence the abundance, composition and properties of secondary organic aerosol (SOA). Only recently have SOA models been developed that explicitly represent multi-generational SOA formation. In this work, we integrated the statistical oxidation model (SOM) into SAPRC-11 to simulate the multi-generational oxidation and gas/particle partitioning of SOA in the regional UCD/CIT air quality model. In SOM, evolution of organic vapors by reaction with the hydroxyl radical is defined by (1) the number of oxygen atoms added per reaction, (2) the decrease in volatility upon addition of an oxygen atom and (3) the probability that a given reaction leads to fragmentation of the organic molecule. These SOM parameter values were fit to laboratory "smog chamber" data for each precursor/compound class. The UCD/CIT model was used to simulate air quality over two-week periods in the South Coast Air Basin of California and the eastern United States. For the regions and episodes tested, the traditional two-product SOA model and SOM produce similar SOA concentrations but a modestly different SOA chemical composition. Predictions of the oxygen-to-carbon ratio qualitatively agree with those measured globally using aerosol mass spectrometers. Overall, the implementation of the SOM in a 3-D model provides a comprehensive framework to simulate the atmospheric evolution of OA.

  16. In vitro model systems for studying the impact of organic chemicals on the skin barrier lipids.

    PubMed

    Groen, Daniël; Berthaud, Fabienne; Bouwstra, Joke A; Chapuis, Christian; Gooris, Gert S; Boncheva, Mila

    2014-01-01

    This paper describes two synthetic lipid models designed to replace human stratum corneum (SC) in studies of the impact of volatile organic chemicals on the molecular organization of the skin barrier lipids. The models built upon previously developed self-assembled lipid membranes which have composition and 3D organization similar to those of the lipid matrix in SC. In one model the target chemicals were incorporated in the lipids before their self-assembly, and in the other one they were applied on top of a preformed lipid membrane. The chemicals could be incorporated within the model membranes in quantities close to those reached within human SC upon heavy surface loading. The dose-dependent effects of the chemicals on the lateral molecular organization in the models were qualitatively identical to those observed by infrared spectroscopy in human SC. The models facilitated the interpretation of X-ray diffraction profiles used to determine the nature of the interactions between the chemicals and the lipid lamellae and the position of the exogenous molecules within the unit cell of the lipid phases. These model systems are suitable for in vitro studies in the areas of skin biophysics, dermatology, transdermal drug delivery, and risk assessment. PMID:24125684

  17. New insights into the organic carbon export in the Mediterranean Sea from 3-D modeling

    NASA Astrophysics Data System (ADS)

    Guyennon, A.; Baklouti, M.; Diaz, F.; Palmieri, J.; Beuvier, J.; Lebaupin-Brossier, C.; Arsouze, T.; Béranger, K.; Dutay, J.-C.; Moutin, T.

    2015-12-01

    The Mediterranean Sea is one of the most oligotrophic regions of the oceans, and nutrients have been shown to limit both phytoplankton and bacterial activities, resulting in a potential major role of dissolved organic carbon (DOC) export in the biological pump. Strong DOC accumulation in surface waters is already well documented, though measurements of DOC stocks and export flux are still sparse and associated with major uncertainties. This study provides the first basin-scale overview and analysis of organic carbon stocks and export fluxes in the Mediterranean Sea through a modeling approach based on a coupled model combining a mechanistic biogeochemical model (Eco3M-MED) and a high-resolution (eddy-resolving) hydrodynamic simulation (NEMO-MED12). The model is shown to reproduce the main spatial and seasonal biogeochemical characteristics of the Mediterranean Sea. Model estimations of carbon export are also of the same order of magnitude as estimations from in situ observations, and their respective spatial patterns are mutually consistent. Strong differences between the western and eastern basins are evidenced by the model for organic carbon export. Though less oligotrophic than the eastern basin, the western basin only supports 39 % of organic carbon (particulate and dissolved) export. Another major result is that except for the Alboran Sea, the DOC contribution to organic carbon export is higher than that of particulate organic carbon (POC) throughout the Mediterranean Sea, especially in the eastern basin. This paper also investigates the seasonality of DOC and POC exports as well as the differences in the processes involved in DOC and POC exports in light of intracellular quotas. Finally, according to the model, strong phosphate limitation of both bacteria and phytoplankton growth is one of the main drivers of DOC accumulation and therefore of export.

  18. Polymer models of the organization of chromosomes in the nucleus of cells

    NASA Astrophysics Data System (ADS)

    Chiariello, Andrea Maria; Bianco, Simona; Piccolo, Andrea; Annunziatella, Carlo; Barbieri, Mariano; Pombo, Ana; Nicodemi, Mario

    2015-04-01

    Understanding the mechanisms that control the organization of chromosomes in the space of the nucleus of cells, and its contribution to gene regulation, is a key open issue in molecular biology. New technologies have shown that chromosomes have a complex 3D organization, which dynamically changes across organisms and cell types. To understand such complex behaviors, quantitative models from polymer physics have been developed, to find the principles of chromosome folding, their origin and function. Here, we provide a short review of recent progress in such an important research field where Physical and Life Sciences meet.

  19. Adsorption of small weak organic acids on goethite: Modeling of mechanisms

    SciTech Connect

    Filius, J.D.; Hiemstra, T.; Riemsdijk, W.H. Van

    1997-11-15

    The adsorption of lactate, oxalate, malonate, phthalate, and citrate has been determined experimentally as a function of concentration, pH, and ionic strength. The data have been described with the CD-MUSIC model of Hiemstra and Van Riemsdijk which allows a distribution of charge of the organic molecule over the surface and the Stern layer. Simultaneously, the concentration, pH, and salt dependency as well as the basic charging behavior of goethite could be described well. On the basis of model calculations, a distinction is made between inner and outer sphere complexation of weak organic acids by goethite. The results indicate that the affinity of the organic acids is dominated by the electrostatic attraction. The intrinsic affinity constants for the exchange reaction of surface water groups and organic acids, expressed per bond, increases with increasing number of reactive groups on the organic molecule. Ion pair formation between noncoordinated carboxylic groups of adsorbed organic acids and cations of the background electrolyte proved to be important for the salt dependency. The knowledge obtained may contribute to the interpretation of the binding of larger organic acids like fulvic and humic acids.

  20. Assessment of survivability of liquid water and organic materials through modeling of large-scale impacts

    NASA Astrophysics Data System (ADS)

    Blank, Jennifer

    Comets, estimated to contain up to 25 wt.% organic material as both ices and more complex, refractory compounds, have been proposed as a vehicle for the delivery of organic compounds to the early Earth and other rocky planets. Successful delivery requires that some of the organic materials survive the extreme temperatures associated with impact, but the response of organic compounds to impact (shock) processing under these conditions is unknown. Several researchers have explored organic-delivery scenarios computationally and experimentally. Here, I will summarize work that addresses the issue of impact delivery and focus on current efforts to track the phase-state of water during a modeled comet-earth collision over a range of impact angles. On the basis of model results generated using a three-dimensional shock physics code (GEODYN), I will infer survivability of organic compounds and liquid water in a range of impact scenarios for comet-Earth and asteroid-Earth collisions. These results will be described in the context of the flux of astromaterials, and organic matter in particular, to young planets.

  1. N-gram analysis of 970 microbial organisms reveals presence of biological language models

    PubMed Central

    2011-01-01

    Background It has been suggested previously that genome and proteome sequences show characteristics typical of natural-language texts such as "signature-style" word usage indicative of authors or topics, and that the algorithms originally developed for natural language processing may therefore be applied to genome sequences to draw biologically relevant conclusions. Following this approach of 'biological language modeling', statistical n-gram analysis has been applied for comparative analysis of whole proteome sequences of 44 organisms. It has been shown that a few particular amino acid n-grams are found in abundance in one organism but occurring very rarely in other organisms, thereby serving as genome signatures. At that time proteomes of only 44 organisms were available, thereby limiting the generalization of this hypothesis. Today nearly 1,000 genome sequences and corresponding translated sequences are available, making it feasible to test the existence of biological language models over the evolutionary tree. Results We studied whole proteome sequences of 970 microbial organisms using n-gram frequencies and cross-perplexity employing the Biological Language Modeling Toolkit and Patternix Revelio toolkit. Genus-specific signatures were observed even in a simple unigram distribution. By taking statistical n-gram model of one organism as reference and computing cross-perplexity of all other microbial proteomes with it, cross-perplexity was found to be predictive of branch distance of the phylogenetic tree. For example, a 4-gram model from proteome of Shigellae flexneri 2a, which belongs to the Gammaproteobacteria class showed a self-perplexity of 15.34 while the cross-perplexity of other organisms was in the range of 15.59 to 29.5 and was proportional to their branching distance in the evolutionary tree from S. flexneri. The organisms of this genus, which happen to be pathotypes of E.coli, also have the closest perplexity values with E. coli. Conclusion Whole

  2. Evaluating mountain goat dairy systems for conversion to the organic model, using a multicriteria method.

    PubMed

    Mena, Y; Nahed, J; Ruiz, F A; Sánchez-Muñoz, J B; Ruiz-Rojas, J L; Castel, J M

    2012-04-01

    Organic farming conserves natural resources, promotes biodiversity, guarantees animal welfare and obtains healthy products from raw materials through natural processes. In order to evaluate possibilities of increasing organic animal production, this study proposes a farm-scale multicriteria method for assessing the conversion of dairy goat systems to the organic model. In addition, a case study in the Northern Sierra of Seville, southern Spain, is analysed. A consensus of expert opinions and a field survey are used to validate a list of potential indicators and issues for assessing the conversion, which consider not only the European Community regulations for organic livestock farming, but also agroecological principles. As a result, the method includes 56 variables integrated in nine indicators: Nutritional management, Sustainable pasture management, Soil fertility and contamination, Weed and pest control, Disease prevention, Breeds and reproduction, Animal welfare, Food safety and Marketing and management. The nine indicators are finally integrated in a global index named OLPI (Organic Livestock Proximity Index). Application of the method to a case study with 24 goat farms reveals an OLPI value of 46.5% for dairy goat farms located in mountain areas of southern Spain. The aspects that differ most from the agroecological model include soil management, animal nutrition and product marketing. Results of the case study indicate that the proposed method is easy to implement and is useful for quantifying the approximation of conventional farms to an organic model. PMID:22436287

  3. Pu-239 organ specific dosimetric model applied to non-human biota

    NASA Astrophysics Data System (ADS)

    Kaspar, Matthew Jason

    There are few locations throughout the world, like the Maralinga nuclear test site located in south western Australia, where sufficient plutonium contaminate concentration levels exist that they can be utilized for studies of the long-term radionuclide accumulation in non-human biota. The information obtained will be useful for the potential human users of the site while also keeping with international efforts to better understand doses to non-human biota. In particular, this study focuses primarily on a rabbit sample set collected from the population located within the site. Our approach is intended to employ the same dose and dose rate methods selected by the International Commission on Radiological Protection and adapted by the scientific community for similar research questions. These models rely on a series of simplifying assumptions on biota and their geometry; in particular; organisms are treated as spherical and ellipsoidal representations displaying the animal mass and volume. These simplifications assume homogeneity of all animal tissues. In collaborative efforts between Colorado State University and the Australian Nuclear Science and Technology Organisation (ANSTO), we are expanding current knowledge on radionuclide accumulation in specific organs causing organ-specific dose rates, such as Pu-239 accumulating in bone, liver, and lungs. Organ-specific dose models have been developed for humans; however, little has been developed for the dose assessment to biota, in particular rabbits. This study will determine if it is scientifically valid to use standard software, in particular ERICA Tool, as a means to determine organ-specific dosimetry due to Pu-239 accumulation in organs. ERICA Tool is normally applied to whole organisms as a means to determine radiological risk to whole ecosystems. We will focus on the aquatic model within ERICA Tool, as animal organs, like aquatic organisms, can be assumed to lie within an infinite uniform medium. This model would

  4. A self-organized model for network evolution. Coupling network evolution and extremal dynamics

    NASA Astrophysics Data System (ADS)

    Caldarelli, G.; Capocci, A.; Garlaschelli, D.

    2008-08-01

    Here we provide a detailed analysis, along with some extensions and additonal investigations, of a recently proposed [1] self-organized model for the evolution of complex networks. Vertices of the network are characterized by a fitness variable evolving through an extremal dynamics process, as in the Bak-Sneppen [2] model representing a prototype of Self-Organized Criticality. The network topology is in turn shaped by the fitness variable itself, as in the fitness network model [3]. The system self-organizes to a nontrivial state, characterized by a power-law decay of dynamical and topological quantities above a critical threshold. The interplay between topology and dynamics in the system is the key ingredient leading to an unexpected behaviour of these quantities.

  5. Universal carrier thermoelectric-transport model based on percolation theory in organic semiconductors

    NASA Astrophysics Data System (ADS)

    Lu, Nianduan; Li, Ling; Liu, Ming

    2015-05-01

    Recent measurements conducted over a large range of temperature and carrier density have found that the Seebeck coefficient exhibits an approaching disorder-free transport feature in high-mobility conjugated polymers [D. Venkateshvaran et al., Nature 515, 384 (2014), 10.1038/nature13854]. It is difficult for the current Seebeck coefficient model to interpret the feature of the charge transport approaching disorder-free transport. We present a general analytical model to describe the Seebeck effect for organic semiconductors based on the hopping transport and percolation theory. The proposed model can well explain the Seebeck feature of the polymers with approaching disorder-free transport, as well as that of the organic semiconductors with the general disorder. The simulated results imply that the Seebeck coefficient in the organic semiconductors would happen to transfer from temperature dependence to temperature independence with the decrease of the energetic disorder.

  6. Molecular model of self diffusion in polar organic liquids: implications for conductivity and fluidity in polar organic liquids and electrolytes.

    PubMed

    Frech, Roger; Petrowsky, Matt

    2014-03-01

    Decades of studying isothermal and temperature-dependent mass and charge transport in polar organic liquids and electrolytes have resulted in two mutually incompatible models and the failure to develop a general molecular level picture. The hydrodynamic model describes conductivity, diffusion, and dielectric relaxation in terms of viscosity, while the inadequacy of the thermal activation model leads to empirical descriptions and fitting procedures whose adjustable parameters have little or no physical significance. We recently demonstrated that transport data can be characterized with a high degree of accuracy and self-consistency using the compensated Arrhenius formalism (CAF), where the transport property of interest assumes an Arrhenius-like form that also includes a dielectric constant dependence in the exponential prefactor. Here, we provide the molecular-level basis for the CAF by first modifying transition state theory, emphasizing the coupling of the diffusing molecule's motion with the dynamical motion of the surrounding matrix. We then explicitly include the polarization energy contribution from the dipolar medium. The polarization energy is related to molecular and system properties through the dipole moment and dipole density, respectively. The energy barrier for transport is coupled to the polarization energy, and we show that accounting for the role of the polarization energy leads naturally to the dielectric constant dependence in the exponential prefactor. PMID:24559237

  7. Partitioning of Organic Ions to Muscle Protein: Experimental Data, Modeling, and Implications for in Vivo Distribution of Organic Ions.

    PubMed

    Henneberger, Luise; Goss, Kai-Uwe; Endo, Satoshi

    2016-07-01

    The in vivo partitioning behavior of ionogenic organic chemicals (IOCs) is of paramount importance for their toxicokinetics and bioaccumulation. Among other proteins, structural proteins including muscle proteins could be an important sorption phase for IOCs, because of their high quantity in the human and other animals' body and their polar nature. Binding data for IOCs to structural proteins are, however, severely limited. Therefore, in this study muscle protein-water partition coefficients (KMP/w) of 51 systematically selected organic anions and cations were determined experimentally. A comparison of the measured KMP/w with bovine serum albumin (BSA)-water partition coefficients showed that anionic chemicals sorb more strongly to BSA than to muscle protein (by up to 3.5 orders of magnitude), while cations sorb similarly to both proteins. Sorption isotherms of selected IOCs to muscle protein are linear (i.e., KMP/w is concentration independent), and KMP/w is only marginally influenced by pH value and salt concentration. Using the obtained data set of KMP/w a polyparameter linear free energy relationship (PP-LFER) model was established. The derived equation fits the data well (R(2) = 0.89, RMSE = 0.29). Finally, it was demonstrated that the in vitro measured KMP/w values of this study have the potential to be used to evaluate tissue-plasma partitioning of IOCs in vivo. PMID:27265315

  8. Multi-Organ Contribution to the Metabolic Plasma Profile Using Hierarchical Modelling

    PubMed Central

    Torell, Frida; Bennett, Kate; Cereghini, Silvia; Rännar, Stefan; Lundstedt-Enkel, Katrin; Moritz, Thomas; Haumaitre, Cecile; Trygg, Johan; Lundstedt, Torbjörn

    2015-01-01

    Hierarchical modelling was applied in order to identify the organs that contribute to the levels of metabolites in plasma. Plasma and organ samples from gut, kidney, liver, muscle and pancreas were obtained from mice. The samples were analysed using gas chromatography time-of-flight mass spectrometry (GC TOF-MS) at the Swedish Metabolomics centre, Umeå University, Sweden. The multivariate analysis was performed by means of principal component analysis (PCA) and orthogonal projections to latent structures (OPLS). The main goal of this study was to investigate how each organ contributes to the metabolic plasma profile. This was performed using hierarchical modelling. Each organ was found to have a unique metabolic profile. The hierarchical modelling showed that the gut, kidney and liver demonstrated the greatest contribution to the metabolic pattern of plasma. For example, we found that metabolites were absorbed in the gut and transported to the plasma. The kidneys excrete branched chain amino acids (BCAAs) and fatty acids are transported in the plasma to the muscles and liver. Lactic acid was also found to be transported from the pancreas to plasma. The results indicated that hierarchical modelling can be utilized to identify the organ contribution of unknown metabolites to the metabolic profile of plasma. PMID:26086868

  9. A framework for implementation of organ effect models in TOPAS with benchmarks extended to proton therapy.

    PubMed

    Ramos-Méndez, J; Perl, J; Schümann, J; Shin, J; Paganetti, H; Faddegon, B

    2015-07-01

    The aim of this work was to develop a framework for modeling organ effects within TOPAS (TOol for PArticle Simulation), a wrapper of the Geant4 Monte Carlo toolkit that facilitates particle therapy simulation. The DICOM interface for TOPAS was extended to permit contour input, used to assign voxels to organs. The following dose response models were implemented: The Lyman-Kutcher-Burman model, the critical element model, the population based critical volume model, the parallel-serial model, a sigmoid-based model of Niemierko for normal tissue complication probability and tumor control probability (TCP), and a Poisson-based model for TCP. The framework allows easy manipulation of the parameters of these models and the implementation of other models. As part of the verification, results for the parallel-serial and Poisson model for x-ray irradiation of a water phantom were compared to data from the AAPM Task Group 166. When using the task group dose-volume histograms (DVHs), results were found to be sensitive to the number of points in the DVH, with differences up to 2.4%, some of which are attributable to differences between the implemented models. New results are given with the point spacing specified. When using Monte Carlo calculations with TOPAS, despite the relatively good match to the published DVH's, differences up to 9% were found for the parallel-serial model (for a maximum DVH difference of 2%) and up to 0.5% for the Poisson model (for a maximum DVH difference of 0.5%). However, differences of 74.5% (in Rectangle1), 34.8% (in PTV) and 52.1% (in Triangle) for the critical element, critical volume and the sigmoid-based models were found respectively. We propose a new benchmark for verification of organ effect models in proton therapy. The benchmark consists of customized structures in the spread out Bragg peak plateau, normal tissue, tumor, penumbra and in the distal region. The DVH's, DVH point spacing, and results of the organ effect models are provided

  10. A framework for implementation of organ effect models in TOPAS with benchmarks extended to proton therapy

    NASA Astrophysics Data System (ADS)

    Ramos-Méndez, J.; Perl, J.; Schümann, J.; Shin, J.; Paganetti, H.; Faddegon, B.

    2015-07-01

    The aim of this work was to develop a framework for modeling organ effects within TOPAS (TOol for PArticle Simulation), a wrapper of the Geant4 Monte Carlo toolkit that facilitates particle therapy simulation. The DICOM interface for TOPAS was extended to permit contour input, used to assign voxels to organs. The following dose response models were implemented: The Lyman-Kutcher-Burman model, the critical element model, the population based critical volume model, the parallel-serial model, a sigmoid-based model of Niemierko for normal tissue complication probability and tumor control probability (TCP), and a Poisson-based model for TCP. The framework allows easy manipulation of the parameters of these models and the implementation of other models. As part of the verification, results for the parallel-serial and Poisson model for x-ray irradiation of a water phantom were compared to data from the AAPM Task Group 166. When using the task group dose-volume histograms (DVHs), results were found to be sensitive to the number of points in the DVH, with differences up to 2.4%, some of which are attributable to differences between the implemented models. New results are given with the point spacing specified. When using Monte Carlo calculations with TOPAS, despite the relatively good match to the published DVH’s, differences up to 9% were found for the parallel-serial model (for a maximum DVH difference of 2%) and up to 0.5% for the Poisson model (for a maximum DVH difference of 0.5%). However, differences of 74.5% (in Rectangle1), 34.8% (in PTV) and 52.1% (in Triangle) for the critical element, critical volume and the sigmoid-based models were found respectively. We propose a new benchmark for verification of organ effect models in proton therapy. The benchmark consists of customized structures in the spread out Bragg peak plateau, normal tissue, tumor, penumbra and in the distal region. The DVH’s, DVH point spacing, and results of the organ effect models are provided

  11. Predictive Multiple Model Switching Control with the Self-Organizing Map

    NASA Technical Reports Server (NTRS)

    Motter, Mark A.

    2000-01-01

    A predictive, multiple model control strategy is developed by extension of self-organizing map (SOM) local dynamic modeling of nonlinear autonomous systems to a control framework. Multiple SOMs collectively model the global response of a nonautonomous system to a finite set of representative prototype controls. Each SOM provides a codebook representation of the dynamics corresponding to a prototype control. Different dynamic regimes are organized into topological neighborhoods where the adjacent entries in the codebook represent the global minimization of a similarity metric. The SOM is additionally employed to identify the local dynamical regime, and consequently implements a switching scheme that selects the best available model for the applied control. SOM based linear models are used to predict the response to a larger family of control sequences which are clustered on the representative prototypes. The control sequence which corresponds to the prediction that best satisfies the requirements on the system output is applied as the external driving signal.

  12. Exploring the patterns and evolution of self-organized urban street networks through modeling

    NASA Astrophysics Data System (ADS)

    Rui, Yikang; Ban, Yifang; Wang, Jiechen; Haas, Jan

    2013-03-01

    As one of the most important subsystems in cities, urban street networks have recently been well studied by using the approach of complex networks. This paper proposes a growing model for self-organized urban street networks. The model involves a competition among new centers with different values of attraction radius and a local optimal principle of both geometrical and topological factors. We find that with the model growth, the local optimization in the connection process and appropriate probability for the loop construction well reflect the evolution strategy in real-world cities. Moreover, different values of attraction radius in centers competition process lead to morphological change in patterns including urban network, polycentric and monocentric structures. The model succeeds in reproducing a large diversity of road network patterns by varying parameters. The similarity between the properties of our model and empirical results implies that a simple universal growth mechanism exists in self-organized cities.

  13. First-Order Transition in a Spin Model for Self-Organization

    NASA Astrophysics Data System (ADS)

    Bauvin, R.; Kamp, Y.

    The paper examines the emergence of self-organization in a population where tandem recruitment is combined with individual memory. The time evolution is modeled as a two-dimensional spin system with local interaction along the time axis and a mean-field interaction along the other axis. We generalize a previous result obtained with this model from the case of two sources to the multisource situation and show a twofold connection with the Potts model. First, when individual memory exceeds a critical value, a phase transition sets in, which is second order for two sources but first order beyond, similarly to the mean-field theory of the Potts model. In addition, the self-organization problem considered here relies on a special case of the one-dimensional nearest-neighbor Potts model with external field, which is shown to be explicitly solvable.

  14. Comparing Organic Aerosol Composition from Marine Biogenic Sources to Seawater and to Physical Sea Spray Models

    NASA Astrophysics Data System (ADS)

    Russell, L. M.; Frossard, A. A.; Sanchez, K.; Massoli, P.; Elliott, S.; Burrows, S. M.; Bates, T. S.; Quinn, P.

    2015-12-01

    In much of the marine atmosphere, organic components in aerosol particles have many sources other than sea spray that contribute organic constituents. For this reason, physical sea spray models provide an important technique for studying the organic composition of particles from marine biogenic sources. The organic composition of particles produced by two different physical sea spray models were measured in three open ocean seawater types: (i) Coastal California in the northeastern Pacific, which is influenced by wind-driven, large-scale upwelling leading to productive or eutrophic (nutrient-rich) seawater and high chl-a concentrations, (ii) George's Bank in the northwestern Atlantic, which is also influenced by nutrient upwelling and eutrophic seawater with phytoplankton productivity and high chl-a concentrations, and (iii) the Sargasso Sea in the subtropical western Atlantic, which is oligotrophic and nutrient-limited, reflected in low phytoplankton productivity and low chl-a concentrations. Fourier transform infrared spectroscopy provides information about the functional group composition that represents the marine organic fraction more completely than is possible with techniques that measure non-refractory mass (vaporizable at 650°C). After separating biogenic marine particles from those from other sources, the measured compositions of atmospheric marine aerosol particles from three ocean regions is 65±12% hydroxyl, 21±9% alkane, 6±6% amine, and 7±8% carboxylic acid functional groups. The organic composition of atmospheric primary marine (ocean-derived) aerosol particles is nearly identical to model generated primary marine aerosol particles from bubbled seawater. Variability in productive and non-productive seawater may be caused by the presence of surfactants that can stabilize the bubble film and lead to preferential drainage of the more soluble (lower alkane group fraction) organic components without substantial changes in overall group composition

  15. MATHEMATICAL MODEL OF PLANT UPTAKE AND TRANSLOCATION OF ORGANIC CHEMICALS: DEVELOPMENT OF THE MODEL

    EPA Science Inventory

    Uptake, transport, and accumulation of organic chemicals by plants are influenced by characteristics of the plant and properties of the chemical, soil, and environmental conditions. valuations of plant contamination cannot be made experimentally for the many thousands of xenobiot...

  16. Model organism databases: essential resources that need the support of both funders and users.

    PubMed

    Oliver, Stephen G; Lock, Antonia; Harris, Midori A; Nurse, Paul; Wood, Valerie

    2016-01-01

    Modern biomedical research depends critically on access to databases that house and disseminate genetic, genomic, molecular, and cell biological knowledge. Even as the explosion of available genome sequences and associated genome-scale data continues apace, the sustainability of professionally maintained biological databases is under threat due to policy changes by major funding agencies. Here, we focus on model organism databases to demonstrate the myriad ways in which biological databases not only act as repositories but actively facilitate advances in research. We present data that show that reducing financial support to model organism databases could prove to be not just scientifically, but also economically, unsound. PMID:27334346

  17. Global modeling of SOA formation from dicarbonyls, epoxides, organic nitrates and peroxides

    NASA Astrophysics Data System (ADS)

    Lin, G.; Penner, J. E.; Sillman, S.; Taraborrelli, D.; Lelieveld, J.

    2012-05-01

    Recent experimental findings indicate that secondary organic aerosol (SOA) represents an important and, under many circumstances, the major fraction of the organic aerosol burden. Here, we use a global 3-D model (IMPACT) to test the results of different mechanisms for the production of SOA. The basic mechanism includes SOA formation from organic nitrates and peroxides produced from an explicit chemical formulation, using partition coefficients based on thermodynamic principles together with assumptions for the rate of formation of low-volatility oligomers. We also include the formation of low-volatility SOA from the reaction of glyoxal and methylglyoxal on aqueous aerosols and cloud droplets as well as from the reaction of epoxides on aqueous aerosols. A model simulation including these SOA formation mechanisms gives an annual global SOA production of 120.5 Tg. The global production of SOA is decreased substantially to 90.8 Tg yr-1 if the HOx regeneration mechanism proposed by Peeters et al. (2009) is used. Model predictions with and without this HOx (OH and HO2 regeneration scheme are compared with multiple surface observation datasets, namely: the Interagency Monitoring of Protected Visual Environments (IMPROVE) for the United States, the European Monitoring and Evaluation Programme (EMEP), and aerosol mass spectrometry (AMS) data measured in both the Northern Hemisphere and tropical forest regions. All model simulations show reasonable agreement with the organic carbon mass observed in the IMPROVE network and the AMS dataset, however observations in Europe are significantly underestimated, which may be caused by an underestimation of primary organic aerosol emissions (POA) in winter and of emissions and/or SOA production in the summer. The modeled organic aerosol concentrations tend to be higher by roughly a factor of three when compared with measurements at three tropical forest sites. This overestimate suggests that more measurements and model studies are

  18. A Modeling substorm Dynamics of the Magnetosphere Using Self-Organized Criticality Approach

    NASA Astrophysics Data System (ADS)

    Bolzan, Mauricio; Rosa, Reinaldo

    2016-07-01

    Responses of Earth magnetic field during substorms exhibits a number of characteristics features such as the power-law spectra of fluctuations on different scales and signatures of low effective dimensions. Due the magnetosphere are constantly out-equilibrium their behavior is similar to real sandpiles during substorms, features of self-organized criticality (SOC) systems. Thus, in this work we presented a simple mathematical model to AE-index based on self-organizing sandpile mentioned by Uritsky and Pudovkin (1998), but we input the dissipation process inside the model. The statistical and multifractal tools to characterization of dynamical processes was used.

  19. Modeling the Self-organized Critical Behavior of the Plasma Sheet Reconnection Dynamics

    NASA Technical Reports Server (NTRS)

    Klimas, Alex; Uritsky, Vadim; Baker, Daniel

    2006-01-01

    Analyses of Polar UVI auroral image data reviewed in our other presentation at this meeting (V. Uritsky, A. Klimas) show that bright night-side high-latitude UV emissions exhibit so many of the key properties of systems in self-organized criticality (SOC) that an alternate interpretation has become virtually impossible. It is now necessary to find and model the source of this behavior. We note that the most common models of self-organized criticality are numerical sandpiles. These are, at root, models that govern the transport of some quantity from a region where it is loaded to another where it is unloaded. Transport is enabled by the excitation of a local threshold instability; it is intermittent and bursty, and it exhibits a number of scale-free statistical properties. Searching for a system in the magnetosphere that is analogous and that, in addition, is known to produce auroral signatures, we focus on the reconnection dynamics of the plasma sheet. In our previous work, a driven reconnection model has been constructed and has been under study. The transport of electromagnetic (primarily magnetic) energy carried by the Poynting flux into the reconnection region of the model has been examined. All of the analysis techniques, and more, that have been applied to the auroral image data have also been applied to this Poynting flux. Here, we report new results showing that this model also exhibits so many of the key properties of systems in self-organized criticality that an alternate interpretation is implausible. Further, we find a strong correlation between these key properties of the model and those of the auroral UV emissions. We suggest that, in general, the driven reconnection model is an important step toward a realistic plasma physical model of self-organized criticality and we conclude, more specifically, that it is also a step in the right direction toward modeling the multiscale reconnection dynamics of the magnetotail.

  20. Modeling the Self-organized Critical Behavior of Earth's Plasma Sheet Reconnection Dynamics

    NASA Technical Reports Server (NTRS)

    Klimas, Alexander J.

    2006-01-01

    Analyses of Polar UVI auroral image data show that bright night-side high-latitude W emissions exhibit so many of the key properties of systems in self-organized criticality that an alternate interpretation has become virtually impossible. These analyses will be reviewed. It is now necessary to find and model the source of this behavior. We note that the most common models of self-organized criticality are numerical sandpiles. These are, at root, models that govern the transport of some quantity from a region where it is loaded to another where it is unloaded. Transport is enabled by the excitation of a local threshold instability; it is intermittent and bursty, and it exhibits a number of scale-free statistical properties. Searching for a system in the magnetosphere that is analogous and that, in addition, is known to produce auroral signatures, we focus on the reconnection dynamics of the magnetotail plasma sheet. In our previous work, a driven reconnection model has been constructed and has been under study. The transport of electromagnetic (primarily magnetic) energy carried by the Poynting flux into the reconnection region of the model has been examined. All of the analysis techniques (and more) that have been applied to the auroral image data have also been applied to this Poynting flux. New results will be presented showing that this model also exhibits so many of the key properties of systems in self-organized criticality that an alternate interpretation is implausible. A strong correlation between these key properties of the model and those of the auroral UV emissions will be demonstrated. We suggest that, in general, the driven reconnection model is an important step toward a realistic plasma physical model of self-organized criticality and we conclude, more specifically, that it is also a step in the right direction toward modeling the multiscale reconnection dynamics of the magnetotail.

  1. Surface models of the male urogenital organs built from the Visible Korean using popular software

    PubMed Central

    Shin, Dong Sun; Park, Jin Seo; Shin, Byeong-Seok

    2011-01-01

    Unlike volume models, surface models, which are empty three-dimensional images, have a small file size, so they can be displayed, rotated, and modified in real time. Thus, surface models of male urogenital organs can be effectively applied to an interactive computer simulation and contribute to the clinical practice of urologists. To create high-quality surface models, the urogenital organs and other neighboring structures were outlined in 464 sectioned images of the Visible Korean male using Adobe Photoshop; the outlines were interpolated on Discreet Combustion; then an almost automatic volume reconstruction followed by surface reconstruction was performed on 3D-DOCTOR. The surface models were refined and assembled in their proper positions on Maya, and a surface model was coated with actual surface texture acquired from the volume model of the structure on specially programmed software. In total, 95 surface models were prepared, particularly complete models of the urinary and genital tracts. These surface models will be distributed to encourage other investigators to develop various kinds of medical training simulations. Increasingly automated surface reconstruction technology using commercial software will enable other researchers to produce their own surface models more effectively. PMID:21829759

  2. Mathematical model of organic substrate degradation in solid waste windrow composting.

    PubMed

    Seng, Bunrith; Kristanti, Risky Ayu; Hadibarata, Tony; Hirayama, Kimiaki; Katayama-Hirayama, Keiko; Kaneko, Hidehiro

    2016-01-01

    Organic solid waste composting is a complex process that involves many coupled physical, chemical and biological mechanisms. To understand this complexity and to ease in planning, design and management of the composting plant, mathematical model for simulation is usually applied. The aim of this paper is to develop a mathematical model of organic substrate degradation and its performance evaluation in solid waste windrow composting system. The present model is a biomass-dependent model, considering biological growth processes under the limitation of moisture, oxygen and substrate contents, and temperature. The main output of this model is substrate content which was divided into two categories: slowly and rapidly degradable substrates. To validate the model, it was applied to a laboratory scale windrow composting of a mixture of wood chips and dog food. The wastes were filled into a cylindrical reactor of 6 cm diameter and 1 m height. The simulation program was run for 3 weeks with 1 s stepwise. The simulated results were in reasonably good agreement with the experimental results. The MC and temperature of model simulation were found to be matched with those of experiment, but limited for rapidly degradable substrates. Under anaerobic zone, the degradation of rapidly degradable substrate needs to be incorporated into the model to achieve full simulation of a long period static pile composting. This model is a useful tool to estimate the changes of substrate content during composting period, and acts as a basic model for further development of a sophisticated model. PMID:26522660

  3. Predicting the acute neurotoxicity of diverse organic solvents using probabilistic neural networks based QSTR modeling approaches.

    PubMed

    Basant, Nikita; Gupta, Shikha; Singh, Kunwar P

    2016-03-01

    Organic solvents are widely used chemicals and the neurotoxic properties of some are well established. In this study, we established nonlinear qualitative and quantitative structure-toxicity relationship (STR) models for predicting neurotoxic classes and neurotoxicity of structurally diverse solvents in rodent test species following OECD guideline principles for model development. Probabilistic neural network (PNN) based qualitative and generalized regression neural network (GRNN) based quantitative STR models were constructed using neurotoxicity data from rat and mouse studies. Further, interspecies correlation based quantitative activity-activity relationship (QAAR) and global QSTR models were also developed using the combined data set of both rodent species for predicting the neurotoxicity of solvents. The constructed models were validated through deriving several statistical coefficients for the test data and the prediction and generalization abilities of these models were evaluated. The qualitative STR models (rat and mouse) yielded classification accuracies of 92.86% in the test data sets, whereas, the quantitative STRs yielded correlation (R(2)) of >0.93 between the measured and model predicted toxicity values in both the test data (rat and mouse). The prediction accuracies of the QAAR (R(2) 0.859) and global STR (R(2) 0.945) models were comparable to those of the independent local STR models. The results suggest the ability of the developed QSTR models to reliably predict binary neurotoxicity classes and the endpoint neurotoxicities of the structurally diverse organic solvents. PMID:26721664

  4. Multi-site validation of a soil organic matter model based on generally available input data

    NASA Astrophysics Data System (ADS)

    Franko, Uwe; Kolbe, Hartmut; Thiel, Enrico; Ließ, Ekkehard

    2010-05-01

    Regionalization of soil organic matter (SOM) dynamics by means of modelling is often restricted by the availability of model inputs on the used scale. Taking this into account the approach of the CANDY model (Franko et al., 1995) has been strongly simplified with a remarkable reduction of input requirements. This simplified model called Candy Carbon balance (CCB) was validated against a large number of long term datasets from arable field experiments mainly situated in Germany but also from some places in Europe altogether containing 41 sites with 65 experiments and a total number of 598 different treatments. The required input data are: - soil: clay content, soil classification - climate: rainfall and air temperature as long term averages - management: crop rotation with yields and organic amendments - SOM: at least one initial value; more observations for validation purpose During the calculation process the model makes use of some other soil parameters like silt content, bulk density, pore volume, field capacity and permanent wilting point. These data may be delivered by the user or if absent they will be calculated from pedotransfer functions. If the initial information includes not only organic Carbon (Corg) but also total Nitrogen (Nt) the SOM dynamics will be modelled for both elements. The CCB model follows the CANDY concept distributing SOM in a long term stabilized and a decomposable fraction. The long term stabilized part is calculated comparable to the CIPS model (Kuka,2005) taking the SOM in soil micro pores as highly stabilized so that its turnover can be neglected for this model application and hence will show no dynamics during simulation. Soil texture, rainfall, irrigation amount and air temperature are used to estimate the site specific biologic activity for SOM turnover in terms of Biological Active Time (BAT). Annual yield data are transformed to the amounts of organic matter input due to cropping that together with organic amendments are the

  5. Modeling the effects of fire severity on soil organic horizons and forest composition in Interior Alaska

    NASA Astrophysics Data System (ADS)

    Genet, H.; Barrett, K. M.; Johnstone, J. F.; McGuire, A. D.; Yuan, F.; Euskirchen, E. S.; Kasischke, E. S.; Rupp, S. T.; Turetsky, M. R.

    2012-12-01

    The fire regime in the boreal region of interior Alaska has been intensifying in terms of both area burned and severity over the last three decades. Based on projections of climate change, this trend is expected to continue throughout the 21st century. Fire causes abrupt changes in energy, nutrient and water balances influencing habitat and vegetation composition. An important factor influencing these changes is the reduction of the soil organic horizon because of differential regeneration capabilities of conifer and evergreen shrubs vs. deciduous and herbaceous vegetation on organic vs. mineral soils. The goal of this study is to develop a prognostic model to simulate the effects of fire severity on soil organic horizons and to evaluate its long-term consequences on forest composition in interior Alaska. Existing field observations were analyzed to build a predictive model of the depth of burning of soil organic horizon after a fire. The model is driven by data sets of fire occurrence, climate, and topography. Post-fire vegetation succession was simulated as a function of post-fire organic horizon depth. The fire severity and post-fire vegetation succession models were then implemented within a biogeochemistry model, the process-based Terrestrial Ecosystem Model. Simulations for 21st century climate scenarios at a 1 by 1km resolution for the Alaska Yukon River Basin were conducted to evaluate the effects of considering vs. ignoring post-fire vegetation succession on carbon dynamics. The results of these simulations indicate that it is important for ecosystem models to represent the influence of fire severity on post-fire vegetation succession in order to fully understand the consequences of changes in climate and disturbance regimes on boreal ecosystems.

  6. 4D cone-beam CT reconstruction using multi-organ meshes for sliding motion modeling.

    PubMed

    Zhong, Zichun; Gu, Xuejun; Mao, Weihua; Wang, Jing

    2016-02-01

    A simultaneous motion estimation and image reconstruction (SMEIR) strategy was proposed for 4D cone-beam CT (4D-CBCT) reconstruction and showed excellent results in both phantom and lung cancer patient studies. In the original SMEIR algorithm, the deformation vector field (DVF) was defined on voxel grid and estimated by enforcing a global smoothness regularization term on the motion fields. The objective of this work is to improve the computation efficiency and motion estimation accuracy of SMEIR for 4D-CBCT through developing a multi-organ meshing model. Feature-based adaptive meshes were generated to reduce the number of unknowns in the DVF estimation and accurately capture the organ shapes and motion. Additionally, the discontinuity in the motion fields between different organs during respiration was explicitly considered in the multi-organ mesh model. This will help with the accurate visualization and motion estimation of the tumor on the organ boundaries in 4D-CBCT. To further improve the computational efficiency, a GPU-based parallel implementation was designed. The performance of the proposed algorithm was evaluated on a synthetic sliding motion phantom, a 4D NCAT phantom, and four lung cancer patients. The proposed multi-organ mesh based strategy outperformed the conventional Feldkamp-Davis-Kress, iterative total variation minimization, original SMEIR and single meshing method based on both qualitative and quantitative evaluations. PMID:26758496

  7. A computationally-efficient secondary organic aerosol module for three-dimensional air quality models

    NASA Astrophysics Data System (ADS)

    Liu, P.; Zhang, Y.

    2008-04-01

    Accurately simulating secondary organic aerosols (SOA) in three-dimensional (3-D) air quality models is challenging due to the complexity of the physics and chemistry involved and the high computational demand required. A computationally-efficient yet accurate SOA module is necessary in 3-D applications for long-term simulations and real-time air quality forecasting. A coupled gas and aerosol box model (i.e., 0-D CMAQ-MADRID 2) is used to optimize relevant processes in order to develop such a SOA module. Solving the partitioning equations for condensable volatile organic compounds (VOCs) and calculating their activity coefficients in the multicomponent mixtures are identified to be the most computationally-expensive processes. The two processes can be speeded up by relaxing the error tolerance levels and reducing the maximum number of iterations of the numerical solver for the partitioning equations for organic species; turning on organic-inorganic interactions only when the water content associated with organic compounds is significant; and parameterizing the calculation of activity coefficients for organic mixtures in the hydrophilic module. The optimal speed-up method can reduce the total CPU cost by up to a factor of 29.7 with ±15% deviation from benchmark results. These speedup methods are applicable to other SOA modules that are based on partitioning theories.

  8. 4D cone-beam CT reconstruction using multi-organ meshes for sliding motion modeling

    NASA Astrophysics Data System (ADS)

    Zhong, Zichun; Gu, Xuejun; Mao, Weihua; Wang, Jing

    2016-02-01

    A simultaneous motion estimation and image reconstruction (SMEIR) strategy was proposed for 4D cone-beam CT (4D-CBCT) reconstruction and showed excellent results in both phantom and lung cancer patient studies. In the original SMEIR algorithm, the deformation vector field (DVF) was defined on voxel grid and estimated by enforcing a global smoothness regularization term on the motion fields. The objective of this work is to improve the computation efficiency and motion estimation accuracy of SMEIR for 4D-CBCT through developing a multi-organ meshing model. Feature-based adaptive meshes were generated to reduce the number of unknowns in the DVF estimation and accurately capture the organ shapes and motion. Additionally, the discontinuity in the motion fields between different organs during respiration was explicitly considered in the multi-organ mesh model. This will help with the accurate visualization and motion estimation of the tumor on the organ boundaries in 4D-CBCT. To further improve the computational efficiency, a GPU-based parallel implementation was designed. The performance of the proposed algorithm was evaluated on a synthetic sliding motion phantom, a 4D NCAT phantom, and four lung cancer patients. The proposed multi-organ mesh based strategy outperformed the conventional Feldkamp-Davis-Kress, iterative total variation minimization, original SMEIR and single meshing method based on both qualitative and quantitative evaluations.

  9. Ethical models in bioethics: theory and application in organ allocation policies.

    PubMed

    Petrini, C

    2010-12-01

    Policies for allocating organs to people awaiting a transplant constitute a major ethical challenge. First and foremost, they demand balance between the principles of beneficence and justice, but many other ethically relevant principles are also involved: autonomy, responsibility, equity, efficiency, utility, therapeutic outcome, medical urgency, and so forth. Various organ allocation models can be developed based on the hierarchical importance assigned to a given principle over the others, but none of the principles should be completely disregarded. An ethically acceptable organ allocation policy must therefore be in conformity, to a certain extent, with the requirements of all the principles. Many models for organ allocation can be derived. The utilitarian model aims to maximize benefits, which can be of various types on a social or individual level, such as the number of lives saved, prognosis, and so forth. The prioritarian model favours the neediest or those who suffer most. The egalitarian model privileges equity and justice, suggesting that all people should have an equal opportunity (casual allocation) or priority should be given to those who have been waiting longer. The personalist model focuses on each individual patient, attempting to mesh together all the various aspects affecting the person: therapeutic needs (urgency), fairness, clinical outcomes, respect for persons. In the individualistic model the main element is free choice and the system of opting-in is privileged. Contrary to the individualistic model, the communitarian model identities in the community the fundamental elements for the legitimacy of choices: therefore, the system of opting-out is privileged. This article does not aim at suggesting practical solutions. Rather, it furnishes to decision makers an overview on the possible ethical approach to this matter. PMID:21196904

  10. Functional genomics and proteomics of the cellular osmotic stress response in 'non-model' organisms.

    PubMed

    Kültz, Dietmar; Fiol, Diego; Valkova, Nelly; Gomez-Jimenez, Silvia; Chan, Stephanie Y; Lee, Jinoo

    2007-05-01

    All organisms are adapted to well-defined extracellular salinity ranges. Osmoregulatory mechanisms spanning all levels of biological organization, from molecules to behavior, are central to salinity adaptation. Functional genomics and proteomics approaches represent powerful tools for gaining insight into the molecular basis of salinity adaptation and euryhalinity in animals. In this review, we discuss our experience in applying such tools to so-called 'non-model' species, including euryhaline animals that are well-suited for studies of salinity adaptation. Suppression subtractive hybridization, RACE-PCR and mass spectrometry-driven proteomics can be used to identify genes and proteins involved in salinity adaptation or other environmental stress responses in tilapia, sharks and sponges. For protein identification in non-model species, algorithms based on sequence homology searches such as MSBLASTP2 are most powerful. Subsequent gene ontology and pathway analysis can then utilize sets of identified genes and proteins for modeling molecular mechanisms of environmental adaptation. Current limitations for proteomics in non-model species can be overcome by improving sequence coverage, N- and C-terminal sequencing and analysis of intact proteins. Dependence on information about biochemical pathways and gene ontology databases for model species represents a more severe barrier for work with non-model species. To minimize such dependence, focusing on a single biological process (rather than attempting to describe the system as a whole) is key when applying 'omics' approaches to non-model organisms. PMID:17449824

  11. An Idealized Model of Organic Carbon Dynamics on the Continental Margin of the Eastern United States

    NASA Astrophysics Data System (ADS)

    Siedlecki, S. A.; Archer, D.; Mahadevan, A.

    2003-12-01

    Continental margins play a significant role in the production and burial of organic carbon in the ocean, bur these areas are poorly resolved global circulation models. In this study, a high-resolution three-dimensional, nonhydrostatic model of an idealized eastern coastal United States after Mahadevan and Archer, 1998, was modified to simulate organic carbon production and export off the shelf. The model assumes a periodic north and south boundary, and an offshore boundary at the shelf-break density front determined by bathymetry. The model uses a free surface and a sigma grid in the vertical. The model is initialized with a vertical nutrient profile taken from the open Atlantic Ocean. As the winds are given time to influence the region, upwelling conditions can result in the vertical movement of water. Vertical diffusion also carries nutrients into the euphotic zone. Excess nutrients in the euphotic zone are converted to particles that advect with the flow while sinking with a velocity of 10-5 m/s. Remineralization is treated as a first-order decay. We will vary the alongshore wind stress, shelf width, and vertical diffusivity to determine their respective impacts on organic carbon export. Eventually, we hope to parameterize the impact of coastal circulation on the carbon cycle with global circulation and carbon models. Mahadevan, A., Archer, D., Modeling a Limited Region of the Ocean, Journal of Computational Physics 145, 555-574, 1998.

  12. Global distribution and climate forcing of marine organic aerosol: 1. Model improvements and evaluation

    SciTech Connect

    Meskhidze, N.; Xu, J.; Gantt, Brett; Zhang, Yang; Nenes, Athanasios; Ghan, Steven J.; Liu, Xiaohong; Easter, Richard C.; Zaveri, Rahul A.

    2011-11-23

    Marine organic aerosol emissions have been implemented and evaluated within the National Center of Atmospheric Research (NCAR)'s Community Atmosphere Model (CAM5) with the Pacific Northwest National Laboratory's 7-mode Modal Aerosol Module (MAM-7). Emissions of marine primary organic aerosols (POA), phytoplanktonproduced isoprene- and monoterpenes-derived secondary organic aerosols (SOA) and methane sulfonate (MS{sup -}) are shown to affect surface concentrations of organic aerosols in remote marine regions. Global emissions of submicron marine POA is estimated to be 7.9 and 9.4 Tg yr{sup -1}, for the Gantt et al. (2011) and Vignati et al. (2010) emission parameterizations, respectively. Marine sources of SOA and particulate MS{sup -} (containing both sulfur and carbon atoms) contribute an additional 0.2 and 5.1 Tg yr{sup -1}, respectively. Widespread areas over productive waters of the Northern Atlantic, Northern Pacific, and the Southern Ocean show marine-source submicron organic aerosol surface concentrations of 100 ngm{sup -3}, with values up to 400 ngm{sup -3} over biologically productive areas. Comparison of long-term surface observations of water insoluble organic matter (WIOM) with POA concentrations from the two emission parameterizations shows that despite revealed discrepancies (often more than a factor of 2), both Gantt et al. (2011) and Vignati et al. (2010) formulations are able to capture the magnitude of marine organic aerosol concentrations, with the Gantt et al. (2011) parameterization attaining better seasonality. Model simulations show that the mixing state of the marine POA can impact the surface number concentration of cloud condensation nuclei (CCN). The largest increases (up to 20 %) in CCN (at a supersaturation (S) of 0.2 %) number concentration are obtained over biologically productive ocean waters when marine organic aerosol is assumed to be externally mixed with sea-salt. Assuming marine organics are internally-mixed with sea

  13. A Novel In Vitro Model for Microvasculature Reveals Regulation of Circumferential ECM Organization by Curvature

    PubMed Central

    Barreto-Ortiz, Sebastian F.; Zhang, Shuming; Davenport, Matthew; Fradkin, Jamie; Ginn, Brian; Mao, Hai-Quan; Gerecht, Sharon

    2013-01-01

    In microvascular vessels, endothelial cells are aligned longitudinally whereas several components of the extracellular matrix (ECM) are organized circumferentially. While current three-dimensional (3D) in vitro models for microvasculature have allowed the study of ECM-regulated tubulogenesis, they have limited control over topographical cues presented by the ECM and impart a barrier for the high-resolution and dynamic study of multicellular and extracellular organization. Here we exploit a 3D fibrin microfiber scaffold to develop a novel in vitro model of the microvasculature that recapitulates endothelial alignment and ECM deposition in a setting that also allows the sequential co-culture of mural cells. We show that the microfibers' nanotopography induces longitudinal adhesion and alignment of endothelial colony-forming cells (ECFCs), and that these deposit circumferentially organized ECM. We found that ECM wrapping on the microfibers is independent of ECFCs' actin and microtubule organization, but it is dependent on the curvature of the microfiber. Microfibers with smaller diameters (100–400 µm) guided circumferential ECM deposition, whereas microfibers with larger diameters (450 µm) failed to support wrapping ECM. Finally, we demonstrate that vascular smooth muscle cells attached on ECFC-seeded microfibers, depositing collagen I and elastin. Collectively, we establish a novel in vitro model for the sequential control and study of microvasculature development and reveal the unprecedented role of the endothelium in organized ECM deposition regulated by the microfiber curvature. PMID:24278378

  14. Entity Model Based Quality Management: A First Step Towards High Reliability Organization Management

    NASA Astrophysics Data System (ADS)

    Engelbrecht, S.; Radestock, Chr.; Bohle, D. K. H.

    2010-09-01

    A management system built upon a generic entity model is presented as an approach towards management systems for High Reliability Organizations(HRO). The entity model is derived from the Ground Systems and Operations standard of the European Cooperation for Space Standardization(ECSS). DLR has launched a first application of the model in its Applied Remote Sensing Cluster, especially for the Center for Satellite based Crisis Information. It is proposed that a management system built upon the entity model systematically enhances a significant number of HRO characteristics.

  15. Variation in pH of Model Secondary Organic Aerosol during Liquid-Liquid Phase Separation.

    PubMed

    Dallemagne, Magda A; Huang, Xiau Ya; Eddingsaas, Nathan C

    2016-05-12

    The majority of atmospheric aerosols consist of both organic and inorganic components. At intermediate relative humidity (RH), atmospheric aerosol can undergo liquid-liquid phase separation (LLPS) in which the organic and inorganic fractions segregate from each other. We have extended the study of LLPS to the effect that phase separation has on the pH of the overall aerosols and the pH of the individual phases. Using confocal microscopy and pH sensitive dyes, the pH of internally mixed model aerosols consisting of polyethylene glycol 400 and ammonium sulfate as well as the pH of the organic fraction during LLPS have been directly measured. During LLPS, the pH of the organic fraction was observed to increase to 4.2 ± 0.2 from 3.8 ± 0.1 under high RH when the aerosol was internally mixed. In addition, the high spatial resolution of the confocal microscope allowed us to characterize the composition of each of the phases, and we have observed that during LLPS the organic shell still contains large quantities of water and should be characterized as an aqueous organic-rich phase rather than simply an organic phase. PMID:27082856

  16. Explicit modeling of volatile organic compounds partitioning in the atmospheric aqueous phase

    NASA Astrophysics Data System (ADS)

    Mouchel-Vallon, C.; Bräuer, P.; Camredon, M.; Valorso, R.; Madronich, S.; Herrmann, H.; Aumont, B.

    2013-01-01

    The gas phase oxidation of organic species is a multigenerational process involving a large number of secondary compounds. Most secondary organic species are water-soluble multifunctional oxygenated molecules. The fully explicit chemical mechanism GECKO-A (Generator of Explicit Chemistry and Kinetics of Organics in the Atmosphere) is used to describe the oxidation of organics in the gas phase and their mass transfer to the aqueous phase. The oxidation of three hydrocarbons of atmospheric interest (isoprene, octane and α-pinene) is investigated for various NOx conditions. The simulated oxidative trajectories are examined in a new two dimensional space defined by the mean oxidation state and the solubility. The amount of dissolved organic matter was found to be very low (yield less than 2% on carbon atom basis) under a water content typical of deliquescent aerosols. For cloud water content, 50% (isoprene oxidation) to 70% (octane oxidation) of the carbon atoms are found in the aqueous phase after the removal of the parent hydrocarbons for low NOx conditions. For high NOx conditions, this ratio is only 5% in the isoprene oxidation case, but remains large for α-pinene and octane oxidation cases (40% and 60%, respectively). Although the model does not yet include chemical reactions in the aqueous phase, much of this dissolved organic matter should be processed in cloud drops and modify both oxidation rates and the speciation of organic species.

  17. Explicit modeling of volatile organic compounds partitioning in the atmospheric aqueous phase

    NASA Astrophysics Data System (ADS)

    Mouchel-Vallon, C.; Bräuer, P.; Camredon, M.; Valorso, R.; Madronich, S.; Herrmann, H.; Aumont, B.

    2012-09-01

    The gas phase oxidation of organic species is a multigenerational process involving a large number of secondary compounds. Most secondary organic species are water-soluble multifunctional oxygenated molecules. The fully explicit chemical mechanism GECKO-A (Generator of Explicit Chemistry and Kinetics of Organics in the Atmosphere) is used to describe the oxidation of organics in the gas phase and their mass transfer to the aqueous phase. The oxidation of three hydrocarbons of atmospheric interest (isoprene, octane and α-pinene) is investigated for various NOx conditions. The simulated oxidative trajectories are examined in a new two dimensional space defined by the mean oxidation state and the solubility. The amount of dissolved organic matter was found to be very low (<2%) under a water content typical of deliquescent aerosols. For cloud water content, 50% (isoprene oxidation) to 70% (octane oxidation) of the carbon atoms are found in the aqueous phase after the removal of the parent hydrocarbons for low NOx conditions. For high NOx conditions, this ratio is only 5% in the isoprene oxidation case, but remains large for α-pinene and octane oxidation cases (40% and 60%, respectively). Although the model does not yet include chemical reactions in the aqueous phase, much of this dissolved organic matter should be processed in cloud drops and modify both oxidation rates and the speciation of organic species.

  18. Can Government Be Self-Organized? A Mathematical Model of the Collective Social Organization of Ancient Teotihuacan, Central Mexico

    PubMed Central

    Froese, Tom; Gershenson, Carlos; Manzanilla, Linda R.

    2014-01-01

    Teotihuacan was the first urban civilization of Mesoamerica and one of the largest of the ancient world. Following a tradition in archaeology to equate social complexity with centralized hierarchy, it is widely believed that the city’s origin and growth was controlled by a lineage of powerful individuals. However, much data is indicative of a government of co-rulers, and artistic traditions expressed an egalitarian ideology. Yet this alternative keeps being marginalized because the problems of collective action make it difficult to conceive how such a coalition could have functioned in principle. We therefore devised a mathematical model of the city’s hypothetical network of representatives as a formal proof of concept that widespread cooperation was realizable in a fully distributed manner. In the model, decisions become self-organized into globally optimal configurations even though local representatives behave and modify their relations in a rational and selfish manner. This self-optimization crucially depends on occasional communal interruptions of normal activity, and it is impeded when sections of the network are too independent. We relate these insights to theories about community-wide rituals at Teotihuacan and the city’s eventual disintegration. PMID:25303308

  19. Can government be self-organized? A mathematical model of the collective social organization of ancient Teotihuacan, central Mexico.

    PubMed

    Froese, Tom; Gershenson, Carlos; Manzanilla, Linda R

    2014-01-01

    Teotihuacan was the first urban civilization of Mesoamerica and one of the largest of the ancient world. Following a tradition in archaeology to equate social complexity with centralized hierarchy, it is widely believed that the city's origin and growth was controlled by a lineage of powerful individuals. However, much data is indicative of a government of co-rulers, and artistic traditions expressed an egalitarian ideology. Yet this alternative keeps being marginalized because the problems of collective action make it difficult to conceive how such a coalition could have functioned in principle. We therefore devised a mathematical model of the city's hypothetical network of representatives as a formal proof of concept that widespread cooperation was realizable in a fully distributed manner. In the model, decisions become self-organized into globally optimal configurations even though local representatives behave and modify their relations in a rational and selfish manner. This self-optimization crucially depends on occasional communal interruptions of normal activity, and it is impeded when sections of the network are too independent. We relate these insights to theories about community-wide rituals at Teotihuacan and the city's eventual disintegration. PMID:25303308

  20. A model of evaluation planning, implementation and management: Toward a ?culture of information? within organizations

    NASA Astrophysics Data System (ADS)

    Bhola, H. S.

    1992-03-01

    The argument underlying the ongoing "paradigm shift" from logical positivism to constructionism is briefly laid out. A model of evaluation planning, implementation and management (called the P-I-M Model, for short) is then presented that assumes a complementarity between the two paradigms. The model further implies that for effective decision-making within human organizations, both "evaluative data" and "descriptive data" are needed. "Evaluative data" generated by evaluation studies must, therefore, be undergirded by an appropriate management information system (MIS) that can generate "descriptive data", concurrently with the process of program implementation. The P-I-M Model, if fully actualized, will enable human organizations to become vibrant "cultures of information" where "informed" decision-making becomes a shared norm among all stakeholders.

  1. Mechanistic modeling of the vertical soil organic matter profile in terrestrial ecosystems

    NASA Astrophysics Data System (ADS)

    Braakhekke, Maarten; Beer, Christian; Hoosbeek, Marcel; Reichstein, Markus; Kruijt, Bart; Wutzler, Thomas; Kattge, Jens; Schrumpf, Marion; Kabat, Pavel

    2010-05-01

    Modelling and measuring studies of soil organic carbon have traditionally focused on the 30 cm of the soil. In the recent past however, interest in the vertical distribution of soil carbon has increased due to 1) estimates suggesting that the deep soil globally stores a large amount of carbon, and 2) increasing evidence that soil carbon stabilization is be controlled by different processes at different depths that are likely to respond varyingly to future global changes, possibly leading to release of previously stabilized carbon. Therefore the ‘bucket' approach employed in traditional soil carbon models is not sufficient to adequately predict future soil carbon dynamics on long time scales. Furthermore, aggregation of soil temperature and moisture response of the whole profile may lead to biased results on short time scales as well. Hence, a more vertically explicit representation is needed, but development and parameterization of such models is hindered by lack of understanding of the processes involved in SOM profile development. Our study aims to answer the following questions: 1) what are the key driving processes that determine the vertical profile of soil organic matter and their comparative strength? and 2) can we improve soil carbon cycle models by accounting for the vertical SOM profile? In this scope we have developed SOMPROF, a new soil carbon model that dynamically simulates the vertical profile of the SOM fraction in the mineral soil, as well as the storage of organic matter in organic surface horizons L, F and H. The model includes two mechanisms of vertical organic matter transport: 1) diffusion, representing bioturbation (mixing of the soil matrix by soil biota), and 2) advection, representing downward movement with infiltrating water. Furthermore organic matter may be input directly at depth by root turnover. The model includes 5 organic carbon pools that differ with respect to their transport behavior and decomposability. The model has been

  2. Modeling organic aerosols in a megacity: potential contribution of semi-volatile and intermediate volatility primary organic compounds to secondary organic aerosol formation

    NASA Astrophysics Data System (ADS)

    Hodzic, A.; Jimenez, J. L.; Madronich, S.; Canagaratna, M. R.; Decarlo, P. F.; Kleinman, L.; Fast, J.

    2010-06-01

    It has been established that observed local and regional levels of secondary organic aerosols (SOA) in polluted areas cannot be explained by the oxidation and partitioning of anthropogenic and biogenic VOC precursors, at least using current mechanisms and parameterizations. In this study, the 3-D regional air quality model CHIMERE is applied to estimate the potential contribution to SOA formation of recently identified semi-volatile and intermediate volatility organic precursors (S/IVOC) in and around Mexico City for the MILAGRO field experiment during March 2006. The model has been updated to include explicitly the volatility distribution of primary organic aerosols (POA), their gas-particle partitioning and the gas-phase oxidation of the vapors. Two recently proposed parameterizations, those of Robinson et al. (2007) ("ROB") and Grieshop et al. (2009) ("GRI") are compared and evaluated against surface and aircraft measurements. The 3-D model results are assessed by comparing with the concentrations of OA components from Positive Matrix Factorization of Aerosol Mass Spectrometer (AMS) data, and for the first time also with oxygen-to-carbon ratios derived from high-resolution AMS measurements. The results show a substantial enhancement in predicted SOA concentrations (2-4 times) with respect to the previously published base case without S/IVOCs (Hodzic et al., 2009), both within and downwind of the city leading to much reduced discrepancies with the total OA measurements. Model improvements in OA predictions are associated with the better-captured SOA magnitude and diurnal variability. The predicted production from anthropogenic and biomass burning S/IVOC represents 40-60% of the total measured SOA at the surface during the day and is somewhat larger than that from commonly measured aromatic VOCs, especially at the T1 site at the edge of the city. The SOA production from the continued multi-generation S/IVOC oxidation products continues actively downwind. Similar

  3. Isotherm-Based Thermodynamic Models for Solute Activities of Organic Acids with Consideration of Partial Dissociation.

    PubMed

    Nandy, Lucy; Ohm, Peter B; Dutcher, Cari S

    2016-06-23

    Organic acids make up a significant fraction of the organic mass in atmospheric aerosol particles. The calculation of gas-liquid-solid equilibrium partitioning of the organic acid is therefore critical for accurate determination of atmospheric aerosol physicochemical properties and processes such as new particle formation and activation to cloud condensation nuclei. Previously, an adsorption isotherm-based statistical thermodynamic model was developed for capturing solute concentration-activity relationships for multicomponent aqueous solutions over the entire concentration range (Dutcher et al. J. Phys. Chem. C/A 2011, 2012, 2013), with model parameters for energies of adsorption successfully related to dipole-dipole electrostatic forces in solute-solvent and solvent-solvent interactions for both electrolytes and organics (Ohm et al. J. Phys. Chem. A 2015). However, careful attention is needed for weakly dissociating semivolatile organic acids. Dicarboxylic acids, such as malonic acid and glutaric acid are treated here as a mixture of nondissociated organic solute (HA) and dissociated solute (H(+) + A(-)). It was found that the apparent dissociation was greater than that predicted by known dissociation constants alone, emphasizing the effect of dissociation on osmotic and activity coefficient predictions. To avoid additional parametrization from the mixture approach, an expression was used to relate the Debye-Hückel hard-core collision diameter to the adjustable solute-solvent intermolecular distance. An improved reference state treatment for electrolyte-organic aqueous mixtures, such as that observed here with partial dissociation, has also been proposed. This work results in predictive correlations for estimation of organic acid and water activities for which there is little or no activity data. PMID:27222917

  4. Agent based model of effects of task allocation strategies in flat organizations

    NASA Astrophysics Data System (ADS)

    Sobkowicz, Pawel

    2016-09-01

    A common practice in many organizations is to pile the work on the best performers. It is easy to implement by the management and, despite the apparent injustice, appears to be working in many situations. In our work we present a simple agent based model, constructed to simulate this practice and to analyze conditions under which the overall efficiency of the organization (for example measured by the backlog of unresolved issues) breaks down, due to the cumulative effect of the individual overloads. The model confirms that the strategy mentioned above is, indeed, rational: it leads to better global results than an alternative one, using equal workload distribution among all workers. The presented analyses focus on the behavior of the organizations close to the limit of the maximum total throughput and provide results for the growth of the unprocessed backlog in several situations, as well as suggestions related to avoiding such buildup.

  5. Modeling of organic light emitting diodes: From molecular to device properties (Presentation Recording)

    NASA Astrophysics Data System (ADS)

    Kordt, Pascal; van der Holst, Jeroen J. M.; Al Helwi, Mustapha; Kowalsky, Wolfgang; May, Falk; Badinski, Alexander; Lennartz, Christian; Andrienko, Denis

    2015-10-01

    We review the progress in modeling of charge transport in disordered organic semiconductors on various length-scales, from atomistic to macroscopic. This includes evaluation of charge transfer rates from first principles, parametrization of coarse-grained lattice and off-lattice models, and solving the master and drift-diffusion equations. Special attention is paid to linking the length-scales and improving the efficiency of the methods. All techniques are illustrated on an amorphous organic semiconductor, DPBIC, a hole conductor and electron blocker used in state of the art organic light emitting diodes (OLEDs). The outlined multiscale scheme can be used to predict OLED properties without fitting parameters, starting from chemical structures of compounds. Reference: Advanced Functional Materials, 2015, doi: 10.1002/adfm.201403004

  6. A fractal model for nuclear organization: current evidence and biological implications

    PubMed Central

    Bancaud, Aurélien; Lavelle, Christophe; Huet, Sébastien; Ellenberg, Jan

    2012-01-01

    Chromatin is a multiscale structure on which transcription, replication, recombination and repair of the genome occur. To fully understand any of these processes at the molecular level under physiological conditions, a clear picture of the polymorphic and dynamic organization of chromatin in the eukaryotic nucleus is required. Recent studies indicate that a fractal model of chromatin architecture is consistent with both the reaction-diffusion properties of chromatin interacting proteins and with structural data on chromatin interminglement. In this study, we provide a critical overview of the experimental evidence that support a fractal organization of chromatin. On this basis, we discuss the functional implications of a fractal chromatin model for biological processes and propose future experiments to probe chromatin organization further that should allow to strongly support or invalidate the fractal hypothesis. PMID:22790985

  7. Child Maltreatment and Emergent Personality Organization: Perspectives from the Five-Factor Model

    ERIC Educational Resources Information Center

    Rogosch, Fred A.; Cicchetti, Dante

    2004-01-01

    The Five-Factor Model was used to examine personality organization in 211 six-year-old children (135 maltreated and 76 nonmaltreated). Longitudinal assessments were conducted at ages 7, 8, and 9. Six-year-old maltreated children exhibited lower agreeableness, conscientiousness, and openness to experience and higher neuroticism than did…

  8. Choosing a Genome Browser for a Model Organism Database (MOD): Surveying the Maize Community

    Technology Transfer Automated Retrieval System (TEKTRAN)

    As the maize genome sequencing is nearing its completion, the Maize Genetics and Genomics Database (MaizeGDB), the Model Organism Database for maize, integrated a genome browser to its already existing Web interface and database. The addition of the MaizeGDB Genome Browser to MaizeGDB will allow it ...

  9. Use of Physicochemical Parameters to Assess the Environmental Fate of Organic Pollutants: The Fugacity Model

    ERIC Educational Resources Information Center

    Domenech, Xavier; Ayllon, Jose Antonio; Peral, Jose

    2006-01-01

    The environmental fate and behavior of different organic pollutants based on the qualitative analysis of thermodynamic and kinetic data is presented. The Fugacity model allows the use of different partition constants in an easy way, to determine the distribution of chemical between different phases in equilibrium of an environmental system.

  10. Entropy in the Bak-Sneppen Model for Self-Organized Criticality

    NASA Astrophysics Data System (ADS)

    Yang, Chun-Bin

    2003-03-01

    The distributions of fitness on the sites of one- and two-dimensional lattices are studied for the nearest-neighbour Bak-Sneppen model on self-organized criticality. The distributions show complicated behaviour showing that the system is far from equilibrium. By introducing the ``energy'' of a site, the entropy flow from the system to its environment is investigated.

  11. Rainfall-induced fecal indicator organisms transport from manured fields: Model sensitivity analysis

    EPA Science Inventory

    Microbial quality of surface waters attracts attention due to food- and waterborne disease outbreaks. Fecal indicator organisms (FIOs) are commonly used for the microbial pollution level evaluation. Models predicting the fate and transport of FIOs are required to design and evalu...

  12. Rapid organic aerosol formation downwind of a highway: Measured and model results from the FEVER study

    NASA Astrophysics Data System (ADS)

    Stroud, Craig A.; Liggio, John; Zhang, Jie; Gordon, Mark; Staebler, Ralf M.; Makar, Paul A.; Zhang, Junhua; Li, Shao-Meng; Mihele, Cristian; Lu, Gang; Wang, Daniel K.; Wentzell, Jeremy; Brook, Jeffrey R.; Evans, Greg J.

    2014-02-01

    The Fast Evolution of Vehicle Emissions from Roadway (FEVER) study was undertaken to strategically measure pollutant gradients perpendicular to a major highway north of Toronto, Canada. A case study period was analyzed when there was an average perpendicular wind direction. Two independent, fast response measurements were used to infer rapid organic aerosol (OA) growth on a spatial scale from 34 m to 285 m at the same time as a decrease was observed in the mixing ratio of primary emitted species, such as CO2 and NOx. An integrated organic gas and particle sampler also showed that near the highway, the aerosol had a larger semivolatile fraction than lower volatile fraction, but over a relatively short distance downwind of the highway, the aerosol transformed to being more low volatile with the change being driven by both evaporation of semivolatile and production of lower volatile organic aerosol. A new 1-D column Lagrangian atmospheric chemistry model was developed to help interpret the measured increase in the ∆OA/∆CO2 curve from 34 m to 285 m downwind of highway, where the ∆ refers to background-corrected concentrations. The model was sensitive to the assumptions for semivolatile organic compounds (SVOCs). Different combinations of SVOC emissions and background mixing ratios were able to yield similar model curves and reproduce the observations. Future measurements of total gas-phase SVOC in equilibrium with aerosol both upwind and downwind of the highway would be helpful to constrain the model.

  13. Bacteria, Yeast, Worms, and Flies: Exploiting Simple Model Organisms to Investigate Human Mitochondrial Diseases

    ERIC Educational Resources Information Center

    Rea, Shane L.; Graham, Brett H.; Nakamaru-Ogiso, Eiko; Kar, Adwitiya; Falk, Marni J.

    2010-01-01

    The extensive conservation of mitochondrial structure, composition, and function across evolution offers a unique opportunity to expand our understanding of human mitochondrial biology and disease. By investigating the biology of much simpler model organisms, it is often possible to answer questions that are unreachable at the clinical level.…

  14. A Model of Institutional Creative Change for Assessing Universities as Learning Organizations

    ERIC Educational Resources Information Center

    Sternberg, Robert J.

    2015-01-01

    Universities, like students, differ in their ability to learn and to recreate themselves. In this article, I present a 3-part model of institutional creative change for assessing universities as learning organizations that can move creatively into the future. The first part, prerequisites, deals with actual ability to change creatively and belief…

  15. AN EMBRYONIC CHICK PANCREAS ORGAN CULTURE MODEL: CHARACTERIZATION AND NEURAL CONTROL OF EXOCRINE RELEASE

    EPA Science Inventory

    An embryonic chick (Gallus domesticus) whole-organ pancreas culture system was developed for use as an in vitro model to study cholinergic regulation of exocrine pancreatic function. The culture system was examined for characteristic exocrine function and viability by measuring e...

  16. MODELING SCALE-DEPENDENT LANDSCAPE PATTERN, DISPERSAL, AND CONNECTIVITY FROM THE PERSPECTIVE OF THE ORGANISM

    EPA Science Inventory

    Effects of fine- to broad-scale patterns of landscape heterogeneity on dispersal success were examined for organisms varying in life history traits. To systematically control spatial pattern, a landscape model was created by merging physiographically-based maps of simulated land...

  17. Validation of Senge's Learning Organization Model with Teachers of Vocational High Schools at the Seoul Megalopolis

    ERIC Educational Resources Information Center

    Park, Joo Ho

    2008-01-01

    This study measured and applied Senge's (1990) fifth discipline model of learning organizations in a culturally distinct population, namely teachers in 17 vocational high schools located in the Seoul megalopolis. The participants were 976 full-time vocational and academic teachers in public trade/industry-technical and business high schools in the…

  18. MATHEMATICAL MODEL FOR THE TRANSPORT AND FATE OF ORGANIC CHEMICALS IN UNSATURATED/SATURATED SOILS

    EPA Science Inventory

    A mathematical model, simulating the transport and fate of nonionizable organic compounds in unsaturated/saturated porous media (soils) in a terrestrial microcosm has been developed. Using the principles of water mass, momentum, heat energy and chemical mass balance, the three fi...

  19. EPIC modeling of soil organic carbon sequestration in croplands of Iowa

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Agricultural lands can mitigate detrimental effects of greenhouse gases because soils can be managed to reduce carbon dioxide emissions and sequester carbon in soil organic matter. Simulation models are useful tools for studying the long-term impacts of crop and soil management practices on soil org...

  20. FROM INDIVIDUALS TO POPULATIONS: MODELING TOXICITY DATA ACROSS LEVELS OF BIOLOGICAL ORGANIZATION

    EPA Science Inventory

    Raimondo, Sandy and Charles L. McKenney, Jr. In press. From Individuals to Populations: Modeling Toxicity Data Across Levels of Biological Organization (Abstract). To be presented at the SETAC Fourth World Congress, 14-18 November 2004, Portland, OR. 1 p. (ERL,GB R1012).

    ...

  1. MODELING MULTICOMPONENT ORGANIC CHEMICAL TRANSPORT IN THREE-FLUID-PHASE POROUS MEDIA

    EPA Science Inventory

    A two dimensional finite-element model was developed to predict coupled transient flow and multicomponent transport of organic chemicals which can partition between NAPL, water, gas and solid phases in porous media under the assumption of local chemical equilibrium. as-phase pres...

  2. PROCESSES, COEFFICIENTS, AND MODELS FOR SIMULATING TOXIC ORGANICS AND HEAVY METALS IN SURFACE WATERS

    EPA Science Inventory

    The reference manual provides kinetics formulations for users of models that compute the fate of toxic organic chemicals and heavy metals in natural surface waters. Rates and coefficients provided in the manual were collected through literature reviews through 1986. The manual de...

  3. MaizeGDB update: New tools, data, and interface for the maize model organism database

    Technology Transfer Automated Retrieval System (TEKTRAN)

    MaizeGDB is a highly curated, community-oriented database and informatics service to researchers focused on the crop plant and model organism Zea mays ssp. mays. Although some form of the maize community database has existed over the last 25 years, there have only been two major releases. In 1991, ...

  4. MODELING MULTICOMPONENT ORGANIC CHEMICAL TRANSPORT IN THREE FLUID PHASE POROUS MEDIA

    EPA Science Inventory

    A two-dimensional finite-element model was developed to predict coupled transient flow and multicomponent transport of organic chemicals which can partition between nonaqueous phase liquid, water, gas and solid phases in porous media under the assumption of local chemical equilib...

  5. Path-Goal Models as a Basis for the Design of Organization Reward Systems.

    ERIC Educational Resources Information Center

    Galbraith, Jay R.

    The purpose of this paper has been to argue the usefulness of path-goal models in theoretical research and practical design of organization reward systems. The reasoning is that the policy choices can be easily related to path-goal attitudes which, in turn, are related to behavior. The major policy choices were identified and related to path-goal…

  6. Coupling Molecular Modeling to the Traditional "IR-ID" Exercise in the Introductory Organic Chemistry Laboratory

    ERIC Educational Resources Information Center

    Stokes-Huby, Heather; Vitale, Dale E.

    2007-01-01

    This exercise integrates the infrared unknown identification ("IR-ID") experiment common to most organic laboratory syllabi with computer molecular modeling. In this modification students are still required to identify unknown compounds from their IR spectra, but must additionally match some of the absorptions with computed frequencies they…

  7. Comparison of measured and modeled effects of residue removal on soil organic carbon

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soil organic carbon (SOC) is an important soil property strongly influenced by management. Changes in SOC are difficult to measure through direct sampling requiring long time periods and intensive sampling to detect small changes in the large, highly variable pool. Models have the potential to predi...

  8. Overcoming the organization-practice barrier in sports injury prevention: A nonhierarchical organizational model.

    PubMed

    Dahlström, Ö; Jacobsson, J; Timpka, T

    2015-08-01

    The organization of sports at the national level has seldom been included in scientific discussions of sports injury prevention. The aim of this study was to develop a model for organization of sports that supports prevention of overuse injuries. The quality function deployment technique was applied in seminars over a two-season period to develop a national organizational structure for athletics in Sweden that facilitates prevention of overuse injuries. Three central features of the resulting model for organization of sports at the national level are (a) diminishment of the organizational hierarchy: participatory safety policy design is introduced through annual meetings where actors from different sectors of the sporting community discuss training, injury prevention, and sports safety policy; (b) introduction of a safety surveillance system: a ubiquitous system for routine collection of injury and illness data; and (c) an open forum for discussion of safety issues: maintenance of a safety forum for participants from different sectors of the sport. A nonhierarchical model for organization of sports at the national level - facilitated by modern information technology - adapted for the prevention of overuse injuries has been developed. Further research is warranted to evaluate the new organizational model in prospective effectiveness studies. PMID:25430864

  9. An Investigation of the Advance Organizer Theory as an Effective Teaching Model.

    ERIC Educational Resources Information Center

    Downing, Agnes

    This paper advocates for the improvement of presentational methods of teaching and expository learning, based on David Ausubel's theory of Meaningful Verbal Learning and its derivative, the Advance Organizer Model of Teaching. This approach to teaching enables teachers to convey large amounts of information as meaningfully and efficiently as…

  10. VOLATILE ORGANIC COMPOUND EMISSION PROJECTION MODEL (VERSION 1.8). USER'S MANUAL

    EPA Science Inventory

    The report discusses a model that can be used to estimate future emissions of volatile organic compounds (VOCs) and costs of their control by applying growth factors, emission constraints, control cost functions, and capacity retirement rates to the base line estimates of VOC emi...

  11. Can the Equivalent Sphere Model Approximate Organ Doses in Space Radiation Environments?

    NASA Technical Reports Server (NTRS)

    Zi-Wei, Lin

    2007-01-01

    In space radiation calculations it is often useful to calculate the dose or dose equivalent in blood-forming organs (BFO). the skin or the eye. It has been customary to use a 5cm equivalent sphere to approximate the BFO dose. However previous studies have shown that a 5cm sphere gives conservative dose values for BFO. In this study we use a deterministic radiation transport with the Computerized Anatomical Man model to investigate whether the equivalent sphere model can approximate organ doses in space radiation environments. We find that for galactic cosmic rays environments the equivalent sphere model with an organ-specific constant radius parameter works well for the BFO dose equivalent and marginally well for the BFO dose and the dose equivalent of the eye or the skin. For solar particle events the radius parameters for the organ dose equivalent increase with the shielding thickness, and the model works marginally for BFO but is unacceptable for the eye or the skin The ranges of the radius parameters are also shown and the BFO radius parameters are found to be significantly larger than 5 cm in all eases.

  12. THE COMPARISON OF TWO VITRO PALATAL ORGAN CULTURE MODELS TO STUDY CELL SIGNALING PATHWAYS DURING PALATOGENESIS

    EPA Science Inventory

    This study was performed to determine the best palatal organ culture model to use in evaluating the role of epidermal growth factor (EGF) signaling in the response to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Previous work has shown that TCDD and EGF can induce teratogenic effe...

  13. MODELING OF MULTICOMPONENT PERVAPORATION FOR REMOVAL OF VOLATILE ORGANIC COMPOUNDS FROM WATER

    EPA Science Inventory

    A resistance-in-series model was used to study the pervaporation of multiple volatile organic compounds (VOCs)-water mixtures. Permeation experiments were carried out for four membranes: poly(dimethylsiloxane) (PDMS), polyether-block-polyamides (PEBA), polyurethane (PUR) and sil...

  14. Rainfall-induced fecal indicator organisms transport from animal waste applied fields: model sensitivity analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The microbial quality of surface waters warrants attention because of associated food- and waterborne-disease outbreaks, and fecal indicator organisms (FIOs) are commonly used to evaluate levels of microbial pollution. Models that predict the fate and transport of FIOs are required for designing and...

  15. Agent-based modeling of hyporheic dissolved organic carbon transport and transformation

    NASA Astrophysics Data System (ADS)

    Gabrielsen, P. J.; Wilson, J. L.; Pullin, M.

    2011-12-01

    Dissolved organic carbon (DOC) is a complex suite of organic compounds present in natural ecosystems, and is particularly studied in river and stream systems. The hyporheic zone (HZ), a region of surface water-shallow groundwater exchange, has been identified as a hotspot of DOC processing and is generally regarded as a net sink of organic matter. More recent studies into stream DOC have shifted to examining DOC quality rather than bulk quantity. DOC quality variability has been linked to hydrologic and climatic variability, both focuses of current climate change research. A new agent-based model in the NetLogo modeling environment couples hydrologic transport with chemical and biological transformation of DOC to simulate changing DOC quality in hyporheic flow. A pore-scale model implements a Lattice Boltzmann fluid dynamic model and surficial interactions to simulate sorption and microbial uptake. Upscaled to a stream meander scale, this model displays spatial variation and evolution of DOC quality. Model output metrics are correlated to field sample analytical results from a hyporheic meander of the East Fork Jemez River, Sandoval Co., NM.

  16. Organ Explant Culture of Neonatal Rat Ventricles: A New Model to Study Gene and Cell Therapy

    PubMed Central

    den Haan, A. Dénise; Veldkamp, Marieke W.; Bakker, Diane; Boink, Geert J. J.; Janssen, Rob B.; de Bakker, Jacques M. T.; Tan, Hanno L.

    2013-01-01

    Testing cardiac gene and cell therapies in vitro requires a tissue substrate that survives for several days in culture while maintaining its physiological properties. The purpose of this study was to test whether culture of intact cardiac tissue of neonatal rat ventricles (organ explant culture) may be used as a model to study gene and cell therapy. We compared (immuno) histology and electrophysiology of organ explant cultures to both freshly isolated neonatal rat ventricular tissue and monolayers. (Immuno) histologic studies showed that organ explant cultures retained their fiber orientation, and that expression patterns of α-actinin, connexin-43, and α-smooth muscle actin did not change during culture. Intracellular voltage recordings showed that spontaneous beating was rare in organ explant cultures (20%) and freshly isolated tissue (17%), but common (82%) in monolayers. Accordingly, resting membrane potential was -83.9±4.4 mV in organ explant cultures, −80.5±3.5 mV in freshly isolated tissue, and −60.9±4.3 mV in monolayers. Conduction velocity, measured by optical mapping, was 18.2±1.0 cm/s in organ explant cultures, 18.0±1.2 cm/s in freshly isolated tissue, and 24.3±0.7 cm/s in monolayers. We found no differences in action potential duration (APD) between organ explant cultures and freshly isolated tissue, while APD of monolayers was prolonged (APD at 70% repolarization 88.8±7.8, 79.1±2.9, and 134.0±4.5 ms, respectively). Organ explant cultures and freshly isolated tissue could be paced up to frequencies within the normal range for neonatal rat (CL 150 ms), while monolayers could not. Successful lentiviral (LV) transduction was shown via Egfp gene transfer. Co-culture of organ explant cultures with spontaneously beating cardiomyocytes increased the occurrence of spontaneous beating activity of organ explant cultures to 86%. We conclude that organ explant cultures of neonatal rat ventricle are structurally and electrophysiologically similar to

  17. Modeling SOAaq Formation: Explicit Organic Chemistry in Cloud Droplets with CMAQ

    NASA Astrophysics Data System (ADS)

    Carlton, A. G.; Sareen, N.; Fahey, K.; Hutzell, W. T.

    2013-12-01

    Aqueous multiphase chemistry in the atmosphere has a substantial impact on climate and can lead to air quality changes that adversely impact human health and the environment. The chemistry is complex because of the variety of compounds present in the atmosphere and the phase transitions associated with multiphase reactions. These reactions can lead to the formation of secondary organic aerosols (SOAAQ) in the atmosphere. When included, current photochemical models typically use a simple parameterization to describe SOAAQ formation. Here, we discuss the implementation of explicit aqueous SOA chemistry in a box model of the CMAQ 5.0.1 aqueous phase chemistry mechanism using the Kinetic PreProcessor (KPP). The expanded chemistry model includes reactions of glyoxal, methylglyoxal, and glycolaldehyde as precursors to form SOAAQ and is based on the mechanism from Lim et. al. 2010. The current aqueous phase chemistry module in CMAQ uses a forward Euler method to solve the system of oxidation equations, estimating the pH with a bisection method assuming electroneutrality, and multiphase processes are solved sequentially. This is not robust for systems with large dynamic range (e.g., multiphase systems), and inhibits expansion of the aqueous phase chemical mechanism to adequately incorporate the growing body of literature that describes multiphase organic chemistry. The KPP solver allows for all processes to be solved simultaneously and facilitates expansion of the current mechanism. Addition of explicit organic reactions and H2O2 photolysis in the KPP box model results in increased mass of organic aerosol and more realistic predictions. For particulate matter focused air quality management strategies to be effective, it is important that models move away from the yield-based approach currently used and expand to include more explicit organic chemistry.

  18. Modeling the formation and aging of secondary organic aerosols during CalNex 2010

    NASA Astrophysics Data System (ADS)

    Hayes, P. L.; Ortega, A. M.; Ahmadov, R.; McKeen, S. A.; Washenfelder, R. A.; Alvarez, S.; Rappenglueck, B.; Holloway, J. S.; Gilman, J. B.; Kuster, W. C.; De Gouw, J. A.; Zotter, P.; Prevot, A. S.; Kleindienst, T. E.; Offenberg, J. H.; Jimenez, J. L.

    2012-12-01

    Several traditional and recently proposed models are applied to predict the concentrations and properties of secondary organic aerosols (SOA) and organic gases at the Pasadena ground site during the CalNex campaign. The models are constrained with and compared against results from available observations. The CalNex campaign and specifically the Pasadena ground site featured a large and sophisticated suite of aerosol and gas phase instrumentation, and thus, it provides a unique opportunity to test SOA models under conditions of strong urban emissions at a range of low photochemical ages. The oxidation of volatile organic compounds (VOCs) using an updated traditional model cannot explain the observed ambient SOA, and under-predicts the measurements by a factor of ~40. Similarly, after accounting for the multi-generation oxidation of VOCs using a volatility basis set (VBS) approach as described by Tsimpidi et al. (2010), SOA is still under-predicted by a factor of ~8. For SOA formed from VOCs (V-SOA) the dominant precursors are aromatics (xylenes, toluene, and trimethylbenzenes). The model SOA formed from the oxidation of primary semivolatile and intermediate volatility organic compounds (P-S/IVOCs, producing SI-SOA) is also predicted using the parameterizations of Robinson et al. (2007) and Grieshop et al. (2009), and the properties of V-SOA + SI-SOA are compared against the measured O:C and volatility. We also compare the results of the different models against fossil/non-fossil carbon measurements as well as tracers of different SOA precursors. Potential Aerosol Mass (PAM) measurements of the SOA forming potential of the Pasadena air masses are also compared against that predicted by the models. The PAM analysis allows for model/measurement comparisons of SOA properties over a range of photochemical ages spanning almost two weeks. Using the V-SOA model, at low photochemical ages (< 1 day) the modeled PAM V-SOA is less than the measured PAM SOA, similar to the

  19. A computationally-efficient secondary organic aerosol module for three-dimensional air quality models

    NASA Astrophysics Data System (ADS)

    Liu, P.; Zhang, Y.

    2008-07-01

    Accurately simulating secondary organic aerosols (SOA) in three-dimensional (3-D) air quality models is challenging due to the complexity of the physics and chemistry involved and the high computational demand required. A computationally-efficient yet accurate SOA module is necessary in 3-D applications for long-term simulations and real-time air quality forecasting. A coupled gas and aerosol box model (i.e., 0-D CMAQ-MADRID 2) is used to optimize relevant processes in order to develop such a SOA module. Solving the partitioning equations for condensable volatile organic compounds (VOCs) and calculating their activity coefficients in the multicomponent mixtures are identified to be the most computationally-expensive processes. The two processes can be speeded up by relaxing the error tolerance levels and reducing the maximum number of iterations of the numerical solver for the partitioning equations for organic species; conditionally activating organic-inorganic interactions; and parameterizing the calculation of activity coefficients for organic mixtures in the hydrophilic module. The optimal speed-up method can reduce the total CPU cost by up to a factor of 31.4 from benchmark under the rural conditions with 2 ppb isoprene and by factors of 10 71 under various test conditions with 2 10 ppb isoprene and >40% relative humidity while maintaining ±15% deviation. These speed-up methods are applicable to other SOA modules that are based on partitioning theories.

  20. Improved AIOMFAC model parameterisation of the temperature dependence of activity coefficients for aqueous organic mixtures

    NASA Astrophysics Data System (ADS)

    Ganbavale, G.; Zuend, A.; Marcolli, C.; Peter, T.

    2015-01-01

    This study presents a new, improved parameterisation of the temperature dependence of activity coefficients in the AIOMFAC (Aerosol Inorganic-Organic Mixtures Functional groups Activity Coefficients) model applicable for aqueous as well as water-free organic solutions. For electrolyte-free organic and organic-water mixtures the AIOMFAC model uses a group-contribution approach based on UNIFAC (UNIversal quasi-chemical Functional-group Activity Coefficients). This group-contribution approach explicitly accounts for interactions among organic functional groups and between organic functional groups and water. The previous AIOMFAC version uses a simple parameterisation of the temperature dependence of activity coefficients, aimed to be applicable in the temperature range from ~ 275 to ~ 400 K. With the goal to improve the description of a wide variety of organic compounds found in atmospheric aerosols, we extend the AIOMFAC parameterisation for the functional groups carboxyl, hydroxyl, ketone, aldehyde, ether, ester, alkyl, aromatic carbon-alcohol, and aromatic hydrocarbon to atmospherically relevant low temperatures. To this end we introduce a new parameterisation for the temperature dependence. The improved temperature dependence parameterisation is derived from classical thermodynamic theory by describing effects from changes in molar enthalpy and heat capacity of a multi-component system. Thermodynamic equilibrium data of aqueous organic and water-free organic mixtures from the literature are carefully assessed and complemented with new measurements to establish a comprehensive database, covering a wide temperature range (~ 190 to ~ 440 K) for many of the functional group combinations considered. Different experimental data types and their processing for the estimation of AIOMFAC model parameters are discussed. The new AIOMFAC parameterisation for the temperature dependence of activity coefficients from low to high temperatures shows an overall improvement of 28% in

  1. Regional modelling of nitrate leaching from Swiss organic and conventional cropping systems under climate change

    NASA Astrophysics Data System (ADS)

    Calitri, Francesca; Necpalova, Magdalena; Lee, Juhwan; Zaccone, Claudio; Spiess, Ernst; Herrera, Juan; Six, Johan

    2016-04-01

    Organic cropping systems have been promoted as a sustainable alternative to minimize the environmental impacts of conventional practices. Relatively little is known about the potential to reduce NO3-N leaching through the large-scale adoption of organic practices. Moreover, the potential to mitigate NO3-N leaching and thus the N pollution under future climate change through organic farming remain unknown and highly uncertain. Here, we compared regional NO3-N leaching from organic and conventional cropping systems in Switzerland using a terrestrial biogeochemical process-based model DayCent. The objectives of this study are 1) to calibrate and evaluate the model for NO3-N leaching measured under various management practices from three experiments at two sites in Switzerland; 2) to estimate regional NO3-N leaching patterns and their spatial uncertainty in conventional and organic cropping systems (with and without cover crops) for future climate change scenario A1B; 3) to explore the sensitivity of NO3-N leaching to changes in soil and climate variables; and 4) to assess the nitrogen use efficiency for conventional and organic cropping systems with and without cover crops under climate change. The data for model calibration/evaluation were derived from field experiments conducted in Liebefeld (canton Bern) and Eschikon (canton Zürich). These experiments evaluated effects of various cover crops and N fertilizer inputs on NO3-N leaching. The preliminary results suggest that the model was able to explain 50 to 83% of the inter-annual variability in the measured soil drainage (RMSE from 12.32 to 16.89 cm y-1). The annual NO3-N leaching was also simulated satisfactory (RMSE = 3.94 to 6.38 g N m-2 y-1), although the model had difficulty to reproduce the inter-annual variability in the NO3-N leaching losses correctly (R2 = 0.11 to 0.35). Future climate datasets (2010-2099) from the 10 regional climate models (RCM) were used in the simulations. Regional NO3-N leaching

  2. Modeling the influence of alkane molecular structure on secondary organic aerosol formation.

    PubMed

    Aumont, Bernard; Camredon, Marie; Mouchel-Vallon, Camille; La, Stéphanie; Ouzebidour, Farida; Valorso, Richard; Lee-Taylor, Julia; Madronich, Sasha

    2013-01-01

    Secondary Organic Aerosols (SOA) production and ageing is a multigenerational oxidation process involving the formation of successive organic compounds with higher oxidation degree and lower vapor pressure. Intermediate Volatility Organic Compounds (IVOC) emitted to the atmosphere are expected to be a substantial source of SOA. These emitted IVOC constitute a complex mixture including linear, branched and cyclic alkanes. The explicit gas-phase oxidation mechanisms are here generated for various linear and branched C10-C22 alkanes using the GECKO-A (Generator for Explicit Chemistry and Kinetics of Organics in the Atmosphere) and SOA formation is investigated for various homologous series. Simulation results show that both the size and the branching of the carbon skeleton are dominant factors driving the SOA yield. However, branching appears to be of secondary importance for the particle oxidation state and composition. The effect of alkane molecular structure on SOA yields appears to be consistent with recent laboratory observations. The simulated SOA composition shows, however, an unexpected major contribution from multifunctional organic nitrates. Most SOA contributors simulated for the oxidation of the various homologous series are far too reduced to be categorized as highly oxygenated organic aerosols (OOA). On a carbon basis, the OOA yields never exceeded 10% regardless of carbon chain length, molecular structure or ageing time. This version of the model appears clearly unable to explain a large production of OOA from alkane precursors. PMID:24600999

  3. Microfabricated Mammalian Organ Systems and Their Integration into Models of Whole Animals and Humans

    PubMed Central

    Sung, Jong H; Esch, Mandy B; Prot, Jean-Matthieu; Long, Christopher J; Smith, Alec; Hickman, James; Shuler, Michael L

    2013-01-01

    While in vitro cell based systems have been an invaluable tool in biology, they often suffer from a lack of physiological relevance. The discrepancy between the in vitro and in vivo systems has been a bottleneck in drug development process and biological sciences. The recent progress in microtechnology has enabled manipulation of cellular environment at a physiologically relevant length scale, which has led to the development of novel in vitro organ systems, often termed ‘organ-on-a-chip’ systems. By mimicking the cellular environment of in vivo tissues, various organ-on-a-chip systems have been reported to reproduce target organ functions better than conventional in vitro model systems. Ultimately, these organ-on-a-chip systems will converge into multi-organ ‘body-on-a-chip’ systems composed of functional tissues that reproduce the dynamics of the whole-body response. Such microscale in vitro systems will open up new possibilities in medical science and in the pharmaceutical industry. PMID:23388858

  4. Position-specific isotope modeling of organic micropollutants transformation through different reaction pathways.

    PubMed

    Jin, Biao; Rolle, Massimo

    2016-03-01

    The degradation of organic micropollutants occurs via different reaction pathways. Compound specific isotope analysis is a valuable tool to identify such degradation pathways in different environmental systems. We propose a mechanism-based modeling approach that provides a quantitative framework to simultaneously evaluate concentration as well as bulk and position-specific multi-element isotope evolution during the transformation of organic micropollutants. The model explicitly simulates position-specific isotopologues for those atoms that experience isotope effects and, thereby, provides a mechanistic description of isotope fractionation occurring at different molecular positions. To demonstrate specific features of the modeling approach, we simulated the degradation of three selected organic micropollutants: dichlorobenzamide (BAM), isoproturon (IPU) and diclofenac (DCF). The model accurately reproduces the multi-element isotope data observed in previous experimental studies. Furthermore, it precisely captures the dual element isotope trends characteristic of different reaction pathways as well as their range of variation consistent with observed bulk isotope fractionation. It was also possible to directly validate the model capability to predict the evolution of position-specific isotope ratios with available experimental data. Therefore, the approach is useful both for a mechanism-based evaluation of experimental results and as a tool to explore transformation pathways in scenarios for which position-specific isotope data are not yet available. PMID:26708763

  5. Vertex-element models for anisotropic growth of elongated plant organs

    PubMed Central

    Fozard, John A.; Lucas, Mikaël; King, John R.; Jensen, Oliver E.

    2013-01-01

    New tools are required to address the challenge of relating plant hormone levels, hormone responses, wall biochemistry and wall mechanical properties to organ-scale growth. Current vertex-based models (applied in other contexts) can be unsuitable for simulating the growth of elongated organs such as roots because of the large aspect ratio of the cells, and these models fail to capture the mechanical properties of cell walls in sufficient detail. We describe a vertex-element model which resolves individual cells and includes anisotropic non-linear viscoelastic mechanical properties of cell walls and cell division whilst still being computationally efficient. We show that detailed consideration of the cell walls in the plane of a 2D simulation is necessary when cells have large aspect ratio, such as those in the root elongation zone of Arabidopsis thaliana, in order to avoid anomalous transverse swelling. We explore how differences in the mechanical properties of cells across an organ can result in bending and how cellulose microfibril orientation affects macroscale growth. We also demonstrate that the model can be used to simulate growth on realistic geometries, for example that of the primary root apex, using moderate computational resources. The model shows how macroscopic root shape can be sensitive to fine-scale cellular geometries. PMID:23847638

  6. A simple model for deep tissue attenuation correction and large organ analysis of Cerenkov luminescence imaging

    NASA Astrophysics Data System (ADS)

    Habte, Frezghi; Natarajan, Arutselvan; Paik, David S.; Gambhir, Sanjiv S.

    2014-03-01

    Cerenkov luminescence imaging (CLI) is an emerging cost effective modality that uses conventional small animal optical imaging systems and clinically available radionuclide probes for light emission. CLI has shown good correlation with PET for organs of high uptake such as kidney, spleen, thymus and subcutaneous tumors in mouse models. However, CLI has limitations for deep tissue quantitative imaging since the blue-weighted spectral characteristics of Cerenkov radiation attenuates highly by mammalian tissue. Large organs such as the liver have also shown higher signal due to the contribution of emission of light from a greater thickness of tissue. In this study, we developed a simple model that estimates the effective tissue attenuation coefficient in order to correct the CLI signal intensity with a priori estimated depth and thickness of specific organs. We used several thin slices of ham to build a phantom with realistic attenuation. We placed radionuclide sources inside the phantom at different tissue depths and imaged it using an IVIS Spectrum (Perkin-Elmer, Waltham, MA, USA) and Inveon microPET (Preclinical Solutions Siemens, Knoxville, TN). We also performed CLI and PET of mouse models and applied the proposed attenuation model to correct CLI measurements. Using calibration factors obtained from phantom study that converts the corrected CLI measurements to %ID/g, we obtained an average difference of less that 10% for spleen and less than 35% for liver compared to conventional PET measurements. Hence, the proposed model has a capability of correcting the CLI signal to provide comparable measurements with PET data.

  7. Impact of Isolated Burns on Major Organs: A Large Animal Model Characterized.

    PubMed

    Burmeister, David M; McIntyre, Matthew K; Baker, Bryan A; Rizzo, Julie A; Brown, Ammon; Natesan, Shanmugasundaram; Chung, Kevin K; Christy, Robert J

    2016-09-01

    Severe burn results in systemic inflammatory response syndrome (SIRS) and multiple organ dysfunction (MOD). Currently, large-animal models of burn-induced SIRS/MOD mostly use secondary insults resulting in a paucity of knowledge on the effect of burn alone on different organ systems. The objective of the current study was to develop and characterize a large animal model of burn-induced SIRS over the course of 2 weeks. Yorkshire swine (n = 16) were randomized to sham controls (n = 4) or 40% total body surface area contact burns (n = 6 at 2 and 14 days post-burn). Blood chemistry and complete blood count analyses were performed at baseline and post-burn days 1, 2, 3, 7, 10, and 14. Upon euthanasia, tissue samples were taken for histopathology. Burns were found to be full thickness and did not re-epithelialize. SIRS was evidenced by increased body temperature, respiration rate, pulse, and white blood cell count for the duration of the experiment. Both acute liver injury and acute kidney injury were induced as determined biochemically and histologically. Histology also revealed atelectasis of the lungs which was associated with increased myeloperoxidase activity. Intestinal structure as well as enterocyte homeostasis was also disrupted. All of these organ abnormalities recovered to varying degrees by 14 days post-burn. We report a unique reproducible large animal model of burn-induced SIRS that can be tailored to specific organ systems for investigation into potential immunomodulatory interventions that prevent organ failure or promote organ recovery after burn injury. PMID:27380531

  8. Three-dimensional models for studying development and disease: moving on from organisms to organs-on-a-chip and organoids.

    PubMed

    Jackson, E L; Lu, H

    2016-06-13

    Human development and disease are challenging to study because of lack of experimental accessibility to in vivo systems and the complex nature of biological processes. For these reasons researchers turn to the use of model systems, ranging in complexity and scale from single cells to model organisms. While the use of model organisms is valuable for studying physiology and pathophysiology in an in vivo context and for aiding pre-clinical development of therapeutics, animal models are costly, difficult to interrogate, and not always equivalent to human biology. For these reasons, three-dimensional (3D) cell cultures have emerged as an attractive model system that contains key aspects of in vivo tissue and organ complexity while being more experimentally tractable than model organisms. In particular, organ-on-a-chip and organoid models represent orthogonal approaches that have been able to recapitulate characteristics of physiology and disease. Here, we review advances in these two categories of 3D cultures and applications in studying development and disease. Additionally, we discuss development of key technologies that facilitate the generation of 3D cultures, including microfluidics, biomaterials, genome editing, and imaging technologies. PMID:27156572

  9. Old knowledge and new technologies allow rapid development of model organisms

    PubMed Central

    Cook, Charles E.; Chenevert, Janet; Larsson, Tomas A.; Arendt, Detlev; Houliston, Evelyn; Lénárt, Péter

    2016-01-01

    Until recently the set of “model” species used commonly for cell biology was limited to a small number of well-understood organisms, and developing a new model was prohibitively expensive or time-consuming. With the current rapid advances in technology, in particular low-cost high-throughput sequencing, it is now possible to develop molecular resources fairly rapidly. Wider sampling of biological diversity can only accelerate progress in addressing cellular mechanisms and shed light on how they are adapted to varied physiological contexts. Here we illustrate how historical knowledge and new technologies can reveal the potential of nonconventional organisms, and we suggest guidelines for selecting new experimental models. We also present examples of nonstandard marine metazoan model species that have made important contributions to our understanding of biological processes. PMID:26976934

  10. Fuzzy model for risk assessment of persistent organic pollutants in aquatic ecosystems.

    PubMed

    Seguí, X; Pujolasus, E; Betrò, S; Agueda, A; Casal, J; Ocampo-Duque, W; Rudolph, I; Barra, R; Páez, M; Barón, E; Eljarrat, E; Barceló, D; Darbra, R M

    2013-07-01

    We developed a model for evaluating the environmental risk of persistent organic pollutants (POPs) to aquatic organisms. The model is based on fuzzy theory and uses information provided by international experts through a questionnaire. It has been tested in two case studies for a particular type of POPs: brominated flame retardants (BFRs). The first case study is related to the EU-funded AQUATERRA project, with sampling campaigns carried out in two Ebro tributaries in Spain (the Cinca and Vero Rivers). The second one, named the BROMACUA project, assessed different aquatic ecosystems in Chile (San Vicente Bay) and Colombia (Santa Marta Marsh). In both projects, the BFRs under study were polybrominated diphenyl ethers (PBDEs) and hexabromocyclododecane (HBCD). However, the model can be extrapolated to other POPs and to different aquatic ecosystems to provide useful results for decision-makers. PMID:23524177

  11. Modelling of environmental impacts from biological treatment of organic municipal waste in EASEWASTE.

    PubMed

    Boldrin, Alessio; Neidel, Trine Lund; Damgaard, Anders; Bhander, Gurbakhash S; Møller, Jacob; Christensen, Thomas H

    2011-04-01

    The waste-LCA model EASEWASTE quantifies potential environmental effects from biological treatment of organic waste, based on mass and energy flows, emissions to air, water, soil and groundwater as well as effects from upstream and downstream processes. Default technologies for composting, anaerobic digestion and combinations hereof are available in the model, but the user can change all key parameters in the biological treatment module so that specific local plants and processes can be modelled. EASEWASTE is one of the newest waste LCA models and the biological treatment module was built partly on features of earlier waste-LCA models, but offers additional facilities, more flexibility, transparency and user-friendliness. The paper presents the main features of the module and provides some examples illustrating the capability of the model in environmentally assessing and discriminating the environmental performance of alternative biological treatment technologies in relation to their mass flows, energy consumption, gaseous emissions, biogas recovery and compost/digestate utilization. PMID:21169006

  12. Colorimetric characterization models based on colorimetric characteristics evaluation for active matrix organic light emitting diode panels.

    PubMed

    Gong, Rui; Xu, Haisong; Tong, Qingfen

    2012-10-20

    The colorimetric characterization of active matrix organic light emitting diode (AMOLED) panels suffers from their poor channel independence. Based on the colorimetric characteristics evaluation of channel independence and chromaticity constancy, an accurate colorimetric characterization method, namely, the polynomial compensation model (PC model) considering channel interactions was proposed for AMOLED panels. In this model, polynomial expressions are employed to calculate the relationship between the prediction errors of XYZ tristimulus values and the digital inputs to compensate the XYZ prediction errors of the conventional piecewise linear interpolation assuming the variable chromaticity coordinates (PLVC) model. The experimental results indicated that the proposed PC model outperformed other typical characterization models for the two tested AMOLED smart-phone displays and for the professional liquid crystal display monitor as well. PMID:23089779

  13. Disordered cellular automaton traffic flow model: phase separated state, density waves and self organized criticality

    NASA Astrophysics Data System (ADS)

    Fourrate, K.; Loulidi, M.

    2006-01-01

    We suggest a disordered traffic flow model that captures many features of traffic flow. It is an extension of the Nagel-Schreckenberg (NaSch) stochastic cellular automata for single line vehicular traffic model. It incorporates random acceleration and deceleration terms that may be greater than one unit. Our model leads under its intrinsic dynamics, for high values of braking probability pr, to a constant flow at intermediate densities without introducing any spatial inhomogeneities. For a system of fast drivers pr→0, the model exhibits a density wave behavior that was observed in car following models with optimal velocity. The gap of the disordered model we present exhibits, for high values of pr and random deceleration, at a critical density, a power law distribution which is a hall mark of a self organized criticality phenomena.

  14. On the inference of function from structure using biomechanical modelling and simulation of extinct organisms.

    PubMed

    Hutchinson, John R

    2012-02-23

    Biomechanical modelling and simulation techniques offer some hope for unravelling the complex inter-relationships of structure and function perhaps even for extinct organisms, but have their limitations owing to this complexity and the many unknown parameters for fossil taxa. Validation and sensitivity analysis are two indispensable approaches for quantifying the accuracy and reliability of such models or simulations. But there are other subtleties in biomechanical modelling that include investigator judgements about the level of simplicity versus complexity in model design or how uncertainty and subjectivity are dealt with. Furthermore, investigator attitudes toward models encompass a broad spectrum between extreme credulity and nihilism, influencing how modelling is conducted and perceived. Fundamentally, more data and more testing of methodology are required for the field to mature and build confidence in its inferences. PMID:21666064

  15. Model Organisms Retain an “Ecological Memory” of Complex Ecologically Relevant Environmental Variation

    PubMed Central

    Beer, Karlyn D.; Wurtmann, Elisabeth J.; Pinel, Nicolás

    2014-01-01

    Although tractable model organisms are essential to characterize the molecular mechanisms of evolution and adaptation, the ecological relevance of their behavior is not always clear because certain traits are easily lost during long-term laboratory culturing. Here, we demonstrate that despite their long tenure in the laboratory, model organisms retain “ecological memory” of complex environmental changes. We have discovered that Halobacterium salinarum NRC-1, a halophilic archaeon that dominates microbial communities in a dynamically changing hypersaline environment, simultaneously optimizes fitness to total salinity, NaCl concentration, and the [K]/[Mg] ratio. Despite being maintained under controlled conditions over the last 50 years, peaks in the three-dimensional fitness landscape occur in salinity and ionic compositions that are not replicated in laboratory culturing but are routinely observed in the natural hypersaline environment of this organism. Intriguingly, adaptation to variations in ion composition was associated with differential regulation of anaerobic metabolism genes, suggesting an intertwined relationship between responses to oxygen and salinity. Our results suggest that the ecological memory of complex environmental variations is imprinted in the networks for coordinating multiple cellular processes. These coordination networks are also essential for dealing with changes in other physicochemically linked factors present during routine laboratory culturing and, hence, retained in model organisms. PMID:24413600

  16. Binding of Iron(III) to Organic Soils: Exafs Spectroscopy And Chemical Equilibrium Modeling

    SciTech Connect

    Gustafsson, J.P.; Persson, I.; Kleja, D.B.; Schaik, J.W.J.van

    2007-07-09

    The complexation of iron(III) to soil organic matter is important for the binding of trace metals in natural environments because of competition effects. In this study, we used extended X-ray absorption fine structure (EXAFS) spectroscopy to characterize the binding mode for iron(III) in two soil samples from organic mor layers, one of which was also treated with iron(III). In most cases the EXAFS spectra had three significant contributions, inner-core Fe-O/N interactions at about 2.02(2) angstroms, Fe-C interactions in the second scattering shell at 3.00(4) angstroms, and a mean Fe-Fe distance at 3.37(3) angstroms. One untreated sample showed features typical for iron (hydr)oxides; however, after treatment of iron(III) the EXAFS spectrum was dominated by organically complexed iron. The presence of a Fe-Fe distance in all samples showed that the major part of the organically complexed iron was hydrolyzed, most likely in a mixture of complexes with an inner core of (O{sub 5}Fe){sub 2}O and (O{sub 5}Fe){sub 3}O. These results were used to constrain a model for metal-humic complexation, the Stockholm Humic Model (SHM). The model was able to describe iron(III) binding very well at low pH considering only one dimeric iron(III)-humic complex. The competition effect on trace metals was also well described.

  17. Hierarchies, boundaries, and representation in a Freudian model of mental organization.

    PubMed

    Grossman, W I

    1992-01-01

    Freud used a spatial model of mental organization, derived from his explanation of aphasia, as an organizing framework for psychoanalytic theory. He introduced the ideas of representation and overdetermination to describe relations of the contents of systems that were joined to form, first, a hierarchical nervous system, then, mental systems. Freud used his basic model to organize aspects of mental function and phenomena, of interpersonal and social phenomena, and some kinds of biological phenomena. His accounts of metapsychology and clinical psychoanalysis are similar to his description of the basic aphasia/nervous system model. Across the boundaries of mental systems, translation of the contents of one system led to their being represented in another. Repeated editing and translation account for many properties of the systems. The mind pictured is a hierarchical structure of agencies, functions, and fantasy organizations. Complexity results from the combination of relatively simple relations and repetition of the same operations. The mind described by Freud's psychoanalysis is the self-reflecting mind and the mental activity of an analyst and of a patient in analysis. PMID:1573160

  18. Contributions of Acid-Catalysed Processes to Secondary Organic Aerosol Mass - A Modelling pproach

    NASA Astrophysics Data System (ADS)

    Ervens, B.; Feingold, G.; Kreidenweis, S. M.

    2005-12-01

    A significant fraction of secondary organic aerosol (SOA) mass is formed by chemical and/or physical processes. However, the amount of organic material found in ambient organic aerosols cannot be explained with current models. Recently, several laboratory studies have been published which suggest that also acid-catalyzed processes that occur either in particles or at their surfaces (heterogeneous) might contribute significantly to mass formation. However, to date there is no general conclusion about the efficiency of such processes due to the great diversity of species and experimental conditions. We present a compilation of literature data (thermodynamic and kinetic) of these processes. The aerosol yields of (i) additional species which are thought previously not contribute to SOA formation (e.g. isoprene, aliphatic aldehydes) and (ii) species which form apparently higher SOA masses on acidic seed aerosols are reported and compared to input data of previous SOA models. Available kinetic data clearly exclude aldol condensation as a significant process for SOA formation on a time scale of typical aerosol life times. Using aerosol size distributions and gas phase concentrations measured during NEAQS2002 as model input data, we show that (even under assumption of equilibrium conditions) these additional processes only contribute a minor fraction to the organic aerosol mass.

  19. Microtechnology-based organ systems and whole-body models for drug screening.

    PubMed

    Lee, Seung Hwan; Ha, Sang Keun; Choi, Inwook; Choi, Nakwon; Park, Tai Hyun; Sung, Jong Hwan

    2016-06-01

    After drug administration, the drugs are absorbed, distributed, metabolized, and excreted (ADME). Because ADME processes affect drug efficacy, various in vitro models have been developed based on the ADME processes. Although these models have been widely accepted as a tool for predicting the effects of drugs, the differences between in vivo and in vitro systems result in high attrition rates of drugs during the development process and remain a major limitation. Recent advances in microtechnology enable more accurate mimicking of the in vivo environment, where cellular behavior and physiological responses to drugs are more realistic; this has led to the development of novel in vitro systems, known as "organ-on-a-chip" systems. The development of organ-on-a-chip systems has progressed to include the reproduction of multiple organ interactions, which is an important step towards "body-on-a-chip" systems that will ultimately predict whole-body responses to drugs. In this review, we summarize the application of microtechnology for the development of in vitro systems that accurately mimic in vivo environments and reconstruct multiple organ models. PMID:27125245

  20. Topsoil organic carbon content of Europe, a new map based on a generalised additive model

    NASA Astrophysics Data System (ADS)

    de Brogniez, Delphine; Ballabio, Cristiano; Stevens, Antoine; Jones, Robert J. A.; Montanarella, Luca; van Wesemael, Bas

    2014-05-01

    There is an increasing demand for up-to-date spatially continuous organic carbon (OC) data for global environment and climatic modeling. Whilst the current map of topsoil organic carbon content for Europe (Jones et al., 2005) was produced by applying expert-knowledge based pedo-transfer rules on large soil mapping units, the aim of this study was to replace it by applying digital soil mapping techniques on the first European harmonised geo-referenced topsoil (0-20 cm) database, which arises from the LUCAS (land use/cover area frame statistical survey) survey. A generalized additive model (GAM) was calibrated on 85% of the dataset (ca. 17 000 soil samples) and a backward stepwise approach selected slope, land cover, temperature, net primary productivity, latitude and longitude as environmental covariates (500 m resolution). The validation of the model (applied on 15% of the dataset), gave an R2 of 0.27. We observed that most organic soils were under-predicted by the model and that soils of Scandinavia were also poorly predicted. The model showed an RMSE of 42 g kg-1 for mineral soils and of 287 g kg-1 for organic soils. The map of predicted OC content showed the lowest values in Mediterranean countries and in croplands across Europe, whereas highest OC content were predicted in wetlands, woodlands and in mountainous areas. The map of standard error of the OC model predictions showed high values in northern latitudes, wetlands, moors and heathlands, whereas low uncertainty was mostly found in croplands. A comparison of our results with the map of Jones et al. (2005) showed a general agreement on the prediction of mineral soils' OC content, most probably because the models use some common covariates, namely land cover and temperature. Our model however failed to predict values of OC content greater than 200 g kg-1, which we explain by the imposed unimodal distribution of our model, whose mean is tilted towards the majority of soils, which are mineral. Finally, average

  1. Preparatory steps for a robust dynamic model for organically bound tritium dynamics in agricultural crops

    SciTech Connect

    Melintescu, A.; Galeriu, D.; Diabate, S.; Strack, S.

    2015-03-15

    The processes involved in tritium transfer in crops are complex and regulated by many feedback mechanisms. A full mechanistic model is difficult to develop due to the complexity of the processes involved in tritium transfer and environmental conditions. First, a review of existing models (ORYZA2000, CROPTRIT and WOFOST) presenting their features and limits, is made. Secondly, the preparatory steps for a robust model are discussed, considering the role of dry matter and photosynthesis contribution to the OBT (Organically Bound Tritium) dynamics in crops.

  2. A material sensitivity study on the accuracy of deformable organ registration using linear biomechanical models

    SciTech Connect

    Chi, Y.; Liang, J.; Yan, D.

    2006-02-15

    Model-based deformable organ registration techniques using the finite element method (FEM) have recently been investigated intensively and applied to image-guided adaptive radiotherapy (IGART). These techniques assume that human organs are linearly elastic material, and their mechanical properties are predetermined. Unfortunately, the accurate measurement of the tissue material properties is challenging and the properties usually vary between patients. A common issue is therefore the achievable accuracy of the calculation due to the limited access to tissue elastic material constants. In this study, we performed a systematic investigation on this subject based on tissue biomechanics and computer simulations to establish the relationships between achievable registration accuracy and tissue mechanical and organ geometrical properties. Primarily we focused on image registration for three organs: rectal wall, bladder wall, and prostate. The tissue anisotropy due to orientation preference in tissue fiber alignment is captured by using an orthotropic or a transversely isotropic elastic model. First we developed biomechanical models for the rectal wall, bladder wall, and prostate using simplified geometries and investigated the effect of varying material parameters on the resulting organ deformation. Then computer models based on patient image data were constructed, and image registrations were performed. The sensitivity of registration errors was studied by perturbating the tissue material properties from their mean values while fixing the boundary conditions. The simulation results demonstrated that registration error for a subvolume increases as its distance from the boundary increases. Also, a variable associated with material stability was found to be a dominant factor in registration accuracy in the context of material uncertainty. For hollow thin organs such as rectal walls and bladder walls, the registration errors are limited. Given 30% in material uncertainty

  3. Sustainability assessment through analogical models: The approach of aerobic living-organism

    NASA Astrophysics Data System (ADS)

    Dassisti, Michele

    2014-10-01

    The most part of scientific discoveries of human being borrow ideas and inspiration from nature. This point gives the rationale of the sustainability assessment approach presented here and based on the aerobic living organism (ALO) already developed by the author, which funds on the basic assumption that it is reasonable and effective to refer to the analogy between an system organized by human (say, manufacturing system, enterprise, etc.) for several decision-making scopes. The critical review of the ALO conceptual model already developed is here discussed through an example of an Italian small enterprise manufacturing metal components for civil furniture to assess its feasibility for sustainability appraisal.

  4. Leader of the pack: gene mapping in dogs and other model organisms.

    PubMed

    Karlsson, Elinor K; Lindblad-Toh, Kerstin

    2008-09-01

    The domestic dog offers a unique opportunity to explore the genetic basis of disease, morphology and behaviour. We share many diseases with our canine companions, including cancer, diabetes and epilepsy, making the dog an ideal model organism for comparative disease genetics. Using newly developed resources, whole-genome association in dog breeds is proving to be exceptionally powerful. Here, we review the different trait-mapping strategies, some key biological findings emerging from recent studies and the implications for human health. We also discuss the development of similar resources for other vertebrate organisms. PMID:18714291

  5. Ellsworth C. Dougherty: A Pioneer in the Selection of Caenorhabditis elegans as a Model Organism

    PubMed Central

    Ferris, Howard

    2015-01-01

    Ellsworth Dougherty (1921–1965) was a man of impressive intellectual dimensions and interests; in a relatively short career he contributed enormously as researcher and scholar to the biological knowledge base for selection of Caenorhabditis elegans as a model organism in neurobiology, genetics, and molecular biology. He helped guide the choice of strains that were eventually used, and, in particular, he developed the methodology and understanding for the nutrition and axenic culture of nematodes and other organisms. Dougherty insisted upon a concise terminology for culture techniques and coined descriptive neologisms that were justified by their linguistic roots. Among other contributions, he refined the classification system for the Protista. PMID:26272995

  6. Primary migration by diffusion through kerogen: I. Model experiments with organic-coated rocks

    SciTech Connect

    Thomas, M.M.; Clouse, J.A. )

    1990-10-01

    Laboratory experiments were performed to assess diffusion through kerogen as a mechanism of hydrocarbon transport through fine-grained rocks. Such transport can be important in primary migration within source rocks and in leakage through seals. To test the concept of diffusion through organic matter networks, model experiments were performed in which hydrocarbon diffusion was measured through Austin chalk cores that had been coated with a monolayer of fatty acids. Hydrocarbon fluxes through the coated cores were compared to hydrocarbon fluxes through uncoated Austin chalk cores. Results showed that the organic coating enhanced transport through the core by a hundredfold over diffusion through its water-filled pore space alone.

  7. Global combustion sources of organic aerosols: model comparison with 84 AMS factor-analysis data sets

    NASA Astrophysics Data System (ADS)

    Tsimpidi, Alexandra P.; Karydis, Vlassis A.; Pandis, Spyros N.; Lelieveld, Jos

    2016-07-01

    Emissions of organic compounds from biomass, biofuel, and fossil fuel combustion strongly influence the global atmospheric aerosol load. Some of the organics are directly released as primary organic aerosol (POA). Most are emitted in the gas phase and undergo chemical transformations (i.e., oxidation by hydroxyl radical) and form secondary organic aerosol (SOA). In this work we use the global chemistry climate model ECHAM/MESSy Atmospheric Chemistry (EMAC) with a computationally efficient module for the description of organic aerosol (OA) composition and evolution in the atmosphere (ORACLE). The tropospheric burden of open biomass and anthropogenic (fossil and biofuel) combustion particles is estimated to be 0.59 and 0.63 Tg, respectively, accounting for about 30 and 32 % of the total tropospheric OA load. About 30 % of the open biomass burning and 10 % of the anthropogenic combustion aerosols originate from direct particle emissions, whereas the rest is formed in the atmosphere. A comprehensive data set of aerosol mass spectrometer (AMS) measurements along with factor-analysis results from 84 field campaigns across the Northern Hemisphere are used to evaluate the model results. Both the AMS observations and the model results suggest that over urban areas both POA (25-40 %) and SOA (60-75 %) contribute substantially to the overall OA mass, whereas further downwind and in rural areas the POA concentrations decrease substantially and SOA dominates (80-85 %). EMAC does a reasonable job in reproducing POA and SOA levels during most of the year. However, it tends to underpredict POA and SOA concentrations during winter indicating that the model misses wintertime sources of OA (e.g., residential biofuel use) and SOA formation pathways (e.g., multiphase oxidation).

  8. Variable C : N : P stoichiometry of dissolved organic matter cycling in the Community Earth System Model

    DOE PAGESBeta

    Letscher, R. T.; Moore, J. K.; Teng, Y. -C.; Primeau, F.

    2015-01-12

    Dissolved organic matter (DOM) plays an important role in the ocean's biological carbon pump by providing an advective/mixing pathway for ~ 20% of export production. DOM is known to have a stoichiometry depleted in nitrogen (N) and phosphorus (P) compared to the particulate organic matter pool, a fact that is often omitted from biogeochemical ocean general circulation models. However the variable C : N : P stoichiometry of DOM becomes important when quantifying carbon export from the upper ocean and linking the nutrient cycles of N and P with that of carbon. Here we utilize recent advances in DOM observationalmore » data coverage and offline tracer-modeling techniques to objectively constrain the variable production and remineralization rates of the DOM C : N : P pools in a simple biogeochemical-ocean model of DOM cycling. The optimized DOM cycling parameters are then incorporated within the Biogeochemical Elemental Cycling (BEC) component of the Community Earth System Model (CESM) and validated against the compilation of marine DOM observations. The optimized BEC simulation including variable DOM C : N : P cycling was found to better reproduce the observed DOM spatial gradients than simulations that used the canonical Redfield ratio. Global annual average export of dissolved organic C, N, and P below 100 m was found to be 2.28 Pg C yr-1 (143 Tmol C yr-1, 16.4 Tmol N yr-1, and 1 Tmol P yr-1, respectively, with an average export C : N : P stoichiometry of 225 : 19 : 1 for the semilabile (degradable) DOM pool. Dissolved organic carbon (DOC) export contributed ~ 25% of the combined organic C export to depths greater than 100 m.« less

  9. Sorption reactivity of mineral surfaces: the model-free conversion of humidity effect on organic vapor sorption to the organic sorbate effect on water-sorbent interactions

    NASA Astrophysics Data System (ADS)

    Borisover, Mikhail

    2013-04-01

    Interaction of water with mineral surfaces is one of the key factors controlling their reactivity towards organic compounds in multiple physical and chemical processes, e.g., in sorption and catalysis. Specifically, water interactions with minerals (as well as with other naturally present sorbents) are of fundamental importance for distribution of organic compounds between different environmental phases. Therefore, it is of basic interest to learn about interrelations between organic sorbate - sorbent and water - sorbent interactions on a local scale, in a microenvironment specific for a given organic sorbate. The understanding of these interrelations can be approached by examining the effect of organic compounds on water - sorbent interactions. However, at environmentally relevant conditions associated with relatively low concentrations of organic compounds, it may be hardly possible to directly measure the effect of sorbed organic molecules on water sorption. This paper reports a thermodynamic approach in which the effect of organic compounds on sorbent-water interactions can be obtained, in a model-free way, from the equilibrium sorption isotherms of organic vapors on a variously hydrated surface (Borisover, M., Adsorption, DOI 10.1007/s10450-012-9446-7). The outcome of this conversion is a "differential" stoichiometry between changes in the amounts of water and organic compounds in the sorbed state. The analysis included the experimental sorption data for various organic vapors on such environmentally important sorbents as quartz, metal oxides, calcite, clay minerals and humic acid. So, based on sorption isotherms of organic compounds obtained at different relative air humidities, the number of water molecules expelled from a sorbent or co-sorbed, per an organic molecule sorbed, may easily be obtained for any humidity range. This "differential" stoichiometry was also examined by means of the Linear Free Energy Relationship (LFER). Based on the LFER analysis

  10. Optical Measurements and Modeling to Estimate Concentrations and Fluxes of Organic Matter in the Southern Ocean

    NASA Technical Reports Server (NTRS)

    Stramski, Dariusz; Mitchell, B. Greg; Marra, John W. (Technical Monitor)

    2001-01-01

    This project was a collaboration between two Principal Investigators, Dr. Dariusz Stramski and Dr. Greg Mitchell of Scripps Institution of Oceanography, University of California San Diego. Our overall goal was to conduct optical measurements and modeling to estimate concentrations of organic matter in the Southern Ocean in support of the U.S. JGOFS Process Study in this region. Key variables and processes of high relevance to accomplish the JGOFS goals include time and space resolution of phytoplankton pigments, particulate organic carbon, and the formation and export of organic carbon. Our project focused on establishing the fundamental relationships for parameterization of these variables and processes in terms of the optical properties of seawater, and developing understanding of why the Southern Ocean differs from other low-latitude systems, or has differentiation within. Our approach builds upon historical observations that optical properties provide a useful proxy for key reservoirs of organic matter such as chlorophyll alpha (Chl) and particulate organic carbon (POC) concentrations, which are of relevance to the JGOFS objectives. We carried out detailed studies of in situ and water sample optical properties including spectral reflectance, absorption, beam attenuation, scattering, and backscattering coefficients. We evaluated the ability to estimate Chl from the spectral reflectance (ocean color) in the Southern Ocean. We examined relationships between the ocean optical properties and particulate organic carbon. We developed, for the first time, an algorithm for estimating particulate organic carbon concentration in the surface ocean from satellite imagery of ocean color. With this algorithm, we obtained maps of POC distribution in the Southern Ocean showing the seasonal progression of POC in the austral spring-summer season. We also developed a semianalytical reflectance model for the investigated polar waters based on our field measurements of absorption

  11. A Study of Cloud Processing of Organic Aerosols Using Models and CHAPS Data

    SciTech Connect

    Ervens, Barbara

    2012-01-17

    The main theme of our work has been the identification of parameters that mostly affect the formation and modification of aerosol particles and their interaction with water vapor. Our detailed process model studies led to simplifications/parameterizations of these effects that bridge detailed aerosol information from laboratory and field studies and the need for computationally efficient expressions in complex atmospheric models. One focus of our studies has been organic aerosol mass that is formed in the atmosphere by physical and/or chemical processes (secondary organic aerosol, SOA) and represents a large fraction of atmospheric particulate matter. Most current models only describe SOA formation by condensation of low volatility (or semivolatile) gas phase products and neglect processes in the aqueous phase of particles or cloud droplets that differently affect aerosol size and vertical distribution and chemical composition (hygroscopicity). We developed and applied models of aqueous phase SOA formation in cloud droplets and aerosol particles (aqSOA). Placing our model results into the context of laboratory, model and field studies suggests a potentially significant contribution of aqSOA to the global organic mass loading. The second focus of our work has been the analysis of ambient data of particles that might act as cloud condensation nuclei (CCN) at different locations and emission scenarios. Our model studies showed that the description of particle chemical composition and mixing state can often be greatly simplified, in particular in aged aerosol. While over the past years many CCN studies have been successful performed by using such simplified composition/mixing state assumptions, much more uncertainty exists in aerosol-cloud interactions in cold clouds (ice or mixed-phase). Therefore we extended our parcel model that describes warm cloud formation by ice microphysics and explored microphysical parameters that determine the phase state and lifetime of

  12. Reconciling modeled and observed atmospheric deposition of soluble organic nitrogen at coastal locations

    NASA Astrophysics Data System (ADS)

    Ito, Akinori; Lin, Guangxing; Penner, Joyce E.

    2014-06-01

    Atmospheric deposition of reactive nitrogen (N) species from air pollutants is a significant source of exogenous nitrogen in marine ecosystems. Here we use an atmospheric chemical transport model to investigate the supply of soluble organic nitrogen (ON) from anthropogenic sources to the ocean. Comparisons of modeled deposition with observations at coastal and marine locations show good overall agreement for inorganic nitrogen and total soluble nitrogen. However, previous modeling approaches result in significant underestimates of the soluble ON deposition if the model only includes the primary soluble ON and the secondary oxidized ON in gases and aerosols. Our model results suggest that including the secondary reduced ON in aerosols as a source of soluble ON contributes to an improved prediction of the deposition rates (g N m-2 yr-1). The model results show a clear distinction in the vertical distribution of soluble ON in aerosols between different processes from the primary sources and the secondary formation. The model results (excluding the biomass burning and natural emission changes) suggest an increase in soluble ON outflow from atmospheric pollution, in particular from East Asia, to the oceans in the twentieth century. These results highlight the necessity of improving the process-based quantitative understanding of the chemical reactions of inorganic nitrogen species with organics in aerosol and cloud water.

  13. Knowledge-based model of hydrogen-bonding propensity in organic crystals.

    PubMed

    Galek, Peter T A; Fábián, László; Motherwell, W D Samuel; Allen, Frank H; Feeder, Neil

    2007-10-01

    A new method is presented to predict which donors and acceptors form hydrogen bonds in a crystal structure, based on the statistical analysis of hydrogen bonds in the Cambridge Structural Database (CSD). The method is named the logit hydrogen-bonding propensity (LHP) model. The approach has a potential application in identifying both likely and unusual hydrogen bonding, which can help to rationalize stable and metastable crystalline forms, of relevance to drug development in the pharmaceutical industry. Whilst polymorph prediction techniques are widely used, the LHP model is knowledge-based and is not restricted by the computational issues of polymorph prediction, and as such may form a valuable precursor to polymorph screening. Model construction applies logistic regression, using training data obtained with a new survey method based on the CSD system. The survey categorizes the hydrogen bonds and extracts model parameter values using descriptive structural and chemical properties from three-dimensional organic crystal structures. LHP predictions from a fitted model are made using two-dimensional observables alone. In the initial cases analysed, the model is highly accurate, achieving approximately 90% correct classification of both observed hydrogen bonds and non-interacting donor-acceptor pairs. Extensive statistical validation shows the LHP model to be robust across a range of small-molecule organic crystal structures. PMID:17873446

  14. A large-scale model for simulating the fate & transport of organic contaminants in river basins.

    PubMed

    Lindim, C; van Gils, J; Cousins, I T

    2016-02-01

    We present STREAM-EU (Spatially and Temporally Resolved Exposure Assessment Model for EUropean basins), a novel dynamic mass balance model for predicting the environmental fate of organic contaminants in river basins. STREAM-EU goes beyond the current state-of-the-science in that it can simulate spatially and temporally-resolved contaminant concentrations in all relevant environmental media (surface water, groundwater, snow, soil and sediments) at the river basin scale. The model can currently be applied to multiple organic contaminants in any river basin in Europe, but the model framework is adaptable to any river basin in any continent. We simulate the environmental fate of perfluoroctanesulfonic acid (PFOS) and perfluorooctanoic acid (PFOA) in the Danube River basin and compare model predictions to recent monitoring data. The model predicts PFOS and PFOA concentrations that agree well with measured concentrations for large stretches of the river. Disagreements between the model predictions and measurements in some river sections are shown to be useful indicators of unknown contamination sources to the river basin. PMID:26414740

  15. Model-data comparison of soil organic oatter cycling: soil core scale

    NASA Astrophysics Data System (ADS)

    Wutzler, Thomas; Reichstein, Markus

    2010-05-01

    Soil organic matter (SOM) cycling is usually modeled as a donor controlled process, most often by first order kinetics. However, evidence of contradition of this donor-paradigm is appearing. One alternative hypothesis is that microbiological consumers of SOM play an important role and need to be taken into account more explicitely. Here we link SOM cycling to the modeling of microbial growth kinetics. We set up a suite of alternative models of microbial growth. Explicitly modelling the cycling of a label across carbon pools allowed to compare the model outputs to data of a soil priming experiment. The experimental data was taken from U. Hamer, & B. Marschner (2002 Journal of Plant Nutrition and Soil Science 165(3)), who incubated several 14C labelled substrates at 20°C in a model system that consisted of sand mixed with lignin for 26 days. Data streams of time series total respiration, respiration from labelled amendment and prior information on model parameters were used to determine the posterior probability density function of the model parameters of each of the model variants and to calculate Bayes-Factors, the ratios of the likelihood of the different model variants. This kind of data and Bayesian analysis is usable to compare model structures adapted to processes that determine the dynamics at this scale: co-limitation of depolymerization of older soil organic matter by both substrate and decomposers, prefererrential substrate usage, activation and deactivation and predation of microbes, and usage of both assimilated carbon and carbon of internal pools for maintenance and growth respiration.

  16. Determining organ dose conversion coefficients for external neutron irradiation by using a voxel mouse model

    PubMed Central

    Zhang, Xiaomin; Xie, Xiangdong; Qu, Decheng; Ning, Jing; Zhou, Hongmei; Pan, Jie; Yang, Guoshan

    2016-01-01

    A set of fluence-to-dose conversion coefficients has been calculated for neutrons with energies <20 MeV using a developed voxel mouse model and Monte Carlo N-particle code (MCNP), for the purpose of neutron radiation effect evaluation. The calculation used 37 monodirectional monoenergetic neutron beams in the energy range 10−9 MeV to 20 MeV, under five different source irradiation configurations: left lateral, right lateral, dorsal–ventral, ventral–dorsal, and isotropic. Neutron fluence-to-dose conversion coefficients for selected organs of the body were presented in the paper, and the effect of irradiation geometry conditions, neutron energy and the organ location on the organ dose was discussed. The results indicated that neutron dose conversion coefficients clearly show sensitivity to irradiation geometry at neutron energy below 1 MeV. PMID:26661852

  17. Towards a compendium of essential genes – From model organisms to synthetic lethality in cancer cells

    PubMed Central

    Zhan, Tianzuo; Boutros, Michael

    2016-01-01

    Abstract Essential genes are defined by their requirement to sustain life in cells or whole organisms. The systematic identification of essential gene sets not only allows insights into the fundamental building blocks of life, but may also provide novel therapeutic targets in oncology. The discovery of essential genes has been tightly linked to the development and deployment of various screening technologies. Here, we describe how gene essentiality was addressed in different eukaryotic model organisms, covering a range of organisms from yeast to mouse. We describe how increasing knowledge of evolutionarily divergent genomes facilitate identification of gene essentiality across species. Finally, the impact of gene essentiality and synthetic lethality on cancer research and the clinical translation of screening results are highlighted. PMID:26627871

  18. Scaling laws and model of words organization in spoken and written language

    NASA Astrophysics Data System (ADS)

    Bian, Chunhua; Lin, Ruokuang; Zhang, Xiaoyu; Ma, Qianli D. Y.; Ivanov, Plamen Ch.

    2016-01-01

    A broad range of complex physical and biological systems exhibits scaling laws. The human language is a complex system of words organization. Studies of written texts have revealed intriguing scaling laws that characterize the frequency of words occurrence, rank of words, and growth in the number of distinct words with text length. While studies have predominantly focused on the language system in its written form, such as books, little attention is given to the structure of spoken language. Here we investigate a database of spoken language transcripts and written texts, and we uncover that words organization in both spoken language and written texts exhibits scaling laws, although with different crossover regimes and scaling exponents. We propose a model that provides insight into words organization in spoken language and written texts, and successfully accounts for all scaling laws empirically observed in both language forms.

  19. Determining organ dose conversion coefficients for external neutron irradiation by using a voxel mouse model.

    PubMed

    Zhang, Xiaomin; Xie, Xiangdong; Qu, Decheng; Ning, Jing; Zhou, Hongmei; Pan, Jie; Yang, Guoshan

    2016-03-01

    A set of fluence-to-dose conversion coefficients has been calculated for neutrons with energies <20 MeV using a developed voxel mouse model and Monte Carlo N-particle code (MCNP), for the purpose of neutron radiation effect evaluation. The calculation used 37 monodirectional monoenergetic neutron beams in the energy range 10(-9) MeV to 20 MeV, under five different source irradiation configurations: left lateral, right lateral, dorsal-ventral, ventral-dorsal, and isotropic. Neutron fluence-to-dose conversion coefficients for selected organs of the body were presented in the paper, and the effect of irradiation geometry conditions, neutron energy and the organ location on the organ dose was discussed. The results indicated that neutron dose conversion coefficients clearly show sensitivity to irradiation geometry at neutron energy below 1 MeV. PMID:26661852

  20. A model for chromosome organization during the cell cycle in live E. coli

    PubMed Central

    Liu, Yuru; Xie, Ping; Wang, Pengye; Li, Ming; Li, Hui; Li, Wei; Dou, Shuoxing

    2015-01-01

    Bacterial chromosomal DNA is a highly compact nucleoid. The organization of this nucleoid is poorly understood due to limitations in the methods used to monitor the complexities of DNA organization in live bacteria. Here, we report that circular plasmid DNA is auto-packaged into a uniform dual-toroidal-spool conformation in response to mechanical stress stemming from sharp bending and un-winding by atomic force microscopic analysis. The mechanism underlying this phenomenon was deduced with basic physical principles to explain the auto-packaging behaviour of circular DNA. Based on our observations and previous studies, we propose a dynamic model of how chromosomal DNA in E. coli may be organized during a cell division cycle. Next, we test the model by monitoring the development of HNS clusters in live E. coli during a cell cycle. The results were in close agreement with the model. Furthermore, the model accommodates a majority of the thus-far-discovered remarkable features of nucleoids in vivo. PMID:26597953

  1. Spectral Color Indices Based Geospatial Modeling of Soil Organic Matter in Chitwan District, Nepal

    NASA Astrophysics Data System (ADS)

    Mandal, Umesh K.

    2016-06-01

    Space Technology provides a resourceful-cost effective means to assess soil nutrients essential for soil management plan. Soil organic matter (SOM) is one of valuable controlling productivity of crops by providing nutrient in farming systems. Geospatial modeling of soil organic matter is essential if there is unavailability of soil test laboratories and its strong spatial correlation. In the present analysis, soil organic matter is modeled from satellite image derived spectral color indices. Brightness Index (BI), Coloration Index (CI), Hue Index (HI), Redness Index (RI) and Saturation Index (SI) were calculated by converting DN value to radiance and radiance to reflectance from Thematic Mapper image. Geospatial model was developed by regressing SOM with color indices and producing multiple regression model using stepwise regression technique. The multiple regression equation between SOM and spectral indices was significant with R = 0. 56 at 95% confidence level. The resulting MLR equation was then used for the spatial prediction for the entire study area. Redness Index was found higher significance in estimating the SOM. It was used to predict SOM as auxiliary variables using cokringing spatial interpolation technique. It was tested in seven VDCs of Chitwan district of Nepal using Thematic Mapper remotely sensed data. SOM was found to be measured ranging from 0.15% to 4.75 %, with a mean of 2.24 %. Remotely sensed data derived spectral color indices have the potential as useful auxiliary variables for estimating SOM content to generate soil fertility management plans.

  2. Comparative evaluation of anaerobic digestion for sewage sludge and various organic wastes with simple modeling.

    PubMed

    Hidaka, Taira; Wang, Feng; Tsumori, Jun

    2015-09-01

    Anaerobic co-digestion of sewage sludge and other organic wastes, such as kitchen garbage, food waste, and agricultural waste, at a wastewater treatment plant (WWTP) is a promising method for both energy and material recovery. Substrate characteristics and the anaerobic digestion performance of sewage sludge and various organic wastes were compared using experiments and modeling. Co-digestion improved the value of digested sewage sludge as a fertilizer. The relationship between total and soluble elemental concentrations was correlated with the periodic table: most Na and K (alkali metals) were soluble, and around 20-40% of Mg and around 10-20% of Ca (alkaline earth metals) were soluble. The ratio of biodegradable chemical oxygen demand of organic wastes was 65-90%. The methane conversion ratio and methane production rate under mesophilic conditions were evaluated using a simplified mathematical model. There was reasonably close agreement between the model simulations and the experimental results in terms of methane production and nitrogen concentration. These results provide valuable information and indicate that the model can be used as a pre-evaluation tool to facilitate the introduction of co-digestion at WWTPs. PMID:26031329

  3. Integrating ecological risk assessments across levels of organization using the Franklin-Noss model of biodiversity

    SciTech Connect

    Brugger, K.E.; Tiebout, H.M. III |

    1994-12-31

    Wildlife toxicologists pioneered methodologies for assessing ecological risk to nontarget species. Historically, ecological risk assessments (ERAS) focused on a limited array of species and were based on a relatively few population-level endpoints (mortality, reproduction). Currently, risk assessment models are becoming increasingly complex that factor in multi-species interactions (across trophic levels) and utilize an increasingly diverse number of ecologically significant endpoints. This trend suggests the increasing importance of safeguarding not only populations of individual species, but also the overall integrity of the larger biotic systems that support them. In this sense, ERAs are in alignment with Conservation Biology, an applied science of ecological knowledge used to conserve biodiversity. A theoretical conservation biology model could be incorporated in ERAs to quantify impacts to biodiversity (structure, function or composition across levels of biological organization). The authors suggest that the Franklin-Noss model for evaluating biodiversity, with its nested, hierarchical approach, may provide a suitable paradigm for assessing and integrating the ecological risk that chemical contaminants pose to biological systems from the simplest levels (genotypes, individual organisms) to the most complex levels of organization (communities and ecosystems). The Franklin-Noss model can accommodate the existing ecotoxicological database and, perhaps more importantly, indicate new areas in which critical endpoints should be identified and investigated.

  4. Modeling the degradation of Portland cement pastes by biogenic organic acids

    SciTech Connect

    De Windt, Laurent; Devillers, Philippe

    2010-08-15

    Reactive transport models can be used to assess the long-term performance of cement-based materials subjected to biodegradation. A bioleaching test (with Aspergillus niger fungi) applied to ordinary Portland cement pastes during 15 months is modeled with HYTEC. Modeling indicates that the biogenic organic acids (acetic, butyric, lactic and oxalic) strongly accelerate hydrate dissolution by acidic hydrolysis whilst their complexation of aluminum has an effect on the secondary gel stability only. The deepest degradation front corresponds to portlandite dissolution and decalcification of calcium silicate hydrates. A complex pattern of sulfate phases dissolution and precipitation takes place in an intermediate zone. The outermost degraded zone consists of alumina and silica gels. The modeling accurateness of calcium leaching, pH evolution and degradation thickness is consistently enhanced whilst considering increase of diffusivity in the degraded zones. Precipitation of calcium oxalate is predicted by modeling but was hindered in the bioleaching reactor.

  5. Estimation of anisotropy parameters in organic-rich shale: Rock physics forward modeling approach

    NASA Astrophysics Data System (ADS)

    Herawati, Ida; Winardhi, Sonny; Priyono, Awali

    2015-09-01

    Anisotropy analysis becomes an important step in processing and interpretation of seismic data. One of the most important things in anisotropy analysis is anisotropy parameter estimation which can be estimated using well data, core data or seismic data. In seismic data, anisotropy parameter calculation is generally based on velocity moveout analysis. However, the accuracy depends on data quality, available offset, and velocity moveout picking. Anisotropy estimation using seismic data is needed to obtain wide coverage of particular layer anisotropy. In anisotropic reservoir, analysis of anisotropy parameters also helps us to better understand the reservoir characteristics. Anisotropy parameters, especially ɛ, are related to rock property and lithology determination. Current research aims to estimate anisotropy parameter from seismic data and integrate well data with case study in potential shale gas reservoir. Due to complexity in organic-rich shale reservoir, extensive study from different disciplines is needed to understand the reservoir. Shale itself has intrinsic anisotropy caused by lamination of their formed minerals. In order to link rock physic with seismic response, it is necessary to build forward modeling in organic-rich shale. This paper focuses on studying relationship between reservoir properties such as clay content, porosity and total organic content with anisotropy. Organic content which defines prospectivity of shale gas can be considered as solid background or solid inclusion or both. From the forward modeling result, it is shown that organic matter presence increases anisotropy in shale. The relationships between total organic content and other seismic properties such as acoustic impedance and Vp/Vs are also presented.

  6. Estimation of anisotropy parameters in organic-rich shale: Rock physics forward modeling approach

    SciTech Connect

    Herawati, Ida Winardhi, Sonny; Priyono, Awali

    2015-09-30

    Anisotropy analysis becomes an important step in processing and interpretation of seismic data. One of the most important things in anisotropy analysis is anisotropy parameter estimation which can be estimated using well data, core data or seismic data. In seismic data, anisotropy parameter calculation is generally based on velocity moveout analysis. However, the accuracy depends on data quality, available offset, and velocity moveout picking. Anisotropy estimation using seismic data is needed to obtain wide coverage of particular layer anisotropy. In anisotropic reservoir, analysis of anisotropy parameters also helps us to better understand the reservoir characteristics. Anisotropy parameters, especially ε, are related to rock property and lithology determination. Current research aims to estimate anisotropy parameter from seismic data and integrate well data with case study in potential shale gas reservoir. Due to complexity in organic-rich shale reservoir, extensive study from different disciplines is needed to understand the reservoir. Shale itself has intrinsic anisotropy caused by lamination of their formed minerals. In order to link rock physic with seismic response, it is necessary to build forward modeling in organic-rich shale. This paper focuses on studying relationship between reservoir properties such as clay content, porosity and total organic content with anisotropy. Organic content which defines prospectivity of shale gas can be considered as solid background or solid inclusion or both. From the forward modeling result, it is shown that organic matter presence increases anisotropy in shale. The relationships between total organic content and other seismic properties such as acoustic impedance and Vp/Vs are also presented.

  7. A modelling approach to find stable and reliable soil organic carbon values for further regionalization.

    NASA Astrophysics Data System (ADS)

    Bönecke, Eric; Franko, Uwe

    2015-04-01

    Soil organic matter (SOM) and carbon (SOC) might be the most important components to describe soil fertility of agricultural used soils. It is sensitive to temporal and spatial changes due to varying weather conditions, uneven crops and soil management practices and still struggles with providing reliable delineation of spatial variability. Soil organic carbon, furthermore, is an essential initial parameter for dynamic modelling, understanding e.g. carbon and nitrogen processes. Alas it requires cost and time intensive field and laboratory work to attain and using this information. The objective of this study is to assess an approach that reduces efforts of laboratory and field analyses by using method to find stable initial soil organic carbon values for further soil process modelling and regionalization on field scale. The demand of strategies, technics and tools to improve reliable soil organic carbon high resolution maps and additionally reducing cost constraints is hence still facing an increasing attention of scientific research. Although, it is nowadays a widely used practice, combining effective sampling schemes with geophysical sensing techniques, to describe within-field variability of soil organic carbon, it is still challenging large uncertainties, even at field scale in both, science and agriculture. Therefore, an analytical and modelling approach might facilitate and improve this strategy on small and large field scale. This study will show a method, how to find reliable steady state values of soil organic carbon at particular points, using the approved soil process model CANDY (Franko et al. 1995). It is focusing on an iterative algorithm of adjusting the key driving components: soil physical properties, meteorological data and management information, for which we quantified the input and the losses of soil carbon (manure, crop residues, other organic inputs, decomposition, leaching). Furthermore, this approach can be combined with geophysical

  8. Organic tank safety project: Preliminary results of energetics and thermal behavior studies of model organic nitrate and/or nitrite mixtures and a simulated organic waste

    SciTech Connect

    Scheele, R.D.; Sell, R.L.; Sobolik, J.L.; Burger, L.L.

    1995-08-01

    As a result of years of production and recovery of nuclear defense materials and subsequent waste management at the Hanford Site, organic-bearing radioactive high-level wastes (HLW) are currently stored in large (up to 3. ML) single-shell storage tanks (SSTs). Because these wastes contain both fuels (organics) and the oxidants nitrate and nitrite, rapid energetic reactions at certain conditions could occur. In support of Westinghouse Hanford Company`s (WHC) efforts to ensure continued safe storage of these organic- and oxidant-bearing wastes and to define the conditions necessary for reactions to occur, we measured the thermal sensitivities and thermochemical and thermokinetic properties of mixtures of selected organics and sodium nitrate and/or nitrite and a simulated Hanford organic-bearing waste using thermoanalytical technologies. These thermoanalytical technologies are used by chemical reactivity hazards evaluation organizations within the chemical industry to assess chemical reaction hazards.

  9. Strategies and Tactics in Multiscale Modeling of Cell-to-Organ Systems

    PubMed Central

    Bassingthwaighte, James B.; Chizeck, Howard Jay; Atlas, Les E.

    2010-01-01

    Modeling is essential to integrating knowledge of human physiology. Comprehensive self-consistent descriptions expressed in quantitative mathematical form define working hypotheses in testable and reproducible form, and though such models are always “wrong” in the sense of being incomplete or partly incorrect, they provide a means of understanding a system and improving that understanding. Physiological systems, and models of them, encompass different levels of complexity. The lowest levels concern gene signaling and the regulation of transcription and translation, then biophysical and biochemical events at the protein level, and extend through the levels of cells, tissues and organs all the way to descriptions of integrated systems behavior. The highest levels of organization represent the dynamically varying interactions of billions of cells. Models of such systems are necessarily simplified to minimize computation and to emphasize the key factors defining system behavior; different model forms are thus often used to represent a system in different ways. Each simplification of lower level complicated function reduces the range of accurate operability at the higher level model, reducing robustness, the ability to respond correctly to dynamic changes in conditions. When conditions change so that the complexity reduction has resulted in the solution departing from the range of validity, detecting the deviation is critical, and requires special methods to enforce adapting the model formulation to alternative reduced-form modules or decomposing the reduced-form aggregates to the more detailed lower level modules to maintain appropriate behavior. The processes of error recognition, and of mapping between different levels of model complexity and shifting the levels of complexity of models in response to changing conditions, are essential for adaptive modeling and computer simulation of large-scale systems in reasonable time. PMID:20463841

  10. MODELING THE EFFECT OF CHLORINE EMISSIONS ON ATMOSPHERIC OZONE AND SECONDARY ORGANIC AEROSOL CONCENTRATIONS ACROSS THE UNITED STATES

    EPA Science Inventory

    This paper presents the modeled effects of natural and anthropogenic chlorine emissions on the atmospheric concentrations of ozone and secondary organic aerosol across the United States. The model calculations include anthropogenic molecular chlorine emissions, anthropogenic hypo...

  11. Secondary organic aerosol in the global aerosol - chemical transport model Oslo CTM2

    NASA Astrophysics Data System (ADS)

    Hoyle, C. R.; Berntsen, T.; Myhre, G.; Isaksen, I. S. A.

    2007-11-01

    The global chemical transport model Oslo CTM2 has been extended to include the formation, transport and deposition of secondary organic aerosol (SOA). Precursor hydrocarbons which are oxidised to form condensible species include both biogenic species such as terpenes and isoprene, as well as species emitted predominantly by anthropogenic activities (toluene, m-xylene, methylbenzene and other aromatics). A model simulation for 2004 gives an annual global SOA production of approximately 55 Tg. Of this total, 2.5 Tg is found to consist of the oxidation products of anthropogenically emitted hydrocarbons, and about 15 Tg is formed by the oxidation products of isoprene. The global production of SOA is increased to about 69 Tg yr-1 by allowing semi-volatile species to partition to ammonium sulphate aerosol. This brings modelled organic aerosol values closer to those observed, however observations in Europe remain significantly underestimated. Allowing SOA to partition into ammonium sulphate aerosol increases the contribution of anthropogenic SOA from about 4.5% to 9.4% of the total production. Total modelled organic aerosol (OA) values are found to represent a lower fraction of the measured values in winter (when primary organic aerosol (POA) is the dominant OA component) than in summer, which may be an indication that estimates of POA emissions are too low. Additionally, for measurement stations where the summer OA values are higher than in winter, the model generally underestimates the increase in summertime OA. In order to correctly model the observed increase in OA in summer, additional SOA sources or formation mechanisms may be necessary. The importance of NO3 as an oxidant of SOA precursors is found to vary regionally, causing up to 50%-60% of the total amount of SOA near the surface in polluted regions and less than 25% in more remote areas, if the yield of condensible oxidation products for β-pinene is used for NO3 oxidation of all terpenes. Reducing the yield

  12. Pore - to - Core Modeling of Soil Organic Matter Decomposition in 3D Soil Structures

    NASA Astrophysics Data System (ADS)

    Falconer, R. E.; Battaia, G.; Baveye, P.; Otten, W.

    2013-12-01

    There is a growing body of literature supporting the need for microbial contributions to be considered explicitly in carbon-climate models. There is also overwhelming evidence that physical protection within aggregates can play a significant role in organic matter dynamics. Yet current models of soil organic matter dynamics divide soil organic matter into conceptual pools with distinct turnover times, assuming that a combination of biochemical and physical properties control decay without explicit description. Albeit robust in their application, such models are not capable to account for changes in soil structure or microbial populations, or accurately predict the effect of wetness or priming. A spatially explicit model is presented that accounts for microbial dynamics and physical processes, permitting consideration of the heterogeneity of the physical and chemical microenvironments at scales relevant for microbes. Exemplified for fungi, we investigate how micro-scale processes manifest at the core scale with particular emphasis on evolution of CO2 and biomass distribution. The microbial model is based upon previous (Falconer et al, 2012) and includes the following processes: uptake, translocation, recycling, enzyme production, growth, spread and respiration. The model is parameterised through a combination of literature data and parameter estimation (Cazelles et al., 2012).The Carbon model comprises two pools, particulate organic matter which through enzymatic activity is converted into dissolved organic matter. The microbial and carbon dynamics occur within a 3D soil structure obtained by X-ray CT. We show that CO2 is affected not only by the amount of Carbon in the soil but also by microbial dynamics, soil structure and the spatial distribution of OM. The same amount of OM can result in substantially different respiration rates, with surprisingly more CO2 with increased clustering of OM. We can explain this from the colony dynamics, production of enzymes and

  13. Ultrafast traveling wave dominates the electric organ discharge of Apteronotus leptorhynchus: an inverse modelling study

    PubMed Central

    Shifman, Aaron R.; Longtin, André; Lewis, John E.

    2015-01-01

    Identifying and understanding the current sources that give rise to bioelectric fields is a fundamental problem in the biological sciences. It is very difficult, for example, to attribute the time-varying features of an electroencephalogram recorded from the head surface to the neural activity of specific brain areas; model systems can provide important insight into such problems. Some species of fish actively generate an oscillating (c. 1000 Hz) quasi-dipole electric field to communicate and sense their environment in the dark. A specialized electric organ comprises neuron-like cells whose collective signal underlies this electric field. As a step towards understanding the detailed biophysics of signal generation in these fish, we use an anatomically-detailed finite-element modelling approach to reverse-engineer the electric organ signal over one oscillation cycle. We find that the spatiotemporal profile of current along the electric organ constitutes a travelling wave that is well-described by two spatial Fourier components varying in time. The conduction velocity of this wave is faster than action potential conduction in any known neuronal axon (>200 m/s), suggesting that the spatiotemporal features of high-frequency electric organ discharges are not constrained by the conduction velocities of spinal neuron pathways. PMID:26514932

  14. Ecotoxicogenomic Approaches for Understanding Molecular Mechanisms of Environmental Chemical Toxicity Using Aquatic Invertebrate, Daphnia Model Organism

    PubMed Central

    Kim, Hyo Jeong; Koedrith, Preeyaporn; Seo, Young Rok

    2015-01-01

    Due to the rapid advent in genomics technologies and attention to ecological risk assessment, the term “ecotoxicogenomics” has recently emerged to describe integration of omics studies (i.e., transcriptomics, proteomics, metabolomics, and epigenomics) into ecotoxicological fields. Ecotoxicogenomics is defined as study of an entire set of genes or proteins expression in ecological organisms to provide insight on environmental toxicity, offering benefit in ecological risk assessment. Indeed, Daphnia is a model species to study aquatic environmental toxicity designated in the Organization for Economic Co-operation and Development’s toxicity test guideline and to investigate expression patterns using ecotoxicology-oriented genomics tools. Our main purpose is to demonstrate the potential utility of gene expression profiling in ecotoxicology by identifying novel biomarkers and relevant modes of toxicity in Daphnia magna. These approaches enable us to address adverse phenotypic outcomes linked to particular gene function(s) and mechanistic understanding of aquatic ecotoxicology as well as exploration of useful biomarkers. Furthermore, key challenges that currently face aquatic ecotoxicology (e.g., predicting toxicant responses among a broad spectrum of phytogenetic groups, predicting impact of temporal exposure on toxicant responses) necessitate the parallel use of other model organisms, both aquatic and terrestrial. By investigating gene expression profiling in an environmentally important organism, this provides viable support for the utility of ecotoxicogenomics. PMID:26035755

  15. How Microstructure Defines Function in Organic Conjugated Materials: Insights from Modelling

    NASA Astrophysics Data System (ADS)

    Olivier, Yoann

    Organic conjugated materials have attracted an increasing interest over the years for their use in organic opto- electronic devices such as light-emitting diodes, solar cells, or field- effect transistors as a result of their low cost, light weight and ease of processing from solution. The improvement of the device performances requires a deep understanding of the electronic processes taking place in these devices down to the molecular scale. Especially, the way organic conjugated molecules or polymer chains organize in the solid state appears as a critical parameter to control in order to fine tune the materials electronic and photophysical properties. In our laboratory, we have developed a multi-faceted modeling scheme that encompasses classical molecular dynamics, quantum-chemistry, non-adiabatic quantum dynamics and kinetic Monte Carlo simulations to assess multiple fundamental opto- electronic processes occurring in conjugated materials used in devices. Here, we will more specifically review work dealing with the modeling of charge transport in conjugated polymers as well as singlet fission and exciton transport in small molecules. In all cases, we will highlight how these processes are sensitive to the relative arrangement of the materials at the nanoscale.

  16. The Buffering Balance: Modeling Arctic river total-, inorganic-, and organic-alkalinity fluxes

    NASA Astrophysics Data System (ADS)

    Hunt, C. W.; Salisbury, J.; Wollheim, W. M.; Mineau, M.; Stewart, R. J.

    2014-12-01

    River-borne inputs of alkalinity influence the pH and pCO2 of coastal ocean waters, and changes in alkalinity inputs also have implications for responses to climate-driven ocean acidification. Recent work has shown that alkalinity fluxes from rivers are not always dominated by inorganic carbon species, and can instead be composed somewhat or mostly of non-carbonate, presumably organic species. Concentrations and proportions of organic alkalinity (O-Alk) are correlated to dissolved organic carbon (DOC) concentrations and fluxes, which are predicted to rise as Arctic permafrost thaws and the hydrologic cycle intensifies. We have scaled results from watershed studies to develop a process-based model to simulate and aggregate Arctic river exports of total alkalinity, DOC, and O-Alk to the coastal sea. Total alkalinity, DOC, and O-Alk were loaded to a river network and routed through a 6-minute hydrologic model (FrAMES). We present results contrasting poorly buffered (e.g. the Kolyma river) and highly buffered (e.g. the Yukon river) systems, the impact of O-Alk on river pH and pCO2, and examine the seasonalities of inorganic and organic influences on coastal ocean carbonate chemistry.

  17. Kinetics of model high molecular weight organic compounds biodegradation in soil aquifer treatment.

    PubMed

    Fox, Peter; Makam, Roshan

    2011-10-01

    Soil Aquifer Treatment (SAT) is a process where treated wastewater is purified during transport through unsaturated and saturated zones. Easily biodegradable compounds are rapidly removed in the unsaturated zone and the residual organic carbon is comprised of primarily high molecular weight compounds. This research focuses on flow in the saturated zone where flow conditions are predictable and high molecular weight compounds are degraded. Flow through the saturated zone was investigated with 4 reactors packed with 2 different particle sizes and operated at 4 different flow rates. The objective was to evaluate the kinetics of transformation for high molecular weight organics during SAT. Dextran was used as a model compound to eliminate the complexity associated with studying a mixture of high molecular weight organics. The hydrolysis products of dextran are easily degradable sugars. Batch experiments with media taken from the reactors were used to determine the distribution of microbial activity in the reactors. Zero-order kinetics were observed for the removal of dextran in batch experiments which is consistent with hydrolysis of high molecular weight organics where extracellular enzymes limit the substrate utilization rate. Biomass and microbial activity measurements demonstrated that the biomass was independent of position in the reactors. A Monod based substrate/biomass growth kinetic model predicted the performance of dextran removal in the reactors. The rate limiting step appears to be hydrolysis and the overall rate was not affected by surface area even though greater biomass accumulation occurred as the surface area decreased. PMID:21723581

  18. Ultrafast traveling wave dominates the electric organ discharge of Apteronotus leptorhynchus: an inverse modelling study

    NASA Astrophysics Data System (ADS)

    Shifman, Aaron R.; Longtin, André; Lewis, John E.

    2015-10-01

    Identifying and understanding the current sources that give rise to bioelectric fields is a fundamental problem in the biological sciences. It is very difficult, for example, to attribute the time-varying features of an electroencephalogram recorded from the head surface to the neural activity of specific brain areas; model systems can provide important insight into such problems. Some species of fish actively generate an oscillating (c. 1000 Hz) quasi-dipole electric field to communicate and sense their environment in the dark. A specialized electric organ comprises neuron-like cells whose collective signal underlies this electric field. As a step towards understanding the detailed biophysics of signal generation in these fish, we use an anatomically-detailed finite-element modelling approach to reverse-engineer the electric organ signal over one oscillation cycle. We find that the spatiotemporal profile of current along the electric organ constitutes a travelling wave that is well-described by two spatial Fourier components varying in time. The conduction velocity of this wave is faster than action potential conduction in any known neuronal axon (>200 m/s), suggesting that the spatiotemporal features of high-frequency electric organ discharges are not constrained by the conduction velocities of spinal neuron pathways.

  19. Ultrafast traveling wave dominates the electric organ discharge of Apteronotus leptorhynchus: an inverse modelling study.

    PubMed

    Shifman, Aaron R; Longtin, André; Lewis, John E

    2015-01-01

    Identifying and understanding the current sources that give rise to bioelectric fields is a fundamental problem in the biological sciences. It is very difficult, for example, to attribute the time-varying features of an electroencephalogram recorded from the head surface to the neural activity of specific brain areas; model systems can provide important insight into such problems. Some species of fish actively generate an oscillating (c. 1000 Hz) quasi-dipole electric field to communicate and sense their environment in the dark. A specialized electric organ comprises neuron-like cells whose collective signal underlies this electric field. As a step towards understanding the detailed biophysics of signal generation in these fish, we use an anatomically-detailed finite-element modelling approach to reverse-engineer the electric organ signal over one oscillation cycle. We find that the spatiotemporal profile of current along the electric organ constitutes a travelling wave that is well-described by two spatial Fourier components varying in time. The conduction velocity of this wave is faster than action potential conduction in any known neuronal axon (>200 m/s), suggesting that the spatiotemporal features of high-frequency electric organ discharges are not constrained by the conduction velocities of spinal neuron pathways. PMID:26514932

  20. The response of selected terrestrial organisms to the Martian environment - A modeling study

    NASA Technical Reports Server (NTRS)

    Kuhn, W. R.; Rogers, S. R.; Macelroy, R. D.

    1979-01-01

    An energy balance model has been developed to investigate how the Martian atmospheric environment could influence a community of photosynthetic microorganisms with properties similar to those of a cyanophyte (blue-green algal mat) and a lichen. Surface moisture and soil nutrients are assumed to be available. The model was developed to approximate equatorial equinox conditions and includes parameters for solar and thermal radiation, convective and conductive energy transport, and evaporative cooling. Calculations include the diurnal variation of organism temperature and transpiration and photosynthetic rates. The influences of different wind speeds and organism size and resistivity are also studied. The temperature of organisms in mats less than a few millimeters thick will not differ from the ground temperature by more than 10 K. Water loss is actually retarded at higher wind speeds, since the organism temperature is lowered, thus reducing the saturation vapor pressure. Typical photosynthetic rates lead to the production of 1 millionth to 100 billionths mole O2 per sq cm/day.