Science.gov

Sample records for model organism podospora

  1. Identification of autophagy as a longevity-assurance mechanism in the aging model Podospora anserina

    PubMed Central

    Knuppertz, Laura; Hamann, Andrea; Pampaloni, Francesco; Stelzer, Ernst; Osiewacz, Heinz D

    2014-01-01

    The filamentous ascomycete Podospora anserina is a well-established aging model in which a variety of different pathways, including those involved in the control of respiration, ROS generation and scavenging, DNA maintenance, proteostasis, mitochondrial dynamics, and programmed cell death have previously been demonstrated to affect aging and life span. Here we address a potential role of autophagy. We provide data demonstrating high basal autophagy levels even in strains cultivated under noninduced conditions. By monitoring an N-terminal fusion of EGFP to the fungal LC3 homolog PaATG8 over the lifetime of the fungus on medium with and without nitrogen supplementation, respectively, we identified a significant increase of GFP puncta in older and in nitrogen-starved cultures suggesting an induction of autophagy during aging. This conclusion is supported by the demonstration of an age-related and autophagy-dependent degradation of a PaSOD1-GFP reporter protein. The deletion of Paatg1, which leads to the lack of the PaATG1 serine/threonine kinase active in early stages of autophagy induction, impairs ascospore germination and development and shortens life span. Under nitrogen-depleted conditions, life span of the wild type is increased almost 4-fold. In contrast, this effect is annihilated in the Paatg1 deletion strain, suggesting that the ability to induce autophagy is beneficial for this fungus. Collectively, our data identify autophagy as a longevity-assurance mechanism in P. anserina and as another surveillance pathway in the complex network of pathways affecting aging and development. These findings provide perspectives for the elucidation of the mechanisms involved in the regulation of individual pathways and their interactions. PMID:24584154

  2. Genetic control of anastomosis in Podospora anserina.

    PubMed

    Tong, Laetitia Chan Ho; Silar, Philippe; Lalucque, Hervé

    2014-09-01

    We developed a new microscopy procedure to study anastomoses in the model ascomycete Podospora anserina and compared it with the previous method involving the formation of balanced heterokaryons. Both methods showed a good correlation. Heterokaryon formation was less quantifiable, but enabled to observe very rare events. Microscopic analysis evidenced that anastomoses were greatly influence by growth conditions and were severely impaired in the IDC mutants of the PaMpk1, PaMpk2, IDC1 and PaNox1 pathways. Yet some mutants readily formed heterokaryons, albeit with a delay when compared to the wild type. We also identified IDC(821), a new mutant presenting a phenotype similar to the other IDC mutants, including lack of anastomosis. Complete genome sequencing revealed that IDC(821) was affected in the orthologue of the Neurospora crassa So gene known to control anastomosis in several other ascomycetes.

  3. 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.

  4. Manganese rescues adverse effects on lifespan and development in Podospora anserina challenged by excess hydrogen peroxide.

    PubMed

    Grimm, Carolin; Osiewacz, Heinz D

    2015-03-01

    For biological systems, balancing cellular levels of reactive oxygen species (ROS) is of great importance because ROS are both, essential for cellular signaling and dangerous in causing molecular damage. Cellular ROS abundance is controlled by a delicate network of molecular pathways. Within this network, superoxide dismutases (SODs) are active in disproportion of the superoxide anion leading to the formation of hydrogen peroxide. The fungal aging model Podospora anserina encodes at least three SODs. One of these is the mitochondrial PaSOD3 isoform containing manganese as a cofactor. Previous work resulted in the selection of strains in which PaSod3 is strongly overexpressed. These strains display impairments in growth and lifespan. A computational model suggests a series of events to occur in Sod3 overexpressing strains leading to adverse effects due to elevated hydrogen peroxide levels. In an attempt to validate this model and to obtain more detailed information about the cellular responses involved in ROS balancing, we further investigated the PaSod3 overexpressing strains. Here we show that hydrogen peroxide levels are indeed strongly increased in the mutant strain. Surprisingly, this phenotype can be rescued by the addition of manganese to the growth medium. Strikingly, while we obtained no evidence for an antioxidant effect of manganese, we found that the metal is required for induction of components of the ROS scavenging network and lowers the hydrogen peroxide level of the mutant. A similar effect of manganese on lifespan reversion was obtained in wild-type strains challenged with exogenous hydrogen peroxide. It appears that manganese is limited under high hydrogen peroxide and suggests that a manganese-dependent activity leads to the induction of ROS scavenging components.

  5. 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

  6. 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

  7. 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

  8. Genome-Wide Gene Expression Profiling of Fertilization Competent Mycelium in Opposite Mating Types in the Heterothallic Fungus Podospora anserina

    PubMed Central

    Coppin, Evelyne; Imbeaud, Sandrine; Grognet, Pierre; Delacroix, Hervé; Debuchy, Robert

    2011-01-01

    Background Mating-type loci in yeasts and ascomycotan filamentous fungi (Pezizomycotina) encode master transcriptional factors that play a critical role in sexual development. Genome-wide analyses of mating-type-specification circuits and mating-type target genes are available in Saccharomyces cerevisiae and Schizosaccharomyces pombe; however, no such analyses have been performed in heterothallic (self-incompatible) Pezizomycotina. The heterothallic fungus Podospora anserina serves as a model for understanding the basic features of mating-type control. Its mat+ and mat− mating types are determined by dissimilar allelic sequences. The mat− sequence contains three genes, designated FMR1, SMR1 and SMR2, while the mat+ sequence contains one gene, FPR1. FMR1 and FPR1 are the major regulators of fertilization, and this study presents a genome-wide view of their target genes and analyzes their target gene regulation. Methodology/Principal Findings The transcriptomic profiles of the mat+ and mat− strains revealed 157 differentially transcribed genes, and transcriptomic analysis of fmr1− and fpr1− mutant strains was used to determine the regulatory actions exerted by FMR1 and FPR1 on these differentially transcribed genes. All possible combinations of transcription repression and/or activation by FMR1 and/or FPR1 were observed. Furthermore, 10 additional mating-type target genes were identified that were up- or down-regulated to the same level in mat+ and mat− strains. Of the 167 genes identified, 32 genes were selected for deletion, which resulted in the identification of two genes essential for the sexual cycle. Interspecies comparisons of mating-type target genes revealed significant numbers of orthologous pairs, although transcriptional profiles were not conserved between species. Conclusions/Significance This study represents the first comprehensive genome-wide analysis of mating-type direct and indirect target genes in a heterothallic filamentous fungus

  9. 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.

  10. 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

  11. What makes a model organism?

    PubMed

    Leonelli, Sabina; Ankeny, Rachel A

    2013-12-01

    This article explains the key role of model organisms within contemporary research, while at the same time acknowledging their limitations as biological models. We analyse the epistemic and social characteristics of model organism biology as a form of "big science", which includes the development of large, centralised infrastructures, a shared ethos and a specific long-term vision about the "right way" to do research. In order to make wise use of existing resources, researchers now find themselves committed to carrying out this vision with its accompanying assumptions. By clarifying the specific characteristics of model organism work, we aim to provide a framework to assess how much funding should be allocated to such research. On the one hand, it is imperative to exploit the resources and knowledge accumulated using these models to study more diverse groups of organisms. On the other hand, this type of research may be inappropriate for research programmes where the processes of interest are much more delimited, can be usefully studied in isolation and/or are simply not captured by model organism biology.

  12. A Network of HMG-box Transcription Factors Regulates Sexual Cycle in the Fungus Podospora anserina

    PubMed Central

    Ait Benkhali, Jinane; Coppin, Evelyne; Brun, Sylvain; Peraza-Reyes, Leonardo; Martin, Tom; Dixelius, Christina; Lazar, Noureddine; van Tilbeurgh, Herman; Debuchy, Robert

    2013-01-01

    High-mobility group (HMG) B proteins are eukaryotic DNA-binding proteins characterized by the HMG-box functional motif. These transcription factors play a pivotal role in global genomic functions and in the control of genes involved in specific developmental or metabolic pathways. The filamentous ascomycete Podospora anserina contains 12 HMG-box genes. Of these, four have been previously characterized; three are mating-type genes that control fertilization and development of the fruit-body, whereas the last one encodes a factor involved in mitochondrial DNA stability. Systematic deletion analysis of the eight remaining uncharacterized HMG-box genes indicated that none were essential for viability, but that seven were involved in the sexual cycle. Two HMG-box genes display striking features. PaHMG5, an ortholog of SpSte11 from Schizosaccharomyces pombe, is a pivotal activator of mating-type genes in P. anserina, whereas PaHMG9 is a repressor of several phenomena specific to the stationary phase, most notably hyphal anastomoses. Transcriptional analyses of HMG-box genes in HMG-box deletion strains indicated that PaHMG5 is at the hub of a network of several HMG-box factors that regulate mating-type genes and mating-type target genes. Genetic analyses revealed that this network also controls fertility genes that are not regulated by mating-type transcription factors. This study points to the critical role of HMG-box members in sexual reproduction in fungi, as 11 out of 12 members were involved in the sexual cycle in P. anserina. PaHMG5 and SpSte11 are conserved transcriptional regulators of mating-type genes, although P. anserina and S. pombe diverged 550 million years ago. Two HMG-box genes, SOX9 and its upstream regulator SRY, also play an important role in sex determination in mammals. The P. anserina and S. pombe mating-type genes and their upstream regulatory factor form a module of HMG-box genes analogous to the SRY/SOX9 module, revealing a commonality of sex

  13. 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.

  14. 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

  15. 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

  16. 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

  17. 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

  18. Two NADPH oxidase isoforms are required for sexual reproduction and ascospore germination in the filamentous fungus Podospora anserina.

    PubMed

    Malagnac, Fabienne; Lalucque, Hervé; Lepère, Gersende; Silar, Philippe

    2004-11-01

    NADPH oxidases are enzymes that produce reactive oxygen species (ROS) using electrons derived from intracellular NADPH. In plants and mammals, ROS have been proposed to be second messengers that signal defence responses or cell proliferation. By inactivating PaNox1 and PaNox2, two genes encoding NADPH oxidases, we demonstrate the crucial role of these enzymes in the control of two key steps of the filamentous fungus Podospora anserina life cycle. PaNox1 mutants are impaired in the differentiation of fruiting bodies from their progenitor cells, and the deletion of the PaNox2 gene specifically blocks ascospore germination. Furthermore, we show that PaNox1 likely acts upstream of PaASK1, a MAPKKK previously implicated in stationary phase differentiation and cell degeneration. Using nitro blue tetrazolium (NBT) and diaminobenzidine (DAB) assays, we detect a regulated secretion of both superoxide and peroxide during P. anserina vegetative growth. In addition, two oxidative bursts are shown to occur during fruiting body development and ascospore germination. Analysis of mutants establishes that PaNox1, PaNox2, and PaASK1, as well as a still unknown additional source of ROS, modulate these secretions. Altogether, our data point toward a role for NADPH oxidases in signalling fungal developmental transitions with respect to nutrient availability. These enzymes are conserved in other multicellular eukaryotes, suggesting that early eukaryotes were endowed with a redox network used for signalling purposes.

  19. 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

  20. 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,…

  1. 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.

  2. Microporoelastic Modeling of Organic-Rich Shales

    NASA Astrophysics Data System (ADS)

    Khosh Sokhan Monfared, S.; Abedi, S.; Ulm, F. J.

    2014-12-01

    Organic-rich shale is an extremely complex, naturally occurring geo-composite. The heterogeneous nature of organic-rich shale and its anisotropic behavior pose grand challenges for characterization, modeling and engineering design The intricacy of organic-rich shale, in the context of its mechanical and poromechanical properties, originates in the presence of organic/inorganic constituents and their interfaces as well as the occurrence of porosity and elastic anisotropy, at multiple length scales. To capture the contributing mechanisms, of 1st order, responsible for organic-rich shale complex behavior, we introduce an original approach for micromechanical modeling of organic-rich shales which accounts for the effect of maturity of organics on the overall elasticity through morphology considerations. This morphology contribution is captured by means of an effective media theory that bridges the gap between immature and mature systems through the choice of system's microtexture; namely a matrix-inclusion morphology (Mori-Tanaka) for immature systems and a polycrystal/granular morphology for mature systems. Also, we show that interfaces play a role on the effective elasticity of mature, organic-rich shales. The models are calibrated by means of ultrasonic pulse velocity measurements of elastic properties and validated by means of nanoindentation results. Sensitivity analyses using Spearman's Partial Rank Correlation Coefficient shows the importance of porosity and Total Organic Carbon (TOC) as key input parameters for accurate model predictions. These modeling developments pave the way to reach a "unique" set of clay properties and highlight the importance of depositional environment, burial and diagenetic processes on overall mechanical and poromechanical behavior of organic-rich shale. These developments also emphasize the importance of understanding and modeling clay elasticity and organic maturity on the overall rock behavior which is of critical importance for a

  3. Primate Models in Organ Transplantation

    PubMed Central

    Anderson, Douglas J.; Kirk, Allan D.

    2013-01-01

    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

  4. 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.

  5. Cardiac electromechanical models: from cell to organ.

    PubMed

    Trayanova, Natalia A; Rice, John Jeremy

    2011-01-01

    The heart is a multiphysics and multiscale system that has driven the development of the most sophisticated mathematical models at the frontiers of computational physiology and medicine. This review focuses on electromechanical (EM) models of the heart from the molecular level of myofilaments to anatomical models of the organ. Because of the coupling in terms of function and emergent behaviors at each level of biological hierarchy, separation of behaviors at a given scale is difficult. Here, a separation is drawn at the cell level so that the first half addresses subcellular/single-cell models and the second half addresses organ models. At the subcellular level, myofilament models represent actin-myosin interaction and Ca-based activation. The discussion of specific models emphasizes the roles of cooperative mechanisms and sarcomere length dependence of contraction force, considered to be the cellular basis of the Frank-Starling law. A model of electrophysiology and Ca handling can be coupled to a myofilament model to produce an EM cell model, and representative examples are summarized to provide an overview of the progression of the field. The second half of the review covers organ-level models that require solution of the electrical component as a reaction-diffusion system and the mechanical component, in which active tension generated by the myocytes produces deformation of the organ as described by the equations of continuum mechanics. As outlined in the review, different organ-level models have chosen to use different ionic and myofilament models depending on the specific application; this choice has been largely dictated by compromises between model complexity and computational tractability. The review also addresses application areas of EM models such as cardiac resynchronization therapy and the role of mechano-electric coupling in arrhythmias and defibrillation.

  6. Cardiac Electromechanical Models: From Cell to Organ

    PubMed Central

    Trayanova, Natalia A.; Rice, John Jeremy

    2011-01-01

    The heart is a multiphysics and multiscale system that has driven the development of the most sophisticated mathematical models at the frontiers of computational physiology and medicine. This review focuses on electromechanical (EM) models of the heart from the molecular level of myofilaments to anatomical models of the organ. Because of the coupling in terms of function and emergent behaviors at each level of biological hierarchy, separation of behaviors at a given scale is difficult. Here, a separation is drawn at the cell level so that the first half addresses subcellular/single-cell models and the second half addresses organ models. At the subcellular level, myofilament models represent actin–myosin interaction and Ca-based activation. The discussion of specific models emphasizes the roles of cooperative mechanisms and sarcomere length dependence of contraction force, considered to be the cellular basis of the Frank–Starling law. A model of electrophysiology and Ca handling can be coupled to a myofilament model to produce an EM cell model, and representative examples are summarized to provide an overview of the progression of the field. The second half of the review covers organ-level models that require solution of the electrical component as a reaction–diffusion system and the mechanical component, in which active tension generated by the myocytes produces deformation of the organ as described by the equations of continuum mechanics. As outlined in the review, different organ-level models have chosen to use different ionic and myofilament models depending on the specific application; this choice has been largely dictated by compromises between model complexity and computational tractability. The review also addresses application areas of EM models such as cardiac resynchronization therapy and the role of mechano-electric coupling in arrhythmias and defibrillation. PMID:21886622

  7. 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.

  8. Condensing Organic Aerosols in a Microphysical Model

    NASA Astrophysics Data System (ADS)

    Gao, Y.; Tsigaridis, K.; Bauer, S.

    2015-12-01

    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.

  9. 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.

  10. 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…

  11. 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.

  12. 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

  13. Geometric modeling of pelvic organs with thickness

    NASA Astrophysics Data System (ADS)

    Bay, T.; Chen, Z.-W.; Raffin, R.; Daniel, M.; Joli, P.; Feng, Z.-Q.; Bellemare, M.-E.

    2012-03-01

    Physiological changes in the spatial configuration of the internal organs in the abdomen can induce different disorders that need surgery. Following the complexity of the surgical procedure, mechanical simulations are necessary but the in vivo factor makes complicate the study of pelvic organs. In order to determine a realistic behavior of these organs, an accurate geometric model associated with a physical modeling is therefore required. Our approach is integrated in the partnership between a geometric and physical module. The Geometric Modeling seeks to build a continuous geometric model: from a dataset of 3D points provided by a Segmentation step, surfaces are created through a B-spline fitting process. An energy function is built to measure the bidirectional distance between surface and data. This energy is minimized with an alternate iterative Hoschek-like method. A thickness is added with an offset formulation, and the geometric model is finally exported in a hexahedral mesh. Afterward, the Physical Modeling tries to calculate the properties of the soft tissues to simulate the organs displacements. The physical parameters attached to the data are determined with a feedback loop between finite-elements deformations and ground-truth acquisition (dynamic MRI).

  14. Polymer models of chromosome (re)organization

    NASA Astrophysics Data System (ADS)

    Mirny, Leonid

    Chromosome Conformation Capture technique (Hi-C) provides comprehensive information about frequencies of spatial interactions between genomic loci. Inferring 3D organization of chromosomes from these data is a challenging biophysical problem. We develop a top-down approach to biophysical modeling of chromosomes. Starting with a minimal set of biologically motivated interactions we build ensembles of polymer conformations that can reproduce major features observed in Hi-C experiments. I will present our work on modeling organization of human metaphase and interphase chromosomes. Our works suggests that active processes of loop extrusion can be a universal mechanism responsible for formation of domains in interphase and chromosome compaction in metaphase.

  15. 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.

  16. Chromatin fiber functional organization: Some plausible models

    NASA Astrophysics Data System (ADS)

    Lesne, A.; Victor, J.-M.

    2006-03-01

    We here present a modeling study of the chromatin fiber functional organization. Multi-scale modeling is required to unravel the complex interplay between the fiber and the DNA levels. It suggests plausible scenarios, including both physical and biological aspects, for fiber condensation, its targeted decompaction, and transcription regulation. We conclude that a major role of the chromatin fiber structure might be to endow DNA with allosteric potentialities and to control DNA transactions by an epigenetic tuning of its mechanical and topological constraints.

  17. Expanding on Successful Concepts, Models, and Organization

    EPA Science Inventory

    If the goal of the AEP framework was to replace existing exposure models or databases for organizing exposure data with a concept, we would share Dr. von Göetz concerns. Instead, the outcome we promote is broader use of an organizational framework for exposure science. The f...

  18. Modeling global organic aerosol formation and growth

    NASA Astrophysics Data System (ADS)

    Tsimpidi, Alexandra; Karydis, Vlasios; Pandis, Spyros; Lelieveld, Jos

    2014-05-01

    A computationally efficient framework for the description of organic aerosol (OA)-gas partitioning and chemical aging has been developed and implemented into the EMAC atmospheric chemistry-climate model. This model simulates the formation of primary (POA) and secondary organic aerosols (SOA) from semi-volatile (SVOC), intermediate-volatile (IVOC) and volatile organic compounds (VOC). POA are divided in two groups with saturation concentrations at 298 K 0.1, 10, 1000, 100000 µg m-3: OA from fossil fuel combustion and biomass burning. The first 2 surrogate species from each group represent the SVOC while the other surrogate species represent the IVOC. Photochemical reactions that change the volatility of the organics in the gas phase are taken into account. The oxidation products from each group of precursors (SVOC, IVOC, and VOC) are lumped into an additional set of oxidized surrogate species (S-SOA, I-SOA, and V-SOA, respectively) in order to track their source of origin. This model is used to i) estimate the relative contributions of SOA and POA to total OA, ii) determine how SOA concentrations are affected by biogenic and anthropogenic emissions, and iii) evaluate the effect of photochemical aging and long-range transport on OA budget over specific regions.

  19. Self-organized model of cascade spreading

    NASA Astrophysics Data System (ADS)

    Gualdi, S.; Medo, M.; Zhang, Y.-C.

    2011-01-01

    We study simultaneous price drops of real stocks and show that for high drop thresholds they follow a power-law distribution. To reproduce these collective downturns, we propose a minimal self-organized model of cascade spreading based on a probabilistic response of the system elements to stress conditions. This model is solvable using the theory of branching processes and the mean-field approximation. For a wide range of parameters, the system is in a critical state and displays a power-law cascade-size distribution similar to the empirically observed one. We further generalize the model to reproduce volatility clustering and other observed properties of real stocks.

  20. Theory and modeling of stereoselective organic reactions.

    PubMed

    Houk, K N; Paddon-Row, M N; Rondan, N G; Wu, Y D; Brown, F K; Spellmeyer, D C; Metz, J T; Li, Y; Loncharich, R J

    1986-03-07

    Theoretical investigations of the transition structures of additions and cycloadditions reveal details about the geometries of bond-forming processes that are not directly accessible by experiment. The conformational analysis of transition states has been developed from theoretical generalizations about the preferred angle of attack by reagents on multiple bonds and predictions of conformations with respect to partially formed bonds. Qualitative rules for the prediction of the stereochemistries of organic reactions have been devised, and semi-empirical computational models have also been developed to predict the stereoselectivities of reactions of large organic molecules, such as nucleophilic additions to carbonyls, electrophilic hydroborations and cycloadditions, and intramolecular radical additions and cycloadditions.

  1. 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

  2. Charophytes: Evolutionary Giants and Emerging Model Organisms

    PubMed Central

    Domozych, David S.; Popper, Zoë A.; Sørensen, Iben

    2016-01-01

    Charophytes are the group of green algae whose ancestral lineage gave rise to land plants in what resulted in a profoundly transformative event in the natural history of the planet. Extant charophytes exhibit many features that are similar to those found in land plants and their relatively simple phenotypes make them efficacious organisms for the study of many fundamental biological phenomena. Several taxa including Micrasterias, Penium, Chara, and Coleochaete are valuable model organisms for the study of cell biology, development, physiology and ecology of plants. New and rapidly expanding molecular studies are increasing the use of charophytes that in turn, will dramatically enhance our understanding of the evolution of plants and the adaptations that allowed for survival on land. The Frontiers in Plant Science series on “Charophytes” provides an assortment of new research reports and reviews on charophytes and their emerging significance as model plants. PMID:27777578

  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.

  4. Modeling Attrition in Organizations from Email Communication

    DTIC Science & Technology

    2013-09-08

    online multiplayer games , user involvement and movement in online social networking plat- forms, and employee turnover within an organization. At... online games . The same problem of reducing churn rates appears in the scenario of social networking platforms. In recent years there has been a...ABSTRACT 16. SECURITY CLASSIFICATION OF: Modeling people’s online behavior in relation to their real-world social context is an interesting and important

  5. 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.

  6. Theory and modeling of stereoselective organic reactions

    SciTech Connect

    Houk, K.N.; Paddon-Row, M.N.; Rondan, N.G.; Wu, Y.D.; Brown, F.K.; Spellmeyer, D.C.; Metz, J.T.; Li, Y.; Loncharich, R.J.

    1986-03-07

    Theoretical investigations of the transition structures of additions and cycloadditions reveal details about the geometrics of bond-forming processes that are not directly accessible by experiment. The conformational analysis of transition states has been developed from theoretical generalizations about the preferred angle of attack by reagents on multiple bonds and predictions of conformations with respect to partially formed bonds. Qualitative rules for the prediction of the stereochemistries of organic reactions have been devised, and semi-empirical computational models have also been developed to predict the stereoselectivities of reactions of large organic molecules, such as nucleophilic additions to carbonyls, electrophilic hydroborations and cycloadditions, and intramolecular radical additions and cycloadditions. 52 references, 7 figures.

  7. Making designer mutants in model organisms.

    PubMed

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

    2014-11-01

    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.

  8. Expanding on Successful Concepts, Models, and Organization

    SciTech Connect

    Teeguarden, Justin G.; Tan, Yu-Mei; Edwards, Stephen W.; Leonard, Jeremy A.; Anderson, Kim A.; Corley, Richard A.; Kile, Molly L.; L. Massey Simonich, Staci; Stone, David; Tanguay, Robert L.; Waters, Katrina M.; Harper, Stacey L.; Williams, David E.

    2016-09-06

    In her letter to the editor1 regarding our recent Feature Article “Completing the Link between Exposure Science and Toxicology for Improved Environmental Health Decision Making: The Aggregate Exposure Pathway Framework” 2, Dr. von Göetz expressed several concerns about terminology, and the perception that we propose the replacement of successful approaches and models for exposure assessment with a concept. We are glad to have the opportunity to address these issues here. If the goal of the AEP framework was to replace existing exposure models or databases for organizing exposure data with a concept, we would share Dr. von Göetz concerns. Instead, the outcome we promote is broader use of an organizational framework for exposure science. The framework would support improved generation, organization, and interpretation of data as well as modeling and prediction, not replacement of models. The field of toxicology has seen the benefits of wide use of one or more organizational frameworks (e.g., mode and mechanism of action, adverse outcome pathway). These frameworks influence how experiments are designed, data are collected, curated, stored and interpreted and ultimately how data are used in risk assessment. Exposure science is poised to similarly benefit from broader use of a parallel organizational framework, which Dr. von Göetz correctly points out, is currently used in the exposure modeling community. In our view, the concepts used so effectively in the exposure modeling community, expanded upon in the AEP framework, could see wider adoption by the field as a whole. The value of such a framework was recognized by the National Academy of Sciences.3 Replacement of models, databases, or any application with the AEP framework was not proposed in our article. The positive role broader more consistent use of such a framework might have in enabling and advancing “general activities such as data acquisition, organization…,” and exposure modeling was discussed

  9. Modeling disordered morphologies in organic semiconductors.

    PubMed

    Neumann, Tobias; Danilov, Denis; Lennartz, Christian; Wenzel, Wolfgang

    2013-12-05

    Organic thin film devices are investigated for many diverse applications, including light emitting diodes, organic photovoltaic and organic field effect transistors. Modeling of their properties on the basis of their detailed molecular structure requires generation of representative morphologies, many of which are amorphous. Because time-scales for the formation of the molecular structure are slow, we have developed a linear-scaling single molecule deposition protocol which generates morphologies by simulation of vapor deposition of molecular films. We have applied this protocol to systems comprising argon, buckminsterfullerene, N,N-Di(naphthalene-1-yl)-N,N'-diphenyl-benzidine, mer-tris(8-hydroxy-quinoline)aluminum(III), and phenyl-C61-butyric acid methyl ester, with and without postdeposition relaxation of the individually deposited molecules. The proposed single molecule deposition protocol leads to formation of highly ordered morphologies in argon and buckminsterfullerene systems when postdeposition relaxation is used to locally anneal the configuration in the vicinity of the newly deposited molecule. The other systems formed disordered amorphous morphologies and the postdeposition local relaxation step has only a small effect on the characteristics of the disordered morphology in comparison to the materials forming crystals.

  10. 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

  11. 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

  12. 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

  13. 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.

  14. 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.

  15. 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

  16. 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

    2016-02-15

    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.

  17. 3D Bioprinting of Tissue/Organ Models.

    PubMed

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

    2016-04-04

    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.

  18. A Topological Model for C2 Organizations

    DTIC Science & Technology

    2011-06-01

    functions of the organization, and the capabilities of its members, as these sets somehow efine the boundaries of organizational performance and the...and functions of the organization, and the capabilities of its members, as these sets somehow efine the boundaries of organizational performance and

  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 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…

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. Sphere-filled organ model for virtual surgery system.

    PubMed

    Suzuki, Shigeyuki; Suzuki, Naoki; Hattori, Asaki; Uchiyama, Akihiko; Kobayashi, Susumu

    2004-06-01

    We have been developing a virtual surgery system that is capable of simulating surgical maneuvers on elastic organs. In order to perform such maneuvers, we have created a deformable organ model using a sphere-filled method instead of the finite element method. This model is suited for real-time simulation and quantitative deformation. Furthermore, we have equipped this model with a sense of touch and a sense of force by connecting it to a force feedback device. However, in the initial stage the model became problematic when faced with complicated incisions. Therefore, we modified this model by developing an algorithm for organ deformation that performs various, complicated incisions while taking into account the effect of gravity. As a result, the sphere-filled model allowed our system to respond to various incisions that deform the organ. Thus, various physical manipulations that involve pressing, pinching, or incising an organ's surface can be performed. Furthermore, the deformation of the internal organ structures and changes in organ vasculature can be observed via the internal spheres' behavior.

  6. 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.

  7. 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…

  8. 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.

  9. 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.…

  10. 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...

  11. Animal models of female pelvic organ prolapse: lessons learned

    PubMed Central

    Couri, Bruna M; Lenis, Andrew T; Borazjani, Ali; Paraiso, Marie Fidela R; Damaser, Margot S

    2012-01-01

    Pelvic organ prolapse is a vaginal protrusion of female pelvic organs. It has high prevalence worldwide and represents a great burden to the economy. The pathophysiology of pelvic organ prolapse is multifactorial and includes genetic predisposition, aberrant connective tissue, obesity, advancing age, vaginal delivery and other risk factors. Owing to the long course prior to patients becoming symptomatic and ethical questions surrounding human studies, animal models are necessary and useful. These models can mimic different human characteristics – histological, anatomical or hormonal, but none present all of the characteristics at the same time. Major animal models include knockout mice, rats, sheep, rabbits and nonhuman primates. In this article we discuss different animal models and their utility for investigating the natural progression of pelvic organ prolapse pathophysiology and novel treatment approaches. PMID:22707980

  12. Self-organizing map models of language acquisition

    PubMed Central

    Li, Ping; Zhao, Xiaowei

    2013-01-01

    Connectionist models have had a profound impact on theories of language. While most early models were inspired by the classic parallel distributed processing architecture, recent models of language have explored various other types of models, including self-organizing models for language acquisition. In this paper, we aim at providing a review of the latter type of models, and highlight a number of simulation experiments that we have conducted based on these models. We show that self-organizing connectionist models can provide significant insights into long-standing debates in both monolingual and bilingual language development. We suggest future directions in which these models can be extended, to better connect with behavioral and neural data, and to make clear predictions in testing relevant psycholinguistic theories. PMID:24312061

  13. Influence of dissolved organic carbon content on modelling natural organic matter acid-base properties.

    PubMed

    Garnier, Cédric; Mounier, Stéphane; Benaïm, Jean Yves

    2004-10-01

    Natural organic matter (NOM) behaviour towards proton is an important parameter to understand NOM fate in the environment. Moreover, it is necessary to determine NOM acid-base properties before investigating trace metals complexation by natural organic matter. This work focuses on the possibility to determine these acid-base properties by accurate and simple titrations, even at low organic matter concentrations. So, the experiments were conducted on concentrated and diluted solutions of extracted humic and fulvic acid from Laurentian River, on concentrated and diluted model solutions of well-known simple molecules (acetic and phenolic acids), and on natural samples from the Seine river (France) which are not pre-concentrated. Titration experiments were modelled by a 6 acidic-sites discrete model, except for the model solutions. The modelling software used, called PROSECE (Programme d'Optimisation et de SpEciation Chimique dans l'Environnement), has been developed in our laboratory, is based on the mass balance equilibrium resolution. The results obtained on extracted organic matter and model solutions point out a threshold value for a confident determination of the studied organic matter acid-base properties. They also show an aberrant decreasing carboxylic/phenolic ratio with increasing sample dilution. This shift is neither due to any conformational effect, since it is also observed on model solutions, nor to ionic strength variations which is controlled during all experiments. On the other hand, it could be the result of an electrode troubleshooting occurring at basic pH values, which effect is amplified at low total concentration of acidic sites. So, in our conditions, the limit for a correct modelling of NOM acid-base properties is defined as 0.04 meq of total analysed acidic sites concentration. As for the analysed natural samples, due to their high acidic sites content, it is possible to model their behaviour despite the low organic carbon concentration.

  14. Predicting long-term organic carbon dynamics in organically-amended soils using the CQESTR model

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A process-based soil C model “CQESTR” was developed to simulate soil organic carbon (SOC) dynamics. The model has been validated successfully for North America, but needs to be tested in other geographic areas. We evaluated the predictive performance of CQESTR in a long-term (34-yr) SOC-depleted Eur...

  15. Drosophila melanogaster as a model organism to study nanotoxicity.

    PubMed

    Ong, Cynthia; Yung, Lin-Yue Lanry; Cai, Yu; Bay, Boon-Huat; Baeg, Gyeong-Hun

    2015-05-01

    Drosophila melanogaster has been used as an in vivo model organism for the study of genetics and development since 100 years ago. Recently, the fruit fly Drosophila was also developed as an in vivo model organism for toxicology studies, in particular, the field of nanotoxicity. The incorporation of nanomaterials into consumer and biomedical products is a cause for concern as nanomaterials are often associated with toxicity in many in vitro studies. In vivo animal studies of the toxicity of nanomaterials with rodents and other mammals are, however, limited due to high operational cost and ethical objections. Hence, Drosophila, a genetically tractable organism with distinct developmental stages and short life cycle, serves as an ideal organism to study nanomaterial-mediated toxicity. This review discusses the basic biology of Drosophila, the toxicity of nanomaterials, as well as how the Drosophila model can be used to study the toxicity of various types of nanomaterials.

  16. Cyberkelp: an integrative approach to the modelling of flexible organisms.

    PubMed Central

    Denny, Mark W; Hale, Ben B

    2003-01-01

    Biomechanical models come in a variety of forms: conceptual models; physical models; and mathematical models (both of the sort written down on paper and the sort carried out on computers). There are model structures (such as insect flight muscle and the tendons of rats' tails), model organisms (such as the flying insect, Manduca sexta), even model systems of organisms (such as the communities that live on wave-swept rocky shores). These different types of models are typically employed separately, but their value often can be enhanced if their insights are integrated. In this brief report we explore a particular example of such integration among models, as applied to flexible marine algae. A conceptual model serves as a template for the construction of a mathematical model of a model species of giant kelp, and the validity of this numerical model is tested using physical models. The validated mathematical model is then used in conjunction with a computer-controlled tensile testing apparatus to simulate the loading regime placed on algal materials. The resulting information can be used to create a more precise mathematical model. PMID:14561344

  17. 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...

  18. 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

  19. 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.

  20. 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.

  1. 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…

  2. 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.

  3. Simple model of self-organized biological evolution

    NASA Astrophysics Data System (ADS)

    de Boer, Jan; Derrida, Bernard; Flyvbjerg, Henrik; Jackson, Andrew D.; Wettig, Tilo

    1994-08-01

    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.

  4. 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.

  5. Xanthusbase: adapting wikipedia principles to a model organism database.

    PubMed

    Arshinoff, Bradley I; Suen, Garret; Just, Eric M; Merchant, Sohel M; Kibbe, Warren A; Chisholm, Rex L; Welch, Roy D

    2007-01-01

    xanthusBase (http://www.xanthusbase.org) is the official model organism database (MOD) for the social bacterium Myxococcus xanthus. In many respects, M.xanthus represents the pioneer model organism (MO) for studying the genetic, biochemical, and mechanistic basis of prokaryotic multicellularity, a topic that has garnered considerable attention due to the significance of biofilms in both basic and applied microbiology research. To facilitate its utility, the design of xanthusBase incorporates open-source software, leveraging the cumulative experience made available through the Generic Model Organism Database (GMOD) project, MediaWiki (http://www.mediawiki.org), and dictyBase (http://www.dictybase.org), to create a MOD that is both highly useful and easily navigable. In addition, we have incorporated a unique Wikipedia-style curation model which exploits the internet's inherent interactivity, thus enabling M.xanthus and other myxobacterial researchers to contribute directly toward the ongoing genome annotation.

  6. The expanding epigenetic landscape of non-model organisms.

    PubMed

    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.

  7. 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

  8. dictyBase, the model organism database for Dictyostelium discoideum.

    PubMed

    Chisholm, Rex L; Gaudet, Pascale; Just, Eric M; Pilcher, Karen E; Fey, Petra; Merchant, Sohel N; Kibbe, Warren A

    2006-01-01

    dictyBase (http://dictybase.org) is the model organism database (MOD) for the social amoeba Dictyostelium discoideum. The unique biology and phylogenetic position of Dictyostelium offer a great opportunity to gain knowledge of processes not characterized in other organisms. The recent completion of the 34 MB genome sequence, together with the sizable scientific literature using Dictyostelium as a research organism, provided the necessary tools to create a well-annotated genome. dictyBase has leveraged software developed by the Saccharomyces Genome Database and the Generic Model Organism Database project. This has reduced the time required to develop a full-featured MOD and greatly facilitated our ability to focus on annotation and providing new functionality. We hope that manual curation of the Dictyostelium genome will facilitate the annotation of other genomes.

  9. Quantitative model studies for interfaces in organic electronic devices

    NASA Astrophysics Data System (ADS)

    Gottfried, J. Michael

    2016-11-01

    In organic light-emitting diodes and similar devices, organic semiconductors are typically contacted by metal electrodes. Because the resulting metal/organic interfaces have a large impact on the performance of these devices, their quantitative understanding is indispensable for the further rational development of organic electronics. A study by Kröger et al (2016 New J. Phys. 18 113022) of an important single-crystal based model interface provides detailed insight into its geometric and electronic structure and delivers valuable benchmark data for computational studies. In view of the differences between typical surface-science model systems and real devices, a ‘materials gap’ is identified that needs to be addressed by future research to make the knowledge obtained from fundamental studies even more beneficial for real-world applications.

  10. 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

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

    MedlinePlus

    ... good understanding of biological complexity, in which many molecular networks operate in synchrony inside our bodies. Researchers ... organisms can also help reveal changes at the molecular level that are associated with diseases and identify ...

  12. 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.

  13. 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.

  14. Considerations when choosing a genetic model organism for metabolomics studies.

    PubMed

    Reed, Laura K; Baer, Charles F; Edison, Arthur S

    2017-02-01

    Model organisms are important in many areas of chemical biology. In metabolomics, model organisms can provide excellent samples for methods development as well as the foundation of comparative phylometabolomics, which will become possible as metabolomics applications expand. Comparative studies of conserved and unique metabolic pathways will help in the annotation of metabolites as well as provide important new targets of investigation in biology and biomedicine. However, most chemical biologists are not familiar with genetics, which needs to be considered when choosing a model organism. In this review we summarize the strengths and weaknesses of several genetic systems, including natural isolates, recombinant inbred lines, and genetic mutations. We also discuss methods to detect targets of selection on the metabolome.

  15. Modelling the fate of oxidisable organic contaminants in groundwater

    NASA Astrophysics Data System (ADS)

    Barry, D. A.; Prommer, H.; Miller, C. T.; Engesgaard, P.; Brun, A.; Zheng, C.

    Subsurface contamination by organic chemicals is a pervasive environmental problem, susceptible to remediation by natural or enhanced attenuation approaches or more highly engineered methods such as pump-and-treat, amongst others. Such remediation approaches, along with risk assessment or the pressing need to address complex scientific questions, have driven the development of integrated modelling tools that incorporate physical, biological and geochemical processes. We provide a comprehensive modelling framework, including geochemical reactions and interphase mass transfer processes such as sorption/desorption, non-aqueous phase liquid dissolution and mineral precipitatation/dissolution, all of which can be in equilibrium or kinetically controlled. This framework is used to simulate microbially mediated transformation/degradation processes and the attendant microbial population growth and decay. Solution algorithms, particularly the split-operator (SO) approach, are described, along with a brief résumé of numerical solution methods. Some of the available numerical models are described, mainly those constructed using available flow, transport and geochemical reaction packages. The general modelling framework is illustrated by pertinent examples, showing the degradation of dissolved organics by microbial activity limited by the availability of nutrients or electron acceptors (i.e., changing redox states), as well as concomitant secondary reactions. Two field-scale modelling examples are discussed, the Vejen landfill (Denmark) and an example where metal contamination is remediated by redox changes wrought by injection of a dissolved organic compound. A summary is provided of current and likely future challenges to modelling of oxidisable organics in the subsurface.

  16. Surface complexation modeling or organic acid sorption to goethite

    SciTech Connect

    Evanko, C.R.; Dzombak, D.A.

    1999-06-15

    Surface complexation modeling was performed using the Generalized Two-Layer Model for a series of low molecular weight organic acids. Sorption of these organic acids to goethite was investigated in a previous study to assess the influence of particular structural features on sorption. Here, the ability to describe the observed sorption behavior for compounds with similar structural features using surface complexation modeling was investigated. A set of surface reactions and equilibrium constants yielding optimal data fits was obtained for each organic acid over a range of total sorbate concentrations. Surface complexation modeling successfully described sorption of a number of the simple organic acids, but an additional hydrophobic component was needed to describe sorption behavior of some compounds with significant hydrophobic character. These compounds exhibited sorption behavior of some compounds with significant hydrophobic character. These compounds exhibited sorption behavior that was inconsistent with ligand exchange mechanisms since sorption behavior of some compounds with significant hydrophobic character. These compounds exhibited sorption behavior that was inconsistent with ligand exchange mechanisms since sorption did not decrease with increasing total sorbate concentration and/or exceeded surface site saturation. Hydrophobic interactions appeared to be most significant for the compound containing a 5-carbon aliphatic chain. Comparison of optimized equilibrium constants for similar surface species showed that model results were consistent with observed sorption behavior: equilibrium constants were highest for compounds having adjacent carboxylic groups, lower for compounds with adjacent phenolic groups, and lowest for compounds with phenolic groups in the ortho position relative to a carboxylic group. Surface complexation modeling was also performed to fit sorption data for Suwannee River fulvic acid. The data could be described well using reactions and

  17. Surface Complexation Modeling of Organic Acid Sorption to Goethite.

    PubMed

    Evanko; Dzombak

    1999-06-15

    Surface complexation modeling was performed using the Generalized Two-Layer Model for a series of low molecular weight organic acids. Sorption of these organic acids to goethite was investigated in a previous study to assess the influence of particular structural features on sorption. Here, the ability to describe the observed sorption behavior for compounds with similar structural features using surface complexation modeling was investigated. A set of surface reactions and equilibrium constants yielding optimal data fits was obtained for each organic acid over a range of total sorbate concentrations. Surface complexation modeling successfully described sorption of a number of the simple organic acids, but an additional hydrophobic component was needed to describe sorption behavior of some compounds with significant hydrophobic character. These compounds exhibited sorption behavior that was inconsistent with ligand exchange mechanisms since sorption did not decrease with increasing total sorbate concentration and/or exceeded surface site saturation. Hydrophobic interactions appeared to be most significant for the compound containing a 5-carbon aliphatic chain. Comparison of optimized equilibrium constants for similar surface species showed that model results were consistent with observed sorption behavior: equilibrium constants were highest for compounds having adjacent carboxylic groups, lower for compounds with adjacent phenolic groups, and lowest for compounds with phenolic groups in the ortho position relative to a carboxylic group. Surface complexation modeling was also performed to fit sorption data for Suwannee River fulvic acid. The data could be described well using reactions and constants similar to those for pyromellitic acid. This four-carboxyl group compound may be useful as a model for fulvic acid with respect to sorption. Other simple organic acids having multiple carboxylic and phenolic functional groups were identified as potential models for humic

  18. Modeling of Spatially Correlated Energetic Disorder in Organic Semiconductors.

    PubMed

    Kordt, Pascal; Andrienko, Denis

    2016-01-12

    Mesoscale modeling of organic semiconductors relies on solving an appropriately parametrized master equation. Essential ingredients of the parametrization are site energies (driving forces), which enter the charge transfer rate between pairs of neighboring molecules. Site energies are often Gaussian-distributed and are spatially correlated. Here, we propose an algorithm that generates these energies with a given Gaussian distribution and spatial correlation function. The method is tested on an amorphous organic semiconductor, DPBIC, illustrating that the accurate description of correlations is essential for the quantitative modeling of charge transport in amorphous mesophases.

  19. Modelling and design of all-organic electromechanic transducers

    NASA Astrophysics Data System (ADS)

    Fortuna, L.; Graziani, S.; La Rosa, M.; Nicolosi, D.; Sicurella, G.; Umana, E.

    2009-04-01

    The recent development of innovative organic materials with intriguing features such as their flexibility, lightness, low cost and easy manufacturability, has driven researchers to develop innovative smart applications based on such kind of materials. In this work, all-organic electromechanical transducers, with both sensing and acting capabilities are proposed. The actuator and sensor models have been identified by using a grey box approach, as a function of membrane geometric parameters. The obtained models have been validated through comparison among estimated and experimental data.

  20. Workshop meeting report Organs-on-Chips: human disease models.

    PubMed

    van de Stolpe, Anja; den Toonder, Jaap

    2013-09-21

    The concept of "Organs-on-Chips" has recently evolved and has been described as 3D (mini-) organs or tissues consisting of multiple and different cell types interacting with each other under closely controlled conditions, grown in a microfluidic chip, and mimicking the complex structures and cellular interactions in and between different cell types and organs in vivo, enabling the real time monitoring of cellular processes. In combination with the emerging iPSC (induced pluripotent stem cell) field this development offers unprecedented opportunities to develop human in vitro models for healthy and diseased organ tissues, enabling the investigation of fundamental mechanisms in disease development, drug toxicity screening, drug target discovery and drug development, and the replacement of animal testing. Capturing the genetic background of the iPSC donor in the organ or disease model carries the promise to move towards "in vitro clinical trials", reducing costs for drug development and furthering the concept of personalized medicine and companion diagnostics. During the Lorentz workshop (Leiden, September 2012) an international multidisciplinary group of experts discussed the current state of the art, available and emerging technologies, applications and how to proceed in the field. Organ-on-a-chip platform technologies are expected to revolutionize cell biology in general and drug development in particular.

  1. 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.

  2. 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.

  3. Quantitative proteomics by metabolic labeling of model organisms.

    PubMed

    Gouw, Joost W; Krijgsveld, Jeroen; Heck, Albert J R

    2010-01-01

    In the biological sciences, model organisms have been used for many decades and have enabled the gathering of a large proportion of our present day knowledge of basic biological processes and their derailments in disease. Although in many of these studies using model organisms, the focus has primarily been on genetics and genomics approaches, it is important that methods become available to extend this to the relevant protein level. Mass spectrometry-based proteomics is increasingly becoming the standard to comprehensively analyze proteomes. An important transition has been made recently by moving from charting static proteomes to monitoring their dynamics by simultaneously quantifying multiple proteins obtained from differently treated samples. Especially the labeling with stable isotopes has proved an effective means to accurately determine differential expression levels of proteins. Among these, metabolic incorporation of stable isotopes in vivo in whole organisms is one of the favored strategies. In this perspective, we will focus on methodologies to stable isotope label a variety of model organisms in vivo, ranging from relatively simple organisms such as bacteria and yeast to Caenorhabditis elegans, Drosophila, and Arabidopsis up to mammals such as rats and mice. We also summarize how this has opened up ways to investigate biological processes at the protein level in health and disease, revealing conservation and variation across the evolutionary tree of life.

  4. Implementing Marine Organic Aerosols Into the GEOS-Chem Model

    NASA Technical Reports Server (NTRS)

    Johnson, Matthew S.

    2015-01-01

    Marine-sourced 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 under-prediction 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.

  5. 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.

  6. GENERAL: Self-organized Criticality Model for Ocean Internal Waves

    NASA Astrophysics Data System (ADS)

    Wang, Gang; Lin, Min; Qiao, Fang-Li; Hou, Yi-Jun

    2009-03-01

    In this paper, we present a simple spring-block model for ocean internal waves based on the self-organized criticality (SOC). The oscillations of the water blocks in the model display power-law behavior with an exponent of -2 in the frequency domain, which is similar to the current and sea water temperature spectra in the actual ocean and the universal Garrett and Munk deep ocean internal wave model [Geophysical Fluid Dynamics 2 (1972) 225; J. Geophys. Res. 80 (1975) 291]. The influence of the ratio of the driving force to the spring coefficient to SOC behaviors in the model is also discussed.

  7. 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...

  8. Green Algae as Model Organisms for Biological Fluid Dynamics.

    PubMed

    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.

  9. 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.

  10. 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

  11. There Is No Simple Model of the Plasma Membrane Organization

    PubMed Central

    Bernardino de la Serna, Jorge; Schütz, Gerhard J.; Eggeling, Christian; Cebecauer, Marek

    2016-01-01

    Ever since technologies enabled the characterization of eukaryotic plasma membranes, heterogeneities in the distributions of its constituents were observed. Over the years this led to the proposal of various models describing the plasma membrane organization such as lipid shells, picket-and-fences, lipid rafts, or protein islands, as addressed in numerous publications and reviews. Instead of emphasizing on one model we in this review give a brief overview over current models and highlight how current experimental work in one or the other way do not support the existence of a single overarching model. Instead, we highlight the vast variety of membrane properties and components, their influences and impacts. We believe that highlighting such controversial discoveries will stimulate unbiased research on plasma membrane organization and functionality, leading to a better understanding of this essential cellular structure. PMID:27747212

  12. 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.

  13. 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.

  14. 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.

  15. A two-site bipolaron model for organic magnetoresistance

    NASA Astrophysics Data System (ADS)

    Wagemans, W.; Bloom, F. L.; Bobbert, P. A.; Wohlgenannt, M.; Koopmans, B.

    2008-04-01

    The recently proposed bipolaron model for large "organic magnetoresistance" (OMAR) at room temperature is extended to an analytically solvable two-site scheme. It is shown that even this extremely simplified approach reproduces some of the key features of OMAR, viz., the possibility to have both positive and negative magnetoresistance, as well as its universal line shapes. Specific behavior and limiting cases are discussed. Extensions of the model, to guide future experiments and numerical Monte Carlo studies, are suggested.

  16. 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…

  17. 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…

  18. Promoting Representational Competence with Molecular Models in Organic Chemistry

    ERIC Educational Resources Information Center

    Stull, Andrew T.; Gainer, Morgan; Padalkar, Shamin; Hegarty, Mary

    2016-01-01

    Mastering the many different diagrammatic representations of molecules used in organic chemistry is challenging for students. This article summarizes recent research showing that manipulating 3-D molecular models can facilitate the understanding and use of these representations. Results indicate that students are more successful in translating…

  19. 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...

  20. Analytical modeling of organic solar cells and photodiodes

    NASA Astrophysics Data System (ADS)

    Altazin, S.; Clerc, R.; Gwoziecki, R.; Pananakakis, G.; Ghibaudo, G.; Serbutoviez, C.

    2011-10-01

    An analytical and physically based expression of organic solar cell I-V characteristic under dark and illuminated conditions has been derived. This model has been found in very good agreement with both experimental data and drift-diffusion numerical simulations accounting for the coupling with Poisson equation and optical propagation.

  1. Waste Reduction Model (WARM) Resources for Small Businesses and Organizations

    EPA Pesticide Factsheets

    This page provides a brief overview of how EPA’s Waste Reduction Model (WARM) can be used by small businesses and organizations. The page includes a brief summary of uses of WARM for the audience and links to other resources.

  2. 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.

  3. 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.

  4. 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

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

    DOE PAGES

    Gantt, B.; Johnson, M. S.; Crippa, M.; ...

    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

  6. The Power of Natural Variation for Model Organism Biology.

    PubMed

    Gasch, Audrey P; Payseur, Bret A; Pool, John E

    2016-03-01

    Genetic background effects have long been recognized and, in some cases studied, but they are often viewed as a nuisance by molecular biologists. We suggest that genetic variation currently represents a critical frontier for molecular studies. Human genetics has seen a surge of interest in genetic variation and its contributions to disease, but insights into disease mechanisms are difficult since information about gene function is lacking. By contrast, model organism genetics has excelled at revealing molecular mechanisms of cellular processes, but often de-emphasizes genetic variation and its functional consequences. We argue that model organism biology would benefit from incorporating natural variation, both to capture how well laboratory lines exemplify the species they represent and to inform on molecular processes and their variability. Such a synthesis would also greatly expand the relevance of model systems for studies of complex trait variation, including disease.

  7. Self-organizing model of motor cortical activities during drawing

    NASA Astrophysics Data System (ADS)

    Lin, Siming H.; Si, Jennie; Schwartz, Andrew B.

    1996-05-01

    The population vector algorithm has been developed to combine the simultaneous direction- related activities of a population of motor cortical neurons to predict the trajectory of the arm movement. In our study, we consider a self-organizing model of a neural representation of the arm trajectory based on neuronal discharge rates. Self-organizing feature mapping (SOFM) is used to select the optimal set of weights in the model to determine the contribution of individual neuron to the overall movement. The correspondence between the movement directions and the discharge patterns of the motor cortical neurons is established in the output map. The topology preserving property of the SOFM is used to analyze real recorded data of a behavior monkey. The data used in this analysis were taken while the monkey was drawing spirals and doing the center out movement. Using such a statistical model, the monkey's arm moving directions could be well predicted based on the motor cortex neuronal firing information.

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

    PubMed Central

    Elliott, Stephen J.; Baumgart, Johannes

    2016-01-01

    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

  9. 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

  10. Structure and Dynamics of a Model Discotic Organic Conducting Material

    NASA Astrophysics Data System (ADS)

    Zbiri, Mohamed; Haverkate, Lucas A.; Kearley, Gordon J.; Johnson, Mark R.; Mulder, Fokko M.

    2016-10-01

    Organic conducting materials exhibit promising functionalities, inducing hence a keen interest due to their potential use as a next generation photoconverters. However, unlike the more expensive inorganic analogues, the underlying properties that give rise to these advantages also cause organic materials to be inherently inefficient as photovoltaics. Understanding their properties at the microscopic level is a major step towards an efficient and targeted design. We probed the morphological and dynamical aspects of a model organic discotic liquid crystal material hexakis(n-hexyloxy)triphenylene (HAT6) by using neutron-based diffraction and quasielastic scattering techniques to gain deeper insights into structure and dynamics. The neutron measurements are accompanied, in a synergistic way, by molecular dynamics simulations for the sake of the analysis and interpretation of the observations

  11. Computational models of molecular self-organization in cellular environments.

    PubMed

    LeDuc, Philip; Schwartz, Russell

    2007-01-01

    The cellular environment creates numerous obstacles to efficient chemistry, as molecular components must navigate through a complex, densely crowded, heterogeneous, and constantly changing landscape in order to function at the appropriate times and places. Such obstacles are especially challenging to self-organizing or self-assembling molecular systems, which often need to build large structures in confined environments and typically have high-order kinetics that should make them exquisitely sensitive to concentration gradients, stochastic noise, and other non-ideal reaction conditions. Yet cells nonetheless manage to maintain a finely tuned network of countless molecular assemblies constantly forming and dissolving with a robustness and efficiency generally beyond what human engineers currently can achieve under even carefully controlled conditions. Significant advances in high-throughput biochemistry and genetics have made it possible to identify many of the components and interactions of this network, but its scale and complexity will likely make it impossible to understand at a global, systems level without predictive computational models. It is thus necessary to develop a clear understanding of how the reality of cellular biochemistry differs from the ideal models classically assumed by simulation approaches and how simulation methods can be adapted to accurately reflect biochemistry in the cell, particularly for the self-organizing systems that are most sensitive to these factors. In this review, we present approaches that have been undertaken from the modeling perspective to address various ways in which self-organization in the cell differs from idealized models.

  12. QSPR Modeling of Bioconcentration Factors of Nonionic Organic Compounds

    PubMed Central

    Deeb, Omar; Khadikar, Padmakar V.; Goodarzi, Mohammad

    2010-01-01

    The terms bioaccumulation and bioconcentration refer to the uptake and build-up of chemicals that can occur in living organisms. Experimental measurement of bioconcentration is time-consuming and expensive, and is not feasible for a large number of chemicals of potential regulatory concern. A highly effective tool depending on a quantitative structure-property relationship (QSPR) can be utilized to describe the tendency of chemical concentration organisms represented by, the important ecotoxicological parameter, the logarithm of Bio Concentration Factor (log BCF) with molecular descriptors for a large set of non-ionic organic compounds. QSPR models were developed using multiple linear regression, partial least squares and neural networks analyses. Linear and non-linear QSPR models to predict log BCF of the compounds developed for the relevant descriptors. The results obtained offer good regression models having good prediction ability. The descriptors used in these models depend on the volume, connectivity, molar refractivity, surface tension and the presence of atoms accepting H-bonds. PMID:20706622

  13. [Discussion on the model organism in acupuncture and meridians researches].

    PubMed

    Zhang, Wei-bo; Wang, Guang-jun; Tian, Yu-ying; Jia, Shu-yong; Yun, Jie

    2014-12-01

    Using model organism to replace human subjects for experimental objects is an important part in basic research on acupuncture therapy. In the process of experimental research, the first thing is that if the animal model is suitable for revealing the underlying mechanism of acupuncture intervention, if it is relatively close to structures of the human body. In addition, some factors such as being easy to feed, larger in the volume and body-surface, lesser in fur, stable in the germline and reasonable in the cost should be considered. In current acupuncture study, most experiments were carried out in mice and rats, some were conducted in rabbits and cats, fewer conducted in larger animals like mini-pigs and monkeys. Due to being smaller in both body size and superficial area in the mouse and rat, soft and comate skin in the rabbit and cat, difficult breeding for cattle and horse, experimental studies of acupuncture-meridians are in fact not ideal in these animals. Mini-pig has a larger body size and body surface, being similar to the human body in the skin structure and easy to breed, and the monkey is mostly close to the human in the gene and body size, and is thus an ideal model organism for acupuncture research. Because acupoint and meridians have their space specificity, the usage of larger animal as the model organism is necessary.

  14. 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.

  15. 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.

  16. A taxonomy of nursing care organization models in hospitals

    PubMed Central

    2012-01-01

    Background Over the last decades, converging forces in hospital care, including cost-containment policies, rising healthcare demands and nursing shortages, have driven the search for new operational models of nursing care delivery that maximize the use of available nursing resources while ensuring safe, high-quality care. Little is known, however, about the distinctive features of these emergent nursing care models. This article contributes to filling this gap by presenting a theoretically and empirically grounded taxonomy of nursing care organization models in the context of acute care units in Quebec and comparing their distinctive features. Methods This study was based on a survey of 22 medical units in 11 acute care facilities in Quebec. Data collection methods included questionnaire, interviews, focus groups and administrative data census. The analytical procedures consisted of first generating unit profiles based on qualitative and quantitative data collected at the unit level, then applying hierarchical cluster analysis to the units’ profile data. Results The study identified four models of nursing care organization: two professional models that draw mainly on registered nurses as professionals to deliver nursing services and reflect stronger support to nurses’ professional practice, and two functional models that draw more significantly on licensed practical nurses (LPNs) and assistive staff (orderlies) to deliver nursing services and are characterized by registered nurses’ perceptions that the practice environment is less supportive of their professional work. Conclusions This study showed that medical units in acute care hospitals exhibit diverse staff mixes, patterns of skill use, work environment design, and support for innovation. The four models reflect not only distinct approaches to dealing with the numerous constraints in the nursing care environment, but also different degrees of approximations to an “ideal” nursing professional practice

  17. Model evaluation of marine primary organic aerosol emission schemes

    NASA Astrophysics Data System (ADS)

    Gantt, B.; Johnson, M. S.; Meskhidze, N.; Sciare, J.; Ovadnevaite, J.; Ceburnis, D.; O'Dowd, C. D.

    2012-09-01

    In this study, several marine primary organic aerosol (POA) emission schemes have been evaluated using the GEOS-Chem chemical transport model in order to provide guidance for their implementation in air quality and climate models. These emission schemes, based on varying dependencies of chlorophyll a concentration ([chl a]) and 10 m wind speed (U10), have large differences in their magnitude, spatial distribution, and seasonality. Model comparison with weekly and monthly mean values of the organic aerosol mass concentration at two coastal sites shows that the source function exclusively related to [chl a] does a better job replicating surface observations. Sensitivity simulations in which the negative U10 and positive [chl a] dependence of the organic mass fraction of sea spray aerosol are enhanced show improved prediction of the seasonality of the marine POA concentrations. A top-down estimate of submicron marine POA emissions based on the parameterization that compares best to the observed weekly and monthly mean values of marine organic aerosol surface concentrations has a global average emission rate of 6.3 Tg yr-1. Evaluation of existing marine POA source functions against a case study during which marine POA contributed the major fraction of submicron aerosol mass shows that none of the existing parameterizations are able to reproduce the hourly-averaged observations. Our calculations suggest that in order to capture episodic events and short-term variability in submicron marine POA concentration over the ocean, new source functions need to be developed that are grounded in the physical processes unique to the organic fraction of sea spray aerosol.

  18. 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.

  19. Culture optimization for the emergent zooplanktonic model organism Oikopleura dioica

    PubMed Central

    Bouquet, Jean-Marie; Spriet, Endy; Troedsson, Christofer; Otterå, Helen; Chourrout, Daniel; Thompson, Eric M.

    2009-01-01

    The pan-global marine appendicularian, Oikopleura dioica, shows considerable promise as a candidate model organism for cross-disciplinary research ranging from chordate genetics and evolution to molecular ecology research. This urochordate, has a simplified anatomical organization, remains transparent throughout an exceptionally short life cycle of less than 1 week and exhibits high fecundity. At 70 Mb, the compact, sequenced genome ranks among the smallest known metazoan genomes, with both gene regulatory and intronic regions highly reduced in size. The organism occupies an important trophic role in marine ecosystems and is a significant contributor to global vertical carbon flux. Among the short list of bona fide biological model organisms, all share the property that they are amenable to long-term maintenance in laboratory cultures. Here, we tested diet regimes, spawn densities and dilutions and seawater treatment, leading to optimization of a detailed culture protocol that permits sustainable long-term maintenance of O. dioica, allowing continuous, uninterrupted production of source material for experimentation. The culture protocol can be quickly adapted in both coastal and inland laboratories and should promote rapid development of the many original research perspectives the animal offers. PMID:19461862

  20. 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.

  1. 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

  2. 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.

  3. Spatial self-organization in hybrid models of multicellular adhesion

    NASA Astrophysics Data System (ADS)

    Bonforti, Adriano; Duran-Nebreda, Salva; Montañez, Raúl; Solé, Ricard

    2016-10-01

    Spatial self-organization emerges in distributed systems exhibiting local interactions when nonlinearities and the appropriate propagation of signals are at work. These kinds of phenomena can be modeled with different frameworks, typically cellular automata or reaction-diffusion systems. A different class of dynamical processes involves the correlated movement of agents over space, which can be mediated through chemotactic movement or minimization of cell-cell interaction energy. A classic example of the latter is given by the formation of spatially segregated assemblies when cells display differential adhesion. Here, we consider a new class of dynamical models, involving cell adhesion among two stochastically exchangeable cell states as a minimal model capable of exhibiting well-defined, ordered spatial patterns. Our results suggest that a whole space of pattern-forming rules is hosted by the combination of physical differential adhesion and the value of probabilities modulating cell phenotypic switching, showing that Turing-like patterns can be obtained without resorting to reaction-diffusion processes. If the model is expanded allowing cells to proliferate and die in an environment where diffusible nutrient and toxic waste are at play, different phases are observed, characterized by regularly spaced patterns. The analysis of the parameter space reveals that certain phases reach higher population levels than other modes of organization. A detailed exploration of the mean-field theory is also presented. Finally, we let populations of cells with different adhesion matrices compete for reproduction, showing that, in our model, structural organization can improve the fitness of a given cell population. The implications of these results for ecological and evolutionary models of pattern formation and the emergence of multicellularity are outlined.

  4. Spatial self-organization in hybrid models of multicellular adhesion.

    PubMed

    Bonforti, Adriano; Duran-Nebreda, Salva; Montañez, Raúl; Solé, Ricard

    2016-10-01

    Spatial self-organization emerges in distributed systems exhibiting local interactions when nonlinearities and the appropriate propagation of signals are at work. These kinds of phenomena can be modeled with different frameworks, typically cellular automata or reaction-diffusion systems. A different class of dynamical processes involves the correlated movement of agents over space, which can be mediated through chemotactic movement or minimization of cell-cell interaction energy. A classic example of the latter is given by the formation of spatially segregated assemblies when cells display differential adhesion. Here, we consider a new class of dynamical models, involving cell adhesion among two stochastically exchangeable cell states as a minimal model capable of exhibiting well-defined, ordered spatial patterns. Our results suggest that a whole space of pattern-forming rules is hosted by the combination of physical differential adhesion and the value of probabilities modulating cell phenotypic switching, showing that Turing-like patterns can be obtained without resorting to reaction-diffusion processes. If the model is expanded allowing cells to proliferate and die in an environment where diffusible nutrient and toxic waste are at play, different phases are observed, characterized by regularly spaced patterns. The analysis of the parameter space reveals that certain phases reach higher population levels than other modes of organization. A detailed exploration of the mean-field theory is also presented. Finally, we let populations of cells with different adhesion matrices compete for reproduction, showing that, in our model, structural organization can improve the fitness of a given cell population. The implications of these results for ecological and evolutionary models of pattern formation and the emergence of multicellularity are outlined.

  5. 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

  6. Combining traits and density to model recruitment of sessile organisms.

    PubMed

    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.

  7. 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

  8. 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

  9. 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.

  10. Modeling the transport of volatile organics in variably saturated media

    SciTech Connect

    Sleep, B.E.; Sykes, J.F. )

    1989-01-01

    The understanding of the processes of dissolution, volatilization, and gas-liquid partitioning in porous media is very limited. The few models which attempt to characterize the transport of volatile organics such as petroleum products and halogenated hydrocarbon solvents in variably saturated media all assume that mass transfer processes are at equilibrium. In addition, gas phase advection is neglected by assuming that gas phase pressures are uniformly atmospheric and that density gradients are negligible. In this study a model was developed to solve for water phase flow and transport and density dependent gas phase flow and transport. Simple expressions for dissolution, volatilization, and gas-liquid partitioning, employing the concept of an overall mass transfer coefficient, were incorporated into the model. The transport of trichloroethylene in a variably saturated vertical cross section, under a variety of conditions, was simulated. Results of the simulations appeared qualitatively correct. The importance of gas phase processes in increasing subsurface contamination from volatile organics, and in dissipating residual amounts of these substances, was demonstrated. The lack of similar analytical and/or numerical models, or suitable experimental studies, excluded the possibility of validating, or verifying, the model.

  11. Self-organized Collaboration Network Model Based on Module Emerging

    NASA Astrophysics Data System (ADS)

    Yang, Hongyong; Lu, Lan; Liu, Qiming

    Recently, the studies of the complex network have gone deep into many scientific fields, such as computer science, physics, mathematics, sociology, etc. These researches enrich the realization for complex network, and increase understands for the new characteristic of complex network. Based on the evolvement characteristic of the author collaboration in the scientific thesis, a self-organized network model of the scientific cooperation network is presented by module emerging. By applying the theoretical analysis, it is shown that this network model is a scale-free network, and the strength degree distribution and the module degree distribution of the network nodes have the same power law. In order to make sure the validity of the theoretical analysis for the network model, we create the computer simulation and demonstration collaboration network. By analyzing the data of the network, the results of the demonstration network and the computer simulation are consistent with that of the theoretical analysis of the model.

  12. 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

  13. A thermodynamic model for organic and aqueous tablet film coating.

    PubMed

    am Ende, Mary Tanya; Berchielli, Alfred

    2005-01-01

    A tablet film-coating model for aqueous- and/or organic-based systems is shown to predict exhaust stream conditions thereby facilitating process optimization and scale-up. This coating model uses the First Law of Thermodynamics and conservation of mass principles to complete a material-energy balance on the coating unit operation for a closed, non-isolated system. Heat loss from the coating pan is incorporated into the model through a parameter called a heat loss factor (HLF) that is directly related to the heat transfer coefficient and pan surface area. For a mixed organic-aqueous coating formulation, the outlet air temperature and humidity are most notably affected by the coating composition and the inlet drying air temperature, which controls the evaporative cooling rate. The coating solution temperature and inlet air relative humidity do not significantly influence the exhaust air temperature, Tair,out. The HLF was determined to be 24 to 62 cal/min degrees C for the LDCS-20 to HCT-30, 360 cal/min degrees C for the HCT-60, 0 cal/min degrees C for the HC-130L and 945 to 1322 cal/min degrees C for the Accela-Cota-48 to Compulab-36 coating pans. This model successfully predicts Tair,out within 3 degrees C for a given coating pan, and within 6 degrees C scaling up from one to 220 kg pans for both organic- and aqueous-based coatings. The model is also useful for probing process and formulation variable sensitivity critical to establishing process robustness.

  14. Modeling organic nitrogen conversions in activated sludge bioreactors.

    PubMed

    Makinia, Jacek; Pagilla, Krishna; Czerwionka, Krzysztof; Stensel, H David

    2011-01-01

    For biological nutrient removal (BNR) systems designed to maximize nitrogen removal, the effluent total nitrogen (TN) concentration may range from 2.0 to 4.0 g N/m(3) with about 25-50% in the form of organic nitrogen (ON). In this study, current approaches to modeling organic N conversions (separate processes vs. constant contents of organic fractions) were compared. A new conceptual model of ON conversions was developed and combined with Activated Sludge Model No. 2d (ASM2d). The model addresses a new insight into the processes of ammonification, biomass decay and hydrolysis of particulate and colloidal ON (PON and CON, respectively). Three major ON fractions incorporated are defined as dissolved (DON) (<0.1 µm), CON (0.1-1.2 µm) and PON (41.2 µm). Each major fraction was further divided into two sub-fractions - biodegradable and non-biodegradable. Experimental data were collected during field measurements and lab experiments conducted at the ''Wschod'' WWTP (570,000 PE) in Gdansk (Poland). The accurate steady-state predictions of DON and CON profiles were possible by varying ammonification and hydrolysis rates under different electron acceptor conditions. With the same model parameter set, the behaviors of both inorganic N forms (NH4-N, NOX-N) and ON forms (DON, CON) in the batch experiments were predicted. The challenges to accurately simulate and predict effluent ON levels from BNR systems are due to analytical methods of direct ON measurement (replacing TKN) and lack of large enough database (in-process measurements, dynamic variations of the ON concentrations) which can be used to determine parameter value ranges.

  15. 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.

  16. 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

  17. 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

  18. Modeling Organic Aerosols during MILAGRO: Application of the CHIMERE Model and Importance of Biogenic Secondary Organic Aerosols

    SciTech Connect

    Hodzic, Alma; Jimenez, Jose L.; Madronich, Sasha; Aiken, Allison; Bessagnet, Bertrand; Curci, Gabriele; Fast, Jerome D.; Lamarque, J.-F.; Onasch, Timothy B.; Roux, Gregory; Schauer, James J.; Stone, Elizabeth A.

    2009-09-22

    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 have 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 first-generation oxidation of anthropogenic (i.e., aromatics, alkanes) and biogenic (i.e., monoterpenes and isoprene) 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 species, with a factor of 5-10 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. However, predicted SOA concentrations were unrealistically low when photochemistry was not active, especially overnight. These nighttime discrepancies were not significantly reduced when greatly enhanced partitioning to the aerosol phase was assumed. Model sensitivity results suggest that observed nighttime SOA concentrations are strongly influenced by the regional background (~2µg/m3) from biogenic origin, which is transported

  19. 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.

  20. Mesoscopic kinetic Monte Carlo modeling of organic photovoltaic device characteristics

    NASA Astrophysics Data System (ADS)

    Kimber, Robin G. E.; Wright, Edward N.; O'Kane, Simon E. J.; Walker, Alison B.; Blakesley, James C.

    2012-12-01

    Measured mobility and current-voltage characteristics of single layer and photovoltaic (PV) devices composed of poly{9,9-dioctylfluorene-co-bis[N,N'-(4-butylphenyl)]bis(N,N'-phenyl-1,4-phenylene)diamine} (PFB) and poly(9,9-dioctylfluorene-co-benzothiadiazole) (F8BT) have been reproduced by a mesoscopic model employing the kinetic Monte Carlo (KMC) approach. Our aim is to show how to avoid the uncertainties common in electrical transport models arising from the need to fit a large number of parameters when little information is available, for example, a single current-voltage curve. Here, simulation parameters are derived from a series of measurements using a self-consistent “building-blocks” approach, starting from data on the simplest systems. We found that site energies show disorder and that correlations in the site energies and a distribution of deep traps must be included in order to reproduce measured charge mobility-field curves at low charge densities in bulk PFB and F8BT. The parameter set from the mobility-field curves reproduces the unipolar current in single layers of PFB and F8BT and allows us to deduce charge injection barriers. Finally, by combining these disorder descriptions and injection barriers with an optical model, the external quantum efficiency and current densities of blend and bilayer organic PV devices can be successfully reproduced across a voltage range encompassing reverse and forward bias, with the recombination rate the only parameter to be fitted, found to be 1×107 s-1. These findings demonstrate an approach that removes some of the arbitrariness present in transport models of organic devices, which validates the KMC as an accurate description of organic optoelectronic systems, and provides information on the microscopic origins of the device behavior.

  1. MIANN models in medicinal, physical and organic chemistry.

    PubMed

    González-Díaz, Humberto; Arrasate, Sonia; Sotomayor, Nuria; Lete, Esther; Munteanu, Cristian R; Pazos, Alejandro; Besada-Porto, Lina; Ruso, Juan M

    2013-01-01

    Reducing costs in terms of time, animal sacrifice, and material resources with computational methods has become a promising goal in Medicinal, Biological, Physical and Organic Chemistry. There are many computational techniques that can be used in this sense. In any case, almost all these methods focus on few fundamental aspects including: type (1) methods to quantify the molecular structure, type (2) methods to link the structure with the biological activity, and others. In particular, MARCH-INSIDE (MI), acronym for Markov Chain Invariants for Networks Simulation and Design, is a well-known method for QSAR analysis useful in step (1). In addition, the bio-inspired Artificial-Intelligence (AI) algorithms called Artificial Neural Networks (ANNs) are among the most powerful type (2) methods. We can combine MI with ANNs in order to seek QSAR models, a strategy which is called herein MIANN (MI & ANN models). One of the first applications of the MIANN strategy was in the development of new QSAR models for drug discovery. MIANN strategy has been expanded to the QSAR study of proteins, protein-drug interactions, and protein-protein interaction networks. In this paper, we review for the first time many interesting aspects of the MIANN strategy including theoretical basis, implementation in web servers, and examples of applications in Medicinal and Biological chemistry. We also report new applications of the MIANN strategy in Medicinal chemistry and the first examples in Physical and Organic Chemistry, as well. In so doing, we developed new MIANN models for several self-assembly physicochemical properties of surfactants and large reaction networks in organic synthesis. In some of the new examples we also present experimental results which were not published up to date.

  2. Genome Editing and Its Applications in Model Organisms.

    PubMed

    Ma, Dongyuan; Liu, Feng

    2015-12-01

    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.

  3. 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.

  4. The Accountable Care Organization (ACO) model: building blocks for success.

    PubMed

    Lowell, Kristina Hanson; Bertko, John

    2010-01-01

    The Accountable Care Organization (ACO) model has received significant attention among policymakers and leaders in the healthcare community in the context of the ongoing debate over health reform, not only because of the unsustainable path on which the country now finds itself but also because it directly focuses on what must be a key goal of the healthcare system: higher value. The model offers a promising approach for achieving this goal. This article provides an overview of the ACO model and its role in the current policy context, highlights the key elements that will be common to all ACOs, and provides details of several challenges that may arise throughout the implementation process, including a host of technical, legal, and operational challenges. These challenges range from issues such as the organizational form and management of the ACO to analytic challenges such as the calculation of spending benchmarks and the selection of quality measures.

  5. Self-organized criticality model for brain plasticity.

    PubMed

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

    2006-01-20

    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.

  6. 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

  7. Thermodynamic Modeling of Organic-Inorganic Aerosols with the Group-Contribution Model AIOMFAC

    NASA Astrophysics Data System (ADS)

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

    2009-04-01

    Liquid aerosol particles are - from a physicochemical viewpoint - mixtures of inorganic salts, acids, water and a large variety of organic compounds (Rogge et al., 1993; Zhang et al., 2007). Molecular interactions between these aerosol components lead to deviations from ideal thermodynamic behavior. Strong non-ideality between organics and dissolved ions may influence the aerosol phases at equilibrium by means of liquid-liquid phase separations into a mainly polar (aqueous) and a less polar (organic) phase. A number of activity models exists to successfully describe the thermodynamic equilibrium of aqueous electrolyte solutions. However, the large number of different, often multi-functional, organic compounds in mixed organic-inorganic particles is a challenging problem for the development of thermodynamic models. The group-contribution concept as introduced in the UNIFAC model by Fredenslund et al. (1975), is a practical method to handle this difficulty and to add a certain predictability for unknown organic substances. We present the group-contribution model AIOMFAC (Aerosol Inorganic-Organic Mixtures Functional groups Activity Coefficients), which explicitly accounts for molecular interactions between solution constituents, both organic and inorganic, to calculate activities, chemical potentials and the total Gibbs energy of mixed systems (Zuend et al., 2008). This model enables the computation of vapor-liquid (VLE), liquid-liquid (LLE) and solid-liquid (SLE) equilibria within one framework. Focusing on atmospheric applications we considered eight different cations, five anions and a wide range of alcohols/polyols as organic compounds. With AIOMFAC, the activities of the components within an aqueous electrolyte solution are very well represented up to high ionic strength. We show that the semi-empirical middle-range parametrization of direct organic-inorganic interactions in alcohol-water-salt solutions enables accurate computations of vapor-liquid and liquid

  8. Mutant generation in vertebrate model organisms by TILLING.

    PubMed

    Winkler, Sylke; Gscheidel, Nicola; Brand, Michael

    2011-01-01

    TILLING (Targeting Induced Local Lesions IN Genomes) is a popular reverse genetic approach that has been successfully applied in several genetic model organisms such as zebrafish, rat, Drosophila, Arabidopsis, or medaka. In contrast to classical targeted knockout technologies that work in mice by directly targeting a gene of interest, TILLING follows an indirect strategy. The first step of the TILLING pipeline is the generation of a TILLING library that consists of large numbers of mutagenized individuals. In a second step, these individuals are screened for mutations in any gene of interest. Screening is performed by PCR amplification of specific exons from each individual of a library followed by mutation detection. This could be done, for example, by direct re-sequencing of PCR fragments or alternatively, by CEL1 endonuclease-mediated mutation discovery. Individuals carrying potentially deleterious point mutations are isolated from the library and mutant lines are established. TILLING allows the identification of a whole range of point mutations, covering nonsense, splice site, and missense mutations in only one screening round, because the generation of mutations by mutagenesis as well as the screening tools is not biased. Potential knockout mutations are initially the mutations of choice, but TILLING screens can also be used to isolate allelic series of point mutations ranging from complete null phenotypes to hypomorphic or even dominant-negative or conditional alleles. These allelic series can be helpful for a comprehensive functional analysis of a gene of interest. TILLING is applicable to any kind of genetically tractable model organism, as long as this model organism is amenable to chemical mutagenesis, and genomic sequence information for a gene of interest is available. This chapter describes the design and pipeline of a TILLING facility as we are currently operating it for zebrafish in Dresden. Protocols for mutation detection by direct re

  9. 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.

  10. Modeling of Electronic Properties in Organic Semiconductor Device Structures

    NASA Astrophysics Data System (ADS)

    Chang, Hsiu-Chuang

    Organic semiconductors (OSCs) have recently become viable for a wide range of electronic devices, some of which have already been commercialized. With the mechanical flexibility of organic materials and promising performance of organic field effect transistors (OFETs) and organic bulk heterojunction devices, OSCs have been demonstrated in applications such as radio frequency identification tags, flexible displays, and photovoltaic cells. Transient phenomena play decisive roles in the performance of electronic devices and OFETs in particular. The dynamics of the establishment and depletion of the conducting channel in OFETs are investigated theoretically. The device structures explored resemble typical organic thin-film transistors with one of the channel contacts removed. By calculating the displacement current associated with charging and discharging of the channel in these capacitors, transient effects on the carrier transport in OSCs may be studied. In terms of the relevant models it is shown that the non-linearity of the process plays a key role. The non-linearity arises in the simplest case from the fact that channel resistance varies during the charging and discharging phases. Traps can be introduced into the models and their effects examined in some detail. When carriers are injected into the device, a conducting channel is established with traps that are initially empty. Gradual filling of the traps then modifies the transport characteristics of the injected charge carriers. In contrast, dc measurements as they are typically performed to characterize the transport properties of organic semiconductor channels investigate a steady state with traps partially filled. Numerical and approximate analytical models of the formation of the conducting channel and the resulting displacement currents are presented. For the process of transient carrier extraction, it is shown that if the channel capacitance is partially or completely discharged through the channel

  11. 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.

  12. Hydrodynamic interaction of two swimming model micro-organisms

    NASA Astrophysics Data System (ADS)

    Ishikawa, Takuji; Simmonds, M. P.; Pedley, T. J.

    2006-12-01

    In order to understand the rheological and transport properties of a suspension of swimming micro-organisms, it is necessary to analyse the fluid-dynamical interaction of pairs of such swimming cells. In this paper, a swimming micro-organism is modelled as a squirming sphere with prescribed tangential surface velocity, referred to as a squirmer. The centre of mass of the sphere may be displaced from the geometric centre (bottom-heaviness). The effects of inertia and Brownian motion are neglected, because real micro-organisms swim at very low Reynolds numbers but are too large for Brownian effects to be important. The interaction of two squirmers is calculated analytically for the limits of small and large separations and is also calculated numerically using a boundary-element method. The analytical and the numerical results for the translational rotational velocities and for the stresslet of two squirmers correspond very well. We sought to generate a database for an interacting pair of squirmers from which one can easily predict the motion of a collection of squirmers. The behaviour of two interacting squirmers is discussed phenomenologically, too. The results for the trajectories of two squirmers show that first the squirmers attract each other, then they change their orientation dramatically when they are in near contact and finally they separate from each other. The effect of bottom-heaviness is considerable. Restricting the trajectories to two dimensions is shown to give misleading results. Some movies of interacting squirmers are available with the online version of the paper.

  13. Regeneration and the need for simpler model organisms.

    PubMed Central

    Sánchez Alvarado, Alejandro

    2004-01-01

    The problem of regeneration is fundamentally a problem of tissue homeostasis involving the replacement of cells lost to normal 'wear and tear' (cell turnover), and/or injury. This attribute is of particular significance to organisms possessing relatively long lifespans, as maintenance of all body parts and their functional integration is essential for their survival. Because tissue replacement is broadly distributed among multicellular life-forms, and the molecules and mechanisms controlling cellular differentiation are considered ancient evolutionary inventions, it should be possible to gain key molecular insights about regenerative processes through the study of simpler animals. We have chosen to study and develop the freshwater planarian Schmidtea mediterranea as a model system because it is one of the simplest metazoans possessing tissue homeostasis and regeneration, and because it has become relatively easy to molecularly manipulate this organism. The developmental plasticity and longevity of S. mediterranea is in marked contrast to its better-characterized invertebrate cohorts: the fruitfly Drosophila melanogaster and the roundworm Caenorhabditis elegans, both of which have short lifespans and are poor at regenerating tissues. Therefore, planarians present us with new, experimentally accessible contexts in which to study the molecular actions guiding cell fate restriction, differentiation and patterning, each of which is crucial not only for regeneration to occur, but also for the survival and perpetuation of all multicellular organisms. PMID:15293803

  14. Determining and modelling hydrophobic organic contaminant speciation in mesocosms

    SciTech Connect

    Ashley, J.T.F.; Baker, J.E.

    1995-12-31

    The bioavailability of hydrophobic organic contaminants (HOCS) in aqueous environments is largely controlled by their interaction with dissolved and particulate organic matter. The binding capacity provides a quantitative means of describing the extent of sequestration of a contaminant. This study was undertaken to evaluate HOC binding capacities within variously sized benthic-planktonic mesocosms during the development of planktonic communities. The ability of each mesocosm to sequester these organic contaminants was followed over time using a gas sparging reactor. Unfiltered water samples, collected from five mesocosms of varying surface area to volume ratios, were spiked with an aliquot of a cocktail containing 16 polychlorinated biphenyls (log K{sub ow}s ranging from 4.55 to 7.65) and chlorpyrifos. After 2 hours, samples were sparged with air. Particulate, dissolved (2 {micro}m nonfilter retained) and vapor phase HOC concentrations were evaluated before and after sparging. Dissolved phase HOC concentrations were separated into colloidally-bound and truly dissolved fractions knowing the vapor phase concentrations and Henry`s Law constants (previously determined using the sparging reactor). Polychlorinated biphenyl congener 97 was found largely in the colloidal and truly dissolved phases (40% and 31%) whereas PCB congener 180 existed largely in the particulate phase (55%). The authors incorporate the results of the HOC binding capacity study into a time-variable, scale-independent model of contaminant speciation in mesocosms.

  15. 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

  16. [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.

  17. 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.

  18. 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.

  19. Empirically based device modeling of bulk heterojunction organic photovoltaics

    NASA Astrophysics Data System (ADS)

    Pierre, Adrien; Lu, Shaofeng; Howard, Ian A.; Facchetti, Antonio; Arias, Ana Claudia

    2013-10-01

    An empirically based, open source, optoelectronic model is constructed to accurately simulate organic photovoltaic (OPV) devices. Bulk heterojunction OPV devices based on a new low band gap dithienothiophene- diketopyrrolopyrrole donor polymer (P(TBT-DPP)) are blended with PC70BM and processed under various conditions, with efficiencies up to 4.7%. The mobilities of electrons and holes, bimolecular recombination coefficients, exciton quenching efficiencies in donor and acceptor domains and optical constants of these devices are measured and input into the simulator to yield photocurrent with less than 7% error. The results from this model not only show carrier activity in the active layer but also elucidate new routes of device optimization by varying donor-acceptor composition as a function of position. Sets of high and low performance devices are investigated and compared side-by-side.

  20. 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.

  1. Modeling financial markets by self-organized criticality.

    PubMed

    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.

  2. 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

  3. 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.

  4. 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.

  5. Rival-model penalized self-organizing map.

    PubMed

    Cheung, Yiu-ming; Law, Lap-tak

    2007-01-01

    As a typical data visualization technique, self-organizing map (SOM) has been extensively applied to data clustering, image analysis, dimension reduction, and so forth. In a conventional adaptive SOM, it needs to choose an appropriate learning rate whose value is monotonically reduced over time to ensure the convergence of the map, meanwhile being kept large enough so that the map is able to gradually learn the data topology. Otherwise, the SOM's performance may seriously deteriorate. In general, it is nontrivial to choose an appropriate monotonically decreasing function for such a learning rate. In this letter, we therefore propose a novel rival-model penalized self-organizing map (RPSOM) learning algorithm that, for each input, adaptively chooses several rivals of the best-matching unit (BMU) and penalizes their associated models, i.e., those parametric real vectors with the same dimension as the input vectors, a little far away from the input. Compared to the existing methods, this RPSOM utilizes a constant learning rate to circumvent the awkward selection of a monotonically decreased function for the learning rate, but still reaches a robust result. The numerical experiments have shown the efficacy of our algorithm.

  6. Digital gene expression for non-model organisms

    PubMed Central

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

    2011-01-01

    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 (106) 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

  7. D. melanogaster, mitochondria and neurodegeneration: small model organism, big discoveries.

    PubMed

    Debattisti, Valentina; Scorrano, Luca

    2013-07-01

    In developed countries, increased life expectancy is accompanied by an increased prevalence of age-related disorders like cancer and neurodegenerative diseases. Albeit the molecular mechanisms behind the clinically, pathologically and etiologically heterogeneous forms of neurodegeneration are often unclear, impairment of mitochondrial fusion-fission and dynamics emerged in recent years as a feature of neuronal dysfunction and death, pinpointing the need for animal models to investigate the relationship between mitochondrial shape and neurodegeneration. While research on mammalian models is slowed down by the complexity of the organisms and their genomes, the long latency of the symptoms and by the difficulty to generate and analyze large cohorts, the lower metazoan Drosophila melanogaster overcomes these problems, proving to be a suitable model to study neurodegenerative diseases and mitochondria-shaping proteins. Here we will summarize our current knowledge on the link between mitochondrial shape and models of neurodegeneration in the fruitfly. This article is part of a Special Issue entitled 'Mitochondrial function and dysfunction in neurodegeneration'.

  8. 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.

  9. 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.

  10. 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.

  11. Modeling organic micro pollutant degradation kinetics during sewage sludge composting.

    PubMed

    Sadef, Yumna; Poulsen, Tjalfe Gorm; Bester, Kai

    2014-11-01

    Degradation of 13 different organic micro-pollutants in sewage sludge during aerobic composting at 5 different temperatures over a 52 day period was investigated. Adequacy of two kinetic models: a single first order, and a dual first order expression (using an early (first 7 days) and a late-time (last 45 days) degradation coefficient), for describing micro-pollutant degradation, and kinetic constant dependency on composting temperature were evaluated. The results showed that both models provide relatively good descriptions of the degradation process, with the dual first order model being most accurate. The single first order degradation coefficient was 0.025 d(-1) on average across all compounds and temperatures. At early times, degradation was about three times faster than at later times. Average values of the early and late time degradation coefficients for the dual first order model were 0.066 d(-1) and 0.022 d(-1), respectively. On average 30% of the initial micro-pollutant mass present in the compost was degraded rapidly during the early stages of the composting process. Single first order and late time dual first order kinetic constants were strongly dependent on composting temperature with maximum values at temperatures of 35-65°C. In contrast the early time degradation coefficients were relatively independent of composting temperature.

  12. 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.

  13. 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

  14. Modeling biogenic and anthropogenic secondary organic aerosol in China

    NASA Astrophysics Data System (ADS)

    Hu, Jianlin; Wang, Peng; Ying, Qi; Zhang, Hongliang; Chen, Jianjun; Ge, Xinlei; Li, Xinghua; Jiang, Jingkun; Wang, Shuxiao; Zhang, Jie; Zhao, Yu; Zhang, Yingyi

    2017-01-01

    A revised Community Multi-scale Air Quality (CMAQ) model with updated secondary organic aerosol (SOA) yields and a more detailed description of SOA formation from isoprene oxidation was applied to study the spatial and temporal distribution of SOA in China in the entire year of 2013. Predicted organic carbon (OC), elemental carbon and volatile organic compounds agreed favorably with observations at several urban areas, although the high OC concentrations in wintertime in Beijing were under-predicted. Predicted summer SOA was generally higher (10-15 µg m-3) due to large contributions of isoprene (country average, 61 %), although the relative importance varies in different regions. Winter SOA was slightly lower and was mostly due to emissions of alkane and aromatic compounds (51 %). Contributions of monoterpene SOA was relatively constant (8-10 %). Overall, biogenic SOA accounted for approximately 75 % of total SOA in summer, 50-60 % in autumn and spring, and 24 % in winter. The Sichuan Basin had the highest predicted SOA concentrations in the country in all seasons, with hourly concentrations up to 50 µg m-3. Approximately half of the SOA in all seasons was due to the traditional equilibrium partitioning of semivolatile components followed by oligomerization, while the remaining SOA was mainly due to reactive surface uptake of isoprene epoxide (5-14 %), glyoxal (14-25 %) and methylglyoxal (23-28 %). Sensitivity analyses showed that formation of SOA from biogenic emissions was significantly enhanced due to anthropogenic emissions. Removing all anthropogenic emissions while keeping the biogenic emissions unchanged led to total SOA concentrations of less than 1 µg m-3, which suggests that manmade emissions facilitated biogenic SOA formation and controlling anthropogenic emissions would result in reduction of both anthropogenic and biogenic SOA.

  15. 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.

  16. Modeling monochloramine loss in the presence of natural organic matter.

    PubMed

    Duirk, Stephen E; Gombert, Bertrand; Croué, Jean-Philippe; Valentine, Richard L

    2005-09-01

    A comprehensive model describing monochloramine loss in the presence of natural organic matter (NOM) is presented. The model incorporates simultaneous monochloramine autodecomposition and reaction pathways resulting in NOM oxidation. These competing pathways were resolved numerically using an iterative process evaluating hypothesized reactions describing NOM oxidation by monochloramine under various experimental conditions. The reaction of monochloramine with NOM was described as biphasic using four NOM specific reaction parameters. NOM pathway 1 involves a direct reaction of monochloramine with NOM (k(doc1) = 1.05 x 10(4)-3.45 x 10(4) M(-1) h(-1)). NOM pathway 2 is slower in terms of monochloramine loss and attributable to free chlorine (HOCl) derived from monochloramine hydrolysis (k(doc2) = 5.72 x 10(5)-6.98 x 10(5) M(-1) h(-1)), which accounted for the majority of monochloramine loss. Also, the free chlorine reactive site fraction in the NOM structure was found to correlate to specific ultraviolet absorbance at 280 nm (SUVA280). Modeling monochloramine loss allowed for insight into disinfectant reaction pathways involving NOM oxidation. This knowledge is of value in assessing monochloramine stability in distribution systems and reaction pathways leading to disinfection by-product (DBP) formation.

  17. The PIRO (predisposition, insult, response, organ dysfunction) model

    PubMed Central

    Marshall, John C

    2014-01-01

    Multimodal therapy for diseases like cancer has only become practicable following the development of staging systems like the TNM (tumor, nodes, metastases) system. Staging enables the identification of subgroups of patients with a disease who not only have a differing prognosis, but who are also more likely to benefit from a specific therapeutic modality. Critically ill patients represent a highly heterogeneous population for whom multiple therapeutic options are potentially available, each carrying not only the potential for differential benefit, but also the potential for differential harm. The PIRO system (predisposition, insult, response, organ dysfunction) is a template proposal for a staging system for acute illness that incorporates assessment of pre-morbid baseline susceptibility (predisposition), the specific disorder responsible for acute illness (insult), the response of the host to that insult, and the resulting degree of organ dysfunction. However the creation of a valid, robust, and clinically useful system presents significant challenges arising from the complexity of the disease state, the lack of a clear phenotype, the confounding influence of the effects of therapy and of cultural and socio-economic factors, and the relatively low profile of acute illness with clinicians and the general public. This review summarizes the rationale for such a model of illness stratification and the results of preliminary cohort studies testing the concept. It further proposes two strategies for building a staging system, recognizing that this will be a demanding undertaking that will require decades of work. PMID:24184604

  18. Autophagy and ageing: insights from invertebrate model organisms.

    PubMed

    Lionaki, Eirini; Markaki, Maria; Tavernarakis, Nektarios

    2013-01-01

    Ageing in diverse species ranging from yeast to humans is associated with the gradual, lifelong accumulation of molecular and cellular damage. Autophagy, a conserved lysosomal, self-destructive process involved in protein and organelle degradation, plays an essential role in both cellular and whole-animal homeostasis. Accumulating evidence now indicates that autophagic degradation declines with age and this gradual reduction of autophagy might have a causative role in the functional deterioration of biological systems during ageing. Indeed, loss of autophagy gene function significantly influences longevity. Moreover, genetic or pharmacological manipulations that extend lifespan in model organisms often activate autophagy. Interestingly, conserved signalling pathways and environmental factors that regulate ageing, such as the insulin/IGF-1 signalling pathway and oxidative stress response pathways converge on autophagy. In this article, we survey recent findings in invertebrates that contribute to advance our understanding of the molecular links between autophagy and the regulation of ageing. In addition, we consider related mechanisms in other organisms and discuss their similarities and idiosyncratic features in a comparative manner.

  19. 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.

  20. 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.

  1. Comparing and modelling land use organization in cities.

    PubMed

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

    2015-12-01

    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.

  2. 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

  3. 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

  4. Self-organized criticality in a computer network model

    PubMed

    Yuan; Ren; Shan

    2000-02-01

    We study the collective behavior of computer network nodes by using a cellular automaton model. The results show that when the load of network is constant, the throughputs and buffer contents of nodes are power-law distributed in both space and time. Also the feature of 1/f noise appears in the power spectrum of the change of the number of nodes that bear a fixed part of the system load. It can be seen as yet another example of self-organized criticality. Power-law decay in the distribution of buffer contents implies that heavy network congestion occurs with small probability. The temporal power-law distribution for throughput might be a reasonable explanation for the observed self-similarity in computer network traffic.

  5. 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...

  6. From organic superconductors to DNA: Fragment orbital-based model

    NASA Astrophysics Data System (ADS)

    Castet, Frédéric; Ducasse, Laurent; Fritsch, Alain

    A semi-empirical valence bond/Hartree-Fock (VB/HF) method is developed to calculate one- and two-electron interactions between molecular fragments in conducting supramolecular stacks. This fragment orbital-based formalism allows for consistent extraction of an effective Hamiltonian defined as a "frontier orbital" model. This Hamiltonian quantitatively describes transfer and electrostatic interactions between conducting electrons, while reducing the active space so dramatically that the electronic eigenstates of very large systems may be investigated. The capabilities of the VB/HF method are illustrated on two different supramolecular stacks involving a π-π interacting fragment. In the first part of this study, the framework of the VB/HF method is used to evaluate the relative magnitude of the electronic interactions between conduction electrons in organic conductors and superconductors derived from Bechgaard salts. In the second part of this study, the VB/HF formalism is extended to derive an effective model for conduction holes along doped DNA double strands. Transferable intra- and intersite parameters were first evaluated from VB/HF calculations carried out on nucleoside pairs. From this interaction databank, the effective Hamiltonian of any type of nucleoside sequence can be defined. The thermalized charge distribution for a single hole delocalized along a DNA sequence containing 240 Watson-Crick pairs is then calculated and compared with the experimental yields of damage revealed by photocleavage experiments.

  7. 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.

  8. Modeling Organic Contaminant Desorption from Municipal Solid Waste Components

    NASA Astrophysics Data System (ADS)

    Knappe, D. R.; Wu, B.; Barlaz, M. A.

    2002-12-01

    Approximately 25% of the sites on the National Priority List (NPL) of Superfund are municipal landfills that accepted hazardous waste. Unlined landfills typically result in groundwater contamination, and priority pollutants such as alkylbenzenes are often present. To select cost-effective risk management alternatives, better information on factors controlling the fate of hydrophobic organic contaminants (HOCs) in landfills is required. The objectives of this study were (1) to investigate the effects of HOC aging time, anaerobic sorbent decomposition, and leachate composition on HOC desorption rates, and (2) to simulate HOC desorption rates from polymers and biopolymer composites with suitable diffusion models. Experiments were conducted with individual components of municipal solid waste (MSW) including polyvinyl chloride (PVC), high-density polyethylene (HDPE), newsprint, office paper, and model food and yard waste (rabbit food). Each of the biopolymer composites (office paper, newsprint, rabbit food) was tested in both fresh and anaerobically decomposed form. To determine the effects of aging on alkylbenzene desorption rates, batch desorption tests were performed after sorbents were exposed to toluene for 30 and 250 days in flame-sealed ampules. Desorption tests showed that alkylbenzene desorption rates varied greatly among MSW components (PVC slowest, fresh rabbit food and newsprint fastest). Furthermore, desorption rates decreased as aging time increased. A single-parameter polymer diffusion model successfully described PVC and HDPE desorption data, but it failed to simulate desorption rate data for biopolymer composites. For biopolymer composites, a three-parameter biphasic polymer diffusion model was employed, which successfully simulated both the initial rapid and the subsequent slow desorption of toluene. Toluene desorption rates from MSW mixtures were predicted for typical MSW compositions in the years 1960 and 1997. For the older MSW mixture, which had a

  9. Age and equity in liver transplantation: An organ allocation model.

    PubMed

    Cucchetti, Alessandro; Ross, Lainie Friedman; Thistlethwaite, J Richard; Vitale, Alessandro; Ravaioli, Matteo; Cescon, Matteo; Ercolani, Giorgio; Burra, Patrizia; Cillo, Umberto; Pinna, Antonio Daniele

    2015-10-01

    A moral liver allocation policy must be fair. We considered a 2-step, 2-principle allocation system called "age mapping." Its first principle, equal opportunity, ensures that candidates of all ages have an equal chance of getting an organ. Its second principle, prudential lifespan equity, allocates younger donor grafts to younger candidates and older donors to older candidates in order to increase the likelihood that all recipients achieve a "full lifespan." Data from 2476 candidates and 1371 consecutive adult liver transplantations (from 1999 to 2012) were used to determine whether age mapping can reduce the gap in years of life lost (YLL) between younger and older recipients. A parametric Weibull prognostic model was developed to estimate total life expectancy after transplantation using survival of the general population matched by sex and age as a reference. Life expectancy from birth was calculated by adding age at transplant and total life expectancy after transplantation. In multivariate analysis, recipient age, hepatitis C virus status, Model for End-Stage Liver Disease score at transplant of >30, and donor age were significantly related to prognosis after surgery (P < 0.05). The mean (and standard deviation) number of years of life from birth, calculated from the current allocation model, for various age groups were: recipients 18-47 years (n = 340) = 65.2 (3.3); 48-55 years (n = 387) = 72.7 (2.1); 56-61 years (n = 372) = 74.7 (1.7) and for recipients >61 years (n = 272) = 77.4 (1.4). The total number of YLL equaled 523 years. Redistributing liver grafts, using an age mapping algorithm, reduces the lifespan gap between younger and older candidates by 33% (from 12.3% to 8.3%) and achieves a 14% overall reduction of YLL (73 years) compared to baseline liver distribution. In conclusion, deliberately incorporating age into an allocation algorithm promotes fairness and increases efficiency.

  10. Empirically based device modeling of bulk heterojunction organic photovoltaics

    NASA Astrophysics Data System (ADS)

    Pierre, Adrien; Lu, Shaofeng; Howard, Ian A.; Facchetti, Antonio; Arias, Ana Claudia

    2013-04-01

    We develop an empirically based optoelectronic model to accurately simulate the photocurrent in organic photovoltaic (OPV) devices with novel materials including bulk heterojunction OPV devices based on a new low band gap dithienothiophene-DPP donor polymer, P(TBT-DPP), blended with PC70BM at various donor-acceptor weight ratios and solvent compositions. Our devices exhibit power conversion efficiencies ranging from 1.8% to 4.7% at AM 1.5G. Electron and hole mobilities are determined using space-charge limited current measurements. Bimolecular recombination coefficients are both analytically calculated using slowest-carrier limited Langevin recombination and measured using an electro-optical pump-probe technique. Exciton quenching efficiencies in the donor and acceptor domains are determined from photoluminescence spectroscopy. In addition, dielectric and optical constants are experimentally determined. The photocurrent and its bias-dependence that we simulate using the optoelectronic model we develop, which takes into account these physically measured parameters, shows less than 7% error with respect to the experimental photocurrent (when both experimentally and semi-analytically determined recombination coefficient is used). Free carrier generation and recombination rates of the photocurrent are modeled as a function of the position in the active layer at various applied biases. These results show that while free carrier generation is maximized in the center of the device, free carrier recombination is most dominant near the electrodes even in high performance devices. Such knowledge of carrier activity is essential for the optimization of the active layer by enhancing light trapping and minimizing recombination. Our simulation program is intended to be freely distributed for use in laboratories fabricating OPV devices.

  11. 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.

  12. 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.

  13. 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.…

  14. Evaluation of approaches focused on modelling of organic carbon stocks using the RothC model

    NASA Astrophysics Data System (ADS)

    Koco, Štefan; Skalský, Rastislav; Makovníková, Jarmila; Tarasovičová, Zuzana; Barančíková, Gabriela

    2014-05-01

    The aim of current efforts in the European area is the protection of soil organic matter, which is included in all relevant documents related to the protection of soil. The use of modelling of organic carbon stocks for anticipated climate change, respectively for land management can significantly help in short and long-term forecasting of the state of soil organic matter. RothC model can be applied in the time period of several years to centuries and has been tested in long-term experiments within a large range of soil types and climatic conditions in Europe. For the initialization of the RothC model, knowledge about the carbon pool sizes is essential. Pool size characterization can be obtained from equilibrium model runs, but this approach is time consuming and tedious, especially for larger scale simulations. Due to this complexity we search for new possibilities how to simplify and accelerate this process. The paper presents a comparison of two approaches for SOC stocks modelling in the same area. The modelling has been carried out on the basis of unique input of land use, management and soil data for each simulation unit separately. We modeled 1617 simulation units of 1x1 km grid on the territory of agroclimatic region Žitný ostrov in the southwest of Slovakia. The first approach represents the creation of groups of simulation units based on the evaluation of results for simulation unit with similar input values. The groups were created after the testing and validation of modelling results for individual simulation units with results of modelling the average values of inputs for the whole group. Tests of equilibrium model for interval in the range 5 t.ha-1 from initial SOC stock showed minimal differences in results comparing with result for average value of whole interval. Management inputs data from plant residues and farmyard manure for modelling of carbon turnover were also the same for more simulation units. Combining these groups (intervals of initial

  15. Development and evaluation of a new sorption model for organic cations in soil: contributions from organic matter and clay minerals.

    PubMed

    Droge, Steven T J; Goss, Kai-Uwe

    2013-12-17

    This study evaluates a newly proposed cation-exchange model that defines the sorption of organic cations to soil as a summed contribution of sorption to organic matter (OM) and sorption to phyllosilicate clay minerals. Sorption to OM is normalized to the fraction organic carbon (fOC), and sorption to clay is normalized to the estimated cation-exchange capacity attributed to clay minerals (CECCLAY). Sorption affinity is specified to a fixed medium composition, with correction factors for other electrolyte concentrations. The model applies measured sorption coefficients to one reference OM material and one clay mineral. If measured values are absent, then empirical relationships are available on the basis of molecular volume and amine type in combination with corrective increments for specific polar moieties. The model is tested using new sorption data generated at pH 6 for two Eurosoils, one enriched in clay and the other, OM, using 29 strong bases (pKa > 8). Using experimental data on reference materials for all tested compounds, model predictions for the two soils differed on average by only -0.1 ± 0.4 log units from measured sorption affinities. Within the chemical applicability domain, the model can also be applied successfully to various reported soil sorption data for organic cations. Particularly for clayish soils, the model shows that sorption of organic cations to clay minerals accounts for more than 90% of the overall affinity.

  16. Modeling Adsorption and Reactions of Organic Molecules at Metal Surfaces

    PubMed Central

    2014-01-01

    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+vdWsurf method that accurately accounts for the collective electronic

  17. 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

  18. 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

  19. 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 ...

  20. 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)

  1. 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…

  2. Dissecting Ubiquitin Folding Using the Self-Organized Polymer Model.

    PubMed

    Reddy, Govardhan; Thirumalai, D

    2015-08-27

    Folding of Ubiquitin (Ub), a functionally important protein found in eukaryotic organisms, is investigated at low and neutral pH at different temperatures using simulations of the coarse-grained self-organized-polymer model with side chains (SOP-SC). The melting temperatures (Tm's), identified with the peaks in the heat capacity curves, decrease as pH decreases, in qualitative agreement with experiments. The calculated radius of gyration, showing dramatic variations with pH, is in excellent agreement with scattering experiments. At Tm, Ub folds in a two-state manner at low and neutral pH. Clustering analysis of the conformations sampled in equilibrium folding trajectories at Tm, with multiple transitions between the folded and unfolded states, shows a network of metastable states connecting the native and unfolded states. At low and neutral pH, Ub folds with high probability through a preferred set of conformations resulting in a pH-dependent dominant folding pathway. Folding kinetics reveal that Ub assembly at low pH occurs by multiple pathways involving a combination of nucleation-collapse and diffusion collision mechanism. The mechanism by which Ub folds is dictated by the stability of the key secondary structural elements responsible for establishing long-range contacts and collapse of Ub. Nucleation collapse mechanism holds if the stability of these elements are marginal, as would be the case at elevated temperatures. If the lifetimes associated with these structured microdomains are on the order of hundreds of microseconds, then Ub folding follows the diffusion-collision mechanism with intermediates, many of which coincide with those found in equilibrium. Folding at neutral pH is a sequential process with a populated intermediate resembling that sampled at equilibrium. The transition state structures, obtained using a Pfold analysis, are homogeneous and globular with most of the secondary and tertiary structures being native-like. Many of our findings for

  3. Structural network analysis of biological networks for assessment of potential disease model organisms.

    PubMed

    Nabhan, Ahmed Ragab; Sarkar, Indra Neil

    2014-02-01

    Model organisms provide opportunities to design research experiments focused on disease-related processes (e.g., using genetically engineered populations that produce phenotypes of interest). For some diseases, there may be non-obvious model organisms that can help in the study of underlying disease factors. In this study, an approach is presented that leverages knowledge about human diseases and associated biological interactions networks to identify potential model organisms for a given disease category. The approach starts with the identification of functional and interaction patterns of diseases within genetic pathways. Next, these characteristic patterns are matched to interaction networks of candidate model organisms to identify similar subsystems that have characteristic patterns for diseases of interest. The quality of a candidate model organism is then determined by the degree to which the identified subsystems match genetic pathways from validated knowledge. The results of this study suggest that non-obvious model organisms may be identified through the proposed approach.

  4. 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...

  5. 76 FR 34712 - Medicare Program; Pioneer Accountable Care Organization Model; Extension of the Submission...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-14

    ...: This notice extends the deadlines for the submission of the Pioneer Accountable Care Organization Model...-coordinated-care-models/pioneer-aco . Application Submission Deadline: Applications must be postmarked on or before August 19, 2011. The Pioneer Accountable Care Organization Model ] Application is available...

  6. 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,…

  7. 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.

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

    DOE PAGES

    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

  9. 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.

  10. Modelling organic crystal structures using distributed multipole and polarizability-based model intermolecular potentials.

    PubMed

    Price, Sarah L; Leslie, Maurice; Welch, Gareth W A; Habgood, Matthew; Price, Louise S; Karamertzanis, Panagiotis G; Day, Graeme M

    2010-08-14

    Crystal structure prediction for organic molecules requires both the fast assessment of thousands to millions of crystal structures and the greatest possible accuracy in their relative energies. We describe a crystal lattice simulation program, DMACRYS, emphasizing the features that make it suitable for use in crystal structure prediction for pharmaceutical molecules using accurate anisotropic atom-atom model intermolecular potentials based on the theory of intermolecular forces. DMACRYS can optimize the lattice energy of a crystal, calculate the second derivative properties, and reduce the symmetry of the spacegroup to move away from a transition state. The calculated terahertz frequency k = 0 rigid-body lattice modes and elastic tensor can be used to estimate free energies. The program uses a distributed multipole electrostatic model (Q, t = 00,...,44s) for the electrostatic fields, and can use anisotropic atom-atom repulsion models, damped isotropic dispersion up to R(-10), as well as a range of empirically fitted isotropic exp-6 atom-atom models with different definitions of atomic types. A new feature is that an accurate model for the induction energy contribution to the lattice energy has been implemented that uses atomic anisotropic dipole polarizability models (alpha, t = (10,10)...(11c,11s)) to evaluate the changes in the molecular charge density induced by the electrostatic field within the crystal. It is demonstrated, using the four polymorphs of the pharmaceutical carbamazepine C(15)H(12)N(2)O, that whilst reproducing crystal structures is relatively easy, calculating the polymorphic energy differences to the accuracy of a few kJ mol(-1) required for applications is very demanding of assumptions made in the modelling. Thus DMACRYS enables the comparison of both known and hypothetical crystal structures as an aid to the development of pharmaceuticals and other speciality organic materials, and provides a tool to develop the modelling of the

  11. 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.

  12. 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

  13. 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

  14. 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.

  15. On the Implications of aerosol liquid water and phase separation for modeled organic aerosol mass

    EPA Science Inventory

    Current chemical transport models assume that organic aerosol (OA)-forming compounds partition mostly to a water-poor, organic-rich phase in accordance with their vapor pressures. However, in the southeast United States, a significant fraction of ambient organic compounds are wat...

  16. 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

  17. Comparison of activity coefficient models for atmospheric aerosols containing mixtures of electrolytes, organics, and water

    NASA Astrophysics Data System (ADS)

    Tong, Chinghang; Clegg, Simon L.; Seinfeld, John H.

    Atmospheric aerosols generally comprise a mixture of electrolytes, organic compounds, and water. Determining the gas-particle distribution of volatile compounds, including water, requires equilibrium or mass transfer calculations, at the heart of which are models for the activity coefficients of the particle-phase components. We evaluate here the performance of four recent activity coefficient models developed for electrolyte/organic/water mixtures typical of atmospheric aerosols. Two of the models, the CSB model [Clegg, S.L., Seinfeld, J.H., Brimblecombe, P., 2001. Thermodynamic modelling of aqueous aerosols containing electrolytes and dissolved organic compounds. Journal of Aerosol Science 32, 713-738] and the aerosol diameter dependent equilibrium model (ADDEM) [Topping, D.O., McFiggans, G.B., Coe, H., 2005. A curved multi-component aerosol hygroscopicity model framework: part 2—including organic compounds. Atmospheric Chemistry and Physics 5, 1223-1242] treat ion-water and organic-water interactions but do not include ion-organic interactions; these can be referred to as "decoupled" models. The other two models, reparameterized Ming and Russell model 2005 [Raatikainen, T., Laaksonen, A., 2005. Application of several activity coefficient models to water-organic-electrolyte aerosols of atmospheric interest. Atmospheric Chemistry and Physics 5, 2475-2495] and X-UNIFAC.3 [Erdakos, G.B., Change, E.I., Pandow, J.F., Seinfeld, J.H., 2006. Prediction of activity coefficients in liquid aerosol particles containing organic compounds, dissolved inorganic salts, and water—Part 3: Organic compounds, water, and ionic constituents by consideration of short-, mid-, and long-range effects using X-UNIFAC.3. Atmospheric Environment 40, 6437-6452], include ion-organic interactions; these are referred to as "coupled" models. We address the question—Does the inclusion of a treatment of ion-organic interactions substantially improve the performance of the coupled models over

  18. A depositional model for organic-rich Duvernay Formation mudstones

    NASA Astrophysics Data System (ADS)

    Knapp, Levi J.; McMillan, Julia M.; Harris, Nicholas B.

    2017-01-01

    The Upper Devonian Duvernay Formation of western Canada is an organic-rich shale formation now targeted as a hydrocarbon reservoir. We present a detailed sedimentological analysis of the Duvernay Formation in order to better understand organic-rich mudstone depositional processes and conditions and to characterize the vertical and lateral heterogeneity of mudstone lithofacies that affect petrophysical and geomechanical rock properties. Organic-rich mudstone facies of the Duvernay Formation were deposited in a dynamic depositional environment by a variety of sediment transport mechanisms, including suspension settling, turbidity currents, and bottom water currents in variably oxygenated bottom waters. Suspension settling dominated in distal relatively deep areas of the basin, but evidence for weak turbidity currents and bottom water currents was observed in the form of graded beds and thin grain-supported siltstone laminae. Organic enrichment primarily occurred in distal areas as a result of bottom water anoxia and low depositional rates of inorganic sediment. In deep water locations near platform margins, alternating silty-sandy contourite beds and organic-rich mudstone beds are present, the former interpreted to have been deposited and reworked by bottom water currents flowing parallel to slope. In shallower, more oxygenated settings, mudstone lithologies vary from calcareous to argillaceous. These sediments were deposited from suspension settling, turbidity currents, and bottom water currents, although primary sedimentary structures are often obscured by extensive bioturbation. Locally, organic enrichment in dysoxic rather than anoxic bottom waters was driven by a slightly increased sedimentation rate and possibly also by aggregation of sedimentary particles in the water column due to interaction between organic matter and clay minerals. Large variations observed in sediment composition, from siliceous to calcareous to argillaceous, reflect multiple biogenic

  19. 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…

  20. 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.

  1. Organism and population-level ecological models for ...

    EPA Pesticide Factsheets

    Ecological risk assessment typically focuses on animal populations as endpoints for regulatory ecotoxicology. Scientists at USEPA are developing models for animal populations exposed to a wide range of chemicals from pesticides to emerging contaminants. Modeled taxa include aquatic and terrestrial invertebrates, fish, amphibians, and birds, and employ a wide range of methods, from matrix-based projection models to mechanistic bioenergetics models and spatially explicit population models. not applicable

  2. 76 FR 33306 - Medicare Program; Pioneer Accountable Care Organization Model, Request for Applications; Correction

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-08

    ... Care Organization Model: Request for Applications.'' FOR FURTHER INFORMATION CONTACT: Maria Alexander... http://innovations.cms.gov/areas-of-focus/seamless-and-coordinated-care-models/pioneer-aco... HUMAN SERVICES Centers for Medicare & Medicaid Services Medicare Program; Pioneer Accountable...

  3. A computational model predicts Xenopus meiotic spindle organization.

    PubMed

    Loughlin, Rose; Heald, Rebecca; Nédélec, François

    2010-12-27

    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.

  4. Self-organization, the cascade model, and natural hazards

    PubMed Central

    Turcotte, Donald L.; Malamud, Bruce D.; Guzzetti, Fausto; Reichenbach, Paola

    2002-01-01

    We consider the frequency-size statistics of two natural hazards, forest fires and landslides. Both appear to satisfy power-law (fractal) distributions to a good approximation under a wide variety of conditions. Two simple cellular-automata models have been proposed as analogs for this observed behavior, the forest fire model for forest fires and the sand pile model for landslides. The behavior of these models can be understood in terms of a self-similar inverse cascade. For the forest fire model the cascade consists of the coalescence of clusters of trees; for the sand pile model the cascade consists of the coalescence of metastable regions. PMID:11875206

  5. 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…

  6. 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.

  7. 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.

  8. 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...

  9. 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...

  10. Democracy versus dictatorship in self-organized models of financial markets

    NASA Astrophysics Data System (ADS)

    D'Hulst, R.; Rodgers, G. J.

    2000-06-01

    Models to mimic the transmission of information in financial markets are introduced. As an attempt to generate the demand process, we distinguish between dictatorship associations, where groups of agents rely on one of them to make decision, and democratic associations, where each agent takes part in the group decision. In the dictatorship model, agents segregate into two distinct populations, while the democratic model is driven towards a critical state where groups of agents of all sizes exist. Hence, both models display a level of organization, but only the democratic model is self-organized. We show that the dictatorship model generates less-volatile markets than the democratic model.

  11. Speciation of volatile organic compound emissions for regional air quality modeling of particulate matter and ozone

    NASA Astrophysics Data System (ADS)

    Makar, P. A.; Moran, M. D.; Scholtz, M. T.; Taylor, A.

    2003-01-01

    A new classification scheme for the speciation of organic compound emissions for use in air quality models is described. The scheme uses 81 organic compound classes to preserve both net gas-phase reactivity and particulate matter (PM) formation potential. Chemical structure, vapor pressure, hydroxyl radical (OH) reactivity, freezing point/boiling point, and solubility data were used to create the 81 compound classes. Volatile, semivolatile, and nonvolatile organic compounds are included. The new classification scheme has been used in conjunction with the Canadian Emissions Processing System (CEPS) to process 1990 gas-phase and particle-phase organic compound emissions data for summer and winter conditions for a domain covering much of eastern North America. A simple postprocessing model was used to analyze the speciated organic emissions in terms of both gas-phase reactivity and potential to form organic PM. Previously unresolved compound classes that may have a significant impact on ozone formation include biogenic high-reactivity esters and internal C6-8 alkene-alcohols and anthropogenic ethanol and propanol. Organic radical production associated with anthropogenic organic compound emissions may be 1 or more orders of magnitude more important than biogenic-associated production in northern United States and Canadian cities, and a factor of 3 more important in southern U.S. cities. Previously unresolved organic compound classes such as low vapour pressure PAHs, anthropogenic diacids, dialkyl phthalates, and high carbon number alkanes may have a significant impact on organic particle formation. Primary organic particles (poorly characterized in national emissions databases) dominate total organic particle concentrations, followed by secondary formation and primary gas-particle partitioning. The influence of the assumed initial aerosol water concentration on subsequent thermodynamic calculations suggests that hydrophobic and hydrophilic compounds may form external

  12. Modelling trends in soil organic carbon under Mediterranean and Alpine forests using the Century model.

    NASA Astrophysics Data System (ADS)

    Chiti, T.; Smith, P.; Dalmonech, D.; Yeluripati, J.; Papale, D.; Valentini, R.

    2009-04-01

    In this work, seven Italian eddy covariance flux sites (Mediterranean and Alpine forests) were used to test the performance of the Century 4.5 model in predicting the dynamics of soil organic carbon (SOC) during the first (2008-2012) and the second (2012-2016) commitment periods of the Kyoto Protocol, and further (2100). As the eddy covariance flux sites have been active for 10 years on average (from 1996-1998), the model was evaluated by comparing the modelled SOC values with those measured at each site. In addition, the model was evaluated by comparing estimates of heterotrophic respiration, that were available for each site, with those provided by the model. Since were not available long term observed values for soil carbon, the short term validation of heterotrophic respiration will give confidence on long term model simulations. Once evaluated, two climate change scenarios (based on the emission scenarios) were examined: A1FI (‘‘world markets-fossil fuel intensive'') and B2 (‘‘local sustainability''). In general the model fitted very well with the data measured at each site, providing values that were within the standard error of the measurements. The amount of SOC estimated for the two forthcoming commitment periods was not so different from the actual amount measured in 2008, highlighting the difficulty, given the closeness in time to the present of the commitment periods, of detecting carbon changes by direct measurements. Differences in the total amount of SOC from the actual stock were observed only for a longer observation period (2100). In conclusion, this work shows that models can be effective tools for estimating future changes in SOC amounts as an alternative to direct measurements when short period of time are considered.

  13. 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.

  14. Modeling the release of organic contaminants during compost decomposition in soil.

    PubMed

    Geng, Chunnu; Haudin, Claire-Sophie; Zhang, Yuan; Lashermes, Gwenaëlle; Houot, Sabine; Garnier, Patricia

    2015-01-01

    Composts, incorporated in soils as amendments, may release organic contaminants during their decomposition. COP-Soil is presented here as a new model to simulate the interaction between organic contaminants and compost, using one module for organic matter and one for organic pollutants, with these modules being linked by several assumptions. Published results of laboratory soil incubations using labeled carbon pollutants from compost were used to test the model for one polycyclic aromatic hydrocarbon (PAH), two surfactants and one herbicide. Several simulation scenarios were tested using (i) the organic pollutant module either alone or coupled to the organic matter module, (ii) various methods to estimate the adsorption coefficients (Kd) of contaminants on organic matter and (iii) different degrading biomasses. The simulations were improved if the organic pollutant module was coupled with the organic matter module. Multiple linear regression model for Kd as a function of organic matter quality yielded the most accurate simulation results. The inclusion of specific biomass in the model made it possible to successfully predict the PAH mineralization.

  15. 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.

  16. Modelling Organic Surfaces with Self-Assembled Monolayers

    DTIC Science & Technology

    1989-05-01

    Contsine on i necessary’and identity by block number) The interfacial properties of organic materials are of critical importance in may applcations...orani materials we of critical importance in many applications, especially the control of wetability, adhesion, nibology, and corrosion. The...the Harvard Uiversity Materals Research lUboatory. 3 1. Introduction Much of modern materials scieno has been devoted to the discovery, development and

  17. Surrogacy theory and models of convoluted organic systems.

    PubMed

    Konopka, Andrzej K

    2007-03-01

    The theory of surrogacy is briefly outlined as one of the conceptual foundations of systems biology that has been developed for the last 30 years in the context of Hertz-Rosen modeling relationship. Conceptual foundations of modeling convoluted (biologically complex) systems are briefly reviewed and discussed in terms of current and future research in systems biology. New as well as older results that pertain to the concepts of modeling relationship, sequence of surrogacies, cascade of representations, complementarity, analogy, metaphor, and epistemic time are presented together with a classification of models in a cascade. Examples of anticipated future applications of surrogacy theory in life sciences are briefly discussed.

  18. MODELING VOLATILE ORGANIC COMPOUND PHARMACOKINETICS IN RAT PUPS

    EPA Science Inventory

    PBPK model predictions of internal dosimetry in young rats were compared to adult animals for benzene, chloroform (CHL), methylene chloride, methyl ethly ketone (MEK), perchloroethylene, and trichloroethylene.

  19. 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.

  20. A novel microfluidic model can mimic organ-specific metastasis of circulating tumor cells

    PubMed Central

    Kong, Jing; Luo, Yong; Jin, Dong; An, Fan; Zhang, Wenyuan; Liu, Lilu; Li, Jiao; Fang, Shimeng; Li, Xiaojie; Yang, Xuesong; Lin, Bingcheng; Liu, Tingjiao

    2016-01-01

    A biomimetic microsystem might compensate costly and time-consuming animal metastatic models. Herein we developed a biomimetic microfluidic model to study cancer metastasis. Primary cells isolated from different organs were cultured on the microlfuidic model to represent individual organs. Breast and salivary gland cancer cells were driven to flow over primary cell culture chambers, mimicking dynamic adhesion of circulating tumor cells (CTCs) to endothelium in vivo. These flowing artificial CTCs showed different metastatic potentials to lung on the microfluidic model. The traditional nude mouse model of lung metastasis was performed to investigate the physiological similarity of the microfluidic model to animal models. It was found that the metastatic potential of different cancer cells assessed by the microfluidic model was in agreement with that assessed by the nude mouse model. Furthermore, it was demonstrated that the metastatic inhibitor AMD3100 inhibited lung metastasis effectively in both the microfluidic model and the nude mouse model. Then the microfluidic model was used to mimick liver and bone metastasis of CTCs and confirm the potential for research of multiple-organ metastasis. Thus, the metastasis of CTCs to different organs was reconstituted on the microfluidic model. It may expand the capabilities of traditional cell culture models, providing a low-cost, time-saving, and rapid alternative to animal models. PMID:27191997

  1. 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)

  2. Molecular Dynamics Modeling of Tethered Organics in Confined Spaces

    SciTech Connect

    Waksburg, Avi; Nguyen, M; Chaffe, Alan; Kidder, Michelle; Buchanan III, A C; Britt, Phillip F

    2011-01-01

    A computational method for constructing and evaluating the dynamic behaviour of functionalised hexagonal mesoporous silica (HMS) MCM-41 models is reported. HMS with three pore diameters (1.7, 2.2 and 2.9 nm) were prepared, and, from these, two series of derivative structures were constructed - one with 1,3-diphenylpropyl (DPP) tethers and the other with smaller dimethylsilyl (DMS) tethers attached to the mesopores internal surfaces. Comparison with experimental data shows that simulation results correctly predict the maximum tether density that can be achieved for each tether and each pore diameter. For the smaller pore models, the extent of DPP functionalisation that can be achieved is limited by the available pore volume. However, for the larger pore model, the extent of functionalisation is limited by access to potentially reactive sites on the pore surface. The dynamic behaviour of the models was investigated over a range of temperatures (240-648 K). At lower temperatures (< 400 K), the mobility of DPP tethers in the 2.9 nm model is actually less than that observed in either the 2.2 nm model or the 1.7 nm model due to the extensive non-bonded interactions that are able to develop between tethers and the silica surface at this diameter. At higher temperatures, the free ends of these tethers break away from the surface, extend further into the pore space and the DPP mobility in the 2.9 nm model is higher than in the smaller pore systems.

  3. 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.

  4. Development and evaluation of statistical shape modeling for principal inner organs on torso CT images.

    PubMed

    Zhou, Xiangrong; Xu, Rui; Hara, Takeshi; Hirano, Yasushi; Yokoyama, Ryujiro; Kanematsu, Masayuki; Hoshi, Hiroaki; Kido, Shoji; Fujita, Hiroshi

    2014-07-01

    The shapes of the inner organs are important information for medical image analysis. Statistical shape modeling provides a way of quantifying and measuring shape variations of the inner organs in different patients. In this study, we developed a universal scheme that can be used for building the statistical shape models for different inner organs efficiently. This scheme combines the traditional point distribution modeling with a group-wise optimization method based on a measure called minimum description length to provide a practical means for 3D organ shape modeling. In experiments, the proposed scheme was applied to the building of five statistical shape models for hearts, livers, spleens, and right and left kidneys by use of 50 cases of 3D torso CT images. The performance of these models was evaluated by three measures: model compactness, model generalization, and model specificity. The experimental results showed that the constructed shape models have good "compactness" and satisfied the "generalization" performance for different organ shape representations; however, the "specificity" of these models should be improved in the future.

  5. 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 ...

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

    PubMed

    Faria, Isabel R; Young, Thomas M

    2010-12-01

    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 multisolute model), widely used in the prediction of multisolute sorption equilibrium from single-solute data, were used to simulate competitive sorption in our systems. The goal was to determine which multisolute model best represented the experimentally obtained multisolute 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 toward 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 soil).

  7. 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

  8. Retention modeling in combined pH/organic solvent gradient reversed-phase HPLC.

    PubMed

    Zisi, Ch; Fasoula, S; Nikitas, P; Pappa-Louisi, A

    2013-07-07

    An approach for retention modeling of double pH/organic solvent gradient data easily generated by automatically mixing two mobile phases with different pH and organic content according to a linear pump program is proposed. This approach is based on retention models arising from the evaluation of the retention data of a set of 17 OPA derivatives of amino acids obtained in 27 combined pH/organic solvent gradient runs performed between fixed initial pH/organic modifier values but different final ones and for different gradient duration. The derived general model is a ninth parameter equation easily manageable through a linear least-squares fitting but it requires eighteen initial pH/organic modifier gradient experiments for a satisfactory retention prediction in various double gradients of the same kind with those used in the fitting procedure. Two simplified versions of the general model, which were parameterized based on six only initial pH/organic modifier gradients, were also proposed, when one of the final double gradient conditions, pH or organic content was kept constant. The full and the simplified models allowed us to predict the experimental retention data in simultaneous pH/organic solvent double gradient mode very satisfactorily without the solution of the fundamental equation of gradient elution.

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

    PubMed Central

    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

  10. The Derivation of Sink Functions of Wheat Organs using the GREENLAB Model

    PubMed Central

    Kang, Mengzhen; Evers, Jochem B.; Vos, Jan; de Reffye, Philippe

    2008-01-01

    Background and Aims In traditional crop growth models assimilate production and partitioning are described with empirical equations. In the GREENLAB functional–structural model, however, allocation of carbon to different kinds of organs depends on the number and relative sink strengths of growing organs present in the crop architecture. The aim of this study is to generate sink functions of wheat (Triticum aestivum) organs by calibrating the GREENLAB model using a dedicated data set, consisting of time series on the mass of individual organs (the ‘target data’). Methods An experiment was conducted on spring wheat (Triticum aestivum, ‘Minaret’), in a growth chamber from, 2004 to, 2005. Four harvests were made of six plants each to determine the size and mass of individual organs, including the root system, leaf blades, sheaths, internodes and ears of the main stem and different tillers. Leaf status (appearance, expansion, maturity and death) of these 24 plants was recorded. With the structures and mass of organs of four individual sample plants, the GREENLAB model was calibrated using a non-linear least-square-root fitting method, the aim of which was to minimize the difference in mass of the organs between measured data and model output, and to provide the parameter values of the model (the sink strengths of organs of each type, age and tiller order, and two empirical parameters linked to biomass production). Key Results and Conclusions The masses of all measured organs from one plant from each harvest were fitted simultaneously. With estimated parameters for sink and source functions, the model predicted the mass and size of individual organs at each position of the wheat structure in a mechanistic way. In addition, there was close agreement between experimentally observed and simulated values of leaf area index. PMID:18045794

  11. Principles of Self-Organization in Young Brain—Viewed from Kohonen Model

    NASA Astrophysics Data System (ADS)

    Pallaver, T.; Kröger, H.; Parizeau, M.

    2008-05-01

    We propose a variant of the Kohonen model to study principles of self-organization in a model of young brain. We suggest a function to measure aquired knowledge and use it to auto-adapt the topology of neuronal connectivity, yielding substantial organizational improvement relative to the standard model. In the early phase of organization with most intense learning, we observe that neural connectivity is of Small World type, which is very efficient to organize neurons in response to stimuli. In analogy to human brain where pruning of neural connectivity occurs in early life, this feature is found to stabilize neuronal response to stimuli.

  12. 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.

  13. Modeling the effects of organic nitrogen uptake by plants on the carbon cycling of boreal ecosystems

    NASA Astrophysics Data System (ADS)

    Zhu, Q.; Zhuang, Q.

    2013-08-01

    Boreal forest and tundra are the major ecosystems in the northern high latitudes in which a large amount of carbon is stored. These ecosystems are nitrogen-limited due to slow mineralization rate of the soil organic nitrogen. Recently, abundant field studies have found that organic nitrogen is another important nitrogen supply for boreal ecosystems. In this study, we incorporated a mechanism that allowed boreal plants to uptake small molecular amino acids into a process-based biogeochemical model, the Terrestrial Ecosystem Model (TEM), to evaluate the impact of organic nitrogen uptake on ecosystem carbon cycling. The new version of the model was evaluated at both boreal forest and tundra sites. We found that the modeled organic nitrogen uptake accounted for 36-87% of total nitrogen uptake by plants in tundra ecosystems and 26-50% for boreal forests, suggesting that tundra ecosystem might have more relied on the organic form of nitrogen than boreal forests. The simulated monthly gross ecosystem production (GPP) and net ecosystem production (NEP) tended to be larger with the new version of the model since the plant uptake of organic nitrogen alleviated the soil nitrogen limitation especially during the growing season. The sensitivity study indicated that the most important factors controlling the plant uptake of organic nitrogen were the maximum root uptake rate (Imax) and the radius of the root (r0) in our model. The model uncertainty due to uncertain parameters associated with organic nitrogen uptake at tundra ecosystem was larger than at boreal forest ecosystems. This study suggests that considering the organic nitrogen uptake by plants is important to boreal ecosystem carbon modeling.

  14. 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 ...

  15. An Introduction to Topic Modeling as an Unsupervised Machine Learning Way to Organize Text Information

    ERIC Educational Resources Information Center

    Snyder, Robin M.

    2015-01-01

    The field of topic modeling has become increasingly important over the past few years. Topic modeling is an unsupervised machine learning way to organize text (or image or DNA, etc.) information such that related pieces of text can be identified. This paper/session will present/discuss the current state of topic modeling, why it is important, and…

  16. 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…

  17. 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…

  18. Electromagnetic Model Reliably Predicts Radar Scattering Characteristics of Airborne Organisms

    NASA Astrophysics Data System (ADS)

    Mirkovic, Djordje; Stepanian, Phillip M.; Kelly, Jeffrey F.; Chilson, Phillip B.

    2016-10-01

    The radar scattering characteristics of aerial animals are typically obtained from controlled laboratory measurements of a freshly harvested specimen. These measurements are tedious to perform, difficult to replicate, and typically yield only a small subset of the full azimuthal, elevational, and polarimetric radio scattering data. As an alternative, biological applications of radar often assume that the radar cross sections of flying animals are isotropic, since sophisticated computer models are required to estimate the 3D scattering properties of objects having complex shapes. Using the method of moments implemented in the WIPL-D software package, we show for the first time that such electromagnetic modeling techniques (typically applied to man-made objects) can accurately predict organismal radio scattering characteristics from an anatomical model: here the Brazilian free-tailed bat (Tadarida brasiliensis). The simulated scattering properties of the bat agree with controlled measurements and radar observations made during a field study of bats in flight. This numerical technique can produce the full angular set of quantitative polarimetric scattering characteristics, while eliminating many practical difficulties associated with physical measurements. Such a modeling framework can be applied for bird, bat, and insect species, and will help drive a shift in radar biology from a largely qualitative and phenomenological science toward quantitative estimation of animal densities and taxonomic identification.

  19. Electromagnetic Model Reliably Predicts Radar Scattering Characteristics of Airborne Organisms

    PubMed Central

    Mirkovic, Djordje; Stepanian, Phillip M.; Kelly, Jeffrey F.; Chilson, Phillip B.

    2016-01-01

    The radar scattering characteristics of aerial animals are typically obtained from controlled laboratory measurements of a freshly harvested specimen. These measurements are tedious to perform, difficult to replicate, and typically yield only a small subset of the full azimuthal, elevational, and polarimetric radio scattering data. As an alternative, biological applications of radar often assume that the radar cross sections of flying animals are isotropic, since sophisticated computer models are required to estimate the 3D scattering properties of objects having complex shapes. Using the method of moments implemented in the WIPL-D software package, we show for the first time that such electromagnetic modeling techniques (typically applied to man-made objects) can accurately predict organismal radio scattering characteristics from an anatomical model: here the Brazilian free-tailed bat (Tadarida brasiliensis). The simulated scattering properties of the bat agree with controlled measurements and radar observations made during a field study of bats in flight. This numerical technique can produce the full angular set of quantitative polarimetric scattering characteristics, while eliminating many practical difficulties associated with physical measurements. Such a modeling framework can be applied for bird, bat, and insect species, and will help drive a shift in radar biology from a largely qualitative and phenomenological science toward quantitative estimation of animal densities and taxonomic identification. PMID:27762292

  20. Electromagnetic Model Reliably Predicts Radar Scattering Characteristics of Airborne Organisms.

    PubMed

    Mirkovic, Djordje; Stepanian, Phillip M; Kelly, Jeffrey F; Chilson, Phillip B

    2016-10-20

    The radar scattering characteristics of aerial animals are typically obtained from controlled laboratory measurements of a freshly harvested specimen. These measurements are tedious to perform, difficult to replicate, and typically yield only a small subset of the full azimuthal, elevational, and polarimetric radio scattering data. As an alternative, biological applications of radar often assume that the radar cross sections of flying animals are isotropic, since sophisticated computer models are required to estimate the 3D scattering properties of objects having complex shapes. Using the method of moments implemented in the WIPL-D software package, we show for the first time that such electromagnetic modeling techniques (typically applied to man-made objects) can accurately predict organismal radio scattering characteristics from an anatomical model: here the Brazilian free-tailed bat (Tadarida brasiliensis). The simulated scattering properties of the bat agree with controlled measurements and radar observations made during a field study of bats in flight. This numerical technique can produce the full angular set of quantitative polarimetric scattering characteristics, while eliminating many practical difficulties associated with physical measurements. Such a modeling framework can be applied for bird, bat, and insect species, and will help drive a shift in radar biology from a largely qualitative and phenomenological science toward quantitative estimation of animal densities and taxonomic identification.

  1. Models of Organization and Governance at the Community College.

    ERIC Educational Resources Information Center

    Silverman, Michael

    In order to provide the best management model for the effective and efficient operation of community colleges, it is useful to look briefly at management theories. The three principle theories in use in corporate management are: (1) theory X, involving an autocratic supervisor allowing for minimal group influence; (2) theory Y, in which…

  2. For the Arts To Have Meaning...A Model of Adult Education in Performing Arts Organizations.

    ERIC Educational Resources Information Center

    Kitinoja, L.; Heimlich, J. E.

    A model of adult education appears to function in the outreach programs of three Columbus (Ohio) performing arts organizations. The first tier represents the arts organization's board of trustees, and the second represents the internal administration of the company. Two administrative bodies are arbitrarily labelled as education and marketing,…

  3. 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…

  4. [Structural models of simple sense organs by the example of first metazoans].

    PubMed

    Aronova, M Z

    2009-01-01

    Basic variants of the evolutional program for formation of simple sensor system--structural models of gravitation receptor, organ of vision, chemoreceptor organ as well as of the nervous system at early stages of the metazoan phylogenesis--are considered from results of our own morphofunctional studies and literature data.

  5. 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…

  6. 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.

  7. Developing and Sharing Team Mental Models in a Profession-Driven and Value-Laden Organization

    ERIC Educational Resources Information Center

    Tzeng, Jeng-Yi

    2006-01-01

    While team mental models have been shown to be effective in facilitating team operations in ordinary transactive organizations, their impact on loosely coupled yet value-laden organizations is relatively under studied. Using qualitative inquiry methodology, this study investigates the three referential frameworks (i.e., theoretical knowledge,…

  8. Current progress in public health models addressing the critical organ shortage.

    PubMed

    Shanmugarajah, Kumaran; Villani, Vincenzo; Madariaga, Maria Lucia L; Shalhoub, Joseph; Michel, Sebastian G

    2014-12-01

    Since its inauguration in 1954, the field of modern transplantation has made great strides in surgical technique, the prevention of acute and chronic rejection, the minimization of immunosuppression-related side-effects and transplant tolerance. As such, organ transplantation is used worldwide as a curative, life-saving treatment for people with end-stage organ failure. However, the successes of organ transplantation have resulted in the number of patients on transplant waiting lists far exceeding the number of organs available, with growing numbers of patients dying while awaiting transplants. In order to address this critical organ shortage, a number of legislative changes have been implemented worldwide to increase the number of individuals registering as organ donors. These have included presumed consent donation, incentivized organ donation, commercial organ transplantation and mandated choice models. This article will address these public health policies in turn. The implementation of these strategies and the evidence for their efficacy will be evaluated. Based on this, we have identified that well-supported transplant coordinators approaching next-of-kin, incentives and public health campaigns are key factors that increase organ donation. Finally we propose a modified mandated choice model that may be an alternative option to maximize the number of available organs for transplantation.

  9. 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...

  10. 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 ...

  11. 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).

  12. 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...

  13. Compound prioritization methods increase rates of chemical probe discovery in model organisms

    PubMed Central

    Wallace, Iain M; Urbanus, Malene L; Luciani, Genna M; Burns, Andrew R; Han, Mitchell KL; Wang, Hao; Arora, Kriti; Heisler, Lawrence E; Proctor, Michael; St. Onge, Robert P; Roemer, Terry; Roy, Peter J; Cummins, Carolyn L; Bader, Gary D; Nislow, Corey; Giaever, Guri

    2011-01-01

    SUMMARY Pre-selection of compounds that are more likely to induce a phenotype can increase the efficiency and reduce the costs for model organism screening. To identify such molecules, we screened ~81,000 compounds in S. cerevisiae and identified ~7,500 that inhibit cell growth. Screening these growth-inhibitory molecules across a diverse panel of model organisms resulted in an increased phenotypic hit-rate. This data was used to build a model to predict compounds that inhibit yeast growth. Empirical and in silico application of the model enriched the discovery of bioactive compounds in diverse model organisms. To demonstrate the potential of these molecules as lead chemical probes we used chemogenomic profiling in yeast and identified specific inhibitors of lanosterol synthase and of stearoyl-CoA 9-desaturase. As community resources, the ~7,500 growth-inhibitory molecules has been made commercially available and the computational model and filter used are provided. PMID:22035796

  14. 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.

  15. Self-organized percolation model for stock market fluctuations

    NASA Astrophysics Data System (ADS)

    Stauffer, Dietrich; Sornette, Didier

    1999-09-01

    In the Cont-Bouchaud model [cond-mat /9712318] of stock markets, percolation clusters act as buying or selling investors and their statistics controls that of the price variations. Rather than fixing the concentration controlling each cluster connectivity artificially at or close to the critical value, we propose that clusters shatter and aggregate continuously as the concentration evolves randomly, reflecting the incessant time evolution of groups of opinions and market moods. By the mechanism of “sweeping of an instability” [Sornette, J. Phys. I 4, 209(1994)], this market model spontaneously exhibits reasonable power-law statistics for the distribution of price changes and accounts for the other important stylized facts of stock market price fluctuations.

  16. 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.

  17. Tardigrades as a potential model organism in space research.

    PubMed

    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 gamma-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 gamma-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.

  18. 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.

  19. Characterization of an organic acid analog model in Adirondack, New York, surface waters

    NASA Astrophysics Data System (ADS)

    Fakhraei, H.; Driscoll, C. T.

    2013-12-01

    Natural waters include a variety of organic matter that differs in composition and functional groups. Dissolved organic matter is important but difficult to characterize acidic and metal binding (e.g., Al) functional groups in chemical equilibrium models. In this study data from Adirondack Lake Survey were used to calibrate an organic acid analog model in order to quantify the influence of organic acids on surface water chemistry. The study sites in the Adirondack region of New York have diverse levels of dissolved organic carbon (DOC), used as a surrogate for organic acids. DOC in 55 Adirondack surface waters varies from 180 μmol C/l (in Little Echo Pond) to 1263 μmol C/l (in Sunday Pond). To reduce the variability inherited in the large raw data set, suite of mean observations was constructed by grouping and averaging measured data into pH intervals of 0.05 pH units from pH 4.15 to 7.3. A chemical equilibrium model, which includes major solutes in natural waters, was linked to an optimization algorithm (genetic algorithm) to calibrate a triprotic organic analog model which includes proton and aluminum binding by adjusting the dissociation constants and site density of DOC. The object of fitting procedure was to simultaneously minimize the discrepancy between observed and simulated pH, acid neutralizing capacity (ANC), organic monomeric aluminum and inorganic monomeric aluminum. A sensitivity analysis on calibrated values indicate that the speciation of the modeled solutes are most responsive to the dissociation constant of AlOrg= Al3+ + Org3- reaction (Org3- represents organic anion), the site density of DOC and the second H+ dissociation constant of the triprotic organic analog (i.e. H2Org- = 2H+ + Org3- reaction).

  20. 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.

  1. Acquisition of a comprhensive air quality model evaluation data set for organic compounds

    SciTech Connect

    Fraser, M.P.; CAss, G.R.; Grosjean, E.; Grosjean, D.

    1995-12-01

    In previous work, photochemical airshed models have been formulated and tested that are capable of predicting the concentrations of more than 50 individual vapor-phase organic compounds that are found in the urban atmosphere. In a separate development, air quality models that account for the concentration of nearly 100 particle-phase organic compounds have been tested. The opportunity thus exists to create a combined air quality model that simultaneously tracks both gas-phase, semi-volatile, and particle-phase organic compounds that range in carbon number from C1 to about C34. Such a tool can be used both to explore the relationship between source emissions and ambient air quality, and to study gas-to-particle conversion processes for organic compounds. A major barrier to the development of such a comprehensive model for atmospheric organic air pollution is the absence of an equally comprehensive atmospheric data base against which such a model can be tested. During September, 1993, an experiment designed to acquire such an air quality model validation data set for organics was conducted in Southern California. At four urban locations and at one upwind offshore island, consecutive measurements over four hour averaging limes were made of speciated vapor phase hydrocarbons, chlorinated organics, and certain gas phase oxygenates via stainless steel canister collection followed by GC/FID and GC/MS analysis. Semi-volatile organics were collected on PUF cartridges, and particle phase organics were collected by filtration, followed by GC/MS analysis. Aldehydes were collected on DNPH impregnated cartridges, and PAN`s were measured by electron capture GC. The design and selected results of that experiment will be discussed.

  2. Model of Team Organization and Behavior and Team Description Method

    DTIC Science & Technology

    1984-10-01

    vr’rs ion re’ Ii’rsto fle , final vers iot de’veloped at’ the end of the’ first year oil fit #-4’,I lerI lot ;t elH’ hsversit’on should not he Ce...observation and study of real-world ’Army) teams and teem missionq. Unlike many previous team performance/team behavior models, the m•del described...team research to date.. Most studies of teams and team performance to date have been baiic and .exploratory: attempts to describe and exxolain the

  3. Tracking the long-distance dispersal of marine organisms: sensitivity to ocean model resolution.

    PubMed

    Putman, Nathan F; He, Ruoying

    2013-04-06

    Ocean circulation models are widely used to simulate organism transport in the open sea, where challenges of directly tracking organisms across vast spatial and temporal scales are daunting. Many recent studies tout the use of 'high-resolution' models, which are forced with atmospheric data on the scale of several hours and integrated with a time step of several minutes or seconds. However, in many cases, the model's outputs that are used to simulate organism movement have been averaged to considerably coarser resolutions (e.g. monthly mean velocity fields). To examine the sensitivity of tracking results to ocean circulation model output resolution, we took the native model output of one of the most sophisticated ocean circulation models available, the Global Hybrid Coordinate Ocean Model, and averaged it to commonly implemented spatial and temporal resolutions in studies of basin-scale dispersal. Comparisons between simulated particle trajectories and in situ near-surface drifter trajectories indicated that 'over averaging' model output yields predictions inconsistent with observations. Further analyses focused on the dispersal of juvenile sea turtles indicate that very different inferences regarding the pelagic ecology of these animals are obtained depending on the resolution of model output. We conclude that physical processes occurring at the scale of days and tens of kilometres should be preserved in ocean circulation model output to realistically depict the movement marine organisms and the resulting ecological and evolutionary processes.

  4. Modeling of the fast organic emissions from a wood-finishing product—Floor wax

    NASA Astrophysics Data System (ADS)

    Chang, John C. S.; Guo, Zhishi

    Environmental chamber and full-scale residential house tests were conducted to evaluate the fast organic emissions from a wood-finishing product—floor wax. For the environmental chamber tests, a very small amount of (<5 gm -2) of the wax was applied to an aluminum plate. It was found that the chamber exit organic concentrations can be estimated by a model with an initial condition of instant organic emissions. The model was applied to the house data to interpret the octane and nonane emissions. Significant sink effects were found in the house that prolonged the elevated octane and nonane concentrations for more than 2 days.

  5. 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.

  6. 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

  7. 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

  8. 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.

  9. Lampreys as Diverse Model Organisms in the Genomics Era.

    PubMed

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

    2015-11-01

    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.

  10. 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

  11. Self-organization with equilibration: A model for the intermediate phase in rigidity percolation

    NASA Astrophysics Data System (ADS)

    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 [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.

  12. 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.

  13. 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.

  14. Evaluating a model of anaerobic digestion of organic wastes through system identification

    SciTech Connect

    Anex, R.P.; Kiely, G.

    1999-07-01

    Anaerobic digestion of the organic fraction of municipal solid waste (MSW), on its own or co-digested with primary sewage sludge (PSS), produces high quality biogas, suitable as renewable energy. Parameter estimation and evaluation of a two-stage mathematical model of the anaerobic co-digestion of the organic fraction of MSW and PSS are described. Measured data are from a bench scale laboratory experiment using a continuously stirred tank reactor and operated at 36 C for 115 days. The two-stage model simulates acidogenesis and methanogenesis, including ammonia inhibition. Model parameters are estimated using an output error, Levenberg-Marquardt (LM) algorithm. Sensitivity of the estimated parameter values and the model outputs to non-estimated model parameters and measurement errors are evaluated. The estimated mathematical model successfully predicts the performance of the anaerobic reactor. Sensitivity results provide guidance for improving the model structure and experimental procedures.

  15. Clostridium cellulolyticum: model organism of mesophilic cellulolytic clostridia.

    PubMed

    Desvaux, Mickaël

    2005-09-01

    Clostridium cellulolyticum ATCC 35319 is a non-ruminal mesophilic cellulolytic bacterium originally isolated from decayed grass. As with most truly cellulolytic clostridia, C. cellulolyticum possesses an extracellular multi-enzymatic complex, the cellulosome. The catalytic components of the cellulosome release soluble cello-oligosaccharides from cellulose providing the primary carbon substrates to support bacterial growth. As most cellulolytic bacteria, C. cellulolyticum was initially characterised by limited carbon consumption and subsequent limited growth in comparison to other saccharolytic clostridia. The first metabolic studies performed in batch cultures suggested nutrient(s) limitation and/or by-product(s) inhibition as the reasons for this limited growth. In most recent investigations using chemostat cultures, metabolic flux analysis suggests a self-intoxication of bacterial metabolism resulting from an inefficiently regulated carbon flow. The investigation of C. cellulolyticum physiology with cellobiose, as a model of soluble cellodextrin, and with pure cellulose, as a carbon source more closely related to lignocellulosic compounds, strengthen the idea of a bacterium particularly well adapted, and even restricted, to a cellulolytic lifestyle. The metabolic flux analysis from continuous cultures revealed that (i) in comparison to cellobiose, the cellulose hydrolysis by the cellulosome introduces an extra regulation of entering carbon flow resulting in globally lower metabolic fluxes on cellulose than on cellobiose, (ii) the glucose 1-phosphate/glucose 6-phosphate branch point controls the carbon flow directed towards glycolysis and dissipates carbon excess towards the formation of cellodextrins, glycogen and exopolysaccharides, (iii) the pyruvate/acetyl-CoA metabolic node is essential to the regulation of electronic and energetic fluxes. This in-depth analysis of C. cellulolyticum metabolism has permitted the first attempt to engineer metabolically a

  16. 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

  17. Kinetic modelling of nitrogen and organics removal in vertical and horizontal flow wetlands.

    PubMed

    Saeed, Tanveer; Sun, Guangzhi

    2011-05-01

    This paper provides a comparative evaluation of the kinetic models that were developed to describe the biodegradation of nitrogen and organics removal in wetland systems. Reaction kinetics that were considered in the model development included first order kinetics, Monod and multiple Monod kinetics; these kinetics were combined with continuous-stirred tank reactor (CSTR) or plug flow pattern to produce equations to link inlet and outlet concentrations of each key pollutants across a single wetland. Using three statistical parameters, a critical evaluation of five potential models was made for vertical and horizontal flow wetlands. The results recommended the models that were developed based on Monod models, for predicting the removal of nitrogen and organics in a vertical and horizontal flow wetland system. No clear correlation was observed between influent BOD/COD values and kinetic coefficients of BOD(5) in VF and HF wetlands, illustrating that the removal of biodegradable organics was insensitive to the nature of organic matter. Higher effluent COD/TN values coincided with greater denitrification kinetic coefficients, signifying the dependency of denitrification on the availability of COD in VF wetland systems. In contrast, the trend was opposite in HF wetlands, indicating that availability of NO(3)-N was the main limiting step for nitrogen removal. Overall, the results suggested the possible application of the developed alternative predictive models, for understanding the complex biodegradation routes of nitrogen and organics removal in VF and HF wetland systems.

  18. Homeotic Genes and the ABCDE Model for Floral Organ Formation in Wheat

    PubMed Central

    Murai, Koji

    2013-01-01

    Floral organ formation has been the subject of intensive study for over 20 years, particularly in the model dicot species Arabidopsis thaliana. These studies have led to the establishment of a general model for the development of floral organs in higher plants, the so-called ABCDE model, in which floral whorl-specific combinations of class A, B, C, D, or E genes specify floral organ identity. In Arabidopsis, class A, B, C, D, E genes encode MADS-box transcription factors except for the class A gene APETALA2. Mutation of these genes induces floral organ homeosis. In this review, I focus on the roles of these homeotic genes in bread wheat (Triticum aestivum), particularly with respect to the ABCDE model. Pistillody, the homeotic transformation of stamens into pistil-like structures, occurs in cytoplasmic substitution (alloplasmic) wheat lines that have the cytoplasm of the related wild species Aegilops crassa. This phenomenon is a valuable tool for analysis of the wheat ABCDE model. Using an alloplasmic line, the wheat ortholog of DROOPING LEAF (TaDL), a member of the YABBY gene family, has been shown to regulate pistil specification. Here, I describe the current understanding of the ABCDE model for floral organ formation in wheat. PMID:27137382

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

    PubMed Central

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

    2016-01-01

    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 laev is and Eleutherodactylouscoqui, 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

  20. 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.

  1. 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.

  2. MATHEMATICAL MODEL FOR GAS/PARTICLE PARTITIONING OF SECONDARY ORGANIC AEROSOLS. (R824970)

    EPA Science Inventory

    A dynamic model is developed for gas-particle absorptive partitioning of semi-volatile organic aerosols. The model is applied to simulate a pair of m-xylene/NOx outdoor smog chamber experiments. In the presence of an inorganic seed aerosol a threshold ...

  3. 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...

  4. 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…

  5. 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

  6. 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.

  7. A predictive framework for evaluating models of semantic organization in free recall

    PubMed Central

    Morton, Neal W; Polyn, Sean M.

    2016-01-01

    Research in free recall has demonstrated that semantic associations reliably influence the organization of search through episodic memory. However, the specific structure of these associations and the mechanisms by which they influence memory search remain unclear. We introduce a likelihood-based model-comparison technique, which embeds a model of semantic structure within the context maintenance and retrieval (CMR) model of human memory search. Within this framework, model variants are evaluated in terms of their ability to predict the specific sequence in which items are recalled. We compare three models of semantic structure, latent semantic analysis (LSA), global vectors (GloVe), and word association spaces (WAS), and find that models using WAS have the greatest predictive power. Furthermore, we find evidence that semantic and temporal organization is driven by distinct item and context cues, rather than a single context cue. This finding provides important constraint for theories of memory search.

  8. River Flow Forecasting: a Hybrid Model of Self Organizing Maps and Least Square Support Vector Machine

    NASA Astrophysics Data System (ADS)

    Ismail, S.; Samsudin, R.; Shabri, A.

    2010-10-01

    Successful river flow time series forecasting is a major goal and an essential procedure that is necessary in water resources planning and management. This study introduced a new hybrid model based on a combination of two familiar non-linear method of mathematical modeling: Self Organizing Map (SOM) and Least Square Support Vector Machine (LSSVM) model referred as SOM-LSSVM model. The hybrid model uses the SOM algorithm to cluster the training data into several disjointed clusters and the individual LSSVM is used to forecast the river flow. The feasibility of this proposed model is evaluated to actual river flow data from Bernam River located in Selangor, Malaysia. Their results have been compared to those obtained using LSSVM and artificial neural networks (ANN) models. The experiment results show that the SOM-LSSVM model outperforms other models for forecasting river flow. It also indicates that the proposed model can forecast more precisely and provides a promising alternative technique in river flow forecasting.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. 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

  16. Time lag model for batch bioreactor simulation accounting the effect of micro-organism mortality.

    PubMed

    Zahariev, Andrey; Kiskinov, Hristo; Angelov, Angel; Zlatev, Stoyan

    2015-01-02

    In the present work, a generalization of the classical model of Monod accounting the influence of both delayed and instant mortalities on the dynamics of the micro-organism population is proposed. The model was analysed and compared with respect to its quality and applicability for simulation of the cultivation process of micro-organisms. Existence of a unique global positive solution of the Cauchy problem for the proposed model is proved and explicit relations between the decay parameters and the nutrition substrate concentration are obtained. These mathematical results allow us to calculate the nutrient substrate concentration which guarantees that the biomass concentration is maximal for every specific type of taxonomic groups of micro-organisms (bacteria, yeasts).

  17. A general mathematical model for chemical-enhanced flushing of soil contaminated by organic compounds

    NASA Astrophysics Data System (ADS)

    Ji, Wei; Brusseau, Mark L.

    The use of chemical agents to enhance the in situ removal of hydrophobic organic compounds (HOCs) from porous media is an emerging remediation technology. Whereas surfactants and cosolvents are the primary agents examined to date, others, such as natural organic matter and complexing agents, have also been examined for their ability to enhance the solubilization of HOCs. While the mode of action of each type of enhanced-solubilization agent may be different, they all induce similar responses. In this paper, a general mathematical model is developed to simulate the enhanced-solubilization process for various chemical agents, including cosolvents, surfactants, natural organic matter, and complexing agents. This model is developed using a master-equation approach that incorporates the solubilization mechanisms associated with each type of agent. A limited evaluation of the model is conducted by comparing simulations to the results of two laboratory experiments. A sensitivity analysis is performed to illustrate the influence of various factors on contaminant removal.

  18. Modeling the multiday evolution and aging of secondary organic aerosol during MILAGRO 2006.

    PubMed

    Dzepina, Katja; Cappa, Christopher D; Volkamer, Rainer M; Madronich, Sasha; Decarlo, Peter F; Zaveri, Rahul A; Jimenez, Jose L

    2011-04-15

    In this study, we apply several recently proposed models to the evolution of secondary organic aerosols (SOA) and organic gases advected from downtown Mexico City at an altitude of ∼3.5 km during three days of aging, in a way that is directly comparable to simulations in regional and global models. We constrain the model with and compare its results to available observations. The model SOA formed from oxidation of volatile organic compounds (V-SOA) when using a non-aging SOA parameterization cannot explain the observed SOA concentrations in aged pollution, despite the increasing importance of the low-NO(x) channel. However, when using an aging SOA parameterization, V-SOA alone is similar to the regional aircraft observations, highlighting the wide diversity in current V-SOA formulations. When the SOA formed from oxidation of semivolatile and intermediate volatility organic vapors (SI-SOA) is computed following Robinson et al. (2007) the model matches the observed SOA mass, but its O/C is ∼2× too low. With the parameterization of Grieshop et al. (2009), the total SOA mass is ∼2× too high, but O/C and volatility are closer to the observations. Heating or dilution cause the evaporation of a substantial fraction of the model SOA; this fraction is reduced by aging although differently for heating vs dilution. Lifting of the airmass to the free-troposphere during dry convection substantially increases SOA by condensation of semivolatile vapors; this effect is reduced by aging.

  19. Chemical equilibrium modeling of organic acids, pH, aluminum, and iron in Swedish surface waters.

    PubMed

    Sjöstedt, Carin S; Gustafsson, Jon Petter; Köhler, Stephan J

    2010-11-15

    A consistent chemical equilibrium model that calculates pH from charge balance constraints and aluminum and iron speciation in the presence of natural organic matter is presented. The model requires input data for total aluminum, iron, organic carbon, fluoride, sulfate, and charge balance ANC. The model is calibrated to pH measurements (n = 322) by adjusting the fraction of active organic matter only, which results in an error of pH prediction on average below 0.2 pH units. The small systematic discrepancy between the analytical results for the monomeric aluminum fractionation and the model results is corrected for separately for two different fractionation techniques (n = 499) and validated on a large number (n = 3419) of geographically widely spread samples all over Sweden. The resulting average error for inorganic monomeric aluminum is around 1 µM. In its present form the model is the first internally consistent modeling approach for Sweden and may now be used as a tool for environmental quality management. Soil gibbsite with a log *Ks of 8.29 at 25°C together with a pH dependent loading function that uses molar Al/C ratios describes the amount of aluminum in solution in the presence of organic matter if the pH is roughly above 6.0.

  20. Optimising the anaerobic co-digestion of urban organic waste using dynamic bioconversion mathematical modelling.

    PubMed

    Fitamo, T; Boldrin, A; Dorini, G; Boe, K; Angelidaki, I; Scheutz, C

    2016-12-01

    Mathematical anaerobic bioconversion models are often used as a convenient way to simulate the conversion of organic materials to biogas. The aim of the study was to apply a mathematical model for simulating the anaerobic co-digestion of various types of urban organic waste, in order to develop strategies for controlling and optimising the co-digestion process. The model parameters were maintained in the same way as the original dynamic bioconversion model, albeit with minor adjustments, to simulate the co-digestion of food and garden waste with mixed sludge from a wastewater treatment plant in a continuously stirred tank reactor. The model's outputs were validated with experimental results obtained in thermophilic conditions, with mixed sludge as a single substrate and urban organic waste as a co-substrate at hydraulic retention times of 30, 20, 15 and 10 days. The predicted performance parameter (methane productivity and yield) and operational parameter (concentration of ammonia and volatile fatty acid) values were reasonable and displayed good correlation and accuracy. The model was later applied to identify optimal scenarios for an urban organic waste co-digestion process. The simulation scenario analysis demonstrated that increasing the amount of mixed sludge in the co-substrate had a marginal effect on the reactor performance. In contrast, increasing the amount of food waste and garden waste resulted in improved performance.

  1. A comparison of models to describe the maximal retention of organic molecules in nanofiltration

    SciTech Connect

    Bruggen, B. van der; Schaep, J.; Wilms, D.; Vandecasteele, C.

    2000-01-01

    Nanofiltration is used in a growing number of applications for the treatment of drinking water, wastewater, and process water. Trial-and-error is generally used to test the applicability of nanofiltration and to select the membranes. In particular for organic molecules, a model that describes retention as a function of molecular parameters and membrane characteristics has not yet been established. In this paper four models for maximal retention, represented by the reflection coefficient, were compared: the steric hindrance pore model, the model of Zeman and Wales, the log-normal model, and an adapted version of the log-normal model. The calculated results were compared to reflection coefficients determined experimentally for a broad range of relatively small organic molecules. Each of the models yielded acceptable results, although the steric hindrance pore model and the model of Zeman and Wales are based on a somewhat idealized view of membrane structure. The log-normal model calculates reflection coefficients from a distribution of pore sizes. The adapted log-normal model also includes hydrodynamic lag, caused by sterical hindrance in the membrane pores. It was found that this effect is very small. The log-normal model appeared to be most useful to predict reflection coefficients in practical applications.

  2. 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

    2016-07-05

    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.

  3. 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

  4. Modeling of secondary organic aerosols from mobile sources in Mexico City

    NASA Astrophysics Data System (ADS)

    Zavala, M.; Lei, W.; Bei, N.; Li, G.; Tsimpidi, A. P.; Karydis, V. A.; Pandis, S.; Molina, L. T.

    2009-04-01

    Mobile sources are significant contributors of emissions of CO, NOx, hydrocarbons and particle matter (PM) that constitute critical precursors of ozone as well as secondary organic and inorganic particles that decisively impact the photochemical levels and aerosol loadings in the atmosphere. Currently there are large uncertainties in regional air quality models during the treatment of aerosol formation from aerosol precursors via the production of condensable organic gases. As a result, the modeling of the concentrations and properties of aerosols resulted from mobile emissions sources is an important challenge. In this study we compare aerosol simulations using the PM-CAMx air quality model linked to the SAPRC99 chemical mechanism with measured aerosol data obtained during the MILAGRO/MCMA-2006 field campaign in Mexico City. The PM-CAMx modeling framework is based on the volatility-basis approach: both primary and secondary organic components are assumed to be photochemically reactive and are logarithmically distributed in volatility bins. The distinction of the volatility properties of aerosols precursors is particularly important for diesel and gasoline emission sources due to their different organic carbon speciation emissions profiles. Using this volatility-basis technique, we will present results on the relative contributions from both gasoline and diesel vehicle fleet emission sources to the formation of secondary organic aerosols in an urban area.

  5. Organ data from the developing Göttingen minipig: first steps towards a juvenile PBPK model.

    PubMed

    Van Peer, Els; Downes, Noel; Casteleyn, Christophe; Van Ginneken, Chris; Weeren, Arie; Van Cruchten, Steven

    2016-04-01

    The Göttingen minipig is the most commonly used pig breed in preclinical drug development in Europe and has recently also been explored for physiologically based pharmacokinetic modelling. To develop such a model, not only physiological data from adult animals but also data from juvenile animals are required, especially when using this model for paediatric drug development. Therefore, the aim of our study was to document body and organ weights (brain, heart, lungs, liver, gastrointestinal tract, spleen and kidney), lengths of the small and large intestines and pH values of the gastrointestinal tract in Göttingen minipigs from the foetal stage until the age of 5 months. Postnatal organ and body weights were fitted to regression models to find suitable equations that could be used to estimate organ weights as a function of body weight in the neonatal and juvenile Göttingen minipig. Most organs followed a non-linear growth curve during the first 5 months of life. In general, relative organ weights were the highest during the first week of life, during which the gastric pH was more alkaline than at 28 days of age.

  6. 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

  7. Parameter-free continuous drift-diffusion models of amorphous organic semiconductors.

    PubMed

    Kordt, Pascal; Stodtmann, Sven; Badinski, Alexander; Al Helwi, Mustapha; Lennartz, Christian; Andrienko, Denis

    2015-09-21

    Continuous drift-diffusion models are routinely used to optimize organic semiconducting devices. Material properties are incorporated into these models via dependencies of diffusion constants, mobilities, and injection barriers on temperature, charge density, and external field. The respective expressions are often provided by the generic Gaussian disorder models, parametrized on experimental data. We show that this approach is limited by the fixed range of applicability of analytic expressions as well as approximations inherent to lattice models. To overcome these limitations we propose a scheme which first tabulates simulation results performed on small-scale off-lattice models, corrects for finite size effects, and then uses the tabulated mobility values to solve the drift-diffusion equations. The scheme is tested on DPBIC, a state of the art hole conductor for organic light emitting diodes. We find a good agreement between simulated and experimentally measured current-voltage characteristics for different film thicknesses and temperatures.

  8. The removal of nitrogen and organics in vertical flow wetland reactors: predictive models.

    PubMed

    Saeed, Tanveer; Sun, Guangzhi

    2011-01-01

    Three kinetic models, for predicting the removal of nitrogen and organics in vertical flow wetlands, have been developed and evaluated. These models were established by combining first-order, Monod and multiple Monod kinetics with continuous stirred-tank reactor (CSTR) flow pattern. Critical evaluations of these models using three statistical parameters, coefficient of determination, relative root mean square error and model efficiency, indicated that when the Monod/multiple Monod kinetics was combined with CSTR flow pattern it allowed close match between theoretical prediction and experiment data of nitrogen and organics removal. The kinetic coefficients (derived from Monod/multiple Monod kinetics) was found to increase with pollutant loading, indicating that the coefficients may vary based on different factors, such as influent pollutant concentration, hydraulic loading, and water depth. Overall, this study demonstrated the validity of combining Monod and multiple Monod kinetics with CSTR flow pattern for the modelling and design of vertical flow wetland systems.

  9. Modeling the Free Carrier Recombination Kinetics in PTB7:PCBM Organic Photovoltaics

    SciTech Connect

    Oosterhout, Stefan D.; Ferguson, Andrew J.; Larson, Bryon W.; Olson, Dana C.; Kopidakis, Nikos

    2016-11-03

    Currently the exact recombination mechanism of free carriers in organic photovoltaic (OPV) devices is poorly understood. Often a reduced Langevin model is used to describe the decay behavior of electrons and holes. Here we propose a novel, simple kinetic model that accurately describes the decay behavior of free carriers in the PTB7:PCBM organic photovoltaic blend. This model needs to only take into account free and trapped holes in the polymer, and free electrons in the fullerene, to accurately describe the recombination behavior of free carriers as measured by time-resolved microwave conductivity (TRMC). The model is consistent for different PTB7:PCBM blend ratios and spans a light intensity range of over 3 orders of magnitude. The model demonstrates that dark carriers exist in the polymer and interact with photoinduced charge carriers, and that the trapping and detrapping rates of the holes are of high importance to the overall carrier lifetime.

  10. 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

  11. 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.

  12. 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.

  13. Modeling of multicomponent pervaporation for removal of volatile organic compounds from water

    SciTech Connect

    Ji, W.; Sikdar, S.K.; Hwang, S.T.

    1994-01-01

    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 and three VOCs. The membrane permeability were calculated in terms of the resistance-in-series model. The membrane performances were then compared with each other based on the permeabilities. Both organic and water permeabilities of polyether-block-polyamides (PEBA) membrane for one VOC-water, two VOC-water, and three VOC-water mixtures were found to be comparable with each other.

  14. 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

    2016-06-22

    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.

  15. 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.

  16. 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.

  17. In silico model for predicting soil organic carbon normalized sorption coefficient (K(OC)) of organic chemicals.

    PubMed

    Wang, Ya; Chen, Jingwen; Yang, Xianhai; Lyakurwa, Felichesmi; Li, Xuehua; Qiao, Xianliang

    2015-01-01

    As a kind of in silico method, the methodology of quantitative structure-activity relationship (QSAR) has been shown to be an efficient way to predict soil organic carbon normalized sorption coefficients (KOC) values. In the present study, a total of 824 logKOC values were used to develop and validate a QSAR model for predicting KOC values. The model statistics parameters, adjusted determination coefficient (R(2)adj) of 0.854, the root mean square error (RMSE) of 0.472, the leave-one-out cross-validation squared correlation coefficient (Q(2)LOO) of 0.850, the external validation coefficient Q(2)ext of 0.761 and the RMSEext of 0.558 were obtained, which indicate satisfactory goodness of fit, robustness and predictive ability. The squared Moriguchi octanol-water partition coefficient (MLOGP2) explained 66.5% of the logKOC variance. The applicability domain of the current model has been extended to emerging pollutants like polybrominated diphenyl ethers, perfluorochemicals and heterocyclic toxins. The developed model can be used to predict the compounds with various functional groups including C=C, -C≡C-, -OH, -O-, -CHO, C=O, -C=O(O), -COOH, -C6H5, -NO2, -NH2, -NH-, N-, -N-N-, -NH-C(O)-NH-, -O-C(O)-NH2, -C(O)-NH2, -X(F, Cl, Br, I), -S-, -SH, -S(O)2-, -OS(O)2-, -NH-S(O)2-, (SR)2PH(OR)2 and Si.

  18. Why goldfish? Merits and challenges in employing goldfish as a model organism in comparative endocrinology research.

    PubMed

    Blanco, Ayelén Melisa; Sundarrajan, Lakshminarasimhan; Bertucci, Juan Ignacio; Unniappan, Suraj

    2017-02-07

    Goldfish has been used as an unconventional model organism to study a number of biological processes. For example, goldfish is a well-characterized and widely used model in comparative endocrinology, especially in neuroendocrinology. Several decades of research has established and validated an array of tools to study hormones in goldfish. The detailed brain atlas of goldfish, together with the stereotaxic apparatus, are invaluable tools for the neuroanatomic localization and central administration of endocrine factors. In vitro techniques, such as organ and primary cell cultures, have been developed using goldfish. In vivo approaches using goldfish were used to measure endogenous hormonal milieu, feeding, behaviour and stress. While there are many benefits in using goldfish as a model organism in research, there are also challenges associated with it. One example is its tetraploid genome that results in the existence of multiple isoforms of endocrine factors. The presence of extra endogenous forms of peptides and its receptors adds further complexity to the already redundant multifactorial endocrine milieu. This review will attempt to discuss the importance of goldfish as a model organism in comparative endocrinology. It will highlight some of the merits and challenges in employing goldfish as an animal model for hormone research in the post-genomic era.

  19. Model organism proteomics as a tool for the study of host-microbiome interactions.

    PubMed

    Cassidy, Liam; Tholey, Andreas

    2014-10-01

    All organisms live in constant contact with the microbial world. In recent years it has become evident that these microbial communities are not only responsible for the development of certain diseases, but are also an indispensable factor for homeostasis. The inherent complexity of meta-organisms hampers a straightforward elucidation of the molecular processes regulating the interactions of the host and its microbiome, as well as the influence of exogenic factors, for example, nutrition. Modern approaches such as meta-proteomics are now capable of deciphering the major processes in microbial communities, but the complete analysis of their interactions with their host is still in its infancy. In order to get easier access, the study of nonmammalian model organisms bears great potential. These organisms provide advantages such as reduced complexity, ease of cultivation in great numbers, and amenity to a range of genetic and biochemical manipulations. We highlight the potentials provided by model organism proteomics for the study of host-microbiome interactions and outline major challenges and demands for technological improvements that will be necessary for the understanding of the manifold interactions within meta-organisms.

  20. 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.

  1. 4D cone-beam CT reconstruction using multi-organ meshes for sliding motion modeling

    PubMed Central

    Zhong, Zichun; Gu, Xuejun; Mao, Weihua; Wang, Jing

    2016-01-01

    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

  2. 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.

  3. 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

  4. A novel in vitro model for microvasculature reveals regulation of circumferential ECM organization by curvature.

    PubMed

    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.

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. Impact of Fluorescent Lighting on Oxidation of Model Wine Solutions Containing Organic Acids and Iron.

    PubMed

    Grant-Preece, Paris; Barril, Celia; Schmidtke, Leigh M; Clark, Andrew C

    2017-03-22

    Previous studies have provided evidence that light exposure can increase oxygen consumption in wine and that the photodegradation of iron(III) tartrate could contribute to this process. In the present study, model wine solutions containing iron(III) and various organic acids, either alone or combined, were stored in sealed clear glass wine bottles and exposed to light from fluorescent lamps. Dissolved oxygen was monitored, and afterward the organic acid degradation products were determined and the capacity of the solutions to bind sulfur dioxide, the main wine preservative, was assessed. In the dark controls, little or no dissolved oxygen was consumed and the organic acids were stable. In the irradiated solutions, dissolved oxygen was consumed at a rate that was dependent on the specific organic acid present, and the latter were oxidized to various carbonyl compounds. For the solutions containing tartaric acid, malic acid, and/or citric acid, irradiation increased their sulfur dioxide-binding capacity.

  10. 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

  11. Modeling organic aerosols in a megacity: Potential contribution of semi-volatile and intermediate volatility primary organic compounds to secondary organic aerosol formation

    SciTech Connect

    Hodzic, A.; Kleinman, L.; Jimenez, J. L.; Madronich, S.; Canagaratna, M. R.; DeCarlo, P. F.; 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

  12. Heterogeneous processes affecting metal ion transport in the presence of organic ligands: Reactive transport modeling

    NASA Astrophysics Data System (ADS)

    Kantar, Cetin

    2007-04-01

    The development of models to accurately simulate metal ion transport through saturated systems under variable chemical conditions, e.g., in systems containing organic ligands (L) such as natural organic matter (NOM), has two essential aspects: (1) establishing the ability to simulate metal ion sorption to aquifer solids over a range of metal/ligand ratios; and (2) to incorporate this ability to simulate metal speciation over a range in chemical conditions (e.g., pH, ligand activity) into mass transport models. Modeling approaches to evaluate metal ion sorption and transport in the presence of NOM include: (1) isotherm-based transport models, and (2) multicomponent (MC) transport models. The accuracy of transport models depends on how well the chemical interactions affecting metal ion transport in the presence of organic ligands (e.g., metal/ligand complexation) are described in transport equations. The isotherm-based transport models often fail to accurately describe metal ion transport in the presence of NOM since these models treat NOM as a single solute despite the fact that NOM is a multicomponent mixture of subcomponents with different chemical and polyfunctional behavior. On the other hand, the calculations presented in this study suggest that a multicomponent reactive transport model, in conjunction with a mechanistic modeling approach for the description of metal ion binding by NOM in a manner conducive to the application of surface complexation modeling (SCM), can effectively be used as an important predictive tool in simulating metal ion sorption and transport under variable chemical conditions in the presence of NOM.

  13. Modeling the Thermodynamics of Mixed Organic-Inorganic Aerosols to Predict Water Activities and Phase Equilibria

    NASA Astrophysics Data System (ADS)

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

    2008-12-01

    Tropospheric aerosol particles 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 behavior. While the thermodynamics of aqueous inorganic systems at atmospheric temperatures are well established, little is known about the physicochemistry of mixed organic-inorganic particles. Salting-out and salting-in effects result from organic-inorganic interactions and are used to improve industrial separation processes. In the atmosphere, they may influence the aerosol phases. Liquid-liquid phase separations into a mainly polar (aqueous) and a less polar organic phase may considerably influence the gas/particle partitioning of semi-volatile substances compared to a single phase estimation. Moreover, the phases present in the aerosol define the reaction medium for heterogeneous and multiphase chemistry occurring in aerosol particles. A correct description of these phases is needed when gas- or cloud-phase reaction schemes are adapted to aerosols. Non-ideal thermodynamic behavior in mixtures is usually described by an expression for the excess Gibbs energy. We present the group-contribution model AIOMFAC (Aerosol Inorganic-Organic Mixtures Functional groups Activity Coefficients), which explicitly accounts for molecular interactions between solution constituents, both organic and inorganic, to calculate activities, chemical potentials and the total Gibbs energy of mixed systems. This model allows to compute vapor-liquid (VLE), liquid-liquid (LLE) and solid-liquid (SLE) equilibria within one framework. Focusing on atmospheric applications we considered eight different cations, five anions and a wide range of alcohols/polyols as organic compounds. With AIOMFAC, the activities of the components within an aqueous electrolyte solution are very well represented up to high ionic strength. We show that the semiempirical middle

  14. Modeling of organic light emitting diodes: from molecular to device properties (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Andrienko, Denis; Kordt, Pascal; May, Falk; Badinski, Alexander; Lennartz, Christian

    2016-09-01

    We will 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 will be 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.

  15. 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.

  16. A fractal model for nuclear organization: current evidence and biological implications.

    PubMed

    Bancaud, Aurélien; Lavelle, Christophe; Huet, Sébastien; Ellenberg, Jan

    2012-10-01

    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.

  17. Digital Computer Simulation Models of Library-Based Information Retrieval Systems. Reports on File Organization Studies.

    ERIC Educational Resources Information Center

    Reilly, Kevin D.

    A simulation study of library-based information retrieval systems is described. Basic models for each of several important aspects are presented: (1) user behavior, emphasizing response to quality and delays in services; (2) the scheduling of services and the organization of the machine-readable files; and (3) the distribution of conventional…

  18. 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...

  19. 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.

  20. 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…

  1. 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, ...

  2. 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 ...

  3. 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...

  4. 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...

  5. 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...

  6. 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...

  7. Faculty Organization Policy System as an Illustration of Easton's "Dynamic Response Model of a Political System."

    ERIC Educational Resources Information Center

    Ebersole, Jay F.

    This paper is an exercise in the study of David Easton's "dynamic response model of a political system," as found in "A Systems Analysis of Political Life." After a brief review of the theory, the development of a local "Reduction in Force" policy is described as an example of faculty organization policy influence on…

  8. 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.…

  9. 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.

  10. [Application of zebrafish model organism in the research of Chinese materia medica].

    PubMed

    Chen, Lei; Liu, Yi; Liang, Sheng-Wang

    2012-04-01

    Zebrafish has become an important model organism in many fields of biomedical studies and been increasingly used in Chinese materia medica studies in recent years. This article summarized the achievements and prospect for zebrafish as a pharmacological and toxicological tool in the study and development of Chinese materia medica.

  11. 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.

  12. 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...

  13. 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).

    ...

  14. 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…

  15. A theoretical model to address organizational human conflict and disruptive behavior in health care organizations.

    PubMed

    Piper, Llewellyn E

    2006-01-01

    This article proposes a theoretical model for leaders to use to address organizational human conflict and disruptive behavior in health care organizations. Leadership is needed to improve interpersonal relationships within the workforce. A workforce with a culture of internal conflict will be unable to achieve its full potential to delivery quality patient care.

  16. Using Grunig's "Indices for Models of Public Relations" To Differentiate Job Functions within Organizations.

    ERIC Educational Resources Information Center

    Reagan, Joey; And Others

    A study was conducted to determine the function of a firm within the context of public relations practice. The assessment of James E. Grunig's "Indices for Models of Public Relations" (an instrument for measuring the type of public relations practiced by an organization) was of primary concern. This instrument places public relations…

  17. 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...

  18. 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…

  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. Models Of Lower Extremity Damage In Mice: Time Course of Organ Damage & Immune Response

    PubMed Central

    Menzel, Christoph L; Pfeifer, Roman; Darwiche, Sophie S; Kobbe, Philipp; Gill, Roop; Shapiro, Richard A; Loughran, Patricia; Vodovotz, Yoram; Scott, Melanie J; Zenati, Mazen S; Billiar, Timothy R; Pape, Hans-Christoph

    2011-01-01

    Background Posttraumatic inflammatory changes have been identified as major causes of altered organ function and failure. Both hemorrhage and soft tissue damage induce these inflammatory changes. Exposure to heterologous bone in animal models has recently been shown to mimic this inflammatory response in a stable and reproducible fashion. This follow-up study tests the hypothesis that inflammatory responses are comparable between a novel trauma model (“pseudofracture”, PFx) and a bilateral femur fracture (BFF) model. Materials and Methods In C57BL/6 mice, markers for remote organ dysfunction and inflammatory responses were compared in 4 groups (control/sham/BFF/PFx) at the time points 2, 4, and 6 hours. Results Hepatocellular damage in BFF and PFx was highly comparable in extent and evolution, as shown by similar levels of NFκB activation and plasma ALT. Pulmonary inflammatory responses were also comparably elevated in both trauma models as early as 2h after trauma as measured by myeloperoxidase activity (MPO). Muscle damage was provoked in both BFF and PFx mice over the time course, although BFF induced significantly higher AST and CK levels. IL-6 levels were also similar with early and sustained increases over time in both trauma models. Conclusions Both BFF and PFx create similar reproducible inflammatory and remote organ responses. PFx will be a useful model to study longer term inflammatory effects that cannot be studied using BFF. PMID:21276982

  1. A novel model for estimating organic chemical bioconcentration in agricultural plants

    SciTech Connect

    Hung, H.; Mackay, D.; Di Guardo, A.

    1995-12-31

    There is increasing recognition that much human and wildlife exposure to organic contaminants can be traced through the food chain to bioconcentration in vegetation. For risk assessment, there is a need for an accurate model to predict organic chemical concentrations in plants. Existing models range from relatively simple correlations of concentrations using octanol-water or octanol-air partition coefficients, to complex models involving extensive physiological data. To satisfy the need for a relatively accurate model of intermediate complexity, a novel approach has been devised to predict organic chemical concentrations in agricultural plants as a function of soil and air concentrations, without the need for extensive plant physiological data. The plant is treated as three compartments, namely, leaves, roots and stems (including fruit and seeds). Data readily available from the literature, including chemical properties, volume, density and composition of each compartment; metabolic and growth rate of plant; and readily obtainable environmental conditions at the site are required as input. Results calculated from the model are compared with observed and experimentally-determined concentrations. It is suggested that the model, which includes a physiological database for agricultural plants, gives acceptably accurate predictions of chemical partitioning between plants, air and soil.

  2. [A clinical, health, economic and satisfaction simulation model, CHESS: a tool for healthcare organization management].

    PubMed

    Meilik, Ahuva; Afek, Arnon; Rotstein, Zeev

    2009-03-01

    The management of medical organizations is based on a profound understanding of the essence of the organization, its vision and missions, as well as the methods the organization utilizes to gather and analyze information. In order to maintain a maximal function level in an ever-changing environment, all organization components must function in tandem. In a previous article the authors presented medical organizations as macro systems composed of micro systems, and discussed the challenges these organization face today. Basing optimal system management on micro medical systems allows the organizations to make maximum use of the advantages that professionalism encompasses, in a flexible micro-system environment. In this article, the authors attempt to present an interactive solution for performing assessments and management in the medical arena--the CHESS model. This solution was developed at the Sheba Medical Center. The CHESS Simulator (Clinical Health Economic and Satisfaction Simulator) was formulated to function as a clinical organizational intelligence system, whose function was to supply quantitative, analyzed data regarding activity on the clinical production floor. The system is unique in that it has a differential view of the complex medical procedures which are highly variable, and also has the capability to locate elements that are based in a common similarity. Data gathering will be based on an online system computerized medical file (EMR), which is a priority for a functioning system. This solution allows medical organization (macro-system] managers and the departments (micro system) directors to make informed decisions that will ensure that the organization's goals are achieved. This is defined as evolving from a reactive management pattern to a proactive management pattern that is mandatory in the competitive atmosphere of the 21st Century.

  3. Process based modelling of soil organic carbon redistribution on landscape scale

    NASA Astrophysics Data System (ADS)

    Schindewolf, Marcus; Seher, Wiebke; Amorim, Amorim S. S.; Maeso, Daniel L.; Jürgen, Schmidt

    2014-05-01

    Recent studies have pointed out the great importance of erosion processes in global carbon cycling. Continuous erosion leads to a massive loss of top soils including the loss of organic carbon accumulated over long time in the soil humus fraction. Lal (2003) estimates that 20% of the organic carbon eroded with top soils is emitted into atmosphere, due to aggregate breakdown and carbon mineralization during transport by surface runoff. Furthermore soil erosion causes a progressive decrease of natural soil fertility, since cation exchange capacity is associated with organic colloids. As a consequence the ability of soils to accumulate organic carbon is reduced proportionately to the drop in soil productivity. The colluvial organic carbon might be protected from further degradation depending on the depth of the colluvial cover and local decomposing conditions. Some colluvial sites can act as long-term sinks for organic carbon. The erosional transport of organic carbon may have an effect on the global carbon budget, however, it is uncertain, whether erosion is a sink or a source for carbon in the atmosphere. Another part of eroded soils and organic carbon will enter surface water bodies and might be transported over long distances. These sediments might be deposited in the riparian zones of river networks. Erosional losses of organic carbon will not pass over into atmosphere for the most part. But soil erosion limits substantially the potential of soils to sequester atmospheric CO2 by generating humus. The present study refers to lateral carbon flux modelling on landscape scale using the process based EROSION 3D soil loss simulation model, using existing parameter values. The selective nature of soil erosion results in a preferentially transport of fine particles while less carbonic larger particles remain on site. Consequently organic carbon is enriched in the eroded sediment compared to the origin soil. For this reason it is essential that EROSION 3D provides the

  4. Modeling organic aerosols in a megacity: potential contribution of semi-volatile and intermediate volatility primary organic compounds to secondary organic aerosol formation

    SciTech Connect

    Hodzic, Alma; Jimenez, Jose L.; Madronich, Sasha; Canagaratna, M. R.; DeCarlo, Peter F.; Kleinman, Lawrence I.; Fast, Jerome D.

    2010-06-21

    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 traditional anthropogenic and biogenic VOC precursors. In this study, the 3D regional air quality model CHIMERE is applied to quantify the contribution to SOA formation of recently identified semi-volatile and intermediate volatility organic vapors (S/IVOC) in and around Mexico City for the MILAGRO field experiment during March 2006. The model has been updated to explicitly include 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. For the first time, 3D model results are assessed by comparing with the concentrations of OA components from Positive Matrix Factorization of Aerosol Mass Spectrometer (AMS) data, but also against and oxygen-to-carbon ratios derived from high-resolution AMS measurements. The results show a substantial enhancement in predicted SOA concentrations (3-6 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. The predicted anthropogenic POA levels are found to agree within 20% with the observed HOA concentrations for both the ROB and GRI simulations, consistent with the interpretation of the emissions inventory by previous studies. The impact of biomass burning POA within the city is underestimated in comparison to the AMS BBOA, presumably due to insufficient nighttime smoldering emissions. Model improvements in OA predictions are associated with the better-captured SOA magnitude and diurnal variability. The production from anthropogenic and biomass burning

  5. Modeling the Multiday Evolution and Aging of Secondary Organic Aerosol During MILAGRO 2006

    NASA Astrophysics Data System (ADS)

    Dzepina, K.; Cappa, C. D.; Volkamer, R.; Madronich, S.; Decarlo, P. F.; Zaveri, R. A.; Jimenez, J. L.

    2010-12-01

    In this study we apply several recently-proposed models to the evolution of secondary organic aerosols (SOA) and organic gases advected from downtown Mexico City at an altitude of ~3.5 km during three days of aging. We constrain the model with and compare its results to available observations. The model SOA formed from oxidation of volatile organic compounds (V-SOA) alone cannot explain the observed mass loadings in aged pollution. Over the regional scale ~5% of the model SOA is due to the low-NOx aromatic V-SOA pathway, which has a higher yield and produces comparably “low-volatility” species that remain in the particle phase as dilution proceeds and more volatile components evaporate. The model SOA formed from oxidation of both semivolatile and intermediate volatility organic vapors (SI-SOA) accounts for most of the predicted SOA mass concentration. With the SI-SOA parameterization of Robinson et al. (2007) the model matches the observed SOA mass, but its O/C is too low by a factor of 2. With the parameterization of Grieshop et al. (2009) the total SOA mass is overpredicted by a factor of ~2 but O/C and volatility are much closer to the observations. Heating or dilution of the air results in evaporation of a substantial fraction of the model SOA; this fraction is reduced by aging although differently for heating vs. dilution. Finally, lifting of the airmass to the free-troposphere during dry convection results in a substantial increase of SOA by condensation of semivolatile vapors, with this effect being reduced by aging.

  6. 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.

  7. Mathematical modeling of atmospheric fine particle-associated primary organic compound concentrations

    NASA Astrophysics Data System (ADS)

    Rogge, Wolfgang F.; Hildemann, Lynn M.; Mazurek, Monica A.; Cass, Glen R.; Simoneit, Bernd R. T.

    1996-08-01

    An atmospheric transport model has been used to explore the relationship between source emissions and ambient air quality for individual particle phase organic compounds present in primary aerosol source emissions. An inventory of fine particulate organic compound emissions was assembled for the Los Angeles area in the year 1982. Sources characterized included noncatalyst- and catalyst-equipped autos, diesel trucks, paved road dust, tire wear, brake lining dust, meat cooking operations, industrial oil-fired boilers, roofing tar pots, natural gas combustion in residential homes, cigarette smoke, fireplaces burning oak and pine wood, and plant leaf abrasion products. These primary fine particle source emissions were supplied to a computer-based model that simulates atmospheric transport, dispersion, and dry deposition based on the time series of hourly wind observations and mixing depths. Monthly average fine particle organic compound concentrations that would prevail if the primary organic aerosol were transported without chemical reaction were computed for more than 100 organic compounds within an 80 km × 80 km modeling area centered over Los Angeles. The monthly average compound concentrations predicted by the transport model were compared to atmospheric measurements made at monitoring sites within the study area during 1982. The predicted seasonal variation and absolute values of the concentrations of the more stable compounds are found to be in reasonable agreement with the ambient observations. While model predictions for the higher molecular weight polycyclic aromatic hydrocarbons (PAH) are in agreement with ambient observations, lower molecular weight PAH show much higher predicted than measured atmospheric concentrations in the particle phase, indicating atmospheric decay by chemical reactions or evaporation from the particle phase. The atmospheric concentrations of dicarboxylic acids and aromatic polycarboxylic acids greatly exceed the contributions that

  8. Modeling the elution of organic chemicals from a melting homogeneous snow pack.

    PubMed

    Meyer, Torsten; Wania, Frank

    2011-06-01

    Organic chemicals are often released in peak concentrations from melting snow packs. A simple, mechanistic snowmelt model was developed to simulate and predict the elution of organic substances from melting, homogeneous snow, as influenced by chemical properties and snow pack characteristics. The model calculates stepwise the chemical transport along with the melt water flow in a multi-layered snow pack, based on chemical equilibrium partitioning between the individual bulk snow phases. The model succeeds in reproducing the elution behavior of several organic contaminants observed in previously conducted cold room experiments. The model aided in identifying four different types of enrichment of organic substances during snowmelt. Water soluble substances experience peak releases early during a melt period (type 1), whereas chemicals that strongly sorb to particulate matter (PM) or snow grain surfaces elute at the end of melting (type 2). Substances that are somewhat water soluble and at the same time have a high affinity for snow grain surfaces may exhibit increasing concentrations in the melt water (type 3). Finally, elution sequences involving peak loads both at the beginning and the end of melting are simulated for chemicals that are partially dissolved in the aqueous melt water phase and partially sorbed to PM (type 4). The extent of type 1 enrichment mainly depends on the snow depth, whereby deeper snow generates more pronounced concentration peaks. PM influences the elution behavior of organic chemicals strongly because of the very large natural variability in the type and amount of particles present in snow. Urban and road-side snow rich in PM can generate type 2 concentration peaks at the end of the melt period for even relatively water soluble substances. From a clean, melting snow pack typical for remote regions, even fairly hydrophobic chemicals can be released in type 1 mode while being almost completely dissolved in the aqueous melt water phase. The

  9. A 3-D mathematical model to identify organ-specific risks in rats during thermal stress.

    PubMed

    Rakesh, Vineet; Stallings, Jonathan D; Helwig, Bryan G; Leon, Lisa R; Jackson, David A; Reifman, Jaques

    2013-12-01

    Early prediction of the adverse outcomes associated with heat stress is critical for effective management and mitigation of injury, which may sometimes lead to extreme undesirable clinical conditions, such as multiorgan dysfunction syndrome and death. Here, we developed a computational model to predict the spatiotemporal temperature distribution in a rat exposed to heat stress in an attempt to understand the correlation between heat load and differential organ dysfunction. The model includes a three-dimensional representation of the rat anatomy obtained from medical imaging and incorporates the key mechanisms of heat transfer during thermoregulation. We formulated a novel approach to estimate blood temperature by accounting for blood mixing from the different organs and to estimate the effects of the circadian rhythm in body temperature by considering day-night variations in metabolic heat generation and blood perfusion. We validated the model using in vivo core temperature measurements in control and heat-stressed rats and other published experimental data. The model predictions were within 1 SD of the measured data. The liver demonstrated the greatest susceptibility to heat stress, with the maximum temperature reaching 2°C higher than the measured core temperature and 95% of its volume exceeding the targeted experimental core temperature. Other organs also attained temperatures greater than the core temperature, illustrating the need to monitor multiple organs during heat stress. The model facilitates the identification of organ-specific risks during heat stress and has the potential to aid in the development of improved clinical strategies for thermal-injury prevention and management.

  10. Organic complexation of rare earth elements in natural waters: Evaluating model calculations from ultrafiltration data

    NASA Astrophysics Data System (ADS)

    Pourret, Olivier; Davranche, Mélanie; Gruau, Gérard; Dia, Aline

    2007-06-01

    The Stockholm Humic Model (SHM) and Humic Ion-Binding Models V and VI were compared for their ability to predict the role of dissolved organic matter (DOM) in the speciation of rare earth elements (REE) in natural waters. Unlike Models V and VI, SHM is part of a speciation code that also allows us to consider dissolution/precipitation, sorption/desorption and oxidation/reduction reactions. In this context, it is particularly interesting to test the performance of SHM. The REE specific equilibrium constants required by the speciation models were estimated using linear free-energy relationships (LFER) between the first hydrolysis constants and the stability constants for REE complexation with lactic and acetic acid. Three datasets were used for the purpose of comparison: (i) World Average River Water (Dissolved Organic Carbon (DOC) = 5 mg L -1), previously investigated using Model V, was reinvestigated using SHM and Model VI; (ii) two natural organic-rich waters (DOC = 18-24 mg L -1), whose REE speciation has already been determined with both Model V and ultrafiltration studies, were also reinvestigated using SHM and Model VI; finally, (iii) new ultrafiltration experiments were carried out on samples of circumneutral-pH (pH 6.2-7.1), organic-rich (DOC = 7-20 mg L -1) groundwaters from the Kervidy-Naizin and Petit-Hermitage catchments, western France. The results were then compared with speciation predictions provided by Model VI and SHM, successively. When applied to World Average River Water, both Model VI and SHM yield comparable results, confirming the earlier finding that a large fraction of the dissolved REE in rivers occurs as organic complexes This implies that the two models are equally valid for calculating REE speciation in low-DOC waters at circumneutral-pH. The two models also successfully reproduced ultrafiltration results obtained for DOC-rich acidic groundwaters and river waters. By contrast, the two models yielded different results when compared to

  11. Three-phase modeling of polycyclic aromatic hydrocarbon association with pore-water-dissolved organic carbon

    SciTech Connect

    Mitra, S. ); Dickhut, R.M. )

    1999-06-01

    Log-log plots of measured organic carbon-normalized sediment pore-water distribution coefficients (K[prime][sub OC]s) for several polycyclic aromatic hydrocarbons (PAHs) versus their octanol-water partition coefficients (K[prime][sub OW]s) at two sites in the Elizabeth River, Virginia, show large deviations from linearity. Organic-carbon normalized distribution coefficients for these PAHs between sediments and pore waters decreased by more than two orders of magnitude with depth as well. To determine to what extent pore water dissolved and colloidal organic carbon (DOC) was responsible for the observed nonlinearity and decrease in K[prime][sub OC], a three-phase model was used to estimate pore-water PAH-DOC binding coefficients (K[sub DOC]). Partitioning of PAHs to pore-water DOC (i.e., K[sub DOC])enhances the observed dissolved phase PAH concentration, especially for high-K[sub OW] compounds, contributing to the nonlinearity in K[prime][sub OC]-K[sub OW] plots. However, the application of the three-phase partitioning model to these data indicate that, at most, pore-water PAH-DOC binding accounts for one order of magnitude of the observed decrease in K[prime][sub OC] with depth in the sediment bed. The results of this study are consistent with three-phase partitioning theory for hydrophobic organic compounds between sediment organic matter, pore-water DOC, and freely dissolved aqueous phases in natural systems.

  12. 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

  13. 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

  14. Spatiotemporal modeling of soil organic carbon stocks across a subtropical region.

    PubMed

    Ross, Christopher Wade; Grunwald, Sabine; Myers, David Brenton

    2013-09-01

    Given the significance and complex nature of soil organic carbon in the context of the global carbon cycle, the need exists for more accurate and economically feasible means of soil organic carbon analysis and its underlying spatial variation at regional scale. The overarching goal of this study was to assess both the spatial and temporal variability of soil organic carbon within a subtropical region of Florida, USA. Specifically, the objectives were to: i) quantify regional soil organic carbon stocks for historical and current conditions and ii) determine whether the soils have acted as a net sink or a net source for atmospheric carbon-dioxide over an approximate 40 year time period. To achieve these objectives, geostatistical interpolation models were used in conjunction with "historical" and "current" datasets to predict soil organic carbon stocks for the upper 20 cm soil profile of the study area. Soil organic carbon estimates derived from the models ranged from 102 to 108 Tg for historical conditions and 211 to 320 Tg for current conditions, indicating that soils in the study area have acted as a net sink for atmospheric carbon over the last 40 years. A paired resampling of historical sites supported the geostatistical estimates, and resulted in an average increase of 0.8 g carbon m(-2) yr(-1) across all collocated samples. Accurately assessing the spatial and temporal state of soil organic carbon at regional scale is critical to further our understanding of global carbon stocks and provide a baseline so that the effects sustainable land use policy can be evaluated.

  15. 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

  16. 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.

  17. 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.

  18. Mathematical model for describing reactions of residual chlorine with organic matter in reclaimed wastewater.

    PubMed

    Funamizu, N; Iwamoto, T; Takakuwa, T

    2004-01-01

    Among several applications of urban wastewater reuse, use of reclaimed wastewater to sustain stream flows has become attractive in the urban area. Since these rivers are used for recreational purposes and for restoring aquatic eco-system, the adequate control of residual chlorine is essential. Mathematical model for describing reactions between residual chlorine and organic matter in reclaimed wastewater has been developed. The model considers the effect of molecular weight distribution of organic matter on the reaction rate. Lab-scale experiments were performed to estimate reaction rates constants and to examine their temperature dependency. The experiments showed that 1) the smaller organic matter gave the larger reaction rate; 2) temperature effect on reaction rate was described by the Arrhenius formula; 3) decline of free chlorine had more temperature dependency than combined chlorine. The comparison of computed results with data from lab-scale experiments confirmed the validity of the model. We used the one-dimensional dispersion model with proposed reaction model and examined the seasonal variation of residual chlorine profile along the river sustained by reclaimed wastewater in Sapporo. Simulation showed that seasonal variation of nitrification performance in secondary treatment as well as change in temperature caused seasonal variation in residual chlorine profile along the river.

  19. 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.

  20. Dosimetric treatment course simulation based on a statistical model of deformable organ motion.

    PubMed

    Söhn, M; Sobotta, B; Alber, M

    2012-06-21

    We present a method of modeling dosimetric consequences of organ deformation and correlated motion of adjacent organ structures in radiotherapy. Based on a few organ geometry samples and the respective deformation fields as determined by deformable registration, principal component analysis (PCA) is used to create a low-dimensional parametric statistical organ deformation model (Söhn et al 2005 Phys. Med. Biol. 50 5893-908). PCA determines the most important geometric variability in terms of eigenmodes, which represent 3D vector fields of correlated organ deformations around the mean geometry. Weighted sums of a few dominating eigenmodes can be used to simulate synthetic geometries, which are statistically meaningful inter- and extrapolations of the input geometries, and predict their probability of occurrence. We present the use of PCA as a versatile treatment simulation tool, which allows comprehensive dosimetric assessment of the detrimental effects that deformable geometric uncertainties can have on a planned dose distribution. For this, a set of random synthetic geometries is generated by a PCA model for each simulated treatment course, and the dose of a given treatment plan is accumulated in the moving tissue elements via dose warping. This enables the calculation of average voxel doses, local dose variability, dose-volume histogram uncertainties, marginal as well as joint probability distributions of organ equivalent uniform doses and thus of TCP and NTCP, and other dosimetric and biologic endpoints. The method is applied to the example of deformable motion of prostate/bladder/rectum in prostate IMRT. Applications include dosimetric assessment of the adequacy of margin recipes, adaptation schemes, etc, as well as prospective 'virtual' evaluation of the possible benefits of new radiotherapy schemes.

  1. Applications of a simulation model to description of anaerobic conversion of complex organic matter into methane

    SciTech Connect

    Vavilin, V.A.; Rytow, S.V.; Lokshina, L.Ya.

    1996-12-31

    Three years passed since the generalized model of anaerobic degradation of complex organic matter has been developed. Now the new modifications were created. Anaerobic degradation was described as a multistep process of series and parallel reactions in which several groups of bacteria take part. Hydrolysis, acidogenesis, acetogenesis and methanogenesis were considered in the model with the various kinetic functions. A two-phase equation describing a particulate substrate degradation as a heterogeneous reaction has been developed. Acetic, butyric, and propionic groups of acidogenic bacteria producing the particular products were considered. The additional group of homoacetogenic bacteria producing acetate from hydrogen and carbon dioxide was involved into new version of the model. Ammonia and hydrogen sulfide inhibition were described previously. In that paper, it was shown by simulation of several case-studies that unionized volatile fatty acids (VFA) are the inhibitors of key stages of anaerobic conversion of complex organic matter: hydrolysis, acetogenesis and methanogenesis.

  2. 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

  3. Optical modeling of sunlight by using partially coherent sources in organic solar cells.

    PubMed

    Alaibakhsh, Hamzeh; Darvish, Ghafar

    2016-03-01

    We investigate the effects of coherent and partially coherent sources in optical modeling of organic solar cells. Two different organic solar cells are investigated: one without substrate and the other with a millimeter-sized glass substrate. The coherent light absorption is calculated with rigorous coupled-wave analysis. The result of this method is convolved with a distribution function to calculate the partially coherent light absorption. We propose a new formulation to accurately model sunlight as a set of partially coherent sources. In the structure with glass substrate, the accurate sunlight modeling results in the elimination of coherent effects in the thick substrate, but the coherency in other layers is not affected. Using partially coherent sources instead of coherent sources for simulations with sunlight results in a smoother absorption spectrum, but the change in the absorption efficiency is negligible.

  4. A multilayer self-organizing model for convex-hull computation.

    PubMed

    Pal, S; Datta, A; Pal, N R

    2001-01-01

    A self-organizing neural-network model is proposed for computation of the convex-hull of a given set of planar points. The network evolves in such a manner that it adapts itself to the hull-vertices of the convex-hull. The proposed network consists of three layers of processors. The bottom layer computes some angles which are passed to the middle layer. The middle layer is used for computation of the minimum angle (winner selection). These information are passed to the topmost layer as well as fed back to the bottom layer. The network in the topmost layer self-organizes by labeling the hull-processors in an orderly fashion so that the final convex-hull is obtained from the topmost layer. Time complexity of the proposed model is analyzed and is compared with existing models of similar nature.

  5. 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.

  6. Hyperbolic and kinetic models for self-organized biological aggregations and movement: a brief review.

    PubMed

    Eftimie, Raluca

    2012-07-01

    We briefly review hyperbolic and kinetic models for self-organized biological aggregations and traffic-like movement. We begin with the simplest models described by an advection-reaction equation in one spatial dimension. We then increase the complexity of models in steps. To this end, we begin investigating local hyperbolic systems of conservation laws with constant velocity. Next, we proceed to investigate local hyperbolic systems with density-dependent speed, systems that consider population dynamics (i.e., birth and death processes), and nonlocal hyperbolic systems. We conclude by discussing kinetic models in two spatial dimensions and their limiting hyperbolic models. This structural approach allows us to discuss the complexity of the biological problems investigated, and the necessity for deriving complex mathematical models that would explain the observed spatial and spatiotemporal group patterns.

  7. 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.

  8. 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

  9. Structure of Spontaneous UP and DOWN Transitions Self-Organizing in a Cortical Network Model

    PubMed Central

    Kang, Siu; Kitano, Katsunori; Fukai, Tomoki

    2008-01-01

    Synaptic plasticity is considered to play a crucial role in the experience-dependent self-organization of local cortical networks. In the absence of sensory stimuli, cerebral cortex exhibits spontaneous membrane potential transitions between an UP and a DOWN state. To reveal how cortical networks develop spontaneous activity, or conversely, how spontaneous activity structures cortical networks, we analyze the self-organization of a recurrent network model of excitatory and inhibitory neurons, which is realistic enough to replicate UP–DOWN states, with spike-timing-dependent plasticity (STDP). The individual neurons in the self-organized network exhibit a variety of temporal patterns in the two-state transitions. In addition, the model develops a feed-forward network-like structure that produces a diverse repertoire of precise sequences of the UP state. Our model shows that the self-organized activity well resembles the spontaneous activity of cortical networks if STDP is accompanied by the pruning of weak synapses. These results suggest that the two-state membrane potential transitions play an active role in structuring local cortical circuits. PMID:18369421

  10. A conceptual model of psychosomatic illness in children. Family organization and family therapy.

    PubMed

    Minuchin, S; Baker, L; Rosman, B L; Liebman, R; Milman, L; Todd, T C

    1975-08-01

    Linear and open systems (multiple feedback) models of psychosomatic illness in children are contrasted in terms of their implications for cause and treatment. An open systems family model is presented that describes three necessary (but not independently sufficient) conditions for the development and maintenance of severe psychosomatic problems in children: (1) a certain type of family organization that encourages somatization; (2) involvement of the child in parental conflict; and (3) physiological vulnerability. Predisposition for psychosomatic illness, symptom choice, and maintenance are discussed within this conceptual framework. We report on family therapy strategies based on this model and the results of family treatment with 48 cases of "brittle" diabetes, psychosomatic asthma, and anorexia nervosa.

  11. 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.

  12. 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

  13. Modeling substorm dynamics of the magnetosphere: from self-organization and self-organized criticality to nonequilibrium phase transitions.

    PubMed

    Sitnov, M I; Sharma, A S; Papadopoulos, K; Vassiliadis, D

    2002-01-01

    Earth's magnetosphere during substorms exhibits a number of characteristic features such as the signatures of low effective dimension, hysteresis, and power-law spectra of fluctuations on different scales. The largest substorm phenomena are in reasonable agreement with low-dimensional magnetospheric models and in particular those of inverse bifurcation. However, deviations from the low-dimensional picture are also quite considerable, making the nonequilibrium phase transition more appropriate as a dynamical analog of the substorm activity. On the other hand, the multiscale magnetospheric dynamics cannot be limited to the features of self-organized criticality (SOC), which is based on a class of mathematical analogs of sandpiles. Like real sandpiles, during substorms the magnetosphere demonstrates features, that are distinct from SOC and are closer to those of conventional phase transitions. While the multiscale substorm activity resembles second-order phase transitions, the largest substorm avalanches are shown to reveal the features of first-order nonequilibrium transitions including hysteresis phenomena and a global structure of the type of a temperature-pressure-density diagram. Moreover, this diagram allows one to find a critical exponent, that reflects the multiscale aspect of the substorm activity, different from the power-law frequency and scale spectra of autonomous systems, although quite consistent with second-order phase transitions. In contrast to SOC exponents, this exponent relates input and output parameters of the magnetosphere. Using an analogy to the dynamical Ising model in the mean-field approximation, we show the connection between the data-derived exponent of nonequilibrium transitions in the magnetosphere and the standard critical exponent beta of equilibrium second-order phase transitions.

  14. An integrated model for continuous quality improvement and productivity improvement in health services organizations.

    PubMed

    Rakich, J S; Darr, K; Longest, B B

    1993-01-01

    The health services paradigm with respect to quality has shifted to that of conformance to requirements (the absence of defects) and fitness for use (meeting customer expectations and needs). This article presents an integrated model of continuous quality improvement (CQI) (often referred to as total quality management) and productivity improvement for health services organizations. It incorporates input-output theory and focuses on the CQI challenge--"How can we be certain that we do the right things right the first time, every time?" The twin pillars of CQI are presented. Achievement of both will result in productivity improvement and enhancement of the health services organization's competitive position.

  15. A material sensitivity study on the accuracy of deformable organ registration using linear biomechanical models.

    PubMed

    Chi, Y; Liang, J; Yan, D

    2006-02-01

    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

  16. 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

  17. 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

  18. Organ Culture as a Model System for Studies on Enterotoxin Interactions with the Intestinal Epithelium.

    PubMed

    Lorenzen, Ulver Spangsberg; Hansen, Gert H; Danielsen, E Michael

    2016-01-01

    Studies on bacterial enterotoxin-epithelium interactions require model systems capable of mimicking the events occurring at the molecular and cellular levels during intoxication. In this chapter, we describe organ culture as an often neglected alternative to whole-animal experiments or enterocyte-like cell lines. Like cell culture, organ culture is versatile and suitable for studying rapidly occurring events, such as enterotoxin binding and uptake. In addition, it is advantageous in offering an epithelium with more authentic permeability/barrier properties than any cell line, as well as a subepithelial lamina propria, harboring the immune cells of the gut mucosa.

  19. Ellsworth C. Dougherty: A Pioneer in the Selection of Caenorhabditis elegans as a Model Organism.

    PubMed

    Ferris, Howard; Hieb, W F

    2015-08-01

    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.

  20. Use of Artificial Neural Network Models to Predict Indicator Organism Concentrations in an Urban Watershed

    NASA Astrophysics Data System (ADS)

    Mas, D. M.; Ahlfeld, D. P.

    2004-05-01

    Forecasting stream water quality is important for numerous aspects of resource protection and management. Fecal coliform and enteroccocus are primary indicator organisms used to assess potential pathogen contamination. Consequently, modeling the occurrence and concentration of fecal coliform and enterococcus is an important tool in watershed management. In addition, analyzing the relationship between model input and predicted indicator organisms is useful for elucidating possible sources of contamination and mechanisms of transport. While many process-based, statistical, and empirical models exist for water quality prediction, artificial neural network (ANN) models are increasingly being used for forecasting of water resources variables because ANNs are often capable of modeling complex systems for which behavioral rules are either unknown or difficult to simulate. The performance of ANNs compared to more established modeling approaches such as multiple linear regression (MLR) remains an importance research question. Data collected the U.S. Geological Survey in the lower Charles River in Massachusetts, USA in 1999-2000 was examined to determine correlation between various water quality constituents and indicator organisms and to explore the relationship between rainfall characteristics and indicator organism concentrations. Using the results of the statistical analysis to guide the selection of explanatory variables, MLR was performed to develop predictive equations for wet weather and dry weather conditions. The results show that the best-performing predictor variables are generally consistent for both indicator organisms considered. In addition, the regression equations show increasing indicator organism concentrations as a function of suspended sediment concentrations and length of time since last precipitation event, suggesting accumulation and wash off as a key mechanism of pathogen transport under wet weather conditions. This research also presents the

  1. 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).

  2. Variable C : N : P stoichiometry of dissolved organic matter cycling in the Community Earth System Model

    DOE PAGES

    Letscher, R. T.; Moore, J. K.; Teng, Y. -C.; ...

    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

  3. The Zebrafish Model Organism Database: new support for human disease models, mutation details, gene expression phenotypes and searching.

    PubMed

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

    2017-01-04

    The Zebrafish Model Organism Database (ZFIN; http://zfin.org) is the central resource for zebrafish (Danio rerio) genetic, genomic, phenotypic and developmental data. ZFIN curators provide expert manual curation and integration of comprehensive data involving zebrafish genes, mutants, transgenic constructs and lines, phenotypes, genotypes, gene expressions, morpholinos, TALENs, CRISPRs, antibodies, anatomical structures, models of human disease and publications. We integrate curated, directly submitted, and collaboratively generated data, making these available to zebrafish research community. Among the vertebrate model organisms, zebrafish are superbly suited for rapid generation of sequence-targeted mutant lines, characterization of phenotypes including gene expression patterns, and generation of human disease models. The recent rapid adoption of zebrafish as human disease models is making management of these data particularly important to both the research and clinical communities. Here, we describe recent enhancements to ZFIN including use of the zebrafish experimental conditions ontology, 'Fish' records in the ZFIN database, support for gene expression phenotypes, models of human disease, mutation details at the DNA, RNA and protein levels, and updates to the ZFIN single box search.

  4. The Zebrafish Model Organism Database: new support for human disease models, mutation details, gene expression phenotypes and searching

    PubMed Central

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

    2017-01-01

    The Zebrafish Model Organism Database (ZFIN; http://zfin.org) is the central resource for zebrafish (Danio rerio) genetic, genomic, phenotypic and developmental data. ZFIN curators provide expert manual curation and integration of comprehensive data involving zebrafish genes, mutants, transgenic constructs and lines, phenotypes, genotypes, gene expressions, morpholinos, TALENs, CRISPRs, antibodies, anatomical structures, models of human disease and publications. We integrate curated, directly submitted, and collaboratively generated data, making these available to zebrafish research community. Among the vertebrate model organisms, zebrafish are superbly suited for rapid generation of sequence-targeted mutant lines, characterization of phenotypes including gene expression patterns, and generation of human disease models. The recent rapid adoption of zebrafish as human disease models is making management of these data particularly important to both the research and clinical communities. Here, we describe recent enhancements to ZFIN including use of the zebrafish experimental conditions ontology, ‘Fish’ records in the ZFIN database, support for gene expression phenotypes, models of human disease, mutation details at the DNA, RNA and protein levels, and updates to the ZFIN single box search. PMID:27899582

  5. 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

  6. 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

  7. Universal predictive models on octanol-air partition coefficients at different temperatures for persistent organic pollutants.

    PubMed

    Chen, Jingwen; Harner, Tom; Ding, Guanghui; Quan, Xie; Schramm, Karl-Werner; Kettrup, Antonius

    2004-10-01

    Owing to the importance of octanol-air partition coefficients (KOA) in describing the partition of organic pollutants from air to environmental organic phases, the paucity of KOA data at different environmental temperatures, and the difficulty or high expenditures involved in experimental determination, the development of predictive models for KOA is necessary. Approaches such as this are greatly needed to evaluate the environmental fate of the ever-increasing list of production chemicals. Partial least squares (PLS) regression with 18 molecular structural descriptors was used to develop predictive models based on directly measured KOA values of selected chlorobenzenes, polychlorinated biphenyls (PCBs), polychlorinated naphthalenes, polychlorinated dibenzo-p-dioxins/dibenzofurans, polybrominated diphenyl ethers, polycyclic aromatic hydrocarbons, and organochlorine pesticides (OPs). An optimization procedure resulted in two temperature-dependent universal predictive models that explained at least 91 % of the variance of log KOA. Model 1 was the more general of the two models that could be used for all the persistent organic pollutant (POP) classes investigated. Although model 1 performed poorly for select OPs, this was attributed to wide variability in structural types within this subset of POPs and their diversity compared to the other POP classes that were investigated. The exclusion of the structurally complex OP subset resulted in a more precise model, model 5. Intermolecular dispersive interactions (induced dipole-induced dipole forces) between octanol and solute molecules play a decisive role in governing KOA and its temperature dependence. Further investigations are needed to better characterize the steric structures of the POPs under study, especially of OPs.

  8. Theoretical model for mesoscopic-level scale-free self-organization of functional brain networks.

    PubMed

    Piersa, Jaroslaw; Piekniewski, Filip; Schreiber, Tomasz

    2010-11-01

    In this paper, we provide theoretical and numerical analysis of a geometric activity flow network model which is aimed at explaining mathematically the scale-free functional graph self-organization phenomena emerging in complex nervous systems at a mesoscale level. In our model, each unit corresponds to a large number of neurons and may be roughly seen as abstracting the functional behavior exhibited by a single voxel under functional magnetic resonance imaging (fMRI). In the course of the dynamics, the units exchange portions of formal charge, which correspond to waves of activity in the underlying microscale neuronal circuit. The geometric model abstracts away the neuronal complexity and is mathematically tractable, which allows us to establish explicit results on its ground states and the resulting charge transfer graph modeling functional graph of the network. We show that, for a wide choice of parameters and geometrical setups, our model yields a scale-free functional connectivity with the exponent approaching 2, which is in agreement with previous empirical studies based on fMRI. The level of universality of the presented theory allows us to claim that the model does shed light on mesoscale functional self-organization phenomena of the nervous system, even without resorting to closer details of brain connectivity geometry which often remain unknown. The material presented here significantly extends our previous work where a simplified mean-field model in a similar spirit was constructed, ignoring the underlying network geometry.

  9. 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.

  10. Community organizing goes to college: A practice-based model of community organizing to implement environmental strategies to reduce high-risk drinking on college campuses

    PubMed Central

    Wagoner, Kimberly G.; Rhodes, Scott D.; Lentz, Ashley W.; Wolfson, Mark

    2013-01-01

    Community organizing is a successful method to leverage resources and build community capacity to identify and intervene upon health issues. However, published accounts documenting the systematic facilitation of the process are limited. This qualitative analysis explored community organizing using data collected as part of the Study to Prevent Alcohol Related Consequences (SPARC), a randomized community trial of 10 North Carolina colleges focused on reducing consequences of high-risk drinking among college students. We sought to develop and confirm use of a community-organizing model, based in practice, illustrating an authentic process of organizing campus and community stakeholders for public health change. Using the grounded theory approach, we analyzed and interpreted data from three waves of individual interviews with full-time community organizers on five SPARC intervention campuses. A five-phase community-organizing model was developed and its use was confirmed. This model may serve as a practical guide for public health interventions utilizing community-organizing approaches. PMID:20530638

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. Prediction of the thermal decomposition of organic peroxides by validated QSPR models.

    PubMed

    Prana, Vinca; Rotureau, Patricia; Fayet, Guillaume; André, David; Hub, Serge; Vicot, Patricia; Rao, Li; Adamo, Carlo

    2014-07-15

    Organic peroxides are unstable chemicals which can easily decompose and may lead to explosion. Such a process can be characterized by physico-chemical parameters such as heat and temperature of decomposition, whose determination is crucial to manage related hazards. These thermal stability properties are also required within many regulatory frameworks related to chemicals in order to assess their hazardous properties. In this work, new quantitative structure-property relationships (QSPR) models were developed to predict accurately the thermal stability of organic peroxides from their molecular structure respecting the OECD guidelines for regulatory acceptability of QSPRs. Based on the acquisition of 38 reference experimental data using DSC (differential scanning calorimetry) apparatus in homogenous experimental conditions, multi-linear models were derived for the prediction of the decomposition heat and the onset temperature using different types of molecular descriptors. Models were tested by internal and external validation tests and their applicability domains were defined and analyzed. Being rigorously validated, they presented the best performances in terms of fitting, robustness and predictive power and the descriptors used in these models were linked to the peroxide bond whose breaking represents the main decomposition mechanism of organic peroxides.

  16. Modeling the Multiday Evolution and Aging of Secondary Organic Aerosol During MILAGRO 2006

    SciTech Connect

    Dzepina, K.; Cappa, Christopher D.; Volkamer, Rainer M.; Madronich, Sasha; DeCarlo, Peter; Zaveri, Rahul A.; Jimenez, Jose L.

    2011-03-22

    In this study we apply several recently-proposed models to the evolution of secondary organic aerosols (SOA) and organic gases advected from downtown Mexico City at an altitude of ~3.5 km during three days of aging. We constrain the model with and compare its results to available observations. The model SOA formed from oxidation of volatile organic compounds (V-SOA) when using the aromatic SOA parameterization of Ng et al. (2007) cannot explain the observed SOA concentrations in aged pollution, even as the low-NOx channel becomes more important away from the city. However, when using the aromatic SOA parameterization of Tsimpidi et al. (2010), V-SOA alone is similar to the regional aircraft observations, highlighting the wide diversity in current V-SOA formulations. When the SOA formed from oxidation of both semivolatile and intermediate volatility organic vapors (SI-SOA) is computed following Robinson et al. (2007) the model matches the observed SOA mass, but its O/C is too low by a factor of 2. With the parameterization of Grieshop et al. (2009) the total SOA mass is overpredicted by a factor of ~2 but O/C and volatility are closer to the observations. Heating or dilution of the air results in evaporation of a substantial fraction of the model SOA; this fraction is reduced by aging although differently for heating vs. dilution. Finally, lifting of the airmass tothe free-troposphere during dry convection results in a substantial increase of SOA bycondensation of semivolatile vapors, with this effect being reduced by aging.

  17. 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.

  18. Numerical Modeling of Immiscible Organic Transport at the Hyde Park Landfill

    NASA Astrophysics Data System (ADS)

    Osborne, M.; Sykes, J.

    1986-01-01

    In this paper, a two-dimensional two-phase mathematical model based on Darcy's law and conservation of mass for each liquid is presented. The numerical model is based on a generalized method of weighted residuals in conjunction with the finite element method and linear quadrilateral isoparametric elements. To alleviate numerical problems associated with hyperbolic equations, upstream weighting of the spatial terms in the model has been incorporated. The theoretical and numerical accuracy of the model is verified by comparison of simulation results with those from an existing one-dimensional two-phase flow simulator. The finite element model is used to simulate the migration of an immiscible organic solvent in groundwater, from a chemical waste disposal site located north of Niagara Falls, New York. The effects of uncertainty regarding porous media heterogeneities and anisotropy are examined, and it is concluded that the extent of immiscible contaminant migration is greatly sensitive to these parameters.

  19. A segregated model for plasmid content and product synthesis in unstable binary fission recombinant organisms.

    PubMed

    Seo, J H; Bailey, J E

    1985-02-01

    Plasmid propagation in populations of unstable, binary fission recombinant organisms has been studied using a segregated, population balance mathematical model. Segregated models have the advantage of direct incorporation of basic information on mechanisms and kinetics of plasmid replication and segregation at the single-cell level. The distribution of cellular plasmid content and specific rates of plasmid gene expression have been obtained for several single-cell models of plasmid replication, partition, and gene expression. Plasmid replication kinetics during cell growth significantly influence the plasmid content distribution. In the case of transient growth of plasmid-containing and plasmid-free cells in partially selective medium, the degree of selection required for stable maintenance of plasmid-containing cells has been determined. Guidelines are presented for applicability of simpler, nonsegregated models and for evaluation of the parameters in these models based on single-cell mechanisms and associated parameters.

  20. A student leadership model for promoting educational programs in organ donation and transplantation.

    PubMed

    Reville, P; Zhao, C; Perez, T; Nowacki, A S; Phillips, D; Bowen, G; Starling, N; Pflaum, B; Strickland, R; Fung, J; Askar, M

    2013-05-01

    The global organ shortage is the strongest factor for the increase in transplant wait time and deaths on waitlists. Here we describe a model for involving high school students in education research around organ donation and transplantation and capitalize on the strength of a pre-existing educational program offered by the local organ procurement organization (OPO). While training in education research at Cleveland Clinic, a high school student embarked on a collaborative project with the local OPO. The project involved evaluating three educational programs, selecting the most appropriate program for administration at her school, coordinating with the student's school administration and teachers, administering an assessment tool for the effectiveness of the program, and analyzing the results. The local OPO program that was selected for implementation consisted of a video presentation entitled "Share your life, share your decision" prepared by the United States Health Resources and Services Administration (HRSA), lectures by invited speakers and an educational assessment (pre- and post-education). The assessment survey included 3 multiple choice and 7 true/false questions. Compared to the over 2500 programs administered in the last 5 years by the local OPO, this program had a higher volume of participation (n = 353 compared to an average of 150 students/day). Students correctly classified transplantation status of more organ and tissues post-education (P < .0001 for both). For 5 out of the 7 true/false questions, students correctly answered questions more frequently post-education (P ≤ .002 for all). This experience included for the first time a formal assessment of the program which will be utilized to address targeted areas for specific improvements. This student collaborative model of involving students in organ donation and transplantation related education research has the potential to promote and maximize the effectiveness of educational programs targeting

  1. 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.

  2. A model organism for new gene discovery by cDNA sequencing

    SciTech Connect

    El-Saved, N.M.; Donelson, J.E.; Alarcon, C.M.

    1994-09-01

    One method of new gene discovery is single pass sequencing of cDNAs to identify expressed sequence tags (ESTs). Model organisms can have biological properties which makes their use advantageous over studies with humans. One such model organism with advantages for cDNA sequencing is the African trypanosome T. brucei rhodesiense. This organism has the same 40 nucleotide sequence (splice leader sequence) on the 5{prime} end of all mRNAs. We have constructed a 5{prime} cDNA library by priming off the splice leader sequence and have begun sequencing this cDNA library. To date, over nearly 500 such cDNA expressed sequence tags (ESTs) have been examined. Forty-three percent of the sequences sampled from the trypanosome cDNA library have significant similarities to sequences already in the protein and translated nucleic acid databases. Among these are cDNA sequences which encode previously reported T. brucej proteins such as the VSG, tubulin, calflagin, etc., and proteins previously identified in other trypanosomatids. Other cDNAs display significant similarities to genes in unrelated organisms encoding several ribosomal proteins, metabolic enzymes, GTP binding proteins, transcription factors, cyclophillin, nucleosomal histones, histone H1, and a macrophage stress protein, among others. The 57% of the cDNAs that are not similar to sequences currently in the databases likely encode both trypanosome-specific proteins and housekeeping proteins shared with other eukaryotes. These cDNA ESTs provide new avenues of research for exploring both the biochemistry and the genome organization of this parasite, as well as a resource for identifying the 5{prime} sequence of novel genes likely to have homology to genes expressed in other organisms.

  3. 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.

  4. Separation of organic pollutants by reverse osmosis and nanofiltration membranes: Mathematical models and experimental verification

    SciTech Connect

    Williams, M.E.; Hestekin, J.A.; Smothers, C.N.; Bhattacharyya, D.

    1999-10-01

    Predictive reverse osmosis (RO) models have been well-developed for many systems. However, the applications to dilute organic-water systems require the modification of transport models and the understanding of solute-polymer interactions. Studies with various substituted, nonionized phenolic compounds showed that these could cause substantial membrane water flux drop, even in dilute solutions with negligible osmotic pressure. Further, the organics could significantly adsorb on the cross-linked aromatic polyamide active layer. In some cases, even concentrations as low as 0.2 mM, 2,4-dinitrophenol (solution in particle-free, double-distilled water) can cause as much as a 70% flux drop with an aromatic polyamide membrane. Two models are presented in this paper: a modified steady-state solution diffusion model and an unsteady-state diffusion adsorption model which are able to predict flux and permeate concentrations from a single RO experiment. Further, the development of these models allows for the understanding of the mechanisms of organic-membrane interactions. For instance, it has been proposed that increased adsorption inherently leads to an increase in flux drop. However, the authors have found, on one hand, that due to specific interactions with membrane water transport groups, chloro-, and nitro-substituted phenols cause significant flux drops. On the other hand, benzene had a high physical adsorption but caused negligible flux drop. The results were further extended to nanofiltration experiments with an aromatic pollutant containing two types of charge groups. The adsorption and separation results are explained according to an ionization model.

  5. 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

  6. 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.

  7. 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...

  8. Using cell and organ culture models to analyze responses of bone cells to mechanical stimulation.

    PubMed

    Pitsillides, Andrew A; Rawlinson, Simon C F

    2012-01-01

    Bone cells of the osteoblastic lineage are responsive to the local mechanical environment. Through integration of a number of possible loading-induced regulatory stimuli, osteocyte, osteoblast, and osteoclast behaviour is organized to fashion a skeletal element of sufficient strength and toughness to resist fracture and crack propagation. Early pre-osteogenic responses had been determined in vivo and this led to the development of bone organ culture models to elucidate other pre-osteogenic responses where osteocytes and osteoblasts retain the natural orientation, connections and attachments to their native extracellular matrix. The application of physiological mechanical loads to bone in these organ culture models generates the regulatory stimuli. As a consequence, these experiments can be used to illustrate the distinctive mechanisms by which osteocytes and osteoblasts respond to mechanical loads and also differences in these responses, suggesting co-ordinated and cooperatively between cell populations. Organ explant cultures are awkward to maintain, and have a limited life, but length of culture times are improving. Monolayer cultures are much easier to maintain and permit the application of a particular mechanical stimulation to be studied in isolation; mainly direct mechanical strain or fluid shear strains. These allow for the response of a single cell type to the applied mechanical stimulation to be monitored precisely.The techniques that can be used to apply mechanical strain to bone and bone cells have not advanced greatly since the first edition. The output from such experiments has, however, increased substantially and their importance is now more broadly accepted. This suggests a growing use of these approaches and an increasing awareness of the importance of the mechanical environment in controlling normal bone cell behaviour. We expand the text to include additions and modifications made to the straining apparatus and update the research cited to

  9. Role of sedimentary organic matter in bacterial sulfate reduction: the G model tested

    SciTech Connect

    Westrich, J.T.; Berner, R.A.

    1984-03-01

    Laboratory study of the bacterial decomposition of Long Island Sound plankton in oxygenated seawater over a period of 2 years shows that the organic material undergoes decomposition via first-order kinetics and can be divided into two decomposable fractions, of considerably different reactivity, and a nonmetabolized fraction. This planktonic material, after undergoing varying degrees of oxic degradation, was added in the laboratory to anoxic sediment taken from a depth of 1 m at the NWC site of Long Island Sound and the rate of bacterial sulfate reduction in the sediment measured by the /sup 35/S radiotracer technique. The stimulated rate of sulfate reduction was in direct proportion to the amount of planktonic carbon added. This provides direct confirmation of the first-order decomposition, or G model, for marine sediments and proves that the in situ rate of sulfate reduction is organic-matter limited. Slower sulfate reduction rates resulted when oxically degraded plankton rather than fresh plankton was added, and the results confirm the presence of the same two fractions of organic matter deduced from the oxic degradation studies. Near-surface Long Island Sound sediment, which already contains abundant readily decomposable organic matter, was also subjected to anoxic decomposition by bacterial sulfate reduction. The decrease in sulfate reduction rate with time parallels decreases in the amount of organic matter, and these results also indicate the presence of two fractions of organic carbon of distinctly different reactivity. From plots of the log of reduction rate vs. time two first-order rate constants were obtained that agree well with those derived from the plankton addition experiment. Together, the two experiments confirm the use of a simple multi-first-order rate law for organic matter decomposition in marine sediments.

  10. Modeling short-term variability of semivolatile organic chemicals in air at a local scale: an integrated modeling approach.

    PubMed

    Morselli, Melissa; Ghirardello, Davide; Semplice, Matteo; Di Guardo, Antonio

    2011-05-01

    Monitoring campaigns from different locations have recently shown how air concentrations of persistent semivolatile contaminants such as polychlorinated biphenyls (PCBs) often exhibit short-term (less than 24 h) variations. The observed patterns have been ascribed to different factors, such as temperature-mediated air-surface exchange and variability of planetary boundary layer (PBL) height and dynamics. Here, we present a new modeling approach developed in order to investigate the short-term variability in air concentrations of organic pollutants at a local scale. A new dynamic multimedia box model is supplied by a meteorological preprocessor (AERMET) with hourly values of air compartment height and wind speed. The resulting model is tested against an existing dataset of PCB air concentrations measured in Zurich, Switzerland. Results show the importance of such modeling approach in elucidating the short- and long-term behavior of semivolatile contaminants in the air/soil system.

  11. 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.

  12. Ultrafast traveling wave dominates the electric organ discharge of Apteronotus leptorhynchus: an inverse modelling study.

    PubMed

    Shifman, Aaron R; Longtin, André; Lewis, John E

    2015-10-30

    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.

  13. 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.

  14. Ecotoxicogenomic approaches for understanding molecular mechanisms of environmental chemical toxicity using aquatic invertebrate, Daphnia model organism.

    PubMed

    Kim, Hyo Jeong; Koedrith, Preeyaporn; Seo, Young Rok

    2015-05-29

    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.

  15. 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

  16. 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

  17. MyMpn: a database for the systems biology model organism Mycoplasma pneumoniae.

    PubMed

    Wodke, Judith A H; Alibés, Andreu; Cozzuto, Luca; Hermoso, Antonio; Yus, Eva; Lluch-Senar, Maria; Serrano, Luis; Roma, Guglielmo

    2015-01-01

    MyMpn (http://mympn.crg.eu) is an online resource devoted to studying the human pathogen Mycoplasma pneumoniae, a minimal bacterium causing lower respiratory tract infections. Due to its small size, its ability to grow in vitro, and the amount of data produced over the past decades, M. pneumoniae is an interesting model organisms for the development of systems biology approaches for unicellular organisms. Our database hosts a wealth of omics-scale datasets generated by hundreds of experimental and computational analyses. These include data obtained from gene expression profiling experiments, gene essentiality studies, protein abundance profiling, protein complex analysis, metabolic reactions and network modeling, cell growth experiments, comparative genomics and 3D tomography. In addition, the intuitive web interface provides access to several visualization and analysis tools as well as to different data search options. The availability and--even more relevant--the accessibility of properly structured and organized data are of up-most importance when aiming to understand the biology of an organism on a global scale. Therefore, MyMpn constitutes a unique and valuable new resource for the large systems biology and microbiology community.

  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. Parameterizing liquid crystal variable retarder structural organization with a fractal-Born approximation model

    NASA Astrophysics Data System (ADS)

    Gladish, James C.; Duncan, Donald D.

    2016-05-01

    Liquid crystal variable retarders (LCVRs) are computer-controlled birefringent devices that contain nanometer-sized birefringent liquid crystals (LCs). These devices impart retardance effects through a global, uniform orientation change of the LCs, which is based on a user-defined drive voltage input. In other words, the LC structural organization dictates the device functionality. The LC structural organization also produces a spectral scatter component which exhibits an inverse power law dependence. We investigate LC structural organization by measuring the voltage-dependent LC spectral scattering signature with an integrating sphere and then relate this observable to a fractal-Born model based on the Born approximation and a Von Kármán spectrum. We obtain LCVR light scattering spectra at various drive voltages (i.e., different LC orientations) and then parameterize LCVR structural organization with voltage-dependent correlation lengths. The results can aid in determining performance characteristics of systems using LCVRs and can provide insight into interpreting structural organization measurements.

  20. Confinement-Induced Glassy Dynamics in a Model for Chromosome Organization

    NASA Astrophysics Data System (ADS)

    Kang, Hongsuk; Yoon, Young-Gui; Thirumalai, D.; Hyeon, Changbong

    2015-11-01

    Recent experiments showing scaling of the intrachromosomal contact probability, P (s )˜s-1 with the genomic distance s , are interpreted to mean a self-similar fractal-like chromosome organization. However, scaling of P (s ) varies across organisms, requiring an explanation. We illustrate dynamical arrest in a highly confined space as a discriminating marker for genome organization, by modeling chromosomes inside a nucleus as a homopolymer confined to a sphere of varying sizes. Brownian dynamics simulations show that the chain dynamics slows down as the polymer volume fraction (ϕ ) inside the confinement approaches a critical value ϕc. The universal value of ϕc∞≈0.44 for a sufficiently long polymer (N ≫1 ) allows us to discuss genome dynamics using ϕ as the sole parameter. Our study shows that the onset of glassy dynamics is the reason for the segregated chromosome organization in humans (N ≈3 ×109, ϕ ≳ϕc∞), whereas chromosomes of budding yeast (N ≈108, ϕ <ϕc∞) are equilibrated with no clear signature of such organization.