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Sample records for replicated actively-used permeable

  1. Permeability of Aluminium Foams Produced by Replication Casting

    Directory of Open Access Journals (Sweden)

    Maxim L. Cherny

    2012-12-01

    Full Text Available The replication casting process is used for manufacturing open-pore aluminum foams with advanced performances, such as stability and repeatability of foam structure with porosity over 60%. A simple foam structure model based on the interaction between sodium chloride solid particles poorly wetted by melted aluminum, which leads to the formation of air pockets (or “air collars”, is proposed for the permeability of porous material. The equation for the minimum pore radius of replicated aluminum foam is derived. According to the proposed model, the main assumption of the permeability model consists in a concentration of flow resistance in a circular aperture of radius rmin. The permeability of aluminum open-pore foams is measured using transformer oil as the fluid, changing the fractions of initial sodium chloride. Measured values of minimum pore size are close to theoretically predicted ones regardless of the particle shape. The expression for the permeability of replicated aluminum foam derived on the basis of the “bottleneck” model of porous media agrees well with the experimental data. The obtained data can be applied for commercial filter cells and pneumatic silencers.

  2. Three-dimensional quantitative structure-permeability relationship analysis for a series of inhibitors of rhinovirus replication.

    Science.gov (United States)

    Ekins, S; Durst, G L; Stratford, R E; Thorner, D A; Lewis, R; Loncharich, R J; Wikel, J H

    2001-01-01

    Multiple three-dimensional quantitative structure-activity relationship (3D-QSAR) approaches were applied to predicting passive Caco-2 permeability for a series of 28 inhibitors of rhinovirus replication. Catalyst, genetic function approximation (GFA) with MS-WHIM descriptors, CoMFA, and VolSurf were all used for generating 3D-quantitative structure permeability relationships utilizing a training set of 19 molecules. Each of these approaches was then compared using a test set of nine molecules not present in the training set. Statistical parameters for the test set predictions (r(2) and leave-one-out q(2)) were used to compare the models. It was found that the Catalyst pharmacophore model was the most predictive (test set of predicted versus observed permeability, r(2) = 0.94). This model consisted of a hydrogen bond acceptor, hydrogen bond donor, and ring aromatic feature with a training set correlation of r(2) = 0.83. The CoMFA model consisted of three components with an r(2) value of 0.96 and produced good predictions for the test set (r(2) = 0.84). VolSurf resulted in an r(2) value of 0.76 and good predictions for the test set (r(2) = 0.83). Test set predictions with GFA/WHIM descriptors (r(2) = 0.46) were inferior when compared with the Catalyst, CoMFA, and VolSurf model predictions in this evaluation. In summary it would appear that the 3D techniques have considerable value in predicting passive permeability for a congeneric series of molecules, representing a valuable asset for drug discovery.

  3. Notional Permeability

    NARCIS (Netherlands)

    Kik, R.; Van den Bos, J.P.; Maertens, J.; Verhagen, H.J.; Van der Meer, J.W.

    2012-01-01

    Different layer design of a rock slope and under layers has a large effect on the strengths on the rock slope itself. In the stability formula developed of VAN DER MEER [1988] this effect is represented by the term Notional Permeability with symbol P. A more open, or permeable, structure underneath

  4. Notional Permeability

    OpenAIRE

    Kik, R.; Van den Bos, J.P.; Maertens, J.; Verhagen, H.J.; van der Meer, J W

    2012-01-01

    Different layer design of a rock slope and under layers has a large effect on the strengths on the rock slope itself. In the stability formula developed of VAN DER MEER [1988] this effect is represented by the term Notional Permeability with symbol P. A more open, or permeable, structure underneath the armour layer has the ability to dissipate more wave energy and therefore requires less weight of the armour layer. The influence of this parameter is thus very important in economic sense. Up u...

  5. Cell cycle profiling by image and flow cytometry: The optimised protocol for the detection of replicational activity using 5-Bromo-2′-deoxyuridine, low concentration of hydrochloric acid and exonuclease III

    Science.gov (United States)

    Konečný, Petr; Frydrych, Ivo; Koberna, Karel

    2017-01-01

    The approach for the detection of replicational activity in cells using 5-bromo-2′-deoxyuridine, a low concentration of hydrochloric acid and exonuclease III is presented in the study. The described method was optimised with the aim to provide a fast and robust tool for the detection of DNA synthesis with minimal impact on the cellular structures using image and flow cytometry. The approach is based on the introduction of breaks into the DNA by the low concentration of hydrochloric acid followed by the subsequent enzymatic extension of these breaks using exonuclease III. Our data showed that the method has only a minimal effect on the tested protein localisations and is applicable both for formaldehyde- and ethanol-fixed cells. The approach partially also preserves the fluorescence of the fluorescent proteins in the HeLa cells expressing Fluorescent Ubiquitin Cell Cycle Indicator. In the case of the short labelling pulses that disabled the use of 5-ethynyl-2′-deoxyuridine because of the low specific signal, the described method provided a bright signal enabling reliable recognition of replicating cells. The optimized protocol was also successfully tested for the detection of trifluridine, the nucleoside used as an antiviral drug and in combination with tipiracil also for the treatment of some types of cancer. PMID:28426799

  6. Cell cycle profiling by image and flow cytometry: The optimised protocol for the detection of replicational activity using 5-Bromo-2'-deoxyuridine, low concentration of hydrochloric acid and exonuclease III.

    Science.gov (United States)

    Ligasová, Anna; Konečný, Petr; Frydrych, Ivo; Koberna, Karel

    2017-01-01

    The approach for the detection of replicational activity in cells using 5-bromo-2'-deoxyuridine, a low concentration of hydrochloric acid and exonuclease III is presented in the study. The described method was optimised with the aim to provide a fast and robust tool for the detection of DNA synthesis with minimal impact on the cellular structures using image and flow cytometry. The approach is based on the introduction of breaks into the DNA by the low concentration of hydrochloric acid followed by the subsequent enzymatic extension of these breaks using exonuclease III. Our data showed that the method has only a minimal effect on the tested protein localisations and is applicable both for formaldehyde- and ethanol-fixed cells. The approach partially also preserves the fluorescence of the fluorescent proteins in the HeLa cells expressing Fluorescent Ubiquitin Cell Cycle Indicator. In the case of the short labelling pulses that disabled the use of 5-ethynyl-2'-deoxyuridine because of the low specific signal, the described method provided a bright signal enabling reliable recognition of replicating cells. The optimized protocol was also successfully tested for the detection of trifluridine, the nucleoside used as an antiviral drug and in combination with tipiracil also for the treatment of some types of cancer.

  7. Database Replication

    CERN Document Server

    Kemme, Bettina

    2010-01-01

    Database replication is widely used for fault-tolerance, scalability and performance. The failure of one database replica does not stop the system from working as available replicas can take over the tasks of the failed replica. Scalability can be achieved by distributing the load across all replicas, and adding new replicas should the load increase. Finally, database replication can provide fast local access, even if clients are geographically distributed clients, if data copies are located close to clients. Despite its advantages, replication is not a straightforward technique to apply, and

  8. Estimation of soil permeability

    Directory of Open Access Journals (Sweden)

    Amr F. Elhakim

    2016-09-01

    Full Text Available Soils are permeable materials because of the existence of interconnected voids that allow the flow of fluids when a difference in energy head exists. A good knowledge of soil permeability is needed for estimating the quantity of seepage under dams and dewatering to facilitate underground construction. Soil permeability, also termed hydraulic conductivity, is measured using several methods that include constant and falling head laboratory tests on intact or reconstituted specimens. Alternatively, permeability may be measured in the field using insitu borehole permeability testing (e.g. [2], and field pumping tests. A less attractive method is to empirically deduce the coefficient of permeability from the results of simple laboratory tests such as the grain size distribution. Otherwise, soil permeability has been assessed from the cone/piezocone penetration tests (e.g. [13,14]. In this paper, the coefficient of permeability was measured using field falling head at different depths. Furthermore, the field coefficient of permeability was measured using pumping tests at the same site. The measured permeability values are compared to the values empirically deduced from the cone penetration test for the same location. Likewise, the coefficients of permeability are empirically obtained using correlations based on the index soil properties of the tested sand for comparison with the measured values.

  9. Permeability prediction in chalks

    DEFF Research Database (Denmark)

    Alam, Mohammad Monzurul; Fabricius, Ida Lykke; Prasad, Manika

    2011-01-01

    The velocity of elastic waves is the primary datum available for acquiring information about subsurface characteristics such as lithology and porosity. Cheap and quick (spatial coverage, ease of measurement) information of permeability can be achieved, if sonic velocity is used for permeability....... The relationships between permeability and porosity from core data were first examined using Kozeny’s equation. The data were analyzed for any correlations to the specific surface of the grain, Sg, and to the hydraulic property defined as the flow zone indicator (FZI). These two methods use two different approaches...... to enhance permeability prediction fromKozeny’s equation. The FZI is based on a concept of a tortuous flow path in a granular bed. The Sg concept considers the pore space that is exposed to fluid flow and models permeability resulting from effective flow parallel to pressure drop. The porosity-permeability...

  10. Archaeal DNA replication.

    Science.gov (United States)

    Kelman, Lori M; Kelman, Zvi

    2014-01-01

    DNA replication is essential for all life forms. Although the process is fundamentally conserved in the three domains of life, bioinformatic, biochemical, structural, and genetic studies have demonstrated that the process and the proteins involved in archaeal DNA replication are more similar to those in eukaryal DNA replication than in bacterial DNA replication, but have some archaeal-specific features. The archaeal replication system, however, is not monolithic, and there are some differences in the replication process between different species. In this review, the current knowledge of the mechanisms governing DNA replication in Archaea is summarized. The general features of the replication process as well as some of the differences are discussed.

  11. Permeability of edible coatings.

    Science.gov (United States)

    Mishra, B; Khatkar, B S; Garg, M K; Wilson, L A

    2010-01-01

    The permeabilities of water vapour, O2 and CO2 were determined for 18 coating formulations. Water vapour transmission rate ranged from 98.8 g/m(2).day (6% beeswax) to 758.0 g/m(2).day (1.5% carboxymethyl cellulose with glycerol). O2 permeability at 14 ± 1°C and 55 ± 5% RH ranged from 1.50 to 7.95 cm(3)cm cm(-2)s(-1)Pa(-1), with CO2 permeability 2 to 6 times as high. Permeability to noncondensable gases (O2 and CO2) was higher for hydrophobic (peanut oil followed by beeswax) coatings as compared to hydrophilic (whey protein concentrate and carboxymethyl cellulose).

  12. Permeability of edible coatings

    OpenAIRE

    B Mishra; Khatkar, B. S.; Garg, M. K.; Wilson, L.A.

    2010-01-01

    The permeabilities of water vapour, O2 and CO2 were determined for 18 coating formulations. Water vapour transmission rate ranged from 98.8 g/m2.day (6% beeswax) to 758.0 g/m2.day (1.5% carboxymethyl cellulose with glycerol). O2 permeability at 14 ± 1°C and 55 ± 5% RH ranged from 1.50 to 7.95 cm3cm cm−2s−1Pa−1, with CO2 permeability 2 to 6 times as high. Permeability to noncondensable gases (O2 and CO2) was higher for hydrophobic (peanut oil followed by beeswax) coatings as compared to hydrop...

  13. Soils - Mean Permeability

    Data.gov (United States)

    Kansas Data Access and Support Center — This digital spatial data set provides information on the magnitude and spatial pattern of depth-weighted, mean soil permeability throughout the State of Kansas. The...

  14. Permeable pavement study (Edison)

    Data.gov (United States)

    U.S. Environmental Protection Agency — While permeable pavement is increasingly being used to control stormwater runoff, field-based, side-by-side investigations on the effects different pavement types...

  15. Biostable glucose permeable polymer

    DEFF Research Database (Denmark)

    2017-01-01

    A new biostable glucose permeable polymer has been developed which is useful, for example, in implantable glucose sensors. This biostable glucose permeable polymer has a number of advantageous characteristics and, for example, does not undergo hydrolytic cleavage and degradation, thereby providing...... a composition that facilitates long term sensor stability in vivo. The versatile characteristics of this polymer allow it to be used in a variety of contexts, for example to form the body of an implantable glucose sensor. The invention includes the polymer composition, sensor systems formed from this polymer...

  16. Replication Restart in Bacteria.

    Science.gov (United States)

    Michel, Bénédicte; Sandler, Steven J

    2017-07-01

    In bacteria, replication forks assembled at a replication origin travel to the terminus, often a few megabases away. They may encounter obstacles that trigger replisome disassembly, rendering replication restart from abandoned forks crucial for cell viability. During the past 25 years, the genes that encode replication restart proteins have been identified and genetically characterized. In parallel, the enzymes were purified and analyzed in vitro, where they can catalyze replication initiation in a sequence-independent manner from fork-like DNA structures. This work also revealed a close link between replication and homologous recombination, as replication restart from recombination intermediates is an essential step of DNA double-strand break repair in bacteria and, conversely, arrested replication forks can be acted upon by recombination proteins and converted into various recombination substrates. In this review, we summarize this intense period of research that led to the characterization of the ubiquitous replication restart protein PriA and its partners, to the definition of several replication restart pathways in vivo, and to the description of tight links between replication and homologous recombination, responsible for the importance of replication restart in the maintenance of genome stability. Copyright © 2017 American Society for Microbiology.

  17. DNA replication and cancer

    DEFF Research Database (Denmark)

    Boyer, Anne-Sophie; Walter, David; Sørensen, Claus Storgaard

    2016-01-01

    A dividing cell has to duplicate its DNA precisely once during the cell cycle to preserve genome integrity avoiding the accumulation of genetic aberrations that promote diseases such as cancer. A large number of endogenous impacts can challenge DNA replication and cells harbor a battery of pathways...... causing DNA replication stress and genome instability. Further, we describe cellular and systemic responses to these insults with a focus on DNA replication restart pathways. Finally, we discuss the therapeutic potential of exploiting intrinsic replicative stress in cancer cells for targeted therapy....

  18. Relative permeability through fractures

    Energy Technology Data Exchange (ETDEWEB)

    Diomampo, Gracel, P.

    2001-08-01

    The mechanism of two-phase flow through fractures is of importance in understanding many geologic processes. Currently, two-phase flow through fractures is still poorly understood. In this study, nitrogen-water experiments were done on both smooth and rough parallel plates to determine the governing flow mechanism for fractures and the appropriate methodology for data analysis. The experiments were done using a glass plate to allow visualization of flow. Digital video recording allowed instantaneous measurement of pressure, flow rate and saturation. Saturation was computed using image analysis techniques. The experiments showed that gas and liquid phases flow through fractures in nonuniform separate channels. The localized channels change with time as each phase path undergoes continues breaking and reforming due to invasion of the other phase. The stability of the phase paths is dependent on liquid and gas flow rate ratio. This mechanism holds true for over a range of saturation for both smooth and rough fractures. In imbibition for rough-walled fractures, another mechanism similar to wave-like flow in pipes was also observed. The data from the experiments were analyzed using Darcy's law and using the concept of friction factor and equivalent Reynold's number for two-phase flow. For both smooth- and rough-walled fractures a clear relationship between relative permeability and saturation was seen. The calculated relative permeability curves follow Corey-type behavior and can be modeled using Honarpour expressions. The sum of the relative permeabilities is not equal one, indicating phase interference. The equivalent homogeneous single-phase approach did not give satisfactory representation of flow through fractures. The graphs of experimentally derived friction factor with the modified Reynolds number do not reveal a distinctive linear relationship.

  19. Replicating animal mitochondrial DNA

    Directory of Open Access Journals (Sweden)

    Emily A. McKinney

    2013-01-01

    Full Text Available The field of mitochondrial DNA (mtDNA replication has been experiencing incredible progress in recent years, and yet little is certain about the mechanism(s used by animal cells to replicate this plasmid-like genome. The long-standing strand-displacement model of mammalian mtDNA replication (for which single-stranded DNA intermediates are a hallmark has been intensively challenged by a new set of data, which suggests that replication proceeds via coupled leading-and lagging-strand synthesis (resembling bacterial genome replication and/or via long stretches of RNA intermediates laid on the mtDNA lagging-strand (the so called RITOLS. The set of proteins required for mtDNA replication is small and includes the catalytic and accessory subunits of DNA polymerase y, the mtDNA helicase Twinkle, the mitochondrial single-stranded DNA-binding protein, and the mitochondrial RNA polymerase (which most likely functions as the mtDNA primase. Mutations in the genes coding for the first three proteins are associated with human diseases and premature aging, justifying the research interest in the genetic, biochemical and structural properties of the mtDNA replication machinery. Here we summarize these properties and discuss the current models of mtDNA replication in animal cells.

  20. Permeability measuremens of brazilian Eucalyptus

    Directory of Open Access Journals (Sweden)

    Marcio Rogério da Silva

    2010-09-01

    Full Text Available The permeability of Brazilian Eucalyptus grandis and Eucalyptus citriodora wood was measured in a custom build gas analysis chamber in order to determine which species could be successfully treated with preservatives. Liquid permeability was tested using an emulsion of Neen oil and a control of distillated water. Air was used to test the gas phase permeability. For both Eucalyptus grandis and Eucalyptus citriodora, the longitudinal permeability of gas was shown to be about twice as great as the liquid phase permeability. No radial permeability was observed for either wood. The permeability of air and water through the sapwood of Eucalyptus grandis was greater than that through the sapwood of Eucalyptus citriodora. The permeability of neen oil preservative through the sapwood of Eucalyptus grandis was also greater than through the sapwood of E. Citradora, but the difference was not statistically significant. Scanning Electron Microscopy images showed that the distribution and obstruction in the vessels could be correlated with observed permeability properties. Irrespective of the causes of differences in permeability between the species, the fluid phase flux through the sapwood of both species was significant, indicating that both Eucalyptus grandis and Eucalyptus citriodora could be successfully treated with wood preservative.

  1. Low Permeability Polyimide Insulation Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Resodyn Technologies proposes a new technology that enables the application of polyimide based cryogenic insulation with low hydrogen permeability. This effort...

  2. The Replication Recipe: What makes for a convincing replication?

    NARCIS (Netherlands)

    Brandt, M.J.; IJzerman, H.; Dijksterhuis, A.J.; Farach, F.J.; Geller, J.; Giner-Sorolla, R.; Grange, J.A.; Perugini, M.; Spies, J.R.; Veer, A. van 't

    2014-01-01

    Psychological scientists have recently started to reconsider the importance of close replications in building a cumulative knowledge base; however, there is no consensus about what constitutes a convincing close replication study. To facilitate convincing close replication attempts we have developed

  3. Modeling DNA Replication.

    Science.gov (United States)

    Bennett, Joan

    1998-01-01

    Recommends the use of a model of DNA made out of Velcro to help students visualize the steps of DNA replication. Includes a materials list, construction directions, and details of the demonstration using the model parts. (DDR)

  4. Eukaryotic DNA Replication Fork.

    Science.gov (United States)

    Burgers, Peter M J; Kunkel, Thomas A

    2017-06-20

    This review focuses on the biogenesis and composition of the eukaryotic DNA replication fork, with an emphasis on the enzymes that synthesize DNA and repair discontinuities on the lagging strand of the replication fork. Physical and genetic methodologies aimed at understanding these processes are discussed. The preponderance of evidence supports a model in which DNA polymerase ε (Pol ε) carries out the bulk of leading strand DNA synthesis at an undisturbed replication fork. DNA polymerases α and δ carry out the initiation of Okazaki fragment synthesis and its elongation and maturation, respectively. This review also discusses alternative proposals, including cellular processes during which alternative forks may be utilized, and new biochemical studies with purified proteins that are aimed at reconstituting leading and lagging strand DNA synthesis separately and as an integrated replication fork.

  5. Abiotic self-replication.

    Science.gov (United States)

    Meyer, Adam J; Ellefson, Jared W; Ellington, Andrew D

    2012-12-18

    The key to the origins of life is the replication of information. Linear polymers such as nucleic acids that both carry information and can be replicated are currently what we consider to be the basis of living systems. However, these two properties are not necessarily coupled. The ability to mutate in a discrete or quantized way, without frequent reversion, may be an additional requirement for Darwinian evolution, in which case the notion that Darwinian evolution defines life may be less of a tautology than previously thought. In this Account, we examine a variety of in vitro systems of increasing complexity, from simple chemical replicators up to complex systems based on in vitro transcription and translation. Comparing and contrasting these systems provides an interesting window onto the molecular origins of life. For nucleic acids, the story likely begins with simple chemical replication, perhaps of the form A + B → T, in which T serves as a template for the joining of A and B. Molecular variants capable of faster replication would come to dominate a population, and the development of cycles in which templates could foster one another's replication would have led to increasingly complex replicators and from thence to the initial genomes. The initial genomes may have been propagated by RNA replicases, ribozymes capable of joining oligonucleotides and eventually polymerizing mononucleotide substrates. As ribozymes were added to the genome to fill gaps in the chemistry necessary for replication, the backbone of a putative RNA world would have emerged. It is likely that such replicators would have been plagued by molecular parasites, which would have been passively replicated by the RNA world machinery without contributing to it. These molecular parasites would have been a major driver for the development of compartmentalization/cellularization, as more robust compartments could have outcompeted parasite-ridden compartments. The eventual outsourcing of metabolic

  6. Adenovirus DNA Replication

    OpenAIRE

    Hoeben, Rob C.; Uil, Taco G.

    2013-01-01

    Adenoviruses have attracted much attention as probes to study biological processes such as DNA replication, transcription, splicing, and cellular transformation. More recently these viruses have been used as gene-transfer vectors and oncolytic agents. On the other hand, adenoviruses are notorious pathogens in people with compromised immune functions. This article will briefly summarize the basic replication strategy of adenoviruses and the key proteins involved and will deal with the new deve...

  7. Minichromosome replication in vitro: inhibition of re-replication by replicatively assembled nucleosomes.

    Science.gov (United States)

    Krude, T; Knippers, R

    1994-08-19

    Single-stranded circular DNA, containing the SV40 origin sequence, was used as a template for complementary DNA strand synthesis in cytosolic extracts from HeLa cells. In the presence of the replication-dependent chromatin assembly factor CAF-1, defined numbers of nucleosomes were assembled during complementary DNA strand synthesis. These minichromosomes were then induced to semiconservatively replicate by the addition of the SV40 initiator protein T antigen (re-replication). The results indicate that re-replication of minichromosomes appears to be inhibited by two independent mechanisms. One acts at the initiation of minichromosome re-replication, and the other affects replicative chain elongation. To directly demonstrate the inhibitory effect of replicatively assembled nucleosomes, two types of minichromosomes were prepared: (i) post-replicative minichromosomes were assembled in a reaction coupled to replication as above; (ii) pre-replicative minichromosomes were assembled independently of replication on double-stranded DNA. Both types of minichromosomes were used as templates for DNA replication under identical conditions. Replicative fork movement was found to be impeded only on post-replicative minichromosome templates. In contrast, pre-replicative minichromosomes allowed one unconstrained replication cycle, but re-replication was inhibited due to a block in fork movement. Thus, replicatively assembled chromatin may have a profound influence on the re-replication of DNA.

  8. Investigating variation in replicability: A "Many Labs" replication project

    NARCIS (Netherlands)

    Klein, R.A.; Ratliff, K.A.; Vianello, M.; Adams, R.B.; Bahnik, S.; Bernstein, M.J.; Bocian, K.; Brandt, M.J.; Brooks, B.; Brumbaugh, C.C.; Cemalcilar, Z.; Chandler, J.; Cheong, W.; Davis, W.E.; Devos, T.; Eisner, M.; Frankowska, N.; Furrow, D.; Galliani, E.M.; Hasselman, F.W.; Hicks, J.A.; Hovermale, J.F.; Hunt, S.J.; Huntsinger, J.R.; IJzerman, H.; John, M.S.; Joy-Gaba, J.A.; Kappes, H.B.; Krueger, L.E.; Kurtz, J.; Levitan, C.A.; Mallett, R.K.; Morris, W.L.; Nelson, A.J.; Nier, J.A.; Packard, G.; Pilati, R.; Rutchick, A.M.; Schmidt, K.; Skorinko, J.L.M.; Smith, R.; Steiner, T.G.; Storbeck, J.; Van Swol, L.M.; Thompson, D.; Veer, A.E. van 't; Vaughn, L.A.; Vranka, M.; Wichman, A.L.; Woodzicka, J.A.; Nosek, B.A.

    2014-01-01

    Although replication is a central tenet of science, direct replications are rare in psychology. This research tested variation in the replicability of 13 classic and contemporary effects across 36 independent samples totaling 6,344 participants. In the aggregate, 10 effects replicated consistently.

  9. Hepatitis B virus replication

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Hepadnaviruses, including human hepatitis B virus (HBV), replicate through reverse transcription of an RNA intermediate, the pregenomic RNA (pgRNA). Despite this kinship to retroviruses, there are fundamental differences beyond the fact that hepadnavirions contain DNA instead of RNA. Most peculiar is the initiation of reverse transcription: it occurs by protein-priming, is strictly committed to using an RNA hairpin on the pgRNA,ε, as template, and depends on cellular chaperones;moreover, proper replication can apparently occur only in the specialized environment of intact nucleocapsids.This complexity has hampered an in-depth mechanistic understanding. The recent successful reconstitution in the test tube of active replication initiation complexes from purified components, for duck HBV (DHBV),now allows for the analysis of the biochemistry of hepadnaviral replication at the molecular level. Here we review the current state of knowledge at all steps of the hepadnaviral genome replication cycle, with emphasis on new insights that turned up by the use of such cellfree systems. At this time, they can, unfortunately,not be complemented by three-dimensional structural information on the involved components. However, at least for the s RNA element such information is emerging,raising expectations that combining biophysics with biochemistry and genetics will soon provide a powerful integrated approach for solving the many outstanding questions. The ultimate, though most challenging goal,will be to visualize the hepadnaviral reverse transcriptase in the act of synthesizing DNA, which will also have strong implications for drug development.

  10. Water-permeability measurement of high performance concrete using a high-pressure triaxial cell

    Energy Technology Data Exchange (ETDEWEB)

    El-Dieb, A.S. [Ain Shams Univ., Cairo (Egypt). Dept. of Civil Engineering; Hooton, R.D. [Univ. of Toronto, Ontario (Canada). Dept. of Civil Engineering

    1995-08-01

    Water permeability of concrete is used to indicate its durability. Accurate and reproducible measurement of water permeability is difficult and becomes more difficult as the quality of concrete increases. When high-performance concrete (HPC) is tested, these concerns become more pronounced. HPC is used widely to improve the durability and performance of structures but there are few test procedures able to evaluate its permeability-related properties. In this study the water permeabilities of concretes including HPC were measured using a high-pressure triaxial cell with a sensitive and automated measurement capability. Special analysis procedures were developed to obtain useful data from the extremely low volume of water being measured. This method was able to measure a wide range of permeability values from 10{sup {minus}12} m/s to 10{sup {minus}16} m/s, with reproducible measurements on replicates.

  11. Permeability testing of biomaterial membranes

    Energy Technology Data Exchange (ETDEWEB)

    Dreesmann, L; Hajosch, R; Nuernberger, J Vaz; Schlosshauer, B [NMI Natural and Medical Sciences Institute at University Tuebingen, Markwiesenstr. 55, D-72770 Reutlingen (Germany); Ahlers, M [GELITA AG, Gammelsbacher Str. 2, D-69412 Eberbach (Germany)], E-mail: schlosshauer@nmi.de

    2008-09-01

    The permeability characteristics of biomaterials are critical parameters for a variety of implants. To analyse the permeability of membranes made from crosslinked ultrathin gelatin membranes and the transmigration of cells across the membranes, we combined three technical approaches: (1) a two-chamber-based permeability assay, (2) cell culturing with cytochemical analysis and (3) biochemical enzyme electrophoresis (zymography). Based on the diffusion of a coloured marker molecule in conjunction with photometric quantification, permeability data for a gelatin membrane were determined in the presence or absence of gelatin degrading fibroblasts. Cytochemical evaluation after cryosectioning of the membranes was used to ascertain whether fibroblasts had infiltrated the membrane inside. Zymography was used to investigate the potential release of proteases from fibroblasts, which are known to degrade collagen derivatives such as gelatin. Our data show that the diffusion equilibrium of a low molecular weight dye across the selected gelatin membrane is approached after about 6-8 h. Fibroblasts increase the permeability due to cavity formation in the membrane inside without penetrating the membrane for an extended time period (>21 days in vitro). Zymography indicates that cavity formation is most likely due to the secretion of matrix metalloproteinases. In summary, the combination of the depicted methods promises to facilitate a more rational development of biomaterials, because it provides a rapid means of determining permeability characteristics and bridges the gap between descriptive methodology and the mechanistic understanding of permeability alterations due to biological degradation.

  12. Psychology, replication & beyond.

    Science.gov (United States)

    Laws, Keith R

    2016-06-01

    Modern psychology is apparently in crisis and the prevailing view is that this partly reflects an inability to replicate past findings. If a crisis does exists, then it is some kind of 'chronic' crisis, as psychologists have been censuring themselves over replicability for decades. While the debate in psychology is not new, the lack of progress across the decades is disappointing. Recently though, we have seen a veritable surfeit of debate alongside multiple orchestrated and well-publicised replication initiatives. The spotlight is being shone on certain areas and although not everyone agrees on how we should interpret the outcomes, the debate is happening and impassioned. The issue of reproducibility occupies a central place in our whig history of psychology.

  13. Methods to Measure Water Permeability.

    Science.gov (United States)

    Solenov, Evgeniy I; Baturina, Galina S; Katkova, Liubov E; Zarogiannis, Sotirios G

    2017-01-01

    Water permeability is a key feature of the cell plasma membranes and it has seminal importance for a number of cell functions such as cell volume regulation, cell proliferation, cell migration, and angiogenesis to name a few. The transport of water occurs mainly through plasma membrane water channels , the aquaporins, who have very important function in physiological and pathophysiological states. Due to the above the experimental assessment of the water permeability of cells and tissues is necessary. The development of new methodologies of measuring water permeability is a vibrant scientific field that constantly develops during the past three decades along with the advances in imaging mainly. In this chapter we describe and critically assess several methods that have been developed for the measurement of water permeability both in living cells as well as in tissues with a focus in the first category.

  14. Geothermal Permeability Enhancement - Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Joe Beall; Mark Walters

    2009-06-30

    The overall objective is to apply known permeability enhancement techniques to reduce the number of wells needed and demonstrate the applicability of the techniques to other undeveloped or under-developed fields. The Enhanced Geothermal System (EGS) concept presented in this project enhances energy extraction from reduced permeability zones in the super-heated, vapor-dominated Aidlin Field of the The Geysers geothermal reservoir. Numerous geothermal reservoirs worldwide, over a wide temperature range, contain zones of low permeability which limit the development potential and the efficient recovery of heat from these reservoirs. Low permeability results from poorly connected fractures or the lack of fractures. The Enhanced Geothermal System concept presented here expands these technologies by applying and evaluating them in a systematic, integrated program.

  15. DNA replication origins in archaea

    OpenAIRE

    Zhenfang eWu; Jingfang eLiu; Haibo eYang; Hua eXiang

    2014-01-01

    DNA replication initiation, which starts at specific chromosomal site (known as replication origins), is the key regulatory stage of chromosome replication. Archaea, the third domain of life, use a single or multiple origin(s) to initiate replication of their circular chromosomes. The basic structure of replication origins is conserved among archaea, typically including an AT-rich unwinding region flanked by several conserved repeats (origin recognition box, ORB) that are located adjacent to ...

  16. Replication studies in longevity

    DEFF Research Database (Denmark)

    Varcasia, O; Garasto, S; Rizza, T

    2001-01-01

    In Danes we replicated the 3'APOB-VNTR gene/longevity association study previously carried out in Italians, by which the Small alleles (less than 35 repeats) had been identified as frailty alleles for longevity. In Danes, neither genotype nor allele frequencies differed between centenarians and 20...

  17. Replication-Fork Dynamics

    NARCIS (Netherlands)

    Duderstadt, Karl E.; Reyes-Lamothe, Rodrigo; van Oijen, Antoine M.; Sherratt, David J.

    2014-01-01

    The proliferation of all organisms depends on the coordination of enzymatic events within large multiprotein replisomes that duplicate chromosomes. Whereas the structure and function of many core replisome components have been clarified, the timing and order of molecular events during replication re

  18. Coronavirus Attachment and Replication

    Science.gov (United States)

    1988-03-28

    synthesis during RNA replication of vesicular stomatitis virus. J. Virol. 49:303-309. Pedersen, N.C. 1976a. Feline infectious peritonitis: Something old...receptors on intestinal brush border membranes from normal host species were developed for canine (CCV), feline (FIPV), porcine (TGEV), human (HCV...gastroenteritis receptor on pig BBMs ...... ................. ... 114 Feline infectious peritonitis virus receptor on cat BBMs ... .............. 117 Human

  19. Reversible Switching of Cooperating Replicators

    Science.gov (United States)

    Urtel, Georg C.; Rind, Thomas; Braun, Dieter

    2017-02-01

    How can molecules with short lifetimes preserve their information over millions of years? For evolution to occur, information-carrying molecules have to replicate before they degrade. Our experiments reveal a robust, reversible cooperation mechanism in oligonucleotide replication. Two inherently slow replicating hairpin molecules can transfer their information to fast crossbreed replicators that outgrow the hairpins. The reverse is also possible. When one replication initiation site is missing, single hairpins reemerge from the crossbreed. With this mechanism, interacting replicators can switch between the hairpin and crossbreed mode, revealing a flexible adaptation to different boundary conditions.

  20. Evaluation of Various Pulse-Decay Laboratory Permeability Measurement Techniques for Highly Stressed Coals

    Science.gov (United States)

    Feng, Ruimin; Harpalani, Satya; Pandey, Rohit

    2017-02-01

    The transient technique for laboratory permeability measurement, proposed by Brace et al. (J Geophys Res 73:2225-2236, 1968) and widely used for conventional gas reservoir rocks, is the preferred method when testing low-permeability rocks in the laboratory. However, Brace et al.'s solution leads to considerable errors since it does not take into account compressive storage and sorption effect when applied to sorptive rocks, such as, coals and shales. To verify the applicability of this solution when used to characterize fluid flow behavior of coal, an in-depth investigation of permeability evolution for flow of helium and methane depletion was conducted for San Juan coals using the pressure pulse-decay method under best replicated in situ conditions. Three permeability solutions, Brace et al.'s (1968), Dicker and Smits's (International meeting on petroleum engineering, Society of Petroleum Engineers, 1988) and Cui et al.'s (Geofluids 9:208-223, 2009), were utilized to establish the permeability trends. Both helium and methane permeability results exhibited very small difference between the Brace et al.'s solution and Dicker and Smits's solution, indicating that the effect of compressive storage is negligible. However, methane permeability enhancement at low pressures due to coal matrix shrinkage resulting from gas desorption can be significant and this was observed in pressure response plots and the estimated permeability values using Cui et al.'s solution only. Therefore, it is recommended that Cui et al.'s solution be employed to correctly include the sorption effect when testing coal permeability using the transient technique. A series of experiments were also carried out to establish the stress-dependent permeability trend under constant effective stress condition, and then quantify the sole contribution of the sorption effect on permeability variation. By comparison with the laboratory data obtained under in situ stress/strain condition, it was verified that

  1. Bentonite Permeability at Elevated Temperature

    Directory of Open Access Journals (Sweden)

    Katherine A. Daniels

    2017-01-01

    Full Text Available Repository designs frequently favour geological disposal of radioactive waste with a backfill material occupying void space around the waste. The backfill material must tolerate the high temperatures produced by decaying radioactive waste to prevent its failure or degradation, leading to increased hydraulic conductivity and reduced sealing performance. The results of four experiments investigating the effect of temperature on the permeability of a bentonite backfill are presented. Bentonite is a clay commonly proposed as the backfill in repository designs because of its high swelling capacity and very low permeability. The experiments were conducted in two sets of purpose-built, temperature controlled apparatus, designed to simulate isotropic pressure and constant volume conditions within the testing range of 4–6 MPa average effective stress. The response of bentonite during thermal loading at temperatures up to 200 °C was investigated, extending the previously considered temperature range. The results provide details of bentonite’s intrinsic permeability, total stress, swelling pressure and porewater pressure during thermal cycles. We find that bentonite’s hydraulic properties are sensitive to thermal loading and the type of imposed boundary condition. However, the permeability change is not large and can mostly be accounted for by water viscosity changes. Thus, under 150 °C, temperature has a minimal impact on bentonite’s hydraulic permeability.

  2. Chromatin replication and epigenome maintenance

    DEFF Research Database (Denmark)

    Alabert, Constance; Groth, Anja

    2012-01-01

    initiates, whereas the replication process itself disrupts chromatin and challenges established patterns of genome regulation. Specialized replication-coupled mechanisms assemble new DNA into chromatin, but epigenome maintenance is a continuous process taking place throughout the cell cycle. If DNA...

  3. Chromatin replication and epigenome maintenance

    DEFF Research Database (Denmark)

    Alabert, Constance; Groth, Anja

    2012-01-01

    initiates, whereas the replication process itself disrupts chromatin and challenges established patterns of genome regulation. Specialized replication-coupled mechanisms assemble new DNA into chromatin, but epigenome maintenance is a continuous process taking place throughout the cell cycle. If DNA...

  4. Initiation of adenovirus DNA replication.

    OpenAIRE

    Reiter, T; Fütterer, J; Weingärtner, B; Winnacker, E L

    1980-01-01

    In an attempt to study the mechanism of initiation of adenovirus DNA replication, an assay was developed to investigate the pattern of DNA synthesis in early replicative intermediates of adenovirus DNA. By using wild-type virus-infected cells, it was possible to place the origin of adenovirus type 2 DNA replication within the terminal 350 to 500 base pairs from either of the two molecular termini. In addition, a variety of parameters characteristic of adenovirus DNA replication were compared ...

  5. Chromatin replication and epigenome maintenance

    DEFF Research Database (Denmark)

    Alabert, Constance; Groth, Anja

    2012-01-01

    Stability and function of eukaryotic genomes are closely linked to chromatin structure and organization. During cell division the entire genome must be accurately replicated and the chromatin landscape reproduced on new DNA. Chromatin and nuclear structure influence where and when DNA replication...... initiates, whereas the replication process itself disrupts chromatin and challenges established patterns of genome regulation. Specialized replication-coupled mechanisms assemble new DNA into chromatin, but epigenome maintenance is a continuous process taking place throughout the cell cycle. If DNA...

  6. Replication Research and Special Education

    Science.gov (United States)

    Travers, Jason C.; Cook, Bryan G.; Therrien, William J.; Coyne, Michael D.

    2016-01-01

    Replicating previously reported empirical research is a necessary aspect of an evidence-based field of special education, but little formal investigation into the prevalence of replication research in the special education research literature has been conducted. Various factors may explain the lack of attention to replication of special education…

  7. Replication Research and Special Education

    Science.gov (United States)

    Travers, Jason C.; Cook, Bryan G.; Therrien, William J.; Coyne, Michael D.

    2016-01-01

    Replicating previously reported empirical research is a necessary aspect of an evidence-based field of special education, but little formal investigation into the prevalence of replication research in the special education research literature has been conducted. Various factors may explain the lack of attention to replication of special education…

  8. Replication data collection highlights value in diversity of replication attempts

    Science.gov (United States)

    DeSoto, K. Andrew; Schweinsberg, Martin

    2017-01-01

    Researchers agree that replicability and reproducibility are key aspects of science. A collection of Data Descriptors published in Scientific Data presents data obtained in the process of attempting to replicate previously published research. These new replication data describe published and unpublished projects. The different papers in this collection highlight the many ways that scientific replications can be conducted, and they reveal the benefits and challenges of crucial replication research. The organizers of this collection encourage scientists to reuse the data contained in the collection for their own work, and also believe that these replication examples can serve as educational resources for students, early-career researchers, and experienced scientists alike who are interested in learning more about the process of replication. PMID:28291224

  9. Anatomy of Mammalian Replication Domains

    Science.gov (United States)

    Takebayashi, Shin-ichiro; Ogata, Masato; Okumura, Katsuzumi

    2017-01-01

    Genetic information is faithfully copied by DNA replication through many rounds of cell division. In mammals, DNA is replicated in Mb-sized chromosomal units called “replication domains.” While genome-wide maps in multiple cell types and disease states have uncovered both dynamic and static properties of replication domains, we are still in the process of understanding the mechanisms that give rise to these properties. A better understanding of the molecular basis of replication domain regulation will bring new insights into chromosome structure and function. PMID:28350365

  10. Capillary permeability in adipose tissue

    DEFF Research Database (Denmark)

    Paaske, W P; Nielsen, S L

    1976-01-01

    of about 7 ml/100 g-min. This corresponds to a capillary diffusion capacity of 2.0 ml/100 g-min which is half the value reported for vasodilated skeletal muscle having approximately twice as great capillary surface area. Thus, adipose tissue has about the same capillary permeability during slight metabolic...

  11. Modeling inhomogeneous DNA replication kinetics.

    Directory of Open Access Journals (Sweden)

    Michel G Gauthier

    Full Text Available In eukaryotic organisms, DNA replication is initiated at a series of chromosomal locations called origins, where replication forks are assembled proceeding bidirectionally to replicate the genome. The distribution and firing rate of these origins, in conjunction with the velocity at which forks progress, dictate the program of the replication process. Previous attempts at modeling DNA replication in eukaryotes have focused on cases where the firing rate and the velocity of replication forks are homogeneous, or uniform, across the genome. However, it is now known that there are large variations in origin activity along the genome and variations in fork velocities can also take place. Here, we generalize previous approaches to modeling replication, to allow for arbitrary spatial variation of initiation rates and fork velocities. We derive rate equations for left- and right-moving forks and for replication probability over time that can be solved numerically to obtain the mean-field replication program. This method accurately reproduces the results of DNA replication simulation. We also successfully adapted our approach to the inverse problem of fitting measurements of DNA replication performed on single DNA molecules. Since such measurements are performed on specified portion of the genome, the examined DNA molecules may be replicated by forks that originate either within the studied molecule or outside of it. This problem was solved by using an effective flux of incoming replication forks at the model boundaries to represent the origin activity outside the studied region. Using this approach, we show that reliable inferences can be made about the replication of specific portions of the genome even if the amount of data that can be obtained from single-molecule experiments is generally limited.

  12. FRAUDULENT ACTIVITIES USING VIRTUAL MEETINGS

    Directory of Open Access Journals (Sweden)

    Anne James

    2013-05-01

    Full Text Available This paper investigates fraudulent and illegal activities that take place through virtual meeting systems. The first section gives an introduction to the problem. Section two describes some cases of fraudulent activity using virtual meeting systems. Section three explores some means of capturing such fraudulent activities so thatcriminals can be brought to justice. Section four provides a solution for capturing virtual meeting conversations in a way that could be admissible in court. Section five discusses tell-tale signs that indicates that a conversation maybe fraudulent. Section six discusses Artificial Intelligence (AI techniques that might be used to detectvirtual meeting crime. Section seven discusses the conclusion to the paper.

  13. Quantifying Evaporation in a Permeable Pavement System

    Science.gov (United States)

    Studies quantifying evaporation from permeable pavement systems are limited to a few laboratory studies and one field application. This research quantifies evaporation for a larger-scale field application by measuring the water balance from lined permeable pavement sections. Th...

  14. Replicated Spectrographs in Astronomy

    CERN Document Server

    Hill, Gary J

    2014-01-01

    As telescope apertures increase, the challenge of scaling spectrographic astronomical instruments becomes acute. The next generation of extremely large telescopes (ELTs) strain the availability of glass blanks for optics and engineering to provide sufficient mechanical stability. While breaking the relationship between telescope diameter and instrument pupil size by adaptive optics is a clear path for small fields of view, survey instruments exploiting multiplex advantages will be pressed to find cost-effective solutions. In this review we argue that exploiting the full potential of ELTs will require the barrier of the cost and engineering difficulty of monolithic instruments to be broken by the use of large-scale replication of spectrographs. The first steps in this direction have already been taken with the soon to be commissioned MUSE and VIRUS instruments for the Very Large Telescope and the Hobby-Eberly Telescope, respectively. MUSE employs 24 spectrograph channels, while VIRUS has 150 channels. We compa...

  15. SUMO and KSHV Replication

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Pei-Ching [Institute of Microbiology and Immunology, National Yang-Ming University, Taipei 112, Taiwan (China); Kung, Hsing-Jien, E-mail: hkung@nhri.org.tw [Institute for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan (China); Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616 (United States); UC Davis Cancer Center, University of California, Davis, CA 95616 (United States); Division of Molecular and Genomic Medicine, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 35053, Taiwan (China)

    2014-09-29

    Small Ubiquitin-related MOdifier (SUMO) modification was initially identified as a reversible post-translational modification that affects the regulation of diverse cellular processes, including signal transduction, protein trafficking, chromosome segregation, and DNA repair. Increasing evidence suggests that the SUMO system also plays an important role in regulating chromatin organization and transcription. It is thus not surprising that double-stranded DNA viruses, such as Kaposi’s sarcoma-associated herpesvirus (KSHV), have exploited SUMO modification as a means of modulating viral chromatin remodeling during the latent-lytic switch. In addition, SUMO regulation allows the disassembly and assembly of promyelocytic leukemia protein-nuclear bodies (PML-NBs), an intrinsic antiviral host defense, during the viral replication cycle. Overcoming PML-NB-mediated cellular intrinsic immunity is essential to allow the initial transcription and replication of the herpesvirus genome after de novo infection. As a consequence, KSHV has evolved a way as to produce multiple SUMO regulatory viral proteins to modulate the cellular SUMO environment in a dynamic way during its life cycle. Remarkably, KSHV encodes one gene product (K-bZIP) with SUMO-ligase activities and one gene product (K-Rta) that exhibits SUMO-targeting ubiquitin ligase (STUbL) activity. In addition, at least two viral products are sumoylated that have functional importance. Furthermore, sumoylation can be modulated by other viral gene products, such as the viral protein kinase Orf36. Interference with the sumoylation of specific viral targets represents a potential therapeutic strategy when treating KSHV, as well as other oncogenic herpesviruses. Here, we summarize the different ways KSHV exploits and manipulates the cellular SUMO system and explore the multi-faceted functions of SUMO during KSHV’s life cycle and pathogenesis.

  16. Permeability of Non-Crimp Fabric Preforms

    NARCIS (Netherlands)

    Loendersloot, Richard; Lomov, Stepan V.

    2011-01-01

    Experimental permeability data of non-crimp fabrics (NCFs) is discussed in this chapter. The chapter starts with a general introduction on permeability, followed by a discussion on experimental permeability data. The infl uence of geometrical features of the textile architecture, in particular the s

  17. Different Methods of Predicting Permeability in Shale

    DEFF Research Database (Denmark)

    Mbia, Ernest Ncha; Fabricius, Ida Lykke; Krogsbøll, Anette

    Permeability is often very difficult to measure or predict in shale lithology. In this work we are determining shale permeability from consolidation tests data using Wissa et al., (1971) approach and comparing the results with predicted permeability from Kozeny’s model. Core and cuttings materials...

  18. Efficient usage of Adabas replication

    CERN Document Server

    Storr, Dieter W

    2011-01-01

    In today's IT organization replication becomes more and more an essential technology. This makes Software AG's Event Replicator for Adabas an important part of your data processing. Setting the right parameters and establishing the best network communication, as well as selecting efficient target components, is essential for successfully implementing replication. This book provides comprehensive information and unique best-practice experience in the field of Event Replicator for Adabas. It also includes sample codes and configurations making your start very easy. It describes all components ne

  19. Solving the Telomere Replication Problem

    Science.gov (United States)

    Maestroni, Laetitia; Matmati, Samah; Coulon, Stéphane

    2017-01-01

    Telomeres are complex nucleoprotein structures that protect the extremities of linear chromosomes. Telomere replication is a major challenge because many obstacles to the progression of the replication fork are concentrated at the ends of the chromosomes. This is known as the telomere replication problem. In this article, different and new aspects of telomere replication, that can threaten the integrity of telomeres, will be reviewed. In particular, we will focus on the functions of shelterin and the replisome for the preservation of telomere integrity. PMID:28146113

  20. Permeability equipment for porous friction surfaces

    Science.gov (United States)

    Standiford, D. L.; Graul, R. A.; Lenke, L. R.

    1985-04-01

    Hydroplaning is the loss of traction between tires and pavement due to the presence of a layer of water. This loss of traction can result in loss of vehicle control. A porous friction surface (PFS) applied over an existing pavement permits the water to drain laterally and vertically away from the tire path, effectively lowering hydroplaning potential. Equipment used to measure pavement drainage (permeability) is discussed with respect to usage on porous friction surface. Background information on hydroplaning, flow theory, and PFS field performance as they are affected by permeability are also presented. Two dynamic test devices and four static devices are considered for measuring PFS permeability. Permeability tests are recommended to measure PFS permeability for maintenance purposes and construction control. Dynamic devices cited could possibly estimate hydroplaning potential; further research must be done to determine this. Permeability devices cannot be used to accurately estimate friction of a pavement surface, however, decreased permeability of a pavement infers a decrease in friction.

  1. On the permeability of fractal tube bundles

    CERN Document Server

    Zinovik, I

    2011-01-01

    The permeability of a porous medium is strongly affected by its local geometry and connectivity, the size distribution of the solid inclusions and the pores available for flow. Since direct measurements of the permeability are time consuming and require experiments that are not always possible, the reliable theoretical assessment of the permeability based on the medium structural characteristics alone is of importance. When the porosity approaches unity, the permeability-porosity relationships represented by the Kozeny-Carman equations and Archie's law predict that permeability tends to infinity and thus they yield unrealistic results if specific area of the porous media does not tend to zero. The goal of this paper is an evaluation of the relationships between porosity and permeability for a set of fractal models with porosity approaching unity and a finite permeability. It is shown that the two-dimensional foams generated by finite iterations of the corresponding geometric fractals can be used to model poro...

  2. Charter School Replication. Policy Guide

    Science.gov (United States)

    Rhim, Lauren Morando

    2009-01-01

    "Replication" is the practice of a single charter school board or management organization opening several more schools that are each based on the same school model. The most rapid strategy to increase the number of new high-quality charter schools available to children is to encourage the replication of existing quality schools. This policy guide…

  3. LHCb experience with LFC replication

    CERN Document Server

    Bonifazi, F; Perez, E D; D'Apice, A; dell'Agnello, L; Düllmann, D; Girone, M; Re, G L; Martelli, B; Peco, G; Ricci, P P; Sapunenko, V; Vagnoni, V; Vitlacil, D

    2008-01-01

    Database replication is a key topic in the framework of the LHC Computing Grid to allow processing of data in a distributed environment. In particular, the LHCb computing model relies on the LHC File Catalog, i.e. a database which stores information about files spread across the GRID, their logical names and the physical locations of all the replicas. The LHCb computing model requires the LFC to be replicated at Tier-1s. The LCG 3D project deals with the database replication issue and provides a replication service based on Oracle Streams technology. This paper describes the deployment of the LHC File Catalog replication to the INFN National Center for Telematics and Informatics (CNAF) and to other LHCb Tier-1 sites. We performed stress tests designed to evaluate any delay in the propagation of the streams and the scalability of the system. The tests show the robustness of the replica implementation with performance going much beyond the LHCb requirements.

  4. DATABASE REPLICATION IN HETEROGENOUS PLATFORM

    Directory of Open Access Journals (Sweden)

    Hendro Nindito

    2014-01-01

    Full Text Available The application of diverse database technologies in enterprises today is increasingly a common practice. To provide high availability and survavibality of real-time information, a database replication technology that has capability to replicate databases under heterogenous platforms is required. The purpose of this research is to find the technology with such capability. In this research, the data source is stored in MSSQL database server running on Windows. The data will be replicated to MySQL running on Linux as the destination. The method applied in this research is prototyping in which the processes of development and testing can be done interactively and repeatedly. The key result of this research is that the replication technology applied, which is called Oracle GoldenGate, can successfully manage to do its task in replicating data in real-time and heterogeneous platforms.

  5. LHCb experience with LFC replication

    CERN Document Server

    Carbone, Angelo; Dafonte Perez, Eva; D'Apice, Antimo; dell'Agnello, Luca; Duellmann, Dirk; Girone, Maria; Lo Re, Giuseppe; Martelli, Barbara; Peco, Gianluca; Ricci, Pier Paolo; Sapunenko, Vladimir; Vagnoni, Vincenzo; Vitlacil, Dejan

    2007-01-01

    Database replication is a key topic in the framework of the LHC Computing Grid to allow processing of data in a distributed environment. In particular, the LHCb computing model relies on the LHC File Catalog, i.e. database which stores information about files spread across the GRID, their logical names and the physical locations of all the replicas. The LHCb computing model requires the LFC to be replicated at Tier-1s. The LCG 3D project deals with the database replication issue and provides a replication service based on Oracle Streams technology. This paper describes the deployment of the LHC File Catalog replication to the INFN National Center for Telematics and Informations (CNAF) and to other LHCb Tier-1 sites. We performed stress tests designed to evaluate any delay in the propagation of the streams and the scalability of the system. The tests show the robustness of the replica implementation with performance going much beyond the LHCb requirements.

  6. Structural determinants of glomerular permeability.

    Science.gov (United States)

    Deen, W M; Lazzara, M J; Myers, B D

    2001-10-01

    Recent progress in relating the functional properties of the glomerular capillary wall to its unique structure is reviewed. The fenestrated endothelium, glomerular basement membrane (GBM), and epithelial filtration slits form a series arrangement in which the flow diverges as it enters the GBM from the fenestrae and converges again at the filtration slits. A hydrodynamic model that combines morphometric findings with water flow data in isolated GBM has predicted overall hydraulic permeabilities that are consistent with measurements in vivo. The resistance of the GBM to water flow, which accounts for roughly half that of the capillary wall, is strongly dependent on the extent to which the GBM surfaces are blocked by cells. The spatial frequency of filtration slits is predicted to be a very important determinant of the overall hydraulic permeability, in keeping with observations in several glomerular diseases in humans. Whereas the hydraulic resistances of the cell layers and GBM are additive, the overall sieving coefficient for a macromolecule (its concentration in Bowman's space divided by that in plasma) is the product of the sieving coefficients for the individual layers. Models for macromolecule filtration reveal that the individual sieving coefficients are influenced by one another and by the filtrate velocity, requiring great care in extrapolating in vitro observations to the living animal. The size selectivity of the glomerular capillary has been shown to be determined largely by the cellular layers, rather than the GBM. Controversial findings concerning glomerular charge selectivity are reviewed, and it is concluded that there is good evidence for a role of charge in restricting the transmural movement of albumin. Also discussed is an effect of albumin that has received little attention, namely, its tendency to increase the sieving coefficients of test macromolecules via steric interactions. Among the unresolved issues are the specific contributions of the

  7. The Membrane Permeability Outcome study.

    Science.gov (United States)

    Locatelli, Francesco; Cavalli, Andrea; Manzoni, Celestina; Pontoriero, Giuseppe

    2011-01-01

    Many observational studies have consistently shown that high-flux hemodialysis has positive effects on the survival and morbidity of uremic patients when compared with low-flux hemodialysis. However, the HEMO study, a randomized trial designed to evaluate the effect of membrane permeability on patient survival, showed only an 8% non-statistically significant reduction of mortality, albeit a secondary analysis suggested an advantage for high-flux membranes in certain patient subgroups. The prospective, randomized Membrane Permeability Outcome (MPO) study investigated the impact of membrane permeability on survival in incident hemodialysis patients who had low albumin (≤4 g/dl) and normal albumin ( >4 g/dl) as separate randomization groups. Patients with serum albumin ≤4 g/dl had significantly better survival rates in the high-flux group compared with the low-flux group (p = 0.032). Moreover, a post-hoc secondary analysis showed that high-flux membranes may significantly improve survival in diabetic patients. No difference was found in patients with normal albumin levels. Considering the increasing number of dialysis patients with low serum albumin levels and with diabetes, the relevance of the MPO study led to the publication of a position statement by the European Renal Best Practice Advisory Board. This board strongly recommended that high-flux hemodialysis should be used for high-risk patients and, with a lower degree of evidence, even also for low-risk subjects due to the substantial reduction in β(2)-microglobulin levels observed in the high-flux group. Copyright © 2011 S. Karger AG, Basel.

  8. Permeability of normal versus carious dentin.

    Science.gov (United States)

    Pashley, E L; Talman, R; Horner, J A; Pashley, D H

    1991-10-01

    Although a number of reports have been published demonstrating that carious dentin is less permeable than normal dentin, these reports have been qualitative rather than quantitative. The purpose of this in vitro study was to apply a quantitative technique to the study of the permeability of carious human teeth before and after excavation, before and after removal of the smear layer and before and after preparation of a control cavity of similar size and depth in normal dentin subjected to the same measurements, for comparative purposes. Dentin permeability was measured as a hydraulic conductance. The permeability values measured at each step in the protocol were expressed as a percent of the maximum permeability of both cavities, permitting each tooth the serve as its own control. Carious lesions exhibited a slight degree of permeability (2.3 +/- 0.6% of controls) which remained unchanged after excavation of the lesions. Removal of the smear layer in the excavated carious lesions increased the permeability significantly to 6.9 +/- 3.2%. Preparation of a control cavity of the same area and depth increased the permeability slightly. Removal of its smear layer increased the permeability of the dentin 91%. These results confirm previous qualitative studies that carious dentin, even after excavation and removal of the smear layer has a very low permeability.

  9. NACSA Charter School Replication Guide: The Spectrum of Replication Options. Authorizing Matters. Replication Brief 1

    Science.gov (United States)

    O'Neill, Paul

    2010-01-01

    One of the most important and high-profile issues in public education reform today is the replication of successful public charter school programs. With more than 5,000 failing public schools in the United States, there is a tremendous need for strong alternatives for parents and students. Replicating successful charter school models is an…

  10. Steam-water relative permeability

    Energy Technology Data Exchange (ETDEWEB)

    Ambusso, W.; Satik, C.; Home, R.N. [Stanford Univ., CA (United States)

    1997-12-31

    A set of relative permeability relations for simultaneous flow of steam and water in porous media have been measured in steady state experiments conducted under the conditions that eliminate most errors associated with saturation and pressure measurements. These relations show that the relative permeabilities for steam-water flow in porous media vary approximately linearly with saturation. This departure from the nitrogen/water behavior indicates that there are fundamental differences between steam/water and nitrogen/water flows. The saturations in these experiments were measured by using a high resolution X-ray computer tomography (CT) scanner. In addition the pressure gradients were obtained from the measurements of liquid phase pressure over the portions with flat saturation profiles. These two aspects constitute a major improvement in the experimental method compared to those used in the past. Comparison of the saturation profiles measured by the X-ray CT scanner during the experiments shows a good agreement with those predicted by numerical simulations. To obtain results that are applicable to general flow of steam and water in porous media similar experiments will be conducted at higher temperature and with porous rocks of different wetting characteristics and porosity distribution.

  11. International Expansion through Flexible Replication

    DEFF Research Database (Denmark)

    Jonsson, Anna; Foss, Nicolai Juul

    2011-01-01

    to local environments and under the impact of new learning. To illuminate these issues, we draw on a longitudinal in-depth study of Swedish home furnishing giant IKEA, involving more than 70 interviews. We find that IKEA has developed organizational mechanisms that support an ongoing learning process aimed......, etc.) are replicated in a uniform manner across stores, and change only very slowly (if at all) in response to learning (“flexible replication”). We conclude by discussing the factors that influence the approach to replication adopted by an international replicator....

  12. The Psychology of Replication and Replication in Psychology.

    Science.gov (United States)

    Francis, Gregory

    2012-11-01

    Like other scientists, psychologists believe experimental replication to be the final arbiter for determining the validity of an empirical finding. Reports in psychology journals often attempt to prove the validity of a hypothesis or theory with multiple experiments that replicate a finding. Unfortunately, these efforts are sometimes misguided because in a field like experimental psychology, ever more successful replication does not necessarily ensure the validity of an empirical finding. When psychological experiments are analyzed with statistics, the rules of probability dictate that random samples should sometimes be selected that do not reject the null hypothesis, even if an effect is real. As a result, it is possible for a set of experiments to have too many successful replications. When there are too many successful replications for a given set of experiments, a skeptical scientist should be suspicious that null or negative findings have been suppressed, the experiments were run improperly, or the experiments were analyzed improperly. This article describes the implications of this observation and demonstrates how to test for too much successful replication by using a set of experiments from a recent research paper.

  13. Regulation of Replication Recovery and Genome Integrity

    DEFF Research Database (Denmark)

    Colding, Camilla Skettrup

    Preserving genome integrity is essential for cell survival. To this end, mechanisms that supervise DNA replication and respond to replication perturbations have evolved. One such mechanism is the replication checkpoint, which responds to DNA replication stress and acts to ensure replication pausing...

  14. Vortex rings impinging on permeable boundaries

    Science.gov (United States)

    Mujal-Colilles, Anna; Dalziel, Stuart B.; Bateman, Allen

    2015-01-01

    Experiments with vortex rings impinging permeable and solid boundaries are presented in order to investigate the influence of permeability. Utilizing Particle Image Velocimetry, we compared the behaviour of a vortex ring impinging four different reticulated foams (with permeability k ˜ 26 - 85 × 10-8 m2) and a solid boundary. Results show how permeability affects the stretching phenomena of the vortex ring and the formation and evolution of the secondary vortex ring with opposite sign. Moreover, permeability also affects the macroscopic no-slip boundary condition found on the solid boundary, turning it into an apparent slip boundary condition for the most permeable boundary. The apparent slip-boundary condition and the flux exchange between the ambient fluid and the foam are jointly responsible for both the modified formation of the secondary vortex and changes on the vortex ring diameter increase.

  15. Clogging in permeable concrete: A review.

    Science.gov (United States)

    Kia, Alalea; Wong, Hong S; Cheeseman, Christopher R

    2017-05-15

    Permeable concrete (or "pervious concrete" in North America) is used to reduce local flooding in urban areas and is an important sustainable urban drainage system. However, permeable concrete exhibits reduction in permeability due to clogging by particulates, which severely limits service life. This paper reviews the clogging mechanism and current mitigating strategies in order to inform future research needs. The pore structure of permeable concrete and characteristics of flowing particulates influence clogging, which occurs when particles build-up and block connected porosity. Permeable concrete requires regular maintenance by vacuum sweeping and pressure washing, but the effectiveness and viability of these methods is questionable. The potential for clogging is related to the tortuosity of the connected porosity, with greater tortuosity resulting in increased potential for clogging. Research is required to develop permeable concrete that can be poured on-site, which produces a pore structure with significantly reduced tortuosity. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. Modelling of water permeability in cementitious materials

    DEFF Research Database (Denmark)

    Guang, Ye; Lura, Pietro; van Breugel, K.

    2006-01-01

    This paper presents a network model to predict the permeability of cement paste from a numerical simulation of its microstructure. Based on a linked list pore network structure, the effective hydraulic conductivity is estimated and the fluid flow is calculated according to the Hagen-Poiseuille law....... The pressure gradient at all nodes is calculated with the Gauss elimination method and the absolute permeability of the pore network is calculated directly from Darcy's law. Finally, the permeability model is validated by comparison with direct water permeability measurements. According to this model......, the predicted permeability of hydrating cement pastes is extremely sensitive to the particle size distribution of the cement and especially to the minimum size of the cement particles. Both in simulations and experiments, the permeability of cement pastes is mainly determined by the critical diameter...

  17. Permeability of Electrospun Superhydrophobic Nanofiber Mats

    Directory of Open Access Journals (Sweden)

    Sarfaraz U. Patel

    2012-01-01

    Full Text Available This paper discusses the fabrication and characterization of electrospun nanofiber mats made up of poly(4-methyl-1-pentene polymer. The polymer was electrospun in different weight concentrations. The mats were characterized by their basis weight, fiber diameter distribution, contact angles, contact angle hysteresis, and air permeability. All of the electrospun nonwoven fiber mats had water contact angles greater than 150 degrees making them superhydrophobic. The permeabilities of the mats were empirically fitted to the mat basis weight by a linear relation. The experimentally measured air permeabilities were significantly larger than the permeabilities predicted by the Kuwabara model for fibrous media.

  18. Vascular permeability in cerebral cavernous malformations.

    Science.gov (United States)

    Mikati, Abdul G; Khanna, Omaditya; Zhang, Lingjiao; Girard, Romuald; Shenkar, Robert; Guo, Xiaodong; Shah, Akash; Larsson, Henrik B W; Tan, Huan; Li, Luying; Wishnoff, Matthew S; Shi, Changbin; Christoforidis, Gregory A; Awad, Issam A

    2015-10-01

    Patients with the familial form of cerebral cavernous malformations (CCMs) are haploinsufficient for the CCM1, CCM2, or CCM3 gene. Loss of corresponding CCM proteins increases RhoA kinase-mediated endothelial permeability in vitro, and in mouse brains in vivo. A prospective case-controlled observational study investigated whether the brains of human subjects with familial CCM show vascular hyperpermeability by dynamic contrast-enhanced quantitative perfusion magnetic resonance imaging, in comparison with CCM cases without familial disease, and whether lesional or brain vascular permeability correlates with CCM disease activity. Permeability in white matter far (WMF) from lesions was significantly greater in familial than in sporadic cases, but was similar in CCM lesions. Permeability in WMF increased with age in sporadic patients, but not in familial cases. Patients with more aggressive familial CCM disease had greater WMF permeability compared to those with milder disease phenotype, but similar lesion permeability. Subjects receiving statin medications for routine cardiovascular indications had a trend of lower WMF, but not lesion, permeability. This is the first demonstration of brain vascular hyperpermeability in humans with an autosomal dominant disease, as predicted mechanistically. Brain permeability, more than lesion permeability, may serve as a biomarker of CCM disease activity, and help calibrate potential drug therapy.

  19. Biomarkers of replicative senescence revisited

    DEFF Research Database (Denmark)

    Nehlin, Jan

    2016-01-01

    Biomarkers of replicative senescence can be defined as those ultrastructural and physiological variations as well as molecules whose changes in expression, activity or function correlate with aging, as a result of the gradual exhaustion of replicative potential and a state of permanent cell cycle...... with their chronological age and present health status, help define their current rate of aging and contribute to establish personalized therapy plans to reduce, counteract or even avoid the appearance of aging biomarkers....

  20. Nucleotide Metabolism and DNA Replication.

    Science.gov (United States)

    Warner, Digby F; Evans, Joanna C; Mizrahi, Valerie

    2014-10-01

    The development and application of a highly versatile suite of tools for mycobacterial genetics, coupled with widespread use of "omics" approaches to elucidate the structure, function, and regulation of mycobacterial proteins, has led to spectacular advances in our understanding of the metabolism and physiology of mycobacteria. In this article, we provide an update on nucleotide metabolism and DNA replication in mycobacteria, highlighting key findings from the past 10 to 15 years. In the first section, we focus on nucleotide metabolism, ranging from the biosynthesis, salvage, and interconversion of purine and pyrimidine ribonucleotides to the formation of deoxyribonucleotides. The second part of the article is devoted to DNA replication, with a focus on replication initiation and elongation, as well as DNA unwinding. We provide an overview of replication fidelity and mutation rates in mycobacteria and summarize evidence suggesting that DNA replication occurs during states of low metabolic activity, and conclude by suggesting directions for future research to address key outstanding questions. Although this article focuses primarily on observations from Mycobacterium tuberculosis, it is interspersed, where appropriate, with insights from, and comparisons with, other mycobacterial species as well as better characterized bacterial models such as Escherichia coli. Finally, a common theme underlying almost all studies of mycobacterial metabolism is the potential to identify and validate functions or pathways that can be exploited for tuberculosis drug discovery. In this context, we have specifically highlighted those processes in mycobacterial DNA replication that might satisfy this critical requirement.

  1. Plasmid Rolling-Circle Replication.

    Science.gov (United States)

    Ruiz-Masó, J A; MachóN, C; Bordanaba-Ruiseco, L; Espinosa, M; Coll, M; Del Solar, G

    2015-02-01

    Plasmids are DNA entities that undergo controlled replication independent of the chromosomal DNA, a crucial step that guarantees the prevalence of the plasmid in its host. DNA replication has to cope with the incapacity of the DNA polymerases to start de novo DNA synthesis, and different replication mechanisms offer diverse solutions to this problem. Rolling-circle replication (RCR) is a mechanism adopted by certain plasmids, among other genetic elements, that represents one of the simplest initiation strategies, that is, the nicking by a replication initiator protein on one parental strand to generate the primer for leading-strand initiation and a single priming site for lagging-strand synthesis. All RCR plasmid genomes consist of a number of basic elements: leading strand initiation and control, lagging strand origin, phenotypic determinants, and mobilization, generally in that order of frequency. RCR has been mainly characterized in Gram-positive bacterial plasmids, although it has also been described in Gram-negative bacterial or archaeal plasmids. Here we aim to provide an overview of the RCR plasmids' lifestyle, with emphasis on their characteristic traits, promiscuity, stability, utility as vectors, etc. While RCR is one of the best-characterized plasmid replication mechanisms, there are still many questions left unanswered, which will be pointed out along the way in this review.

  2. Reactivation of DNA replication in nuclei from terminally differentiated cells: nuclear membrane permeabilization is required for initiation in Xenopus egg extract.

    Science.gov (United States)

    Leno, G H; Munshi, R

    1997-05-01

    We have used Xenopus egg extract to investigate the requirements for reactivation of DNA replication in nuclei isolated from terminally differentiated chicken erythrocytes. Previous work has shown that reactivation of erythrocyte nuclei in egg extract is accompanied by chromatin decondensation, nuclear envelope reformation, and the accumulation of egg lamin, LIII. However, in those studies, erythrocyte nuclei were prepared by methods that were not designed to maintain the selective permeability of the nuclear membrane, and as such, it is not clear if loss of nuclear membrane integrity played a role in the reactivation process. Therefore, the purpose of this study was to determine if changes in nuclear membrane permeability are required for reactivation of erythrocyte nuclei in egg extract. Nuclei with intact nuclear membranes were prepared from erythrocytes with streptolysin O and permeable nuclei by treatment of intact nuclei with the detergent Nonidet-P40. Like permeable nuclei, most intact nuclei decondensed, imported nuclear protein, and accumulated lamin LIII from the extract. However, unlike permeable nuclei, which replicated extensively in the extract, few intact nuclei initiated replication under the same conditions. These data demonstrate that permeabilization of the nuclear membrane is required for reactivation of DNA replication in terminally differentiated erythrocyte nuclei by egg extract and suggest that loss of nuclear membrane integrity may be a general requirement for replication of quiescent cell nuclei by this system.

  3. Intercomparison on measurement of water vapour permeability

    DEFF Research Database (Denmark)

    Hansen, Kurt Kielsgaard

    Three different materials are tested - hard woodfibre board - damp proof course - underlay for roofing The water vapour permeability has been measured according to EN ISO 12572 (2001).......Three different materials are tested - hard woodfibre board - damp proof course - underlay for roofing The water vapour permeability has been measured according to EN ISO 12572 (2001)....

  4. Crustal permeability: Introduction to the special issue

    Science.gov (United States)

    Ingebritsen, Steven E.; Gleeson, Tom

    2015-01-01

    The topic of crustal permeability is of broad interest in light of the controlling effect of permeability on diverse geologic processes and also timely in light of the practical challenges associated with emerging technologies such as hydraulic fracturing for oil and gas production (‘fracking’), enhanced geothermal systems, and geologic carbon sequestration. This special issue of Geofluids is also motivated by the historical dichotomy between the hydrogeologic concept of permeability as a static material property that exerts control on fluid flow and the perspective of economic geologists, geophysicists, and crustal petrologists who have long recognized permeability as a dynamic parameter that changes in response to tectonism, fluid production, and geochemical reactions. Issues associated with fracking, enhanced geothermal systems, and geologic carbon sequestration have already begun to promote a constructive dialog between the static and dynamic views of permeability, and here we have made a conscious effort to include both viewpoints. This special issue also focuses on the quantification of permeability, encompassing both direct measurement of permeability in the uppermost crust and inferential permeability estimates, mainly for the deeper crust.

  5. Accurate determination of characteristic relative permeability curves

    Science.gov (United States)

    Krause, Michael H.; Benson, Sally M.

    2015-09-01

    A recently developed technique to accurately characterize sub-core scale heterogeneity is applied to investigate the factors responsible for flowrate-dependent effective relative permeability curves measured on core samples in the laboratory. The dependency of laboratory measured relative permeability on flowrate has long been both supported and challenged by a number of investigators. Studies have shown that this apparent flowrate dependency is a result of both sub-core scale heterogeneity and outlet boundary effects. However this has only been demonstrated numerically for highly simplified models of porous media. In this paper, flowrate dependency of effective relative permeability is demonstrated using two rock cores, a Berea Sandstone and a heterogeneous sandstone from the Otway Basin Pilot Project in Australia. Numerical simulations of steady-state coreflooding experiments are conducted at a number of injection rates using a single set of input characteristic relative permeability curves. Effective relative permeability is then calculated from the simulation data using standard interpretation methods for calculating relative permeability from steady-state tests. Results show that simplified approaches may be used to determine flowrate-independent characteristic relative permeability provided flow rate is sufficiently high, and the core heterogeneity is relatively low. It is also shown that characteristic relative permeability can be determined at any typical flowrate, and even for geologically complex models, when using accurate three-dimensional models.

  6. Permeability Tests on Eastern Scheldt Sand

    DEFF Research Database (Denmark)

    Jakobsen, Kim Parsberg

    The flow through porous media plays an important role in various engineering disciplines, as for example in ground water hydrology and soil mechanics. In the present study the permeability is determined for a fine, saturated sand. As the flow through a porous media strongly depends on the charact......The flow through porous media plays an important role in various engineering disciplines, as for example in ground water hydrology and soil mechanics. In the present study the permeability is determined for a fine, saturated sand. As the flow through a porous media strongly depends...... on the characteristics of the soil matrix, the permeability is determined for different void ratios. All tests are performed on reconstituted specimens of Eastern Scheldt Sand. The permeability is determined by use of a falling head apparatus. Finally the test results are briefly summarised and a relationship between...... void ratio and permeability is established....

  7. Macro fluid analysis of laminated fabric permeability

    Directory of Open Access Journals (Sweden)

    Qiu Li

    2016-01-01

    Full Text Available A porous jump model is put forward to predict the breathability of laminated fabrics by utilizing fluent software. To simplify the parameter setting process, the methods of determining the parameters of jump porous model by means of fabric layers are studied. Also, effects of single/multi-layer fabrics and thickness on breathability are analyzed, indicating that fabric breathability reduces with the increase of layers. Multi-layer fabric is simplified into a single layer, and the fabric permeability is calculated by proportion. Moreover, the change curve of fabric layer and face permeability, as well as the equation between the fabric layer and the face permeability are obtained. Then, face permeability and pressure-jump coefficient parameters setting of porous jump model could be integrated into single parameter (i. e. fabric layers, which simplifies the fluent operation process and realizes the prediction of laminated fabric permeability.

  8. Permeability measurement and control for epoxy composites

    Science.gov (United States)

    Chang, Tsun-Hsu; Tsai, Cheng-Hung; Wong, Wei-Syuan; Chen, Yen-Ren; Chao, Hsien-Wen

    2017-08-01

    The coupling of the electric and magnetic fields leads to a strong interplay in materials' permittivity and permeability. Here, we proposed a specially designed cavity, called the mu cavity. The mu cavity, consisting of a mushroom structure inside a cylindrical resonator, is exclusively sensitive to permeability, but not to permittivity. It decouples materials' electromagnetic properties and allows an accurate measurement of the permeability. With the help of an epsilon cavity, these two cavities jointly determine the complex permeability and permittivity of the materials at microwave frequencies. Homemade epoxy-based composite materials were prepared and tested. Measurement and manipulation of the permeability and permittivity of the epoxy composites will be shown. The results will be compared with the effective medium theories.

  9. Compact rock material gas permeability properties

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Huanling, E-mail: whl_hm@163.com [Key Laboratory of Coastal Disaster and Defence, Ministry of Education, Hohai University, Nanjing 210098 (China); LML, University of Lille, Cite Scientifique, 59655 Villeneuve d’Ascq (France); Xu, Weiya; Zuo, Jing [Institutes of Geotechnical Engineering, Hohai University, Nanjing 210098 (China)

    2014-09-15

    Natural compact rocks, such as sandstone, granite, and rock salt, are the main materials and geological environment for storing underground oil, gas, CO{sub 2,} shale gas, and radioactive waste because they have extremely low permeabilities and high mechanical strengths. Using the inert gas argon as the fluid medium, the stress-dependent permeability and porosity of monzonitic granite and granite gneiss from an underground oil storage depot were measured using a permeability and porosity measurement system. Based on the test results, models for describing the relationships among the permeability, porosity, and confining pressure of rock specimens were analyzed and are discussed. A power law is suggested to describe the relationship between the stress-dependent porosity and permeability; for the monzonitic granite and granite gneiss (for monzonitic granite (A-2), the initial porosity is approximately 4.05%, and the permeability is approximately 10{sup −19} m{sup 2}; for the granite gneiss (B-2), the initial porosity is approximately 7.09%, the permeability is approximately 10{sup −17} m{sup 2}; and the porosity-sensitivity exponents that link porosity and permeability are 0.98 and 3.11, respectively). Compared with moderate-porosity and high-porosity rocks, for which φ > 15%, low-porosity rock permeability has a relatively lower sensitivity to stress, but the porosity is more sensitive to stress, and different types of rocks show similar trends. From the test results, it can be inferred that the test rock specimens’ permeability evolution is related to the relative particle movements and microcrack closure.

  10. Gas and Water Permeability of Concrete

    Energy Technology Data Exchange (ETDEWEB)

    Villar, M. V.; Martin, P. L.; Romero, F. J.; Gutierrez-Rodirgo, V.; Barcala, J. M.

    2012-11-01

    The gas pressure of concrete samples was measured in an unsteady-state equipment working under low injection pressures and in a newly fine tuned steady-state setup working under different pressures. These measurements allowed the estimation of the intrinsic and relative gas permeability of the concrete and of the effect of boundary conditions on them. Permeability decreased with water content, but it was also greatly affected by the hydraulic history of concrete, i.e. if it had been previously dried or wetted. In particular, and for a given degree of saturation, the gas permeability of concrete previously saturated was lower than if the concrete had been just air dried or saturated after air drying. In any case, the gas permeability was about two orders of magnitude higher than the liquid water permeability (10-16 vs. 10-18 m2), probably due to the chemical reactions taking place during saturation (carbonation). The relative gas permeability of concrete increased sharply for water degrees of saturation smaller than 50%. The boundary conditions also affected the gas permeability, which seemed to be mostly conditioned by the back pressure and the confining pressure, increasing as the former increased and decreasing as the latter increased, i.e. decreasing as the effective pressure increased. Overall the increase of pressure head or injection pressure implied a decrease in gas permeability. External,microcracking during air-drying could not be ruled out as responsible for the decrease of permeability with confining pressure. The apparent permeability obtained applying the Klinkenberg method for a given effective pressure was only slightly smaller than the average of all the values measured for the same confining pressure range. For this reason it is considered that the Klinkenberg effect was not relevant in the range of pressures applied. (Author) 37 refs.

  11. Defects of mitochondrial DNA replication.

    Science.gov (United States)

    Copeland, William C

    2014-09-01

    Mitochondrial DNA is replicated by DNA polymerase γ in concert with accessory proteins such as the mitochondrial DNA helicase, single-stranded DNA binding protein, topoisomerase, and initiating factors. Defects in mitochondrial DNA replication or nucleotide metabolism can cause mitochondrial genetic diseases due to mitochondrial DNA deletions, point mutations, or depletion, which ultimately cause loss of oxidative phosphorylation. These genetic diseases include mitochondrial DNA depletion syndromes such as Alpers or early infantile hepatocerebral syndromes, and mitochondrial DNA deletion disorders, such as progressive external ophthalmoplegia, ataxia-neuropathy, or mitochondrial neurogastrointestinal encephalomyopathy. This review focuses on our current knowledge of genetic defects of mitochondrial DNA replication (POLG, POLG2, C10orf2, and MGME1) that cause instability of mitochondrial DNA and mitochondrial disease.

  12. Regulation of beta cell replication

    DEFF Research Database (Denmark)

    Lee, Ying C; Nielsen, Jens Høiriis

    2008-01-01

    Beta cell mass, at any given time, is governed by cell differentiation, neogenesis, increased or decreased cell size (cell hypertrophy or atrophy), cell death (apoptosis), and beta cell proliferation. Nutrients, hormones and growth factors coupled with their signalling intermediates have been...... suggested to play a role in beta cell mass regulation. In addition, genetic mouse model studies have indicated that cyclins and cyclin-dependent kinases that determine cell cycle progression are involved in beta cell replication, and more recently, menin in association with cyclin-dependent kinase...... inhibitors has been demonstrated to be important in beta cell growth. In this review, we consider and highlight some aspects of cell cycle regulation in relation to beta cell replication. The role of cell cycle regulation in beta cell replication is mostly from studies in rodent models, but whether...

  13. Shell Separation for Mirror Replication

    Science.gov (United States)

    1999-01-01

    NASA's Space Optics Manufacturing Center has been working to expand our view of the universe via sophisticated new telescopes. The Optics Center's goal is to develop low-cost, advanced space optics technologies for the NASA program in the 21st century - including the long-term goal of imaging Earth-like planets in distant solar systems. To reduce the cost of mirror fabrication, Marshall Space Flight Center (MSFC) has developed replication techniques, the machinery, and materials to replicate electro-formed nickel mirrors. Optics replication uses reusable forms, called mandrels, to make telescope mirrors ready for final finishing. MSFC optical physicist Bill Jones monitors a device used to chill a mandrel, causing it to shrink and separate from the telescope mirror without deforming the mirror's precisely curved surface.

  14. Personality and Academic Motivation: Replication, Extension, and Replication

    Science.gov (United States)

    Jones, Martin H.; McMichael, Stephanie N.

    2015-01-01

    Previous work examines the relationships between personality traits and intrinsic/extrinsic motivation. We replicate and extend previous work to examine how personality may relate to achievement goals, efficacious beliefs, and mindset about intelligence. Approximately 200 undergraduates responded to the survey with a 150 participants replicating…

  15. Plant actin controls membrane permeability.

    Science.gov (United States)

    Hohenberger, Petra; Eing, Christian; Straessner, Ralf; Durst, Steffen; Frey, Wolfgang; Nick, Peter

    2011-09-01

    The biological effects of electric pulses with low rise time, high field strength, and durations in the nanosecond range (nsPEFs) have attracted considerable biotechnological and medical interest. However, the cellular mechanisms causing membrane permeabilization by nanosecond pulsed electric fields are still far from being understood. We investigated the role of actin filaments for membrane permeability in plant cells using cell lines where different degrees of actin bundling had been introduced by genetic engineering. We demonstrate that stabilization of actin increases the stability of the plasma membrane against electric permeabilization recorded by penetration of Trypan Blue into the cytoplasm. By use of a cell line expressing the actin bundling WLIM domain under control of an inducible promotor we can activate membrane stabilization by the glucocorticoid analog dexamethasone. By total internal reflection fluorescence microscopy we can visualize a subset of the cytoskeleton that is directly adjacent to the plasma membrane. We conclude that this submembrane cytoskeleton stabilizes the plasma membrane against permeabilization through electric pulses. Copyright © 2011 Elsevier B.V. All rights reserved.

  16. Regulation of Replication Recovery and Genome Integrity

    DEFF Research Database (Denmark)

    Colding, Camilla Skettrup

    facilitate replication recovery after MMS-induced replication stress. Our data reveal that control of Mrc1 turnover through the interplay between posttranslational modifications and INQ localization adds another layer of regulation to the replication checkpoint. We also add replication recovery to the list...... is mediated by Mrc1, which ensures Mec1 presence at the stalled replication fork thus facilitating Rad53 phosphorylation. When replication can be resumed safely, the replication checkpoint is deactivated and replication forks restart. One mechanism for checkpoint deactivation is the ubiquitin......-targeted proteasomal degradation of Mrc1. In this study, we describe a novel nuclear structure, the intranuclear quality control compartment (INQ), which regulates protein turnover and is important for recovery after replication stress. We find that upon methyl methanesulfonate (MMS)-induced replication stress, INQ...

  17. A Negative Permeability Material at Red Light

    DEFF Research Database (Denmark)

    Yuan, Hsiao-Kuan; Chettiar, Uday K.; Cai, Wenshan;

    2007-01-01

    A negative permeability in a periodic array of pairs of thin silver strips is demonstrated experimentally for two distinct samples. The effect of the strip surface roughness on negative permeability is evaluated. The first sample, Sample A, is fabricated of thinner strips with a root mean square...... roughness of 7 nm, while Sample B is made of thicker strips with 3-nm roughness. The real part of permeability, μ ′ , is −1 at a wavelength of 770 nm in Sample A and −1.7 at 725 nm in Sample B. Relative to prototypes simulated with ideal strips, larger strip roughness acts to decrease μ ′ by a factor of 7...

  18. Gut Permeability in Autism Spectrum Disorders

    OpenAIRE

    2014-01-01

    ObjectiveTo test whether gut permeability is increased in autism spectrum disorders (ASD) by evaluating gut permeability in a population-derived cohort of children with ASD compared with age- and intelligence quotient-matched controls without ASD but with special educational needs (SEN).Patients and MethodsOne hundred thirty-three children aged 10–14 years, 103 with ASD and 30 with SEN, were given an oral test dose of mannitol and lactulose and urine collected for 6 hr. Gut permeability was a...

  19. Hyperthermia stimulates HIV-1 replication.

    Directory of Open Access Journals (Sweden)

    Ferdinand Roesch

    Full Text Available HIV-infected individuals may experience fever episodes. Fever is an elevation of the body temperature accompanied by inflammation. It is usually beneficial for the host through enhancement of immunological defenses. In cultures, transient non-physiological heat shock (42-45°C and Heat Shock Proteins (HSPs modulate HIV-1 replication, through poorly defined mechanisms. The effect of physiological hyperthermia (38-40°C on HIV-1 infection has not been extensively investigated. Here, we show that culturing primary CD4+ T lymphocytes and cell lines at a fever-like temperature (39.5°C increased the efficiency of HIV-1 replication by 2 to 7 fold. Hyperthermia did not facilitate viral entry nor reverse transcription, but increased Tat transactivation of the LTR viral promoter. Hyperthermia also boosted HIV-1 reactivation in a model of latently-infected cells. By imaging HIV-1 transcription, we further show that Hsp90 co-localized with actively transcribing provirus, and this phenomenon was enhanced at 39.5°C. The Hsp90 inhibitor 17-AAG abrogated the increase of HIV-1 replication in hyperthermic cells. Altogether, our results indicate that fever may directly stimulate HIV-1 replication, in a process involving Hsp90 and facilitation of Tat-mediated LTR activity.

  20. Hyperthermia stimulates HIV-1 replication.

    Science.gov (United States)

    Roesch, Ferdinand; Meziane, Oussama; Kula, Anna; Nisole, Sébastien; Porrot, Françoise; Anderson, Ian; Mammano, Fabrizio; Fassati, Ariberto; Marcello, Alessandro; Benkirane, Monsef; Schwartz, Olivier

    2012-01-01

    HIV-infected individuals may experience fever episodes. Fever is an elevation of the body temperature accompanied by inflammation. It is usually beneficial for the host through enhancement of immunological defenses. In cultures, transient non-physiological heat shock (42-45°C) and Heat Shock Proteins (HSPs) modulate HIV-1 replication, through poorly defined mechanisms. The effect of physiological hyperthermia (38-40°C) on HIV-1 infection has not been extensively investigated. Here, we show that culturing primary CD4+ T lymphocytes and cell lines at a fever-like temperature (39.5°C) increased the efficiency of HIV-1 replication by 2 to 7 fold. Hyperthermia did not facilitate viral entry nor reverse transcription, but increased Tat transactivation of the LTR viral promoter. Hyperthermia also boosted HIV-1 reactivation in a model of latently-infected cells. By imaging HIV-1 transcription, we further show that Hsp90 co-localized with actively transcribing provirus, and this phenomenon was enhanced at 39.5°C. The Hsp90 inhibitor 17-AAG abrogated the increase of HIV-1 replication in hyperthermic cells. Altogether, our results indicate that fever may directly stimulate HIV-1 replication, in a process involving Hsp90 and facilitation of Tat-mediated LTR activity.

  1. Cellular Responses to Replication Problems

    NARCIS (Netherlands)

    M. Budzowska (Magdalena)

    2008-01-01

    textabstractDuring every S-phase cells need to duplicate their genomes so that both daughter cells inherit complete copies of genetic information. It is a tremendous task, given the large sizes of mammalian genomes and the required precision of DNA replication. A major threat to the accuracy and eff

  2. Covert Reinforcement: A Partial Replication.

    Science.gov (United States)

    Ripstra, Constance C.; And Others

    A partial replication of an investigation of the effect of covert reinforcement on a perceptual estimation task is described. The study was extended to include an extinction phase. There were five treatment groups: covert reinforcement, neutral scene reinforcement, noncontingent covert reinforcement, and two control groups. Each subject estimated…

  3. Crinivirus replication and host interactions

    Directory of Open Access Journals (Sweden)

    Zsofia A Kiss

    2013-05-01

    Full Text Available Criniviruses comprise one of the genera within the family Closteroviridae. Members in this family are restricted to the phloem and rely on whitefly vectors of the genera Bemisia and/or Trialeurodes for plant-to-plant transmission. All criniviruses have bipartite, positive-sense ssRNA genomes, although there is an unconfirmed report of one having a tripartite genome. Lettuce infectious yellows virus (LIYV is the type species of the genus, the best studied so far of the criniviruses and the first for which a reverse genetics system was available. LIYV RNA 1 encodes for proteins predicted to be involved in replication, and alone is competent for replication in protoplasts. Replication results in accumulation of cytoplasmic vesiculated membranous structures which are characteristic of most studied members of the Closteroviridae. These membranous structures, often referred to as BYV-type vesicles, are likely sites of RNA replication. LIYV RNA 2 is replicated in trans when co-infecting cells with RNA 1, but is temporally delayed relative to RNA1. Efficient RNA 2 replication also is dependent on the RNA 1-encoded RNA binding protein, P34. No LIYV RNA 2-encoded proteins have been shown to affect RNA replication, but at least four, CP, CPm, Hsp70h, and p59 are virion structural components and CPm is a determinant of whitefly transmissibility. Roles of other LIYV RNA 2-encoded proteins are largely as yet unknown, but P26 is a non-virion protein that accumulates in cells as characteristic plasmalemma deposits which in plants are localized within phloem parenchyma and companion cells over plasmodesmata connections to sieve elements. The two remaining crinivirus-conserved RNA 2-encoded proteins are P5 and P9. P5 is 39 amino acid protein and is encoded at the 5’ end of RNA 2 as ORF1 and is part of the hallmark closterovirus gene array. The orthologous gene in BYV has been shown to play a role in cell-to-cell movement and indicated to be localized to the

  4. Variability of permeability with diameter of conduit

    Indian Academy of Sciences (India)

    J A Adegoke; J A Olowofela

    2008-05-01

    An entry length is always observed before laminar flow is achieved in fluid flowing in a conduit. This depends on the Reynolds number of the flow and the degree of smoothness of the conduit. This work examined this region and the point where laminar flow commences in the context of flow through conduit packed with porous material like beads, of known porosity. Using some theoretical assumptions, it is demonstrated that permeability varies from zero at wall-fluid boundary to maximum at mid-stream, creating a permeability profile similar to the velocity profile. An equation was obtained to establish this. We also found that peak values of permeability increase with increasing porosity, and therefore entry length increases with increasing porosity with all other parameters kept constant. A plot of peak permeability versus porosity revealed that they are linearly related.

  5. Effect of temperature on sandstone permeability

    DEFF Research Database (Denmark)

    Rosenbrand, Esther; Kjøller, Claus

    assumptions would be required in order to estimate sandstone permeability based on the Kozeny equation. An effective specific surface area per pore volume for permeability was estimated by using image analysis and pore size distributions as from nuclear magnetic resonance (NMR) transverse relaxation data...... be determined based on the Klinkenberg (1941) procedure, which accounts for effects on permeability of gas slip on the fluid-solid interface by means of several permeability measurements with different pore pressures. A comparison between the equivalent pore sizes as estimated using the Kozeny equation...... at 80°C than at 20°C; at 80°C the main effect might be due to an alteration of pore fluid rheology, whereas at 20°C particles might be filtered in pore constrictions. DLVO theory (Derjaguin and Landau (1941); Verwey and Overbeek (1948)) was used to compare effects of temperature and salinity on surface...

  6. Measuring Permeability of Composite Cryotank Laminants

    Science.gov (United States)

    Oliver, Stanley T.; Selvidge, Shawn; Watwood, Michael C.

    2004-01-01

    This paper describes a test method developed to identify whether certain materials and material systems are suitable candidates for large pressurized reusable cryogenic tanks intended for use in current and future manned launch systems. It provides a quick way to screen numerous candidate materials for permeability under anticipated loading environments consistent with flight conditions, as well as addressing reusability issues. cryogenic tank, where the major design issue was hydrogen permeability. It was successfully used to evaluate samples subjected to biaxial loading while maintaining test temperatures near liquid hydrogen. After each sample was thermally preconditioned, a cyclic pressure load was applied to simulate the in-plane strain. First permeability was measured while a sample was under load. Then the sample was unloaded and allowed to return to ambient temperature. The test was repeated to simulate reusability, in order to evaluate its effects on material permeability.

  7. Lunar electrical conductivity and magnetic permeability

    Science.gov (United States)

    Dyal, P.; Parkin, C. W.; Daily, W. D.

    1975-01-01

    Improved analytical techniques are applied to a large Apollo magnetometer data set to yield values of electroconductivity, temperature, magnetic permeability, and iron abundance. Average bulk electroconductivity of the moon is calculated to be .0007 mho/m; a rapid increase with depth to about .003 mho/m within 250 km is indicated. The temperature profile, obtained from the electroconductivity profile for olivine, indicates high lunar temperatures at relatively shallow depths. Magnetic permeability of the moon relative to its environment is calculated to be 1.008 plus or minus .005; a permeability relative to free space of 1.012 plus 0.011, minus 0.008 is obtained. Lunar iron abundances corresponding to this permeability value are 2.5 plus 2.3, minus 1.7 wt% free iron and 5.0-13.5 wt% total iron for a moon composed of a combination of free iron, olivine, and orthopyroxene.

  8. Permeable landscapes for wildlife in the Northeast

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Landscape permeability, also referred to as "habitat connectivity," is the ability of a diverse land area to provide for passage of animals. This project will...

  9. Replication-Uncoupled Histone Deposition during Adenovirus DNA Replication

    OpenAIRE

    Komatsu, Tetsuro; Nagata, Kyosuke

    2012-01-01

    In infected cells, the chromatin structure of the adenovirus genome DNA plays critical roles in its genome functions. Previously, we reported that in early phases of infection, incoming viral DNA is associated with both viral core protein VII and cellular histones. Here we show that in late phases of infection, newly synthesized viral DNA is also associated with histones. We also found that the knockdown of CAF-1, a histone chaperone that functions in the replication-coupled deposition of his...

  10. Food Packaging Permeability Behaviour: A Report

    OpenAIRE

    Valentina Siracusa

    2012-01-01

    The use of polymer materials in food packaging field is one of the largest growing market area. Actually the optimization behaviour of packaging permeability is of crucial importance, in order to extend the food shelf-life and to reach the best engineering solution. Studying the permeability characterization of the different polymer material (homogeneous and heterogeneous polymer system) to the different packaging gases, in different environmental condition, is crucial to understand if the se...

  11. Pneumatic fracturing of low permeability media

    Energy Technology Data Exchange (ETDEWEB)

    Schuring, J.R. [New Jersey Institute of Technology, Newark, NJ (United States)

    1996-08-01

    Pneumatic fracturing of soils to enhance the removal and treatment of dense nonaqueous phase liquids is described. The process involves gas injection at a pressure exceeding the natural stresses and at a flow rate exceeding the permeability of the formation. The paper outlines geologic considerations, advantages and disadvantages, general technology considerations, low permeability media considerations, commercial availability, efficiency, and costs. Five case histories of remediation using pneumatic fracturing are briefly summarized. 11 refs., 2 figs., 1 tab.

  12. REPLICATION TOOL AND METHOD OF PROVIDING A REPLICATION TOOL

    DEFF Research Database (Denmark)

    2016-01-01

    structured master surface (3a, 3b, 3c, 3d) having a lateral master pattern and a vertical master profile. The microscale structured master surface (3a, 3b, 3c, 3d) has been provided by localized pulsed laser treatment to generate microscale phase explosions. A method for producing a part with microscale......The invention relates to a replication tool (1, 1a, 1b) for producing a part (4) with a microscale textured replica surface (5a, 5b, 5c, 5d). The replication tool (1, 1a, 1b) comprises a tool surface (2a, 2b) defining a general shape of the item. The tool surface (2a, 2b) comprises a microscale...... energy directors on flange portions thereof uses the replication tool (1, 1a, 1b) to form an item (4) with a general shape as defined by the tool surface (2a, 2b). The formed item (4) comprises a microscale textured replica surface (5a, 5b, 5c, 5d) with a lateral arrangement of polydisperse microscale...

  13. Relations Between Permeability and Structure of Wood

    Institute of Scientific and Technical Information of China (English)

    Bao Fucheng; Zhao Youke; Lü Jianxiong

    2003-01-01

    The permeability and the structure of heartwood and sapwood of the solvent-exchange dried and the air-dried green-wood of Chinese-fir (Cunninghamia lanceolata (Lamb.) Hook.) and masson pine (Pinus massoniana Lamb.) were measured inorder to study the relations between the permeability and the structure. The results showed that the permeability of sapwood of boththe air-dried and the solvent-exchange dried wood was higher than that of heartwood, and the permeability of the solvent-exchangeddried heartwood and sapwood was higher than that of the air-dried. A higher permeability of wood was attributed to, on the one hand,a bigger number of flow path per unit area of the wood perpendicular to the flow direction resulted from a bigger number ofunaspirated pits per unit area and a bigger number of effective pit openings per membrane, and on the other hand, a smaller numberof tracheid in series connection per unit length parallel to flow direction resulted from a longer tracheid length and an effectivetracheid length for permeability.

  14. Permeability of lateritic soil by various methods

    Directory of Open Access Journals (Sweden)

    Tatiana Tavares Rodriguez

    2015-10-01

    Full Text Available Soil Permeability is an important property of soil used to dimension several types of engineering works, and it can be quantified by the permeability rates. Despite of the great use, the type of the re doubts about the best way to determine de permeability rates. The main questions are: (1 the type of the method and (2 the reproducibility of samples in tropical soils. So, the objective of this work is to evaluate the permeability of a lateritic soil by comparing values of permeability coefficient determined for laboratory and in situ testing. For this, it was chosen the lateritic soil of Campo Experimental de Engenharia Geotécncia (CEEG of the Universidade Estadual de Londrina (UEL and four equipments: constant and variable head permeameters, Guelph permeameter and infiltrometer. The results show that all the methods present mean value of permeability coefficient on the order of 10-3 cm/s whit variation coefficient in range of 37% to 92% , except the constant permeameter. The heterogeneous structure of lateritic soil (in macro and micro pores is the probably determinant of the variability observed.

  15. Comparative field permeability measurement of permeable pavements using ASTM C1701 and NCAT permeameter methods.

    Science.gov (United States)

    Li, Hui; Kayhanian, Masoud; Harvey, John T

    2013-03-30

    Fully permeable pavement is gradually gaining support as an alternative best management practice (BMP) for stormwater runoff management. As the use of these pavements increases, a definitive test method is needed to measure hydraulic performance and to evaluate clogging, both for performance studies and for assessment of permeability for construction quality assurance and maintenance needs assessment. Two of the most commonly used permeability measurement tests for porous asphalt and pervious concrete are the National Center for Asphalt Technology (NCAT) permeameter and ASTM C1701, respectively. This study was undertaken to compare measured values for both methods in the field on a variety of permeable pavements used in current practice. The field measurements were performed using six experimental section designs with different permeable pavement surface types including pervious concrete, porous asphalt and permeable interlocking concrete pavers. Multiple measurements were performed at five locations on each pavement test section. The results showed that: (i) silicone gel is a superior sealing material to prevent water leakage compared with conventional plumbing putty; (ii) both methods (NCAT and ASTM) can effectively be used to measure the permeability of all pavement types and the surface material type will not impact the measurement precision; (iii) the permeability values measured with the ASTM method were 50-90% (75% on average) lower than those measured with the NCAT method; (iv) the larger permeameter cylinder diameter used in the ASTM method improved the reliability and reduced the variability of the measured permeability.

  16. Frictional stability-permeability relationships for fractures in shales: Friction-Permeability Relationships

    Energy Technology Data Exchange (ETDEWEB)

    Fang, Yi [Department of Energy and Mineral Engineering, EMS Energy Institute, and G3 Center, Pennsylvania State University, University Park Pennsylvania USA; Elsworth, Derek [Department of Energy and Mineral Engineering, EMS Energy Institute, and G3 Center, Pennsylvania State University, University Park Pennsylvania USA; Department of Geosciences, EMS Energy Institute, and G3 Center, Pennsylvania State University, University Park Pennsylvania USA; Wang, Chaoyi [Department of Energy and Mineral Engineering, EMS Energy Institute, and G3 Center, Pennsylvania State University, University Park Pennsylvania USA; Ishibashi, Takuya [Department of Energy and Mineral Engineering, EMS Energy Institute, and G3 Center, Pennsylvania State University, University Park Pennsylvania USA; Fukushima Renewable Energy Institute, National Institute of Advanced Industrial Science and Technology, Koriyama Japan; Fitts, Jeffrey P. [Department of Civil and Environmental Engineering, Princeton University, Princeton New Jersey USA

    2017-01-01

    There is wide concern that fluid injection in the subsurface, such as for the stimulation of shale reservoirs or for geological CO2 sequestration (GCS), has the potential to induce seismicity that may change reservoir permeability due to fault slip. However, the impact of induced seismicity on fracture permeability evolution remains unclear due to the spectrum of modes of fault reactivation (e.g., stable versus unstable). As seismicity is controlled by the frictional response of fractures, we explore friction-stability-permeability relationships through the concurrent measurement of frictional and hydraulic properties of artificial fractures in Green River shale (GRS) and Opalinus shale (OPS). We observe that carbonate-rich GRS shows higher frictional strength but weak neutral frictional stability. The GRS fracture permeability declines during shearing while an increased sliding velocity reduces the rate of permeability decline. By comparison, the phyllosilicate-rich OPS has lower friction and strong stability while the fracture permeability is reduced due to the swelling behavior that dominates over the shearing induced permeability reduction. Hence, we conclude that the friction-stability-permeability relationship of a fracture is largely controlled by mineral composition and that shale mineral compositions with strong frictional stability may be particularly subject to permanent permeability reduction during fluid infiltration.

  17. Replicator dynamics in value chains

    DEFF Research Database (Denmark)

    Cantner, Uwe; Savin, Ivan; Vannuccini, Simone

    2016-01-01

    The pure model of replicator dynamics though providing important insights in the evolution of markets has not found much of empirical support. This paper extends the model to the case of firms vertically integrated in value chains. We show that i) by taking value chains into account, the replicator...... dynamics may revert its effect. In these regressive developments of market selection, firms with low fitness expand because of being integrated with highly fit partners, and the other way around; ii) allowing partner's switching within a value chain illustrates that periods of instability in the early...... stage of industry life-cycle may be the result of an 'optimization' of partners within a value chain providing a novel and simple explanation to the evidence discussed by Mazzucato (1998); iii) there are distinct differences in the contribution to market selection between the layers of a value chain...

  18. Therapeutic targeting of replicative immortality

    OpenAIRE

    Yaswen, Paul; MacKenzie, Karen L.; Keith, W. Nicol; Hentosh, Patricia; Rodier, Francis; Zhu, Jiyue; Firestone, Gary L.; Matheu, Ander; Carnero, Amancio; Bilsland, Alan; Sundin, Tabetha; Honoki, Kanya; Fujii, Hiromasa; Georgakilas, Alexandros G.; Amedei, Amedeo

    2015-01-01

    One of the hallmarks of malignant cell populations is the ability to undergo continuous proliferation. This property allows clonal lineages to acquire sequential aberrations that can fuel increasingly autonomous growth, invasiveness, and therapeutic resistance. Innate cellular mechanisms have evolved to regulate replicative potential as a hedge against malignant progression. When activated in the absence of normal terminal differentiation cues, these mechanisms can result in a state of persis...

  19. Alphavirus polymerase and RNA replication.

    Science.gov (United States)

    Pietilä, Maija K; Hellström, Kirsi; Ahola, Tero

    2017-01-16

    Alphaviruses are typically arthropod-borne, and many are important pathogens such as chikungunya virus. Alphaviruses encode four nonstructural proteins (nsP1-4), initially produced as a polyprotein P1234. nsP4 is the core RNA-dependent RNA polymerase but all four nsPs are required for RNA synthesis. The early replication complex (RC) formed by the polyprotein P123 and nsP4 synthesizes minus RNA strands, and the late RC composed of fully processed nsP1-nsP4 is responsible for the production of genomic and subgenomic plus strands. Different parts of nsP4 recognize the promoters for minus and plus strands but the binding also requires the other nsPs. The alphavirus polymerase has been purified and is capable of de novo RNA synthesis only in the presence of the other nsPs. The purified nsP4 also has terminal adenylyltransferase activity, which may generate the poly(A) tail at the 3' end of the genome. Membrane association of the nsPs is vital for replication, and alphaviruses induce membrane invaginations called spherules, which form a microenvironment for RNA synthesis by concentrating replication components and protecting double-stranded RNA intermediates. The RCs isolated as crude membrane preparations are active in RNA synthesis in vitro, but high-resolution structure of the RC has not been achieved, and thus the arrangement of viral and possible host components remains unknown. For some alphaviruses, Ras-GTPase-activating protein (Src-homology 3 (SH3) domain)-binding proteins (G3BPs) and amphiphysins have been shown to be essential for RNA replication and are present in the RCs. Host factors offer an additional target for antivirals, as only few alphavirus polymerase inhibitors have been described.

  20. Dynamic replication of Web contents

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The phenomenal growth of the World Wide Web has brought huge increase in the traffic to the popular web sites.Long delays and denial of service experienced by the end-users,especially during the peak hours,continues to be the common problem while accessing popular sites.Replicating some of the objects at multiple sites in a distributed web-server environment is one of the possible solutions to improve the response time/Iatency. The decision of what and where to replicate requires solving a constraint optimization problem,which is NP-complete in general.In this paper, we consider the problem of placing copies of objects in a distributed web server system to minimize the cost of serving read and write requests when the web servers have Iimited storage capacity.We formulate the problem as a 0-1 optimization problem and present a polynomial time greedy algorithm with backtracking to dynamically replicate objects at the appropriate sites to minimize a cost function.To reduce the solution search space,we present necessary condi tions for a site to have a replica of an object jn order to minimize the cost function We present simulation resuIts for a variety of problems to illustrate the accuracy and efficiency of the proposed algorithms and compare them with those of some well-known algorithms.The simulation resuIts demonstrate the superiority of the proposed algorithms.

  1. Relative permeability in dual porosity porous media

    Energy Technology Data Exchange (ETDEWEB)

    Deghmoum, A. [SONATRACH CRD, Boumerdes (Algeria); Tiab, D. [Oklahoma Univ., Norman, OK (United States); Mazouzi, A. [SONATRACH PED (Algeria)

    2000-06-01

    One of the important factors in the field of reservoir simulation of dual-porosity systems is reliable relative permeability data. Laboratory limitations hinder measurements. The real behaviour of naturally fractures reservoirs is not reflected in the reservoir core samples, which as a rule originate from zones without induced or natural fractures. Therefore, it is commonly assumed that the relative permeability of a naturally fractured system is a straight line, which can cause errors. The authors undertook to conduct special core analyses on Berea outcrop core samples, to simulate fracture opening through the cutting of the samples to get different fracture apertures, to study the effects of dual porosity on the shape of capillary pressure curves, and to evaluate absolute and relative permeability, as they are affected by fracture opening. The correlation obtained between absolute permeability and fracture aperture was good, and capillary pressure curves permitted the observation of the effect of dual porosity. High residual oil saturation was present in the matrix, since the fractures became the easiest route for water flow, and this situation prevented the use of unsteady-state tests to measure relative permeability on the samples. Instead, the centrifuge technique was successfully used. A naturally fractured reservoir (NFR), the Tin Fouye Tabankort (TFT) reservoir in Algeria was selected to extend the findings. The site was principally selected due to the availability of naturally fractured cores and published data. Core observations, well test analysis and borehole imager tools were all TFT natural fracture indicators presented in the paper. Representative data of relative permeability was obtained by conducting a displacement test on a full diameter core to solve the laboratory limitations. The correlation between permeability and fracture opening was used to estimate the aperture of natural fractures in TFT reservoir. 17 refs., 2 tabs., 24 figs.

  2. Evaluating replicability of laboratory experiments in economics.

    Science.gov (United States)

    Camerer, Colin F; Dreber, Anna; Forsell, Eskil; Ho, Teck-Hua; Huber, Jürgen; Johannesson, Magnus; Kirchler, Michael; Almenberg, Johan; Altmejd, Adam; Chan, Taizan; Heikensten, Emma; Holzmeister, Felix; Imai, Taisuke; Isaksson, Siri; Nave, Gideon; Pfeiffer, Thomas; Razen, Michael; Wu, Hang

    2016-03-25

    The replicability of some scientific findings has recently been called into question. To contribute data about replicability in economics, we replicated 18 studies published in the American Economic Review and the Quarterly Journal of Economics between 2011 and 2014. All of these replications followed predefined analysis plans that were made publicly available beforehand, and they all have a statistical power of at least 90% to detect the original effect size at the 5% significance level. We found a significant effect in the same direction as in the original study for 11 replications (61%); on average, the replicated effect size is 66% of the original. The replicability rate varies between 67% and 78% for four additional replicability indicators, including a prediction market measure of peer beliefs.

  3. Adenovirus sequences required for replication in vivo.

    OpenAIRE

    Wang, K.; Pearson, G D

    1985-01-01

    We have studied the in vivo replication properties of plasmids carrying deletion mutations within cloned adenovirus terminal sequences. Deletion mapping located the adenovirus DNA replication origin entirely within the first 67 bp of the adenovirus inverted terminal repeat. This region could be further subdivided into two functional domains: a minimal replication origin and an adjacent auxillary region which boosted the efficiency of replication by more than 100-fold. The minimal origin occup...

  4. In vivo human buccal permeability of nicotine

    DEFF Research Database (Denmark)

    Adrian, Charlotte L; Olin, Helle B D; Dalhoff, Kim

    2006-01-01

    The aim was to examine the in vivo buccal pH-dependent permeability of nicotine in humans and furthermore compare the in vivo permeability of nicotine to previous in vitro permeability data. The buccal permeability of nicotine was examined in a three-way cross-over study in eight healthy non......-smokers using a buccal perfusion cell. The disappearance of nicotine from perfusion solutions with pH 6.0, 7.4, and 8.1 was studied for 3h. The apparent permeability of nicotine (P(app)) was determined at each pH value. Parotid saliva was collected in an attempt to assess systemic levels of nicotine....... The disappearance rate of nicotine increased significantly as the pH increased, which resulted in P(app) values of 0.57+/-0.55 x 10(-4), 2.10+/-0.23 x 10(-4), and 3.96+/-0.54 x 10(-4)cms(-1) (mean+/-S.D.) at pH 6.0, 7.4, and 8.1, respectively. A linear relationship (R(2)=0.993) was obtained between the P...

  5. Permeability Tests on Silkeborg Sand No. 0000

    DEFF Research Database (Denmark)

    Lund, Willy; Jakobsen, Kim Parsberg

    The flow through porous media plays an important role in various engineering disciplines, as for example in ground water hydrology and soil mechanics. In the present study the permeability is determined for a fine, saturated sand. As the flow through a porous media strongly depends on the charact......The flow through porous media plays an important role in various engineering disciplines, as for example in ground water hydrology and soil mechanics. In the present study the permeability is determined for a fine, saturated sand. As the flow through a porous media strongly depends...... on the characteristics of the soil matrix, the permeability is determined for different void ratios. All tests are performed on reconstituted specimens of Silkeborg Sand No. 0000. The permeability is determined by use of a falling head apparatus. The apparatus, test procedures and the analysis method are described...... in the succeeding sections. Finally the test results are briefly summarised and a relationship between void ratio l and permeability is established....

  6. Vascular permeability in cerebral cavernous malformations

    DEFF Research Database (Denmark)

    Mikati, Abdul G; Khanna, Omaditya; Zhang, Lingjiao;

    2015-01-01

    Patients with the familial form of cerebral cavernous malformations (CCMs) are haploinsufficient for the CCM1, CCM2, or CCM3 gene. Loss of corresponding CCM proteins increases RhoA kinase-mediated endothelial permeability in vitro, and in mouse brains in vivo. A prospective case-controlled observ......Patients with the familial form of cerebral cavernous malformations (CCMs) are haploinsufficient for the CCM1, CCM2, or CCM3 gene. Loss of corresponding CCM proteins increases RhoA kinase-mediated endothelial permeability in vitro, and in mouse brains in vivo. A prospective case......-controlled observational study investigated whether the brains of human subjects with familial CCM show vascular hyperpermeability by dynamic contrast-enhanced quantitative perfusion magnetic resonance imaging, in comparison with CCM cases without familial disease, and whether lesional or brain vascular permeability...... correlates with CCM disease activity. Permeability in white matter far (WMF) from lesions was significantly greater in familial than in sporadic cases, but was similar in CCM lesions. Permeability in WMF increased with age in sporadic patients, but not in familial cases. Patients with more aggressive...

  7. Honeycomb Core Permeability Under Mechanical Loads

    Science.gov (United States)

    Glass, David E.; Raman, V. V.; Venkat, Venki S.; Sankaran, Sankara N.

    1997-01-01

    A method for characterizing the air permeability of sandwich core materials as a function of applied shear stress was developed. The core material for the test specimens was either Hexcel HRP-3/16-8.0 and or DuPont Korex-1/8-4.5 and was nominally one-half inch thick and six inches square. The facesheets where made of Hercules' AS4/8552 graphite/epoxy (Gr/Ep) composites and were nominally 0.059-in. thick. Cytec's Metalbond 1515-3M epoxy film adhesive was used for co-curing the facesheets to the core. The permeability of the specimens during both static (tension) and dynamic (reversed and non-reversed) shear loads were measured. The permeability was measured as the rate of air flow through the core from a circular 1-in2 area of the core exposed to an air pressure of 10.0 psig. In both the static and dynamic testing, the Korex core experienced sudden increases in core permeability corresponding to a core catastrophic failure, while the URP core experienced a gradual increase in the permeability prior to core failure. The Korex core failed at lower loads than the HRP core both in the transverse and ribbon directions.

  8. Replication Origin Specification Gets a Push.

    Science.gov (United States)

    Plosky, Brian S

    2015-12-03

    During the gap between G1 and S phases when replication origins are licensed and fired, it is possible that DNA translocases could disrupt pre-replicative complexes (pre-RCs). In this issue of Molecular Cell, Gros et al. (2015) find that pre-RCs can be pushed along DNA and retain the ability to support replication.

  9. Exploiting replicative stress to treat cancer

    DEFF Research Database (Denmark)

    Dobbelstein, Matthias; Sørensen, Claus Storgaard

    2015-01-01

    DNA replication in cancer cells is accompanied by stalling and collapse of the replication fork and signalling in response to DNA damage and/or premature mitosis; these processes are collectively known as 'replicative stress'. Progress is being made to increase our understanding of the mechanisms...

  10. Tunable permeability of magnetic wires at microwaves

    Science.gov (United States)

    Panina, L. V.; Makhnovskiy, D. P.; Morchenko, A. T.; Kostishin, V. G.

    2015-06-01

    This paper presents the analysis into microwave magnetic properties of magnetic microwires and their composites in the context of applications in wireless sensors and tunable microwave materials. It is demonstrated that the intrinsic permeability of wires has a wide frequency dispersion with relatively large values in the GHz band. In the case of a specific magnetic anisotropy this results in a tunable microwave impedance which could be used for distributed wireless sensing networks in functional composites. The other range of applications is related with developing the artificial magnetic dielectrics with large and tunable permeability. The composites with magnetic wires with a circumferential anisotropy have the effective permeability which differs substantially from unity for a relatively low concentration (less than 10%). This can make it possible to design the wire media with a negative and tunable index of refraction utilising natural magnetic properties of wires.

  11. Gyroid Nanoporous Membranes with Tunable Permeability

    DEFF Research Database (Denmark)

    Li, Li; Schulte, Lars; Clausen, Lydia D.

    2011-01-01

    Understanding the relevant permeability properties of ultrafiltration membranes is facilitated by using materials and procedures that allow a high degree of control on morphology and chemical composition. Here we present the first study on diffusion permeability through gyroid nanoporous cross......-sided skin membranes, much faster than expected by a naive resistance-in-series model; the flux through the two-sided skin membranes even increases with the membrane thickness. We propose a model that captures the physics behind the observed phenomena, as confirmed by flow visualization experiments...... the effective diffusion coefficients of a series of antibiotics, proteins, and other biomolecules; solute permeation is discussed in terms of hindered diffusion. The combination of uniform bulk morphology, isotropically percolating porosity, controlled surface chemistry, and tunable permeability is distinctive...

  12. Ammonia and urea permeability of mammalian aquaporins

    DEFF Research Database (Denmark)

    Litman, Thomas; Søgaard, Rikke; Zeuthen, Thomas

    2009-01-01

    The human aquaporins,AQP3,AQP7, AQP8,AQP9, and possibly AQP10, are permeable to ammonia, and AQP7, AQP9, and possibly AQP3, are permeable to urea. In humans, these aquaporins supplement the ammonia transport of the Rhesus (Rh) proteins and the urea transporters (UTs). The mechanism by which...... ammonium is transported by aquaporins is not fully resolved. A comparison of transport equations, models, and experimental data shows that ammonia is transported in its neutral form, NH(3). In the presence of NH(3), the aquaporin stimulates H(+) transport. Consequently, this transport of H(+) is only...... significant at alkaline pH. It is debated whether the H(+) ion passes via the aquaporin or by some external route; the investigation of this problem requires the aquaporin-expressing cell to be voltage-clamped. The ammonia-permeable aquaporins differ from other aquaporins by having a less restrictive aromatic...

  13. Permeability of Hollow Microspherical Membranes to Helium

    Science.gov (United States)

    Zinoviev, V. N.; Kazanin, I. V.; Pak, A. Yu.; Vereshchagin, A. S.; Lebiga, V. A.; Fomin, V. M.

    2016-01-01

    This work is devoted to the study of the sorption characteristics of various hollow microspherical membranes to reveal particles most suitable for application in the membrane-sorption technologies of helium extraction from a natural gas. The permeability of the investigated sorbents to helium and their impermeability to air and methane are shown experimentally. The sorption-desorption dependences of the studied sorbents have been obtained, from which the parameters of their specific permeability to helium are calculated. It has been established that the physicochemical modification of the original particles exerts a great influence on the coefficient of the permeability of a sorbent to helium. Specially treated cenospheres have displayed high efficiency as membranes for selective extraction of helium.

  14. Food Packaging Permeability Behaviour: A Report

    Directory of Open Access Journals (Sweden)

    Valentina Siracusa

    2012-01-01

    Full Text Available The use of polymer materials in food packaging field is one of the largest growing market area. Actually the optimization behaviour of packaging permeability is of crucial importance, in order to extend the food shelf-life and to reach the best engineering solution. Studying the permeability characterization of the different polymer material (homogeneous and heterogeneous polymer system to the different packaging gases, in different environmental condition, is crucial to understand if the selected material is adapted to the chosen food contact field. Temperature and humidity parameters are of crucial importance for food quality preservation, especially in real life situations, like food market, and house long-life use. The aim of this report was to collect information about the state of the art on the permeability characteristics of the polymer packages used on food field.

  15. Magnetohydrodynamic Flow Past a Permeable Bed

    Directory of Open Access Journals (Sweden)

    R. Venugopal

    1983-01-01

    Full Text Available The paper evaluates mass flow velocity heat transfer rates and velocity/temperature distributions in the viscous, incompressible and slightly conducting fluid past a permeable bed in three different configurations namely (1 Couette flow (2 Poiseuille flow and (3 free surface flow, under the influence of a uniform transverse magnetic field. To discuss the solution, the flow region is divided into two zones : Zone 1 (from the impermeable upper rigid plate to the permeable bed in which the flow is laminar and governed by Navier-Stokes equations, and Zone 2 (the permeable bed below the nominal surface in which the flow is governed by Darcy law. The paper also investigates the effects of magnetic field, porosity and Biot number on the physical quantities mentioned above.

  16. Quantifying porosity, compressibility and permeability in Shale

    DEFF Research Database (Denmark)

    Mbia, Ernest Ncha; Fabricius, Ida Lykke; Frykman, Peter

    (XRD) of shale samples show about 50% silt and high content of kaolinite in the clay fraction when compared with offshore samples from the Central Graben. Porosity measurements from helium porosimetry-mercury immersion (HPMI), mercury injection capillary pressure (MICP) and nuclear magnetic resonance...... (NMR) show that, the MICP porosity is 9-10% points lower than HPMI and NMR porosity. Compressibility result shows that deep shale is stiffer in situ than normally assumed in geotechnical modelling and that static compressibility corresponds with dynamic one only at the begining of unloading stress...... strain data. We found that Kozeny's modelled permeability fall in the same order of magnitude with measured permeability for shale rich in kaolinite but overestimates permeability by two to three orders of magnitudes for shale with high content of smectite. The empirical Yang and Aplin model gives good...

  17. Magnetic levitation from negative permeability materials

    Energy Technology Data Exchange (ETDEWEB)

    Coffey, Mark W., E-mail: mcoffey@mines.edu [Department of Physics, Colorado School of Mines, Golden, CO 80401 (United States)

    2012-09-03

    As left-handed materials and metamaterials are becoming more prevalent, we examine the effect of negative permeability upon levitation force. We first consider two half spaces of differing permeability and a point magnetic source, so that the method of images may be employed. We determine that the resulting force may be larger than for conventional magnetic materials. We then illustrate the inclusion of a finite sample thickness. -- Highlights: ► The effect of negative permeability upon levitation force is considered. ► Such an effect could be realized with metamaterials. ► The resulting force may be larger than with conventional materials. ► The analysis is extended to allow for a finite sample thickness. ► Representative numerical values are given.

  18. Blood flow and permeability in microvessels

    Science.gov (United States)

    Sugihara-Seki, Masako; Fu, Bingmei M.

    2005-07-01

    The mechanics of blood flow in microvessels and microvessel permeability are reviewed. In the first part, characteristics of blood flow in vivo and in vitro are described from a fluid-mechanical point of view, and mathematical models for blood flow in microvessels are presented. Possible causes of the increased flow resistance obtained in vivo compared to in vitro are examined, including the effects of irregularities of vessel lumen, the presence of endothelial surface glycocalyx and white blood cells. In the second part, the ultrastructural pathways and mechanisms whereby endothelial cells and the clefts between the cells modulate microvessel permeability to water and solutes are introduced. Previous and current models for microvessel permeability to water and solutes are reviewed. These models examine the role of structural components of interendothelial cleft, such as junction strands and surface glycocalyx, in the determination of water and solute transport across the microvessel walls. Transport models in the tissue space surrounding the microvessel are also described.

  19. Replication of micro and nano surface geometries

    DEFF Research Database (Denmark)

    Hansen, Hans Nørgaard; Hocken, R.J.; Tosello, Guido

    2011-01-01

    : manufacture of net-shape micro/nano surfaces, tooling (i.e. master making), and surface quality control (metrology, inspection). Replication processes and methods as well as the metrology of surfaces to determine the degree of replication are presented and classified. Examples from various application areas...... are given including replication for surface texture measurements, surface roughness standards, manufacture of micro and nano structured functional surfaces, replicated surfaces for optical applications (e.g. optical gratings), and process chains based on combinations of repeated surface replication steps....

  20. Replication of prions in differentiated muscle cells.

    Science.gov (United States)

    Herbst, Allen; Aiken, Judd M; McKenzie, Debbie

    2014-01-01

    We have demonstrated that prions accumulate to high levels in non-proliferative C2C12 myotubes. C2C12 cells replicate as myoblasts but can be differentiated into myotubes. Earlier studies indicated that C2C12 myoblasts are not competent for prion replication. (1) We confirmed that observation and demonstrated, for the first time, that while replicative myoblasts do not accumulate PrP(Sc), differentiated post-mitotic myotube cultures replicate prions robustly. Here we extend our observations and describe the implication and utility of this system for replicating prions.

  1. Small-bowel permeability in collagenous colitis

    DEFF Research Database (Denmark)

    Wildt, Signe; Madsen, Jan L; Rumessen, Jüri J

    2006-01-01

    Collagenous colitis (CC) is a chronic inflammatory bowel disease that affects the colon. However, some patients with CC present with accompanying pathologic small-bowel manifestations such as coeliac disease, defects in bile acid absorption and histopathologic changes in small-intestinal biopsies......, indicating that CC is a pan-intestinal disease. In small-intestinal disease, the intestinal barrier function may be impaired, and the permeability of the small intestine altered. The purpose of this research was to study small-bowel function in patients with CC as expressed by intestinal permeability....

  2. Liquid Permeability of Ceramic Foam Filters

    OpenAIRE

    Zhang, Kexu

    2012-01-01

    This project is in support of the PhD project: ‘Removal of Inclusions from Liquid Aluminium using Electromagnetically Modified Filtration’. The purpose of this project was to measure the tortuosity, and permeability of ~50mm thick: 30, 40, 50 and 80 pores per inch (ppi) commercial alumina ceramic foam filters (CFFs). Measurements have been taken of: cell (pore), window and strut sizes, porosity, tortuosity and liquid permeability. Water velocity from ~0.015-0.77 m/s have been used ...

  3. Development of an Improved Permeability Modification Simulator

    Energy Technology Data Exchange (ETDEWEB)

    Gao, H.W.; Elphnick, J.

    1999-03-09

    This report describes the development of an improved permeability modification simulator performed jointly by BDM Petroleum Technologies and Schlumberger Dowell under a cooperative research and development agreement (CRADA) with the US Department of Energy. The improved simulator was developed by modifying NIPER's PC-GEL permeability modification simulator to include a radial model, a thermal energy equation, a wellbore simulator, and a fully implicit time-stepping option. The temperature-dependent gelation kinetics of a delayed gel system (DGS) is also included in the simulator.

  4. The Permeability of Rubble Mound Breakwaters

    DEFF Research Database (Denmark)

    Williams, A.F.; Burcharth, H. F.; Adel, H. den

    1992-01-01

    The results of an extensive series of permeability experiments originally analysed by Shih (1990) are reinterpreted in the light of new experiments. It is proposed that the Forchheimer equation might not fully describe flow at the high Reynolds numbers found in the interior of rubble material....... A new series of tests designed to test for deviations from the Forchheimer equation and investigate the effects of material shape are described. While no evidence can be found to indicate a deviation from the Forchheimer equation a dependency of permeability and the surface roughness the material...

  5. DNA replication stress: causes, resolution and disease.

    Science.gov (United States)

    Mazouzi, Abdelghani; Velimezi, Georgia; Loizou, Joanna I

    2014-11-15

    DNA replication is a fundamental process of the cell that ensures accurate duplication of the genetic information and subsequent transfer to daughter cells. Various pertubations, originating from endogenous or exogenous sources, can interfere with proper progression and completion of the replication process, thus threatening genome integrity. Coordinated regulation of replication and the DNA damage response is therefore fundamental to counteract these challenges and ensure accurate synthesis of the genetic material under conditions of replication stress. In this review, we summarize the main sources of replication stress and the DNA damage signaling pathways that are activated in order to preserve genome integrity during DNA replication. We also discuss the association of replication stress and DNA damage in human disease and future perspectives in the field. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

  6. Replication Stress: A Lifetime of Epigenetic Change

    Directory of Open Access Journals (Sweden)

    Simran Khurana

    2015-09-01

    Full Text Available DNA replication is essential for cell division. Challenges to the progression of DNA polymerase can result in replication stress, promoting the stalling and ultimately collapse of replication forks. The latter involves the formation of DNA double-strand breaks (DSBs and has been linked to both genome instability and irreversible cell cycle arrest (senescence. Recent technological advances have elucidated many of the factors that contribute to the sensing and repair of stalled or broken replication forks. In addition to bona fide repair factors, these efforts highlight a range of chromatin-associated changes at and near sites of replication stress, suggesting defects in epigenome maintenance as a potential outcome of aberrant DNA replication. Here, we will summarize recent insight into replication stress-induced chromatin-reorganization and will speculate on possible adverse effects for gene expression, nuclear integrity and, ultimately, cell function.

  7. Nitric oxide turnover in permeable river sediment

    DEFF Research Database (Denmark)

    Schreiber, Frank; Stief, Peter; Kuypers, Marcel M M

    2014-01-01

    We measured nitric oxide (NO) microprofiles in relation to oxygen (O2) and all major dissolved N-species (ammonium, nitrate, nitrite, and nitrous oxide [N2O]) in a permeable, freshwater sediment (River Weser, Germany). NO reaches peak concentrations of 0.13 μmol L-1 in the oxic zone and is consumed...

  8. Water permeability in human airway epithelium

    DEFF Research Database (Denmark)

    Pedersen, Peter Steen; Procida, Kristina; Larsen, Per Leganger;

    2005-01-01

    Osmotic water permeability (P(f)) was studied in spheroid-shaped human airway epithelia explants derived from nasal polyps by the use of a new improved tissue collection and isolation procedure. The fluid-filled spheroids were lined with a single cell layer with the ciliated apical cell membrane...

  9. Quantitative permeability imaging of plant tissues

    NARCIS (Netherlands)

    Sibgatullin, T.; Vergeldt, F.J.; Gerkema, E.; As, van H.

    2010-01-01

    A method for mapping tissue permeability based on time-dependent diffusion measurements is presented. A pulsed field gradient sequence to measure the diffusion encoding time dependence of the diffusion coefficients based on the detection of stimulated spin echoes to enable long diffusion times is co

  10. Vascular permeability and drug delivery in cancers

    Directory of Open Access Journals (Sweden)

    Sandy eAzzi

    2013-08-01

    Full Text Available The endothelial barrier strictly maintains vascular and tissue homeostasis, and therefore modulates many physiological processes such as angiogenesis, immune responses, and dynamic exchanges throughout organs. Consequently, alteration of this finely tuned function may have devastating consequences for the organism. This is particularly obvious in cancers, where a disorganized and leaky blood vessel network irrigates solid tumors. In this context, vascular permeability drives tumor-induced angiogenesis, blood flow disturbances, inflammatory cell infiltration, and tumor cell extravasation. This can directly restrain the efficacy of conventional therapies by limiting intravenous drug delivery. Indeed, for more effective anti-angiogenic therapies, it is now accepted that not only should excessive angiogenesis be alleviated, but also that the tumor vasculature needs to be normalized. Recovery of normal state vasculature requires diminishing hyperpermeability, increasing pericyte coverage, and restoring the basement membrane, to subsequently reduce hypoxia and interstitial fluid pressure. In this review, we will introduce how vascular permeability accompanies tumor progression and, as a collateral damage, impacts on efficient drug delivery. The molecular mechanisms involved in tumor-driven vascular permeability will next be detailed, with a particular focus on the main factors produced by tumor cells, especially the emblematic vascular endothelial growth factor (VEGF. Finally, new perspectives in cancer therapy will be presented, centered on the use of anti-permeability factors and normalization agents.

  11. [Graphic recording of the maxillary ostium permeability].

    Science.gov (United States)

    Rosique, M; Pastor, A; Hellín, D; García-Ortega, F P

    1993-01-01

    Currently we practise salpingography for evaluating Eustachian tube permeability. In a similar mode, we describe a technique of graphic search, with impedianciometry, of patency in the osteomeatal complex, after puncture and placing Foley's catheter in the maxillary sinus. In several cases without opening, we make topical treatment though catheter. For this technique, we propose the term of infundibulography.

  12. Water permeability of pigmented waterborne coatings

    NARCIS (Netherlands)

    Donkers, P.A.J.; Huinink, H.P.; Erich, S.J.F.; Reuvers, N.J.W.; Adan, O.C.G.

    2013-01-01

    Coatings are used in a variety of applications. Last decades more and more coating systems are transforming from solvent to waterborne coating systems. In this study the influence of pigments on the water permeability of a waterborne coating system is studied, with special interest in the possible i

  13. Pump and treat in low permeability media

    Energy Technology Data Exchange (ETDEWEB)

    Mackay, D.M. [Univ. of Waterloo, Ontario (Canada)

    1996-08-01

    Pump and Treat (P&T) is a commonly applied technology whose primary promise for the low permeability environments of interest to these technology reviews is almost certainly containment of the problem. Conventional P&T would be expected to offer little promise of complete restoration in such environments, unless very long time frames (decades or centuries) are considered. A variety of approaches have been proposed to enhance the efficiency of P&T; some appear to offer little promise in low or mixed permeability environments, while others may offer more promise (e.g. hydro- or pneumatic-fracturing, which are described elsewhere in this document, and application of vacuum to the extraction well(s), which is a proprietary technology whose promise is currently difficult to assess objectively). Understanding the potential advantages and means of optimizing these enhancement approaches requires more understanding of the basic processes limiting P&T performance in low or mixed permeability media. These efforts are probably also necessary to understand the advantages and means of optimizing many of the very different remedial technologies that may be applicable to low or mixed permeability environments. Finally, since a reasonably certain capability of P&T is containment (i.e. prevention of further migration of contaminants), P&T may generally be required as a sort of safety net around sites at which the alternative technologies are being tested or applied. 23 refs.

  14. Oxygen permeable membrane for oxygen enriched combustion

    Energy Technology Data Exchange (ETDEWEB)

    Asakawa, S. (Matsushita Research Inst., Tokyo, Japan); Saito, Y.; Kawahito, M.; Ito, Y.; Tsuchiya, S.; Sugata, K.

    1983-02-01

    An oxygen enriched air production system using gas separation membranes has been developed to be used for fuel combustion systems. High oxygen permeable scopolymers, including three dimensional structure, have been synthesized through condensation of polyvinylphenol with some, ..cap alpha..,..omega..-bis (diethylamino) polydimethylsiloxanes. The experimental results showed that the oxygen permeability through the copolymer varies as a function of the dimethylsiloxane content of the copolymers. Such composition dependence of the oxygen permeability was explained on the basis of polymer constitution. Typical values of the oxygen permeability, 3.4 x 10/sup -8/ (cc x cm/cm/sup 2/ x sec x cmHg) and ..cap alpha.., 2.1, were obtained at 72% of dimethylsiloxane content. The copolymers are soluble in most common organic solvents and uniform, defect-free membranes as thin as 1000 Angstroms have been formed by spreading solutions of the copolymer on water. Composite membranes fabricated by applying the membranes to porous support materials were used for practical gas separation and 30% oxygen enriched air was produced from ambient air. A new type oxygen enriched combustion system, which is more efficient for energy saving, has been developed by utilizing oxygen enriched air thus produced. 15 references, 15 figures, 1 table.

  15. Foam film permeability: theory and experiment.

    Science.gov (United States)

    Farajzadeh, R; Krastev, R; Zitha, Pacelli L J

    2008-02-28

    The mass transfer of gas through foam films is a prototype of various industrial and biological processes. The aim of this paper is to give a perspective and critical overview of studies carried out to date on the mass transfer of gas through foam films. Contemporary experimental data are summarized, and a comprehensive overview of the theoretical models used to explain the observed effects is given. A detailed description of the processes that occur when a gas molecule passes through each layer that forms a foam film is shown. The permeability of the film-building surfactant monolayers plays an important role for the whole permeability process. It can be successfully described by the models used to explain the permeability of surfactant monolayers on aqueous sub-phase. For this reason, the present paper briefly discusses the surfactant-induced resistance to mass transfer of gases through gas-liquid interface. One part of the paper discusses the experimental and theoretical aspects of the foam film permeability in a train of foam films in a matrix or a cylinder. This special case is important to explain the gas transfer in porous media or in foams. Finally, this paper will highlight the gaps and challenges and sketch possible directions for future research.

  16. Tunable permeability of magnetic wires at microwaves

    Energy Technology Data Exchange (ETDEWEB)

    Panina, L.V., E-mail: lpanina@plymouth.ac.uk [National University of Science and Technology, MISiS, Moscow (Russian Federation); Institute for Design Problems in Microelectronics, RAN, Moscow (Russian Federation); Makhnovskiy, D.P. [School of Computing and Mathematics, University of Plymouth (United Kingdom); Morchenko, A.T.; Kostishin, V.G. [National University of Science and Technology, MISiS, Moscow (Russian Federation)

    2015-06-01

    This paper presents the analysis into microwave magnetic properties of magnetic microwires and their composites in the context of applications in wireless sensors and tunable microwave materials. It is demonstrated that the intrinsic permeability of wires has a wide frequency dispersion with relatively large values in the GHz band. In the case of a specific magnetic anisotropy this results in a tunable microwave impedance which could be used for distributed wireless sensing networks in functional composites. The other range of applications is related with developing the artificial magnetic dielectrics with large and tunable permeability. The composites with magnetic wires with a circumferential anisotropy have the effective permeability which differs substantially from unity for a relatively low concentration (less than 10%). This can make it possible to design the wire media with a negative and tunable index of refraction utilising natural magnetic properties of wires. - Highlights: • Applications of magnetic microwires for functional composites and distributed sensor networks are proposed. • Diluted composites with magnetic microwires can demonstrate tunable left-handed properties. • Large microwave permeability combined with a specific magnetic structure lead to a large and sensitive microwave magnetoimpedance. • Microwave magnetoimpedance highly sensitive to temperature is demonstrated.

  17. Self-replication of DNA rings

    Science.gov (United States)

    Kim, Junghoon; Lee, Junwye; Hamada, Shogo; Murata, Satoshi; Ha Park, Sung

    2015-06-01

    Biology provides numerous examples of self-replicating machines, but artificially engineering such complex systems remains a formidable challenge. In particular, although simple artificial self-replicating systems including wooden blocks, magnetic systems, modular robots and synthetic molecular systems have been devised, such kinematic self-replicators are rare compared with examples of theoretical cellular self-replication. One of the principal reasons for this is the amount of complexity that arises when you try to incorporate self-replication into a physical medium. In this regard, DNA is a prime candidate material for constructing self-replicating systems due to its ability to self-assemble through molecular recognition. Here, we show that DNA T-motifs, which self-assemble into ring structures, can be designed to self-replicate through toehold-mediated strand displacement reactions. The inherent design of these rings allows the population dynamics of the systems to be controlled. We also analyse the replication scheme within a universal framework of self-replication and derive a quantitative metric of the self-replicability of the rings.

  18. DNA Replication via Entanglement Swapping

    CERN Document Server

    Pusuluk, Onur

    2010-01-01

    Quantum effects are mainly used for the determination of molecular shapes in molecular biology, but quantum information theory may be a more useful tool to understand the physics of life. Molecular biology assumes that function is explained by structure, the complementary geometries of molecules and weak intermolecular hydrogen bonds. However, both this assumption and its converse are possible if organic molecules and quantum circuits/protocols are considered as hardware and software of living systems that are co-optimized during evolution. In this paper, we try to model DNA replication as a multiparticle entanglement swapping with a reliable qubit representation of nucleotides. In the model, molecular recognition of a nucleotide triggers an intrabase entanglement corresponding to a superposition state of different tautomer forms. Then, base pairing occurs by swapping intrabase entanglements with interbase entanglements.

  19. Permeability Measurements On Hot Rock Samples

    Science.gov (United States)

    Mueller, S.; Spieler, O.; Scheu, B.; Dingwell, D. B.

    Gas permeability is an important issue with regards to the explosive behaviour of Si- rich volcanoes. It directly affects the gas pressure within the volcano which influences the eruptive behaviour of the volcano. To date permeability measurements have only been performed on cold porous rocks (e.g. Eichelberger et al. 1986, Klug &Cashman 1996), because measurements with higher temperatures are not possible with common gas permeameters. Investigating the permeability of volcanic rocks in a hot state (up to 850 C) provides a better insight into the degassing processes under natural condi- tions. Therefore, any new experimental setup is expected to yield information about the temperature dependency of permeability in volcanic rocks. The present experi- ments have been performed on samples with a wide range of porosities. The samples were collected from block-and-ash flows on Merapi (Indonesia), Unzen (Japan) and pumices on Lipari Island (Italy). Permeabiltiy was measured using a modified setup of the fragmentation apparatus. A cylindrical rock sample (Æ = 25mm, l = 60 mm), glued gas tight in a sample container, was placed in a steel autoclave. Below the sample was a defined volume of argon gas at a known pressure. After the rupture of a diaphragm, the pressure above the sample drops rapidly to atmospheric conditions and the pres- surized gas flows through the porous rock sample until the pressure is equalized. The length of time from the beginning of the pressure drop to equilization delivers the basis for the calculation of the gas flow rate. The measurements we have performed at room temperature and at 850C to study the temperature dependency of the permeability.

  20. Therapeutic targeting of replicative immortality.

    Science.gov (United States)

    Yaswen, Paul; MacKenzie, Karen L; Keith, W Nicol; Hentosh, Patricia; Rodier, Francis; Zhu, Jiyue; Firestone, Gary L; Matheu, Ander; Carnero, Amancio; Bilsland, Alan; Sundin, Tabetha; Honoki, Kanya; Fujii, Hiromasa; Georgakilas, Alexandros G; Amedei, Amedeo; Amin, Amr; Helferich, Bill; Boosani, Chandra S; Guha, Gunjan; Ciriolo, Maria Rosa; Chen, Sophie; Mohammed, Sulma I; Azmi, Asfar S; Bhakta, Dipita; Halicka, Dorota; Niccolai, Elena; Aquilano, Katia; Ashraf, S Salman; Nowsheen, Somaira; Yang, Xujuan

    2015-12-01

    One of the hallmarks of malignant cell populations is the ability to undergo continuous proliferation. This property allows clonal lineages to acquire sequential aberrations that can fuel increasingly autonomous growth, invasiveness, and therapeutic resistance. Innate cellular mechanisms have evolved to regulate replicative potential as a hedge against malignant progression. When activated in the absence of normal terminal differentiation cues, these mechanisms can result in a state of persistent cytostasis. This state, termed "senescence," can be triggered by intrinsic cellular processes such as telomere dysfunction and oncogene expression, and by exogenous factors such as DNA damaging agents or oxidative environments. Despite differences in upstream signaling, senescence often involves convergent interdependent activation of tumor suppressors p53 and p16/pRB, but can be induced, albeit with reduced sensitivity, when these suppressors are compromised. Doses of conventional genotoxic drugs required to achieve cancer cell senescence are often much lower than doses required to achieve outright cell death. Additional therapies, such as those targeting cyclin dependent kinases or components of the PI3K signaling pathway, may induce senescence specifically in cancer cells by circumventing defects in tumor suppressor pathways or exploiting cancer cells' heightened requirements for telomerase. Such treatments sufficient to induce cancer cell senescence could provide increased patient survival with fewer and less severe side effects than conventional cytotoxic regimens. This positive aspect is countered by important caveats regarding senescence reversibility, genomic instability, and paracrine effects that may increase heterogeneity and adaptive resistance of surviving cancer cells. Nevertheless, agents that effectively disrupt replicative immortality will likely be valuable components of new combinatorial approaches to cancer therapy. Copyright © 2015 The Authors

  1. Simultaneous estimation of relative permeability and porosity/permeability fields by history matching production data

    Energy Technology Data Exchange (ETDEWEB)

    Eydinov, D. [Scandpower, Kjeller (Norway); Gao, G. [Chevron, San Ramon, CA (United States); Li, G.; Reynolds, A.C. [Tulsa Univ., Tulsa, OK (United States)

    2007-07-01

    Relative permeability curves are typically obtained through core flood tests. This paper provided details of a procedure that used automatic history matching of 3-phase flow production data to estimate permeability curves with grid block porosities. The method used a B-spline approximation to represent sets of permeability curves with a log transformation of parameters to ensure that curves were monotonic or convex. It was assumed that the model vector was a multivariate Gaussian distribution. The history matching problem was considered in a Bayesian framework. The method was then compared with a power law model using the same data from a synthetic reservoir model. Results showed that the B-spline model obtained more accurate permeability curves than the power law model. The randomized maximum likelihood (RML) method was used to quantify uncertainties in the model parameters. 19 refs., 17 figs.

  2. A Novel Empirical Equation for Relative Permeability in Low Permeability Reservoirs☆

    Institute of Scientific and Technical Information of China (English)

    Yulei Ge; Shurong Li; Kexin Qu

    2014-01-01

    In this paper, a novel empirical equation is proposed to calculate the relative permeability of low permeability res-ervoir. An improved item is introduced on the basis of Rose empirical formula and Al-Fattah empirical formula, with one simple model to describe oil/water relative permeability. The position displacement idea of bare bones particle swarm optimization is applied to change the mutation operator to improve the RNA genetic algorithm. The param-eters of the new empirical equation are optimized with the hybrid RNA genetic algorithm (HRGA) based on the ex-perimental data. The data is obtained from a typical low permeability reservoir wel 54 core 27-1 in GuDong by unsteady method. We carry out matlab programming simulation with HRGA. The comparison and error analysis show that the empirical equation proposed is more accurate than the Rose empirical formula and the exponential model. The generalization of the empirical equation is also verified.

  3. Regulation of Unperturbed DNA Replication by Ubiquitylation

    Directory of Open Access Journals (Sweden)

    Sara Priego Moreno

    2015-06-01

    Full Text Available Posttranslational modification of proteins by means of attachment of a small globular protein ubiquitin (i.e., ubiquitylation represents one of the most abundant and versatile mechanisms of protein regulation employed by eukaryotic cells. Ubiquitylation influences almost every cellular process and its key role in coordination of the DNA damage response is well established. In this review we focus, however, on the ways ubiquitylation controls the process of unperturbed DNA replication. We summarise the accumulated knowledge showing the leading role of ubiquitin driven protein degradation in setting up conditions favourable for replication origin licensing and S-phase entry. Importantly, we also present the emerging major role of ubiquitylation in coordination of the active DNA replication process: preventing re-replication, regulating the progression of DNA replication forks, chromatin re-establishment and disassembly of the replisome at the termination of replication forks.

  4. Chromosome replication and segregation in bacteria.

    Science.gov (United States)

    Reyes-Lamothe, Rodrigo; Nicolas, Emilien; Sherratt, David J

    2012-01-01

    In dividing cells, chromosome duplication once per generation must be coordinated with faithful segregation of newly replicated chromosomes and with cell growth and division. Many of the mechanistic details of bacterial replication elongation are well established. However, an understanding of the complexities of how replication initiation is controlled and coordinated with other cellular processes is emerging only slowly. In contrast to eukaryotes, in which replication and segregation are separate in time, the segregation of most newly replicated bacterial genetic loci occurs sequentially soon after replication. We compare the strategies used by chromosomes and plasmids to ensure their accurate duplication and segregation and discuss how these processes are coordinated spatially and temporally with growth and cell division. We also describe what is known about the three conserved families of ATP-binding proteins that contribute to chromosome segregation and discuss their inter-relationships in a range of disparate bacteria.

  5. Semiconservative replication in the quasispecies model

    Science.gov (United States)

    Tannenbaum, Emmanuel; Deeds, Eric J.; Shakhnovich, Eugene I.

    2004-06-01

    This paper extends Eigen’s quasispecies equations to account for the semiconservative nature of DNA replication. We solve the equations in the limit of infinite sequence length for the simplest case of a static, sharply peaked fitness landscape. We show that the error catastrophe occurs when μ , the product of sequence length and per base pair mismatch probability, exceeds 2 ln [2/ ( 1+1/k ) ] , where k>1 is the first-order growth rate constant of the viable “master” sequence (with all other sequences having a first-order growth rate constant of 1 ). This is in contrast to the result of ln k for conservative replication. In particular, as k→∞ , the error catastrophe is never reached for conservative replication, while for semiconservative replication the critical μ approaches 2 ln 2 . Semiconservative replication is therefore considerably less robust than conservative replication to the effect of replication errors. We also show that the mean equilibrium fitness of a semiconservatively replicating system is given by k ( 2 e-μ/2 -1 ) below the error catastrophe, in contrast to the standard result of k e-μ for conservative replication (derived by Kimura and Maruyama in 1966). From this result it is readily shown that semiconservative replication is necessary to account for the observation that, at sufficiently high mutagen concentrations, faster replicating cells will die more quickly than more slowly replicating cells. Thus, in contrast to Eigen’s original model, the semiconservative quasispecies equations are able to provide a mathematical basis for explaining the efficacy of mutagens as chemotherapeutic agents.

  6. Quantitative Prediction of Structural Fractures in Low Permeability Reservoir

    Institute of Scientific and Technical Information of China (English)

    Zeng Lianbo; Tian Chonglu

    1996-01-01

    @@ Low -permeability fractured reservoirs will become increasingly prominent along with the enhanced exploration extent and the emerging moderate-high water content in most of the moderate-high permeability reservoirs of the oil fields in eastern China.

  7. Considerations about the internodal permeability evaluation in reservoir simulation

    Energy Technology Data Exchange (ETDEWEB)

    Cordazzo, Jonas; Maliska, Clovis R. [Santa Catarina Univ., Florianopolis, SC (Brazil). Dept. de Engenharia Mecanica. Lab. Computacional de Dinamica dos Fluidos]. E-mails: jonas@sinmec.ufsc.br; maliska@sinmec.ufsc.br; Romeu, Regis K. [PETROBRAS, Rio de Janeiro, RJ (Brazil). Centro de Pesquisas]. E-mail: regis@cenpes.petrobras.com.br

    2003-07-01

    This work reports some numerical problems caused by the using of harmonic average in the inter nodal permeability calculation during the petroleum reservoir simulation. This paper begins with a brief review, showing, in the sequence the approach used by commercial simulators in interpreting the permeability map. Then, the results of using harmonic averaging to determine the inter nodal permeability are presented by solving the 2D chessboard problem. Finally, the Element-based Finite Volume Method (EbFVM) is analyzed considering the permeability evaluation. It is demonstrated that this method, besides dealing with triangular and quadrilateral elements, can also deal with the permeability map without averaging. The two possibilities of storing the physical properties and their implications in the permeability evaluation are addressed. The permeability storage in the center of the elements, instead of in the center of control volumes, avoids the need of weighting the permeability values in the interfaces of the control volumes. (author)

  8. Influence of salinity on permeability characteristics of marine sediments

    Digital Repository Service at National Institute of Oceanography (India)

    Jose, U.V.; Bhat, S.T.; Nayak, B.U.

    that permeability increases with an increase in salt concentration for a given void ratio. This is explained by diffused double layer theory. Also, the rate of increase in permeability decreases with increase in salt concentration. The effect of salt concentration...

  9. Intestinal permeability study of minoxidil: assessment of minoxidil as a high permeability reference drug for biopharmaceutics classification.

    Science.gov (United States)

    Ozawa, Makoto; Tsume, Yasuhiro; Zur, Moran; Dahan, Arik; Amidon, Gordon L

    2015-01-05

    The purpose of this study was to evaluate minoxidil as a high permeability reference drug for Biopharmaceutics Classification System (BCS). The permeability of minoxidil was determined in in situ intestinal perfusion studies in rodents and permeability studies across Caco-2 cell monolayers. The permeability of minoxidil was compared with that of metoprolol, an FDA reference drug for BCS classification. In rat perfusion studies, the permeability of minoxidil was somewhat higher than that of metoprolol in the jejunum, while minoxidil showed lower permeability than metoprolol in the ileum. The permeability of minoxidil was independent of intestinal segment, while the permeability of metoprolol was region-dependent. Similarly, in mouse perfusion study, the jejunal permeability of minoxidil was 2.5-fold higher than that of metoprolol. Minoxidil and metoprolol showed similar permeability in Caco-2 study at apical pH of 6.5 and basolateral pH of 7.4. The permeability of minoxidil was independent of pH, while metoprolol showed pH-dependent transport in Caco-2 study. Minoxidil exhibited similar permeability in the absorptive direction (AP-BL) in comparison with secretory direction (BL-AP), while metoprolol had higher efflux ratio (ER > 2) at apical pH of 6.5 and basolateral pH of 7.4. No concentration-dependent transport was observed for either minoxidil or metoprolol transport in Caco-2 study. Verapamil did not alter the transport of either compounds across Caco-2 cell monolayers. The permeability of minoxidil was independent of both pH and intestinal segment in intestinal perfusion studies and Caco-2 studies. Caco-2 studies also showed no involvement of carrier mediated transport in the absorption process of minoxidil. These results suggest that minoxidil may be an acceptable reference drug for BCS high permeability classification. However, minoxidil exhibited higher jejunal permeability than metoprolol and thus to use minoxidil as a reference drug would raise the

  10. Regulation of chromosomal replication in Caulobacter crescentus.

    Science.gov (United States)

    Collier, Justine

    2012-03-01

    The alpha-proteobacterium Caulobacter crescentus is characterized by its asymmetric cell division, which gives rise to a replicating stalked cell and a non-replicating swarmer cell. Thus, the initiation of chromosomal replication is tightly regulated, temporally and spatially, to ensure that it is coordinated with cell differentiation and cell cycle progression. Waves of DnaA and CtrA activities control when and where the initiation of DNA replication will take place in C. crescentus cells. The conserved DnaA protein initiates chromosomal replication by directly binding to sites within the chromosomal origin (Cori), ensuring that DNA replication starts once and only once per cell cycle. The CtrA response regulator represses the initiation of DNA replication in swarmer cells and in the swarmer compartment of pre-divisional cells, probably by competing with DnaA for binding to Cori. CtrA and DnaA are controlled by multiple redundant regulatory pathways that include DNA methylation-dependent transcriptional regulation, temporally regulated proteolysis and the targeting of regulators to specific locations within the cell. Besides being critical regulators of chromosomal replication, CtrA and DnaA are also master transcriptional regulators that control the expression of many genes, thus connecting DNA replication with other events of the C. crescentus cell cycle. Copyright © 2012 Elsevier Inc. All rights reserved.

  11. Comparison of three replication strategies in complex multicellular organisms: Asexual replication, sexual replication with identical gametes, and sexual replication with distinct sperm and egg gametes

    Science.gov (United States)

    Tannenbaum, Emmanuel

    2008-01-01

    This paper studies the mutation-selection balance in three simplified replication models. The first model considers a population of organisms replicating via the production of asexual spores. The second model considers a sexually replicating population that produces identical gametes. The third model considers a sexually replicating population that produces distinct sperm and egg gametes. All models assume diploid organisms whose genomes consist of two chromosomes, each of which is taken to be functional if equal to some master sequence, and defective otherwise. In the asexual population, the asexual diploid spores develop directly into adult organisms. In the sexual populations, the haploid gametes enter a haploid pool, where they may fuse with other haploids. The resulting immature diploid organisms then proceed to develop into mature organisms. Based on an analysis of all three models, we find that, as organism size increases, a sexually replicating population can only outcompete an asexually replicating population if the adult organisms produce distinct sperm and egg gametes. A sexual replication strategy that is based on the production of large numbers of sperm cells to fertilize a small number of eggs is found to be necessary in order to maintain a sufficiently low cost for sex for the strategy to be selected for over a purely asexual strategy. We discuss the usefulness of this model in understanding the evolution and maintenance of sexual replication as the preferred replication strategy in complex, multicellular organisms.

  12. Degradation of permeability resistance of high strength concrete after combustion

    Institute of Scientific and Technical Information of China (English)

    Min LI; Hongtao KAO; Chunxiang QIAN

    2008-01-01

    To evaluate the remaining durability of con-crete materials after combustion, the permeability of high strength concrete (HSC) after combustion was studied. The transport behavior of chloride ion, water and air in concrete after combustion and the effect of temperature, strength grade, and aggregation on the permeability of HSC after combustion are investigated by chloride ion permeability coefficient (Dc), water permeability coef-ficient (Dw) and air permeability coefficient (Da). The experiment results show that all three permeability coeffi-cients commendably reflect changes of permeability. The permeability coefficient increases with the evaluation tem-perature. After the same temperature, the permeability coefficient of HSC is lower than that of normal strength concrete (NSC). However, the degree of degradation of permeability coefficient of HSC is greater than that of NSC. The permeability resistance of HSC containing limestone is better than that of HSC containing basalt. Combining changes of compressive strength and per-meability, the remaining durability of concrete materials after combustion is appropriately evaluated.

  13. 21 CFR 886.5916 - Rigid gas permeable contact lens.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Rigid gas permeable contact lens. 886.5916 Section... (CONTINUED) MEDICAL DEVICES OPHTHALMIC DEVICES Therapeutic Devices § 886.5916 Rigid gas permeable contact lens. (a) Identification. A rigid gas permeable contact lens is a device intended to be worn...

  14. Determination of permeability using fractal method for porous media

    Institute of Scientific and Technical Information of China (English)

    施明恒; 陈永平

    2001-01-01

    A theoretical formulation was developed to express permeability as a function of different fractal dimensions and other scales for porous media . The effective fractal void ratio, the spectral dimension and the fractal dimension of particle mass distribution were introduced. The permeabilities for different soils in China are calculated. The predicted permeability for rice soil was compared with the measured data available in literature.

  15. Scanning electron microscopy and dentinal permeability analysis of smear layer.

    Science.gov (United States)

    Prati, C; Mongiorgi, R; Pashley, D H; Riva di Sanseverino, L

    1991-05-01

    The aim of the present study was to evaluate the surface morphology and the permeability of dentine after different acid treatments: polyacrylic acid, maleic acid, phosphoric acid and saline solution as control. Dentine permeability was expressed as hydraulic conductance. All the acid treatments removed the smear layer and increased the dentine permeability.

  16. Replicative Intermediates of Human Papillomavirus Type 11 in Laryngeal Papillomas: Site of Replication Initiation and Direction of Replication

    Science.gov (United States)

    Auborn, K. J.; Little, R. D.; Platt, T. H. K.; Vaccariello, M. A.; Schildkraut, C. L.

    1994-07-01

    We have examined the structures of replication intermediates from the human papillomavirus type 11 genome in DNA extracted from papilloma lesions (laryngeal papillomas). The sites of replication initiation and termination utilized in vivo were mapped by using neutral/neutral and neutral/alkaline two-dimensional agarose gel electrophoresis methods. Initiation of replication was detected in or very close to the upstream regulatory region (URR; the noncoding, regulatory sequences upstream of the open reading frames in the papillomavirus genome). We also show that replication forks proceed bidirectionally from the origin and converge 180circ opposite the URR. These results demonstrate the feasibility of analysis of replication of viral genomes directly from infected tissue.

  17. Electrostatically gated membrane permeability in inorganic protocells

    Science.gov (United States)

    Li, Mei; Harbron, Rachel L.; Weaver, Jonathan V. M.; Binks, Bernard P.; Mann, Stephen

    2013-06-01

    Although several strategies are now available to produce functional microcompartments analogous to primitive cell-like structures, little progress has been made in generating protocell constructs with self-controlled membrane permeability. Here we describe the preparation of water-dispersible colloidosomes based on silica nanoparticles and delineated by a continuous semipermeable inorganic membrane capable of self-activated, electrostatically gated permeability. We use crosslinking and covalent grafting of a pH-responsive copolymer to generate an ultrathin elastic membrane that exhibits selective release and uptake of small molecules. This behaviour, which depends on the charge of the copolymer coronal layer, serves to trigger enzymatic dephosphorylation reactions specifically within the protocell aqueous interior. This system represents a step towards the design and construction of alternative types of artificial chemical cells and protocell models based on spontaneous processes of inorganic self-organization.

  18. Permeability of cork for water and ethanol.

    Science.gov (United States)

    Fonseca, Ana Luisa; Brazinha, Carla; Pereira, Helena; Crespo, Joao G; Teodoro, Orlando M N D

    2013-10-01

    Transport properties of natural (noncompressed) cork were evaluated for water and ethanol in both vapor and liquid phases. The permeability for these permeants has been measured, as well as the sorption and diffusion coefficients. This paper focuses on the differences between the transport of gases' relevant vapors and their liquids (water and ethanol) through cork. A transport mechanism of vapors and liquids is proposed. Experimental evidence shows that both vapors and liquids permeate not only through the small channels across the cells (plasmodesmata), as in the permeation of gases, but also through the walls of cork cells by sorption and diffusion as in dense membranes. The present study also shows that cork permeability for gases was irreversibly and drastically decreased after cork samples were exposed to ethanol or water in liquid phase.

  19. Anisotropic permeability in deterministic lateral displacement arrays

    CERN Document Server

    Vernekar, Rohan; Loutherback, Kevin; Morton, Keith; Inglis, David

    2016-01-01

    We investigate anisotropic permeability of microfluidic deterministic lateral displacement (DLD) arrays. A DLD array can achieve high-resolution bimodal size-based separation of micro-particles, including bioparticles such as cells. Correct operation requires that the fluid flow remains at a fixed angle with respect to the periodic obstacle array. We show via experiments and lattice-Boltzmann simulations that subtle array design features cause anisotropic permeability. The anisotropy, which indicates the array's intrinsic tendency to induce an undesired lateral pressure gradient, can lead to off-axis flows and therefore local changes in the critical separation size. Thus, particle trajectories can become unpredictable and the device useless for the desired separation duty. We show that for circular posts the rotated-square layout, unlike the parallelogram layout, does not suffer from anisotropy and is the preferred geometry. Furthermore, anisotropy becomes severe for arrays with unequal axial and lateral gaps...

  20. Monitoring pulmonary vascular permeability using radiolabeled transferrin

    Energy Technology Data Exchange (ETDEWEB)

    Basran, G.S.; Hardy, J.G.

    1988-07-01

    A simple, noninvasive technique for monitoring pulmonary vascular permeability in patients in critical care units is discussed. High vascular permeability is observed in patients with clinically defined adult respiratory distress syndrome (ARDS) but not in patients with hydrostatic pulmonary edema or in patients with minor pulmonary insults who are considered to be at risk of developing ARDS. The technique has been used in the field of therapeutics and pharmacology to test the effects of the putative antipermeability agents methylprednisolone and terbutaline sulfate. There appears to be a good correlation between the acute inhibitory effect of either drug on transferrin exudation and patient prognosis. Thus, a byproduct of such drug studies may be an index of survival in patients with established ARDS.

  1. Permittivity and permeability tensors for cloaking applications

    CERN Document Server

    Choudhury, Balamati; Jha, Rakesh Mohan

    2016-01-01

    This book is focused on derivations of analytical expressions for stealth and cloaking applications. An optimal version of electromagnetic (EM) stealth is the design of invisibility cloak of arbitrary shapes in which the EM waves can be controlled within the cloaking shell by introducing a prescribed spatial variation in the constitutive parameters. The promising challenge in design of invisibility cloaks lies in the determination of permittivity and permeability tensors for all the layers. This book provides the detailed derivation of analytical expressions of the permittivity and permeability tensors for various quadric surfaces within the eleven Eisenhart co-ordinate systems. These include the cylinders and the surfaces of revolutions. The analytical modeling and spatial metric for each of these surfaces are provided along with their tensors. This mathematical formulation will help the EM designers to analyze and design of various quadratics and their hybrids, which can eventually lead to design of cloakin...

  2. Gravity filtration of suspensions: permeability effects

    Science.gov (United States)

    Soori, Tejaswi; Wang, Mengyu; Ward, Thomas

    2015-11-01

    This paper examines the filtration rates of mono-modal suspensions as a function of time and a cake layer builds up through theory and experimentation. Darcy's Law, which describes fluid flow through porous media, was applied along with the Kynch theory of sedimentation, which provides the basis for analyzing low concentration (ϕ filter media. A CCD camera was used to capture images of the cake formation and fluid drainage processes, and subsequent image and theoretical analysis found the fluid flow experienced a constant pressure loss due to the permeability of the filter media, whereas the experienced pressure loss due to the cake formation varies as a function of time, ϕ and d. The rate of cake formation was also found to be independent of ϕ but dependent on d which can be attributed to a change in porosity affecting permeability. Studies on similar systems with multi-modal suspensions are in-progress.

  3. Changes of Intestinal Permeability in Cholelithiasis Patients

    Institute of Scientific and Technical Information of China (English)

    Shao-long Sun; Shuo-dong Wu; Dong-xu Cui; Bao-lin Liu; Xian-wei Dai

    2009-01-01

    @@ In normal condition,intestine mucosa possesses barrier function.When the barrier function of intestine mucosa was damaged,intestinal bacteria,endotoxin,or other substances would enter blood.It is generally accepted that biliary bacteria origins from the intestine either via duodenal papilla or intestinal mucosa.In this study,we aimed to investigate the intestinal permeability changes of cholelithiasis patients to elucidate the possible pathogenesis of cholelithiasis.

  4. Cation Permeability in Soybean Aleurone Layer

    OpenAIRE

    Noda, Hiroko; Fukuda, Mitsuru

    1998-01-01

    The permeation of water and ions into bean seeds is essential for processing and cooking of beans. The permeability of cations, K, Na, Ca, and Mg ions, into soybean seed tissue, especially aleurone layer, during water uptake was investigated to characterize the ion permeation into soybeans. Aleurone layers and seed coats contained relatively high concentration of endogenous K and Ca ions, and endogenous Ca ion, respectively. The amounts of Ca ion entered seed coats and aleurone layers were gr...

  5. A Reconciliation of Packed Column Permeability Data: Column Permeability as a Function of Particle Porosity

    Directory of Open Access Journals (Sweden)

    Hubert M. Quinn

    2014-01-01

    Full Text Available In his textbook teaching of packed bed permeability, Georges Guiochon uses mobile phase velocity as the fluid velocity term in his elaboration of the Darcy permeability equation. Although this velocity frame makes a lot of sense from a thermodynamic point of view, it is valid only with respect to permeability at a single theoretical boundary condition. In his more recent writings, however, Guiochon has departed from his long-standing mode of discussing permeability in terms of the Darcy equation and has embraced the well-known Kozeny-Blake equation. In this paper, his teaching pertaining to the constant in the Kozeny-Blake equation is examined and, as a result, a new correlation coefficient is identified and defined herein based on the velocity frame used in his teaching. This coefficient correlates pressure drop and fluid velocity as a function of particle porosity. We show that in their experimental protocols, Guiochon et al. have not adhered to a strict material balance of permeability which creates a mismatch of particle porosity and leads to erroneous conclusions regarding the value of the permeability coefficient in the Kozeny-Blake equation. By correcting the experimental data to properly reflect particle porosity we reconcile the experimental results of Guiochon and Giddings, resulting in a permeability reference chart which is presented here for the first time. This reference chart demonstrates that Guiochon’s experimental data, when properly normalized for particle porosity and other related discrepancies, corroborates the value of 267 for the constant in the Kozeny-Blake equation which was derived by Giddings in 1965.

  6. Ammonia gas permeability of meat packaging materials.

    Science.gov (United States)

    Karim, Faris; Hijaz, Faraj; Kastner, Curtis L; Smith, J Scott

    2011-03-01

    Meat products are packaged in polymer films designed to protect the product from exterior contaminants such as light, humidity, and harmful chemicals. Unfortunately, there is almost no data on ammonia permeability of packaging films. We investigated ammonia permeability of common meat packaging films: low-density polyethylene (LDPE; 2.2 mil), multilayer polyolefin (MLP; 3 mil), and vacuum (V-PA/PE; 3 mil, 0.6 mil polyamide/2.4 mil polyethylene). The films were fabricated into 10 × 5 cm pouches and filled with 50 mL deionized water. Pouches were placed in a plexiglass enclosure in a freezer and exposed to 50, 100, 250, or 500 ppm ammonia gas for 6, 12, 24, and 48 h at -17 ± 3 °C and 21 ± 3 °C. At freezing temperatures, no ammonia residues were detected and no differences in pH were found in the water. At room temperature, ammonia levels and pH of the water increased significantly (P packaging materials have low ammonia permeability and protect meat products exposed to ammonia leaks during frozen storage.

  7. Surface micro topography replication in injection moulding

    DEFF Research Database (Denmark)

    Arlø, Uffe Rolf

    of the mechanisms controlling topography replication. Surface micro topography replication in injection moulding depends on the main elements of  Process conditions  Plastic material  Mould topography In this work, the process conditions is the main factor considered, but the impact of plastic material...

  8. Replication and Robustness in Developmental Research

    Science.gov (United States)

    Duncan, Greg J.; Engel, Mimi; Claessens, Amy; Dowsett, Chantelle J.

    2014-01-01

    Replications and robustness checks are key elements of the scientific method and a staple in many disciplines. However, leading journals in developmental psychology rarely include explicit replications of prior research conducted by different investigators, and few require authors to establish in their articles or online appendices that their key…

  9. Completion of DNA replication in Escherichia coli.

    Science.gov (United States)

    Wendel, Brian M; Courcelle, Charmain T; Courcelle, Justin

    2014-11-18

    The mechanism by which cells recognize and complete replicated regions at their precise doubling point must be remarkably efficient, occurring thousands of times per cell division along the chromosomes of humans. However, this process remains poorly understood. Here we show that, in Escherichia coli, the completion of replication involves an enzymatic system that effectively counts pairs and limits cellular replication to its doubling point by allowing converging replication forks to transiently continue through the doubling point before the excess, over-replicated regions are incised, resected, and joined. Completion requires RecBCD and involves several proteins associated with repairing double-strand breaks including, ExoI, SbcDC, and RecG. However, unlike double-strand break repair, completion occurs independently of homologous recombination and RecA. In some bacterial viruses, the completion mechanism is specifically targeted for inactivation to allow over-replication to occur during lytic replication. The results suggest that a primary cause of genomic instabilities in many double-strand-break-repair mutants arises from an impaired ability to complete replication, independent from DNA damage.

  10. Replication and Robustness in Developmental Research

    Science.gov (United States)

    Duncan, Greg J.; Engel, Mimi; Claessens, Amy; Dowsett, Chantelle J.

    2014-01-01

    Replications and robustness checks are key elements of the scientific method and a staple in many disciplines. However, leading journals in developmental psychology rarely include explicit replications of prior research conducted by different investigators, and few require authors to establish in their articles or online appendices that their key…

  11. Using Replication Projects in Teaching Research Methods

    Science.gov (United States)

    Standing, Lionel G.; Grenier, Manuel; Lane, Erica A.; Roberts, Meigan S.; Sykes, Sarah J.

    2014-01-01

    It is suggested that replication projects may be valuable in teaching research methods, and also address the current need in psychology for more independent verification of published studies. Their use in an undergraduate methods course is described, involving student teams who performed direct replications of four well-known experiments, yielding…

  12. How frog embryos replicate their DNA reliably

    Science.gov (United States)

    Bechhoefer, John; Marshall, Brandon

    2007-03-01

    Frog embryos contain three billion base pairs of DNA. In early embryos (cycles 2-12), DNA replication is extremely rapid, about 20 min., and the entire cell cycle lasts only 25 min., meaning that mitosis (cell division) takes place in about 5 min. In this stripped-down cell cycle, there are no efficient checkpoints to prevent the cell from dividing before its DNA has finished replication - a disastrous scenario. Even worse, the many origins of replication are laid down stochastically and are also initiated stochastically throughout the replication process. Despite the very tight time constraints and despite the randomness introduced by origin stochasticity, replication is extremely reliable, with cell division failing no more than once in 10,000 tries. We discuss a recent model of DNA replication that is drawn from condensed-matter theories of 1d nucleation and growth. Using our model, we discuss different strategies of replication: should one initiate all origins as early as possible, or is it better to hold back and initiate some later on? Using concepts from extreme-value statistics, we derive the distribution of replication times given a particular scenario for the initiation of origins. We show that the experimentally observed initiation strategy for frog embryos meets the reliability constraint and is close to the one that requires the fewest resources of a cell.

  13. Mammalian RAD52 Functions in Break-Induced Replication Repair of Collapsed DNA Replication Forks

    DEFF Research Database (Denmark)

    Sotiriou, Sotirios K; Kamileri, Irene; Lugli, Natalia

    2016-01-01

    Human cancers are characterized by the presence of oncogene-induced DNA replication stress (DRS), making them dependent on repair pathways such as break-induced replication (BIR) for damaged DNA replication forks. To better understand BIR, we performed a targeted siRNA screen for genes whose depl...

  14. Multiple—tube Permeable Element for Combined Blowing Converter

    Institute of Scientific and Technical Information of China (English)

    YANGWen-yuan; XUWei-hua; 等

    1994-01-01

    The method consisting of cold test and hot simulating has been proved to be reliable for designing permeable ele-ments.The carbon-magnesia multiple-tube permeable ele-ments which are formed by isostatical pressure have higher density,high heat resistance and good thermoshock resis-tance,The brickwork ,maintenance and erosion meha-nism of permeable elements were studied.The tehnology of combined blowing wa established based on the peculiari-ties of semi-steel refining at Panzhihua Irom& Steel Co.(PZISC).The service life of permeable elements reahed 600 heats,that means the permeable elements can work synchronitially with converter lining.

  15. Rescue from replication stress during mitosis.

    Science.gov (United States)

    Fragkos, Michalis; Naim, Valeria

    2017-04-03

    Genomic instability is a hallmark of cancer and a common feature of human disorders, characterized by growth defects, neurodegeneration, cancer predisposition, and aging. Recent evidence has shown that DNA replication stress is a major driver of genomic instability and tumorigenesis. Cells can undergo mitosis with under-replicated DNA or unresolved DNA structures, and specific pathways are dedicated to resolving these structures during mitosis, suggesting that mitotic rescue from replication stress (MRRS) is a key process influencing genome stability and cellular homeostasis. Deregulation of MRRS following oncogene activation or loss-of-function of caretaker genes may be the cause of chromosomal aberrations that promote cancer initiation and progression. In this review, we discuss the causes and consequences of replication stress, focusing on its persistence in mitosis as well as the mechanisms and factors involved in its resolution, and the potential impact of incomplete replication or aberrant MRRS on tumorigenesis, aging and disease.

  16. Permeability and permeability anisotropy in Crab Orchard sandstone: Experimental insights into spatio-temporal effects

    Science.gov (United States)

    Gehne, Stephan; Benson, Philip M.

    2017-08-01

    Permeability in tight crustal rocks is primarily controlled by the connected porosity, shape and orientation of microcracks, the preferred orientation of cross-bedding, and sedimentary features such as layering. This leads to a significant permeability anisotropy. Less well studied, however, are the effects of time and stress recovery on the evolution of the permeability hysteresis which is becoming increasingly important in areas ranging from fluid migration in ore-forming processes to enhanced resource extraction. Here, we report new data simulating spatio-temporal permeability changes induced using effective pressure, simulating burial depth, on a tight sandstone (Crab Orchard). We find an initially (measured at 5 MPa) anisotropy of 2.5% in P-wave velocity and 180% in permeability anisotropy is significantly affected by the direction of the effective pressure change and cyclicity; anisotropy values decrease to 1% and 10% respectively after 3 cycles to 90 MPa and back. Furthermore, we measure a steadily increasing recovery time (10-20 min) for flow parallel to cross-bedding, and a far slower recovery time (20-50 min) for flow normal to cross-bedding. These data are interpreted via strain anisotropy and accommodation models, similar to the ;seasoning; process often used in dynamic reservoir extraction.

  17. A New Replication Norm for Psychology

    Directory of Open Access Journals (Sweden)

    Etienne P LeBel

    2015-10-01

    Full Text Available In recent years, there has been a growing concern regarding the replicability of findings in psychology, including a mounting number of prominent findings that have failed to replicate via high-powered independent replication attempts. In the face of this replicability “crisis of confidence”, several initiatives have been implemented to increase the reliability of empirical findings. In the current article, I propose a new replication norm that aims to further boost the dependability of findings in psychology. Paralleling the extant social norm that researchers should peer review about three times as many articles that they themselves publish per year, the new replication norm states that researchers should aim to independently replicate important findings in their own research areas in proportion to the number of original studies they themselves publish per year (e.g., a 4:1 original-to-replication studies ratio. I argue this simple approach could significantly advance our science by increasing the reliability and cumulative nature of our empirical knowledge base, accelerating our theoretical understanding of psychological phenomena, instilling a focus on quality rather than quantity, and by facilitating our transformation toward a research culture where executing and reporting independent direct replications is viewed as an ordinary part of the research process. To help promote the new norm, I delineate (1 how each of the major constituencies of the research process (i.e., funders, journals, professional societies, departments, and individual researchers can incentivize replications and promote the new norm and (2 any obstacles each constituency faces in supporting the new norm.

  18. Evaluating Permeability Enchancement Using Electrical Techniques

    Energy Technology Data Exchange (ETDEWEB)

    John W. Pritchett

    2008-09-01

    Enhanced Geothermal Systems (EGS) development projects involve the artificial stimulation of relatively impermeable high-temperature underground regions (at depths of 2-4 kilometers or more) to create sufficient permeability to permit underground fluid circulation, so that hot water can be withdrawn from production wells and used to generate electric power. Several major research projects of this general type have been undertaken in the past in New Mexico (Fenton Hill), Europe, Japan and Australia. Recent U.S. activities along these lines focus mainly on stimulating peripheral areas of existing operating hydrothermal fields rather than on fresh 'greenfield' sites, but the long-term objective of the Department of Energy's EGS program is the development of large-scale power projects based on EGS technology (MIT, 2006; NREL, 2008). Usually, stimulation is accomplished by injecting water into a well at high pressure, enhancing permeability by the creation and propagation of fractures in the surrounding rock (a process known as 'hydrofracturing'). Beyond just a motivation, low initial system permeability is also an essential prerequisite to hydrofracturing. If the formation permeability is too high, excessive fluid losses will preclude the buildup of sufficient pressure to fracture rock. In practical situations, the actual result of injection is frequently to re-open pre-existing hydrothermally-mineralized fractures, rather than to create completely new fractures by rupturing intact rock. Pre-existing fractures can often be opened using injection pressures in the range 5-20 MPa. Creation of completely new fractures will usually require pressures that are several times higher. It is preferable to undertake development projects of this type in regions where tectonic conditions are conducive to shear failure, so that when pre-existing fractures are pressurized they will fail by shearing laterally. If this happens, the fracture will often stay open

  19. Effective stress law for the permeability of a limestone

    CERN Document Server

    Ghabezloo, Siavash; Guédon, Sylvine; Martineau, François

    2008-01-01

    The effective stress law for the permeability of a limestone is studied experimentally by performing constant head permeability tests in a triaxial cell with different conditions of confining pressure and pore pressure. Test results have shown that a pore pressure increase and a confining pressure decrease both result in an increase of the permeability, and that the effect of the pore pressure change on the variation of the permeability is more important than the effect of a change of the confining pressure. A power law is proposed for the variation of the permeability with the effective stress. The permeability effective stress coefficient increases linearly with the differential pressure and is greater than one as soon the differential pressure exceeds few bars. The test results are well reproduced using the proposed permeability-effective stress law. A conceptual pore-shell model based on a detailed observation of the microstructure of the studied limestone is proposed. This model is able to explain the ex...

  20. The Accelerated Test of Chloride Permeability of Concrete

    Institute of Scientific and Technical Information of China (English)

    TAN Ke-feng; ODD E Gjφrv

    2003-01-01

    The availability of accelerated chloride permeability test and the effect of w/c ratio, incorporation of silica fume, maximum aggregate size and aggregate type on the chloride permeability were studied. The mathematic analysis certifies that there is a linear relationship between accelerated test and natural diffusion. Test results show that the chloride permeability of concrete increases as w/c ratio increases whilst a limited amount of replacement of cement with silica fume, the chloride permeability decreases dramatically. The maximum aggregate size in the range of 8 to 25 mm seems also affect chloride permeability but with a much less significant level. The chloride permeability of silica fume lightweight aggregate concrete is very low, especially the concrete made with dry lightweight concrete. The chloride permeability can be evaluated by this accelerated test method.

  1. Upscaling of permeability field of fractured rock system: Numerical examples

    KAUST Repository

    Bao, K.

    2012-01-01

    When the permeability field of a given porous medium domain is heterogeneous by the existence of randomly distributed fractures such that numerical investigation becomes cumbersome, another level of upscaling may be required. That is such complex permeability field could be relaxed (i.e., smoothed) by constructing an effective permeability field. The effective permeability field is an approximation to the real permeability field that preserves certain quantities and provides an overall acceptable description of the flow field. In this work, the effective permeability for a fractured rock system is obtained for different coarsening scenarios starting from very coarse mesh all the way towards the fine mesh simulation. In all these scenarios, the effective permeability as well as the pressure at each cell is obtained. The total flux at the exit boundary is calculated in all these cases, and very good agreement is obtained.

  2. Data from Investigating Variation in Replicability: A “Many Labs” Replication Project

    Directory of Open Access Journals (Sweden)

    Richard A. Klein

    2014-04-01

    Full Text Available This dataset is from the Many Labs Replication Project in which 13 effects were replicated across 36 samples and over 6,000 participants. Data from the replications are included, along with demographic variables about the participants and contextual information about the environment in which the replication was conducted. Data were collected in-lab and online through a standardized procedure administered via an online link. The dataset is stored on the Open Science Framework website. These data could be used to further investigate the results of the included 13 effects or to study replication and generalizability more broadly.

  3. Permeability-porosity relationships of subduction zone sediments

    Science.gov (United States)

    Gamage, K.; Screaton, E.; Bekins, B.; Aiello, I.

    2011-01-01

    Permeability-porosity relationships for sediments from the northern Barbados, Costa Rica, Nankai, and Peru subduction zones were examined based on sediment type, grain size distribution, and general mechanical and chemical compaction history. Greater correlation was observed between permeability and porosity in siliciclastic sediments, diatom oozes, and nannofossil chalks than in nannofossil oozes. For siliciclastic sediments, grouping of sediments by percentage of clay-sized material yields relationships that are generally consistent with results from other marine settings and suggests decreasing permeability as percentage of clay-sized material increases. Correction of measured porosities for smectite content improved the correlation of permeability-porosity relationships for siliciclastic sediments and diatom oozes. The relationship between permeability and porosity for diatom oozes is very similar to the relationship in siliciclastic sediments, and permeabilities of both sediment types are related to the amount of clay-size particles. In contrast, nannofossil oozes have higher permeability values by 1.5 orders of magnitude than siliciclastic sediments of the same porosity and show poor correlation between permeability and porosity. More indurated calcareous sediments, nannofossil chalks, overlap siliciclastic permeabilities at the lower end of their measured permeability range, suggesting similar consolidation patterns at depth. Thus, the lack of correlation between permeability and porosity for nannofossil oozes is likely related to variations in mechanical and chemical compaction at shallow depths. This study provides the foundation for a much-needed global database with fundamental properties that relate to permeability in marine settings. Further progress in delineating controls on permeability requires additional carefully documented permeability measurements on well-characterized samples. ?? 2010 Elsevier B.V.

  4. Replication forks reverse at high frequency upon replication stress in Physarum polycephalum.

    Science.gov (United States)

    Maric, Chrystelle; Bénard, Marianne

    2014-12-01

    The addition of hydroxyurea after the onset of S phase allows replication to start and permits the successive detecting of replication-dependent joint DNA molecules and chicken foot structures in the synchronous nuclei of Physarum polycephalum. We find evidence for a very high frequency of reversed replication forks upon replication stress. The formation of these reversed forks is dependent on the presence of joint DNA molecules, the impediment of the replication fork progression by hydroxyurea, and likely on the propensity of some replication origins to reinitiate replication to counteract the action of this compound. As hydroxyurea treatment enables us to successively detect the appearance of joint DNA molecules and then of reversed replication forks, we propose that chicken foot structures are formed both from the regression of hydroxyurea-frozen joint DNA molecules and from hydroxyurea-stalled replication forks. These experiments underscore the transient nature of replication fork regression, which becomes detectable due to the hydroxyurea-induced slowing down of replication fork progression.

  5. A quantitative model of DNA replication in Xenopus embryos: reliable replication despite stochasticity

    Science.gov (United States)

    Cheng-Hsin Yang, Scott; Bechhoefer, John

    2008-03-01

    DNA synthesis in Xenopus frog embryos initiates stochastically in time at many sites (origins) along the chromosome. Stochastic initiation implies fluctuations in the replication time and may lead to cell death if replication takes longer than the cell cycle time (˜ 25 min.). Surprisingly, although the typical replication time is about 20 min., in vivo experiments show that replication fails to complete only about 1 in 250 times. How is replication timing accurately controlled despite the stochasticity? Biologists have proposed two mechanisms: the first uses a regular spatial distribution of origins, while the second uses randomly located origins but increases their probability of initiation as the cell cycle proceeds. Here, we show that both mechanisms yield similar end-time distributions, implying that regular origin spacing is not needed for control of replication time. Moreover, we show that the experimentally inferred time-dependent initiation rate satisfies the observed low failure probability and nearly optimizes the use of replicative proteins.

  6. Targeting DNA Replication Stress for Cancer Therapy

    Science.gov (United States)

    Zhang, Jun; Dai, Qun; Park, Dongkyoo; Deng, Xingming

    2016-01-01

    The human cellular genome is under constant stress from extrinsic and intrinsic factors, which can lead to DNA damage and defective replication. In normal cells, DNA damage response (DDR) mediated by various checkpoints will either activate the DNA repair system or induce cellular apoptosis/senescence, therefore maintaining overall genomic integrity. Cancer cells, however, due to constitutive growth signaling and defective DDR, may exhibit “replication stress” —a phenomenon unique to cancer cells that is described as the perturbation of error-free DNA replication and slow-down of DNA synthesis. Although replication stress has been proven to induce genomic instability and tumorigenesis, recent studies have counterintuitively shown that enhancing replicative stress through further loosening of the remaining checkpoints in cancer cells to induce their catastrophic failure of proliferation may provide an alternative therapeutic approach. In this review, we discuss the rationale to enhance replicative stress in cancer cells, past approaches using traditional radiation and chemotherapy, and emerging approaches targeting the signaling cascades induced by DNA damage. We also summarize current clinical trials exploring these strategies and propose future research directions including the use of combination therapies, and the identification of potential new targets and biomarkers to track and predict treatment responses to targeting DNA replication stress. PMID:27548226

  7. Oncogene v-jun modulates DNA replication.

    Science.gov (United States)

    Wasylyk, C; Schneikert, J; Wasylyk, B

    1990-07-01

    Cell transformation leads to alterations in both transcription and DNA replication. Activation of transcription by the expression of a number of transforming oncogenes is mediated by the transcription factor AP1 (Herrlich & Ponta, 1989; Imler & Wasylyk, 1989). AP1 is a composite transcription factor, consisting of members of the jun and fos gene-families. c-jun and c-fos are progenitors of oncogenes, suggestion that an important transcriptional event in cell transformation is altered activity of AP1, which may arise either indirectly by oncogene expression or directly by structural modification of AP1. We report here that the v-jun oncogene and its progenitor c-jun, as fusion proteins with the lex-A-repressor DNA binding domain, can activate DNA replication from the Polyoma virus (Py) origin of replication, linked to the lex-A operator. The transcription-activation region of v-jun is required for activation of replication. When excess v-jun is expressed in the cell, replication is inhibited or 'squelched'. These results suggest that one consequence of deregulated jun activity could be altered DNA replication and that there are similarities in the way v-jun activates replication and transcription.

  8. Targeting DNA Replication Stress for Cancer Therapy

    Directory of Open Access Journals (Sweden)

    Jun Zhang

    2016-08-01

    Full Text Available The human cellular genome is under constant stress from extrinsic and intrinsic factors, which can lead to DNA damage and defective replication. In normal cells, DNA damage response (DDR mediated by various checkpoints will either activate the DNA repair system or induce cellular apoptosis/senescence, therefore maintaining overall genomic integrity. Cancer cells, however, due to constitutive growth signaling and defective DDR, may exhibit “replication stress” —a phenomenon unique to cancer cells that is described as the perturbation of error-free DNA replication and slow-down of DNA synthesis. Although replication stress has been proven to induce genomic instability and tumorigenesis, recent studies have counterintuitively shown that enhancing replicative stress through further loosening of the remaining checkpoints in cancer cells to induce their catastrophic failure of proliferation may provide an alternative therapeutic approach. In this review, we discuss the rationale to enhance replicative stress in cancer cells, past approaches using traditional radiation and chemotherapy, and emerging approaches targeting the signaling cascades induced by DNA damage. We also summarize current clinical trials exploring these strategies and propose future research directions including the use of combination therapies, and the identification of potential new targets and biomarkers to track and predict treatment responses to targeting DNA replication stress.

  9. CO2 breakthrough pressure and permeability for unsaturated low-permeability sandstone of the Ordos Basin

    Science.gov (United States)

    Zhao, Yan; Yu, Qingchun

    2017-07-01

    With rising threats from greenhouse gases, capture and injection of CO2 into suitable underground formations is being considered as a method to reduce anthropogenic emissions of CO2 to the atmosphere. As the injected CO2 will remain in storage for hundreds of years, the safety of CO2 geologic sequestration is a major concern. The low-permeability sandstone of the Ordos Basin in China is regarded as both caprock and reservoir rock, so understanding the breakthrough pressure and permeability of the rock is necessary. Because part of the pore volume experiences a non-wetting phase during the CO2 injection and migration process, the rock may be in an unsaturated condition. And if accidental leakage occurs, CO2 will migrate up into the unsaturated zone. In this study, breakthrough experiments were performed at various degrees of water saturation with five core samples of low-permeability sandstone obtained from the Ordos Basin. The experiments were conducted at 40 °C and pressures of >8 MPa to simulate the geological conditions for CO2 sequestration. The results indicate that the degree of water saturation and the pore structure are the main factors affecting the rock breakthrough pressure and permeability, since the influence of calcite dissolution and clay mineral swelling during the saturation process is excluded. Increasing the average pore radius or most probable pore radius leads to a reduction in the breakthrough pressure and an increase by several orders of magnitude in scCO2 effective permeability. In addition, the breakthrough pressure rises and the scCO2 effective permeability decreases when the water saturation increases. However, when the average pore radius is greater than 0.151 μm, the degree of water saturation will has a little effect on the breakthrough pressure. On this foundation, if the most probable pore radius of the core sample reaches 1.760 μm, the breakthrough pressure will not be impacted by the increasing water saturation. We establish

  10. A whole genome RNAi screen identifies replication stress response genes.

    Science.gov (United States)

    Kavanaugh, Gina; Ye, Fei; Mohni, Kareem N; Luzwick, Jessica W; Glick, Gloria; Cortez, David

    2015-11-01

    Proper DNA replication is critical to maintain genome stability. When the DNA replication machinery encounters obstacles to replication, replication forks stall and the replication stress response is activated. This response includes activation of cell cycle checkpoints, stabilization of the replication fork, and DNA damage repair and tolerance mechanisms. Defects in the replication stress response can result in alterations to the DNA sequence causing changes in protein function and expression, ultimately leading to disease states such as cancer. To identify additional genes that control the replication stress response, we performed a three-parameter, high content, whole genome siRNA screen measuring DNA replication before and after a challenge with replication stress as well as a marker of checkpoint kinase signalling. We identified over 200 replication stress response genes and subsequently analyzed how they influence cellular viability in response to replication stress. These data will serve as a useful resource for understanding the replication stress response.

  11. Study on the micro-replication of shark skin

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Direct replication of creatural scarfskins to form biomimetic surfaces with relatively vivid morphology is a new attempt of the bio-replicated forming technology at animal body. Taking shark skins as the replication templates, and the micro-embossing and micro-molding as the material forming methods, the micro-replicating technology of the outward morphology on shark skins was demonstrated. The preliminary analysis on replication precision indicates that the bio-replicated forming technology can replicate the outward morphology of the shark scales with good precision, which validates the application of the bio-replicated forming technology in the direct morphology replication of the firm creatural scarfskins.

  12. Engineered Trehalose Permeable to Mammalian Cells.

    Directory of Open Access Journals (Sweden)

    Alireza Abazari

    Full Text Available Trehalose is a naturally occurring disaccharide which is associated with extraordinary stress-tolerance capacity in certain species of unicellular and multicellular organisms. In mammalian cells, presence of intra- and extracellular trehalose has been shown to confer improved tolerance against freezing and desiccation. Since mammalian cells do not synthesize nor import trehalose, the development of novel methods for efficient intracellular delivery of trehalose has been an ongoing investigation. Herein, we studied the membrane permeability of engineered lipophilic derivatives of trehalose. Trehalose conjugated with 6 acetyl groups (trehalose hexaacetate or 6-O-Ac-Tre demonstrated superior permeability in rat hepatocytes compared with regular trehalose, trehalose diacetate (2-O-Ac-Tre and trehalose tetraacetate (4-O-Ac-Tre. Once in the cell, intracellular esterases hydrolyzed the 6-O-Ac-Tre molecules, releasing free trehalose into the cytoplasm. The total concentration of intracellular trehalose (plus acetylated variants reached as high as 10 fold the extracellular concentration of 6-O-Ac-Tre, attaining concentrations suitable for applications in biopreservation. To describe this accumulation phenomenon, a diffusion-reaction model was proposed and the permeability and reaction kinetics of 6-O-Ac-Tre were determined by fitting to experimental data. Further studies suggested that the impact of the loading and the presence of intracellular trehalose on cellular viability and function were negligible. Engineering of trehalose chemical structure rather than manipulating the cell, is an innocuous, cell-friendly method for trehalose delivery, with demonstrated potential for trehalose loading in different types of cells and cell lines, and can facilitate the wide-spread application of trehalose as an intracellular protective agent in biopreservation studies.

  13. [Corneal permeability of topically applied pirenzepine solution].

    Science.gov (United States)

    Wang, Kai-di; Zhang, Jin-song; Yan, Pan-shi

    2006-06-01

    To study the corneal permeability of three different pirenzepine eye-drop solutions and provide reference for further clinical use. Sixty-three New Zealand white rabbits were divided into three groups. Each group of rabbits received 2% pirenzepine (pirenzepine group), 2% pirenzepine with 0.1% hyaluronic acid (hyaluronic acid group), or 2% pirenzepine with 0.1% azone (azone group). One drop eye-drops was applied to conjunctive sac every 5 min for six times. Aqueous samples were obtained from each group at 0.5, 1.0, 2.0, 4.0, 8.0, 12.0, 24.0 h after the last drop, respectively. Concentration of pirenzepine in these samples was determined by the HPLC (high pressure liquid chromatography). Stimulation symptom of rabbit eyes was also observed. The concentrations of pirenzepine in aqueous humor were (0.40 +/- 0.06) microg/ml at 0.5 h, (0.53 +/- 0.03) microg/ml at 1.0 h, (1.52 +/- 0.33) microg/ml at 2.0 h and (0.15 +/- 0.02) microg/ml at 4.0 h in pirenzepine group. Aqueous humor concentration of pirenzepine in both 2% pirenzepine with 0.1% azone and 2% pirenzepine with 0.1% hyaluronic acid were significantly higher than that of single pirenzepine application, and their bioavailability in the groups with combinations of pirenzepine with 0.1% azone or 0.1% hyaluronic acid were 23.0 times and 3.4 times higher than that of single pirenzepine usage. No obvious irritate symptom was found in rabbit of all three groups after eye-drop applying. The combination application of pirenzepine with azone or hyaluronic acid has higher corneal permeability compared with pirenzepine alone. This result indicates that azone and hyaluronic acid could be used in pirenzepine eye-drop solution to increase corneal permeability.

  14. Replicated Data Management for Mobile Computing

    CERN Document Server

    Douglas, Terry

    2008-01-01

    Managing data in a mobile computing environment invariably involves caching or replication. In many cases, a mobile device has access only to data that is stored locally, and much of that data arrives via replication from other devices, PCs, and services. Given portable devices with limited resources, weak or intermittent connectivity, and security vulnerabilities, data replication serves to increase availability, reduce communication costs, foster sharing, and enhance survivability of critical information. Mobile systems have employed a variety of distributed architectures from client-server

  15. Classification of Sporting Activities Using Smartphone Accelerometers

    Directory of Open Access Journals (Sweden)

    Noel E. O'Connor

    2013-04-01

    Full Text Available In this paper we present a framework that allows for the automatic identification of sporting activities using commonly available smartphones. We extract discriminative informational features from smartphone accelerometers using the Discrete Wavelet Transform (DWT. Despite the poor quality of their accelerometers, smartphones were used as capture devices due to their prevalence in today’s society. Successful classification on this basis potentially makes the technology accessible to both elite and non-elite athletes. Extracted features are used to train different categories of classifiers. No one classifier family has a reportable direct advantage in activity classification problems to date; thus we examine classifiers from each of the most widely used classifier families. We investigate three classification approaches; a commonly used SVM-based approach, an optimized classification model and a fusion of classifiers. We also investigate the effect of changing several of the DWT input parameters, including mother wavelets, window lengths and DWT decomposition levels. During the course of this work we created a challenging sports activity analysis dataset, comprised of soccer and field-hockey activities. The average maximum F-measure accuracy of 87% was achieved using a fusion of classifiers, which was 6% better than a single classifier model and 23% better than a standard SVM approach.

  16. PERMEABILITY OF SALTSTONE MEASUREMENT BY BEAM BENDING

    Energy Technology Data Exchange (ETDEWEB)

    Harbour, J; Tommy Edwards, T; Vickie Williams, V

    2008-01-30

    One of the goals of the Saltstone variability study is to identify (and, quantify the impact of) the operational and compositional variables that control or influence the important processing and performance properties of Saltstone mixes. A performance property for Saltstone mixes that is important but not routinely measured is the liquid permeability or saturated hydraulic conductivity of the cured Saltstone mix. The value for the saturated hydraulic conductivity is an input into the Performance Assessment for the SRS Z-Area vaults. Therefore, it is important to have a method available that allows for an accurate and reproducible measurement of permeability quickly and inexpensively. One such method that could potentially meet these requirements for the measurement of saturated hydraulic conductivity is the technique of beam bending, developed by Professor George Scherer at Princeton University. In order to determine the feasibility of this technique for Saltstone mixes, a summer student, David Feliciano, was hired to work at Princeton under the direction of George Scherer. This report details the results of this study which demonstrated the feasibility and applicability of the beam bending method to measurement of permeability of Saltstone samples. This research effort used samples made at Princeton from a Modular Caustic side solvent extraction Unit based simulant (MCU) and premix at a water to premix ratio of 0.60. The saturated hydraulic conductivities for these mixes were measured by the beam bending technique and the values determined were of the order of 1.4 to 3.4 x 10{sup -9} cm/sec. These values of hydraulic conductivity are consistent with independently measured values of this property on similar MCU based mixes by Dixon and Phifer. These values are also consistent with the hydraulic conductivity of a generic Saltstone mix measured by Langton in 1985. The high water to premix ratio used for Saltstone along with the relatively low degree of hydration for

  17. Altered permeability barrier structure in cholesteatoma matrix

    DEFF Research Database (Denmark)

    Svane-Knudsen, Viggo; Halkier-Sørensen, Lars; Rasmussen, Gurli

    2002-01-01

    The stratum corneum of the cholesteatoma epithelium comprises the greater part of the cholesteatoma matrix. The permeability barrier that militates against diffusion and penetration of infectious and toxic agents into and through the epithelium is situated here. The multiple long sheets of lamellar...... lipid structures filling the intercellular spaces mainly control the barrier function. The barrier in cholesteatoma epithelium is several times thicker than in unaffected skin but presents distinctive features of a defective barrier as seen in other scaling skin diseases. The intercellular spaces appear...

  18. Gas permeability measurements for film envelope materials

    Energy Technology Data Exchange (ETDEWEB)

    Ludtka, Gerard M. (Oak Ridge, TN); Kollie, Thomas G. (Oak Ridge, TN); Watkin, David C. (Clinton, TN); Walton, David G. (Knoxville, TN)

    1998-01-01

    Method and apparatus for measuring the permeability of polymer film materials such as used in super-insulation powder-filled evacuated panels (PEPs) reduce the time required for testing from several years to weeks or months. The method involves substitution of a solid non-outgassing body having a free volume of between 0% and 25% of its total volume for the usual powder in the PEP to control the free volume of the "body-filled panel". Pressure versus time data for the test piece permit extrapolation to obtain long term performance of the candidate materials.

  19. Gas permeability measurements for film envelope materials

    Energy Technology Data Exchange (ETDEWEB)

    Ludtka, G.M.; Kollie, T.G.; Watkin, D.C.; Walton, D.G.

    1998-05-12

    Method and apparatus for measuring the permeability of polymer film materials such as used in super-insulation powder-filled evacuated panels (PEPs) reduce the time required for testing from several years to weeks or months. The method involves substitution of a solid non-outgassing body having a free volume of between 0% and 25% of its total volume for the usual powder in the PEP to control the free volume of the ``body-filled panel.`` Pressure versus time data for the test piece permit extrapolation to obtain long term performance of the candidate materials. 4 figs.

  20. On the dynamic viscous permeability tensor symmetry.

    Science.gov (United States)

    Perrot, Camille; Chevillotte, Fabien; Panneton, Raymond; Allard, Jean-François; Lafarge, Denis

    2008-10-01

    Based on a direct generalization of a proof given by Torquato for symmetry property in static regime, this express letter clarifies the reasons why the dynamic permeability tensor is symmetric for spatially periodic structures having symmetrical axes which do not coincide with orthogonal pairs being perpendicular to the axis of three-, four-, and sixfold symmetry. This somewhat nonintuitive property is illustrated by providing detailed numerical examples for a hexagonal lattice of solid cylinders in the asymptotic and frequency dependent regimes. It may be practically useful for numerical implementation validation and/or convergence assessment.

  1. A transcription and translation-coupled DNA replication system using rolling-circle replication.

    Science.gov (United States)

    Sakatani, Yoshihiro; Ichihashi, Norikazu; Kazuta, Yasuaki; Yomo, Tetsuya

    2015-05-27

    All living organisms have a genome replication system in which genomic DNA is replicated by a DNA polymerase translated from mRNA transcribed from the genome. The artificial reconstitution of this genome replication system is a great challenge in in vitro synthetic biology. In this study, we attempted to construct a transcription- and translation-coupled DNA replication (TTcDR) system using circular genomic DNA encoding phi29 DNA polymerase and a reconstituted transcription and translation system. In this system, phi29 DNA polymerase was translated from the genome and replicated the genome in a rolling-circle manner. When using a traditional translation system composition, almost no DNA replication was observed, because the tRNA and nucleoside triphosphates included in the translation system significantly inhibited DNA replication. To minimize these inhibitory effects, we optimized the composition of the TTcDR system and improved replication by approximately 100-fold. Using our system, genomic DNA was replicated up to 10 times in 12 hours at 30 °C. This system provides a step toward the in vitro construction of an artificial genome replication system, which is a prerequisite for the construction of an artificial cell.

  2. Using autonomous replication to physically and genetically define human origins of replication

    Energy Technology Data Exchange (ETDEWEB)

    Krysan, P.J.

    1993-01-01

    The author previously developed a system for studying autonomous replication in human cells involving the use of sequences from the Epstein-Barr virus (EBV) genome to provide extrachromosomal plasmids with a nuclear retention function. Using this system, it was demonstrated that large fragments of human genomic DNA could be isolated which replicate autonomously in human cells. In this study the DNA sequences which function as origins of replication in human cells are defined physically and genetically. These experiments demonstrated that replication initiates at multiple locations distributed throughout the plasmid. Another line of experiments addressed the DNA sequence requirements for autonomous replication in human cells. These experiments demonstrated that human DNA fragments have a higher replication activity than bacterial fragments do. It was also found, however, that the bacterial DNA sequence could support efficient replication if enough copies of it were present on the plasmid. These findings suggested that autonomous replication in human cells does not depend on extensive, specific DNA sequences. The autonomous replication system which the author has employed for these experiments utilizes a cis-acting sequence from the EBV origin and the trans-acting EBNA-1 protein to provide plasmids with a nuclear retention function. It was therefore relevant to verify that the autonomous replication of human DNA fragments did not depend on the replication activity associated with the EBV sequences utilized for nuclear retention. To accomplish this goal, the author demonstrated that plasmids carrying the EBV sequences and large fragments of human DNA could support long-term autonomous replication in hamster cells, which are not permissive for EBV replication.

  3. Mechanism of chromosomal DNA replication initiation and replication fork stabilization in eukaryotes.

    Science.gov (United States)

    Wu, LiHong; Liu, Yang; Kong, DaoChun

    2014-05-01

    Chromosomal DNA replication is one of the central biological events occurring inside cells. Due to its large size, the replication of genomic DNA in eukaryotes initiates at hundreds to tens of thousands of sites called DNA origins so that the replication could be completed in a limited time. Further, eukaryotic DNA replication is sophisticatedly regulated, and this regulation guarantees that each origin fires once per S phase and each segment of DNA gets duplication also once per cell cycle. The first step of replication initiation is the assembly of pre-replication complex (pre-RC). Since 1973, four proteins, Cdc6/Cdc18, MCM, ORC and Cdt1, have been extensively studied and proved to be pre-RC components. Recently, a novel pre-RC component called Sap1/Girdin was identified. Sap1/Girdin is required for loading Cdc18/Cdc6 to origins for pre-RC assembly in the fission yeast and human cells, respectively. At the transition of G1 to S phase, pre-RC is activated by the two kinases, cyclindependent kinase (CDK) and Dbf4-dependent kinase (DDK), and subsequently, RPA, primase-polα, PCNA, topoisomerase, Cdc45, polδ, and polɛ are recruited to DNA origins for creating two bi-directional replication forks and initiating DNA replication. As replication forks move along chromatin DNA, they frequently stall due to the presence of a great number of replication barriers on chromatin DNA, such as secondary DNA structures, protein/DNA complexes, DNA lesions, gene transcription. Stalled forks must require checkpoint regulation for their stabilization. Otherwise, stalled forks will collapse, which results in incomplete DNA replication and genomic instability. This short review gives a concise introduction regarding the current understanding of replication initiation and replication fork stabilization.

  4. Replicating chromatin: a tale of histones

    DEFF Research Database (Denmark)

    Groth, Anja

    2009-01-01

    Chromatin serves structural and functional roles crucial for genome stability and correct gene expression. This organization must be reproduced on daughter strands during replication to maintain proper overlay of epigenetic fabric onto genetic sequence. Nucleosomes constitute the structural...

  5. Control of chromosome replication in caulobacter crescentus.

    Science.gov (United States)

    Marczynski, Gregory T; Shapiro, Lucy

    2002-01-01

    Caulobacter crescentus permits detailed analysis of chromosome replication control during a developmental cell cycle. Its chromosome replication origin (Cori) may be prototypical of the large and diverse class of alpha-proteobacteria. Cori has features that both affiliate and distinguish it from the Escherichia coli chromosome replication origin. For example, requirements for DnaA protein and RNA transcription affiliate both origins. However, Cori is distinguished by several features, and especially by five binding sites for the CtrA response regulator protein. To selectively repress and limit chromosome replication, CtrA receives both protein degradation and protein phosphorylation signals. The signal mediators, proteases, response regulators, and kinases, as well as Cori DNA and the replisome, all show distinct patterns of temporal and spatial organization during cell cycle progression. Future studies should integrate our knowledge of biochemical activities at Cori with our emerging understanding of cytological dynamics in C. crescentus and other bacteria.

  6. LHCb Data Replication During SC3

    CERN Multimedia

    Smith, A

    2006-01-01

    LHCb's participation in LCG's Service Challenge 3 involves testing the bulk data transfer infrastructure developed to allow high bandwidth distribution of data across the grid in accordance with the computing model. To enable reliable bulk replication of data, LHCb's DIRAC system has been integrated with gLite's File Transfer Service middleware component to make use of dedicated network links between LHCb computing centres. DIRAC's Data Management tools previously allowed the replication, registration and deletion of files on the grid. For SC3 supplementary functionality has been added to allow bulk replication of data (using FTS) and efficient mass registration to the LFC replica catalog.Provisional performance results have shown that the system developed can meet the expected data replication rate required by the computing model in 2007. This paper details the experience and results of integration and utilisation of DIRAC with the SC3 transfer machinery.

  7. Initiation of Replication in Escherichia coli

    DEFF Research Database (Denmark)

    Frimodt-Møller, Jakob

    The circular chromosome of Escherichia coli is replicated by two replisomes assembled at the unique origin and moving in the opposite direction until they meet in the less well defined terminus. The key protein in initiation of replication, DnaA, facilitates the unwinding of double-stranded DNA...... to single-stranded DNA in oriC. Although DnaA is able to bind both ADP and ATP, DnaA is only active in initiation when bound to ATP. Although initiation of replication, and the regulation of this, is thoroughly investigated it is still not fully understood. The overall aim of the thesis was to investigate...... the regulation of initiation, the effect on the cell when regulation fails, and if regulation was interlinked to chromosomal organization. This thesis uncovers that there exists a subtle balance between chromosome replication and reactive oxygen species (ROS) inflicted DNA damage. Thus, failure in regulation...

  8. Surface Micro Topography Replication in Injection Moulding

    DEFF Research Database (Denmark)

    Arlø, Uffe Rolf; Hansen, Hans Nørgaard; Kjær, Erik Michael

    2005-01-01

    carried out with rough EDM (electrical discharge machining) mould surfaces, a PS grade, and by applying established three-dimensional topography parameters. Significant quantitative relationships between process parameters and topography parameters were established. It further appeared that replication...

  9. Estimation of permeability and permeability anisotropy in horizontal wells through numerical simulation of mud filtrate invasion

    Energy Technology Data Exchange (ETDEWEB)

    Pereira, Nelson [PETROBRAS S.A., Rio de Janeiro, RJ (Brazil). Exploracao e Producao; Altman, Raphael; Rasmus, John; Oliveira, Jansen [Schlumberger Servicos de Petroleo Ltda., Rio de Janeiro, RJ (Brazil)

    2008-07-01

    This paper describes how permeability and permeability anisotropy is estimated in horizontal wells using LWD (logging-while-drilling) laterolog resistivity data. Laterolog-while-drilling resistivity passes of while-drilling and timelapse (while reaming) were used to capture the invasion process. Radial positions of water based mud invasion fronts were calculated from while-drilling and reaming resistivity data. The invasion process was then recreated by constructing forward models with a fully implicit, near-wellbore numerical simulation such that the invasion front at a given time was consistent with the position of the front predicted by resistivity inversions. The radial position of the invasion front was shown to be sensitive to formation permeability. The while-drilling environment provides a fertile scenario to investigate reservoir dynamic properties because mud cake integrity and growth is not fully developed which means that the position of the invasion front at a particular point in time is more sensitive to formation permeability. The estimation of dynamic formation properties in horizontal wells is of particular value in marginal fields and deep-water offshore developments where running wireline and obtaining core is not always feasible, and where the accuracy of reservoir models can reduce the risk in field development decisions. (author)

  10. Modeling of microvascular permeability changes after electroporation.

    Directory of Open Access Journals (Sweden)

    Selma Corovic

    Full Text Available Vascular endothelium selectively controls the transport of plasma contents across the blood vessel wall. The principal objective of our preliminary study was to quantify the electroporation-induced increase in permeability of blood vessel wall for macromolecules, which do not normally extravasate from blood into skin interstitium in homeostatic conditions. Our study combines mathematical modeling (by employing pharmacokinetic and finite element modeling approach with in vivo measurements (by intravital fluorescence microscopy. Extravasation of fluorescently labeled dextran molecules of two different sizes (70 kDa and 2000 kDa following the application of electroporation pulses was investigated in order to simulate extravasation of therapeutic macromolecules with molecular weights comparable to molecular weight of particles such as antibodies and plasmid DNA. The increase in blood vessel permeability due to electroporation and corresponding transvascular transport was quantified by calculating the apparent diffusion coefficients for skin microvessel wall (D [μm2/s] for both molecular sizes. The calculated apparent diffusion coefficients were D = 0.0086 μm2/s and D = 0.0045 μm2/s for 70 kDa and 2000 kDa dextran molecules, respectively. The results of our preliminary study have important implications in development of realistic mathematical models for prediction of extravasation and delivery of large therapeutic molecules to target tissues by means of electroporation.

  11. Modeling the pharmacodynamics of passive membrane permeability

    Science.gov (United States)

    Swift, Robert V.; Amaro, Rommie E.

    2011-11-01

    Small molecule permeability through cellular membranes is critical to a better understanding of pharmacodynamics and the drug discovery endeavor. Such permeability may be estimated as a function of the free energy change of barrier crossing by invoking the barrier domain model, which posits that permeation is limited by passage through a single "barrier domain" and assumes diffusivity differences among compounds of similar structure are negligible. Inspired by the work of Rezai and co-workers (JACS 128:14073-14080, 2006), we estimate this free energy change as the difference in implicit solvation free energies in chloroform and water, but extend their model to include solute conformational affects. Using a set of eleven structurally diverse FDA approved compounds and a set of thirteen congeneric molecules, we show that the solvation free energies are dominated by the global minima, which allows solute conformational distributions to be effectively neglected. For the set of tested compounds, the best correlation with experiment is obtained when the implicit chloroform global minimum is used to evaluate the solvation free energy difference.

  12. Haemophilia, AIDS and lung epithelial permeability

    Energy Technology Data Exchange (ETDEWEB)

    O' Doherty, M.J.; Page, C.J.; Harrington, C.; Nunan, T.; Savidge, G. (Haemophilia Centre and Coagulation Research Unit, Department of Nuclear Medicine, Rayne Institute, St. Thomas' Hospital, London (United Kingdom))

    1990-01-01

    Lung {sup 99m}Tc DTPA transfer was measured in HIV antibodypositive haemophiliacs (11 smokers, 26 nonsmokers, 5 patients with Pneumocystis carinii pneumonia (PCP)). Lung {sup 99m}Tc DTPA transfer as a marker of lung epithelial permeability was measured as the half time of transfer (from airspace into blood). This half time was faster in smokers compred to nonsmokers and the transfer curve was monoexponential. In nonsmokers no difference was observed between asymptomatic HIV-positive haemophiliacs and normal subjects, with the exception of the lung bases. At the lung basis in HIV-positive haemophiliac nonsmokers the transfer was faster than in normal individuals, implying increased alveolar permeability. Pneumocystis carinii pneumonia resulted in a rapid transfer of {sup 99m}Tc DTPA (mean T50 of 2 minutes) and the transfer curve was biphasic, confirming previous observations in homosexual HIV antibody-positive patients with PCP. These changes returned to a monoexponential profile by 6 weeks following successful treatment. The DTPA lung transfer study may enable clinicians to instigate therapy for PCP without the need for initial bronchoscopy and provide a noninvasive method for the reassessment of patients should further respiratory signs or symptoms develop. This method is considered to be highly cost-effective in that it obviates the use of factor VIII concentrates required to cover bronchoscopic procedures and, with its early application and ease of use as a follow-up investigation, permits the evaluation of patients on an outpatient basis, thus reducing hospital costs. (au).

  13. Air sparging in low permeability soils

    Energy Technology Data Exchange (ETDEWEB)

    Marley, M.C. [Envirogen, Inc., Canton, MA (United States)

    1996-08-01

    Sparging technology is rapidly growing as a preferred, low cost remediation technique of choice at sites across the United States. The technology is considered to be commercially available and relatively mature. However, the maturity is based on the number of applications of the technology as opposed to the degree of understanding of the mechanisms governing the sparging process. Few well documented case studies exist on the long term operation of the technology. Sparging has generally been applied using modified monitoring well designs in uniform, coarse grained soils. The applicability of sparging for the remediation of DNAPLs in low permeability media has not been significantly explored. Models for projecting the performance of sparging systems in either soils condition are generally simplistic but can be used to provide general insight into the effects of significant changes in soil and fluid properties. The most promising sparging approaches for the remediation of DNAPLs in low permeability media are variations or enhancements to the core technology. Recirculatory sparging systems, sparging/biosparging trenches or curtains and heating or induced fracturing techniques appear to be the most promising technology variants for this type of soil. 21 refs., 9 figs.

  14. Modeling of microvascular permeability changes after electroporation.

    Science.gov (United States)

    Corovic, Selma; Markelc, Bostjan; Dolinar, Mitja; Cemazar, Maja; Jarm, Tomaz

    2015-01-01

    Vascular endothelium selectively controls the transport of plasma contents across the blood vessel wall. The principal objective of our preliminary study was to quantify the electroporation-induced increase in permeability of blood vessel wall for macromolecules, which do not normally extravasate from blood into skin interstitium in homeostatic conditions. Our study combines mathematical modeling (by employing pharmacokinetic and finite element modeling approach) with in vivo measurements (by intravital fluorescence microscopy). Extravasation of fluorescently labeled dextran molecules of two different sizes (70 kDa and 2000 kDa) following the application of electroporation pulses was investigated in order to simulate extravasation of therapeutic macromolecules with molecular weights comparable to molecular weight of particles such as antibodies and plasmid DNA. The increase in blood vessel permeability due to electroporation and corresponding transvascular transport was quantified by calculating the apparent diffusion coefficients for skin microvessel wall (D [μm2/s]) for both molecular sizes. The calculated apparent diffusion coefficients were D = 0.0086 μm2/s and D = 0.0045 μm2/s for 70 kDa and 2000 kDa dextran molecules, respectively. The results of our preliminary study have important implications in development of realistic mathematical models for prediction of extravasation and delivery of large therapeutic molecules to target tissues by means of electroporation.

  15. Dehumidification System with Steam Permeability Films

    Science.gov (United States)

    Ishikwa, Masaaki; Sekimori, Souji; Ogiwara, Shigeaki; Ochiai, Tetsunari; Hirata, Tetsuo

    In a factory with a clean room facility in cold regions, dew-condensation on walls of the facility is one of the most serious problems in winter. In this study, a new dehumidification system in which a steam permeability film is located between humid air in a clean room and dry air from outside to exchange steam is proposed. This system can treat a lot of humid air with small energy only for driving fans to flow air. Some films are examined in two kinds of steam exchangers; double tube type and flat p1ate type. Steam permeability resistance and therma1 resistance of each film are first obtained in a double tube type exchanger. An analytica1 model for a flat plate type exchanger is then proposed, which shows good agreement with experimental data. Steam and heat transfer characteristics of a flat plate type exchanger are also evaluated experimentally. One film on a flat plate type exchanger shows dehumidification capacity of 0.033g/s(=120g/h )with its area of 2.232m2.

  16. Commercial Building Partnerships Replication and Diffusion

    Energy Technology Data Exchange (ETDEWEB)

    Antonopoulos, Chrissi A.; Dillon, Heather E.; Baechler, Michael C.

    2013-09-16

    This study presents findings from survey and interview data investigating replication efforts of Commercial Building Partnership (CBP) partners that worked directly with the Pacific Northwest National Laboratory (PNNL). PNNL partnered directly with 12 organizations on new and retrofit construction projects, which represented approximately 28 percent of the entire U.S. Department of Energy (DOE) CBP program. Through a feedback survey mechanism, along with personal interviews, PNNL gathered quantitative and qualitative data relating to replication efforts by each organization. These data were analyzed to provide insight into two primary research areas: 1) CBP partners’ replication efforts of technologies and approaches used in the CBP project to the rest of the organization’s building portfolio (including replication verification), and, 2) the market potential for technology diffusion into the total U.S. commercial building stock, as a direct result of the CBP program. The first area of this research focused specifically on replication efforts underway or planned by each CBP program participant. Factors that impact replication include motivation, organizational structure and objectives firms have for implementation of energy efficient technologies. Comparing these factors between different CBP partners revealed patterns in motivation for constructing energy efficient buildings, along with better insight into market trends for green building practices. The second area of this research develops a diffusion of innovations model to analyze potential broad market impacts of the CBP program on the commercial building industry in the United States.

  17. Mycobacterium tuberculosis replicates within necrotic human macrophages

    Science.gov (United States)

    Lerner, Thomas R.; Repnik, Urska; Herbst, Susanne; Collinson, Lucy M.; Griffiths, Gareth

    2017-01-01

    Mycobacterium tuberculosis modulation of macrophage cell death is a well-documented phenomenon, but its role during bacterial replication is less characterized. In this study, we investigate the impact of plasma membrane (PM) integrity on bacterial replication in different functional populations of human primary macrophages. We discovered that IFN-γ enhanced bacterial replication in macrophage colony-stimulating factor–differentiated macrophages more than in granulocyte–macrophage colony-stimulating factor–differentiated macrophages. We show that permissiveness in the different populations of macrophages to bacterial growth is the result of a differential ability to preserve PM integrity. By combining live-cell imaging, correlative light electron microscopy, and single-cell analysis, we found that after infection, a population of macrophages became necrotic, providing a niche for M. tuberculosis replication before escaping into the extracellular milieu. Thus, in addition to bacterial dissemination, necrotic cells provide first a niche for bacterial replication. Our results are relevant to understanding the environment of M. tuberculosis replication in the host. PMID:28242744

  18. Therapeutic benefits of enhancing permeability barrier for atopic eczema

    Directory of Open Access Journals (Sweden)

    George Man

    2015-06-01

    Full Text Available The regulatory role of epidermal permeability barrier function in cutaneous inflammation has been well appreciated. While barrier disruption induces cutaneous inflammation, improvement of permeability barrier function alleviates inflammation. Studies have demonstrated that improvement of epidermal permeability barrier function not only prevents the development of atopic eczema, but also delays the relapse of these diseases. Moreover, enhancing the epidermal permeability barrier also alleviates atopic eczema. Furthermore, co-applications of barrier enhancing products with glucocorticoids can increase the therapeutic efficacy and reduce the adverse effects of glucocorticoids in the treatment of atopic eczema. Therefore, utilization of permeability barrier enhancing products alone or in combination with glucocorticoids could be a valuable approach in the treatment of atopic eczema. In this review, we discuss the benefits of improving the epidermal permeability barrier in the management of atopic eczema.

  19. Herbal medicines that benefit epidermal permeability barrier function

    Directory of Open Access Journals (Sweden)

    Lizhi Hu

    2015-06-01

    Full Text Available Epidermal permeability barrier function plays a critical role in regulating cutaneous functions. Hence, researchers have been searching for effective and affordable regimens to enhance epidermal permeability barrier function. In addition to topical stratum corneum lipids, peroxisome proliferator-activated receptor, and liver X receptor ligands, herbal medicines have been proven to benefit epidermal permeability barrier function in both normal and diseased skin, including atopic dermatitis, glucocorticoid-induced skin damage, and UVB-damaged skin. The potential mechanisms by which herbal medicines improve the permeability barrier include stimulation of epidermal differentiation, lipid production, antimicrobial peptide expression, and antioxidation. Therefore, utilization of herbal medicines could be a valuable alternative approach to enhance epidermal permeability barrier function in order to prevent and/or treat skin disorders associated with permeability barrier abnormalities.

  20. Organization of Replication of Ribosomal DNA in Saccharomyces cerevisiae

    NARCIS (Netherlands)

    Linskens, Maarten H.K.; Huberman, Joel A.

    1988-01-01

    Using recently developed replicon mapping techniques, we have analyzed the replication of the ribosomal DNA in Saccharomyces cerevisiae. The results show that (i) the functional origin of replication colocalizes with an autonomously replicating sequence element previously mapped to the

  1. Dynamics of Escherichia coli Chromosome Segregation during Multifork Replication

    DEFF Research Database (Denmark)

    Nielsen, Henrik Jørck; Youngren, Brenda; Hansen, Flemming G.

    2007-01-01

    Slowly growing Escherichia coli cells have a simple cell cycle, with replication and progressive segregation of the chromosome completed before cell division. In rapidly growing cells, initiation of replication occurs before the previous replication rounds are complete. At cell division...

  2. Calculation of large scale relative permeabilities from stochastic properties of the permeability field and fluid properties

    Energy Technology Data Exchange (ETDEWEB)

    Lenormand, R.; Thiele, M.R. [Institut Francais du Petrole, Rueil Malmaison (France)

    1997-08-01

    The paper describes the method and presents preliminary results for the calculation of homogenized relative permeabilities using stochastic properties of the permeability field. In heterogeneous media, the spreading of an injected fluid is mainly sue to the permeability heterogeneity and viscosity fingering. At large scale, when the heterogeneous medium is replaced by a homogeneous one, we need to introduce a homogenized (or pseudo) relative permeability to obtain the same spreading. Generally, is derived by using fine-grid numerical simulations (Kyte and Berry). However, this operation is time consuming and cannot be performed for all the meshes of the reservoir. We propose an alternate method which uses the information given by the stochastic properties of the field without any numerical simulation. The method is based on recent developments on homogenized transport equations (the {open_quotes}MHD{close_quotes} equation, Lenormand SPE 30797). The MHD equation accounts for the three basic mechanisms of spreading of the injected fluid: (1) Dispersive spreading due to small scale randomness, characterized by a macrodispersion coefficient D. (2) Convective spreading due to large scale heterogeneities (layers) characterized by a heterogeneity factor H. (3) Viscous fingering characterized by an apparent viscosity ration M. In the paper, we first derive the parameters D and H as functions of variance and correlation length of the permeability field. The results are shown to be in good agreement with fine-grid simulations. The are then derived a function of D, H and M. The main result is that this approach lead to a time dependent . Finally, the calculated are compared to the values derived by history matching using fine-grid numerical simulations.

  3. Modelling of Longwall Mining-Induced Strata Permeability Change

    Science.gov (United States)

    Adhikary, D. P.; Guo, H.

    2015-01-01

    The field measurement of permeability within the strata affected by mining is a challenging and expensive task, thus such tests may not be carried out in large numbers to cover all the overburden strata and coal seams being affected by mining. However, numerical modelling in conjunction with a limited number of targeted field measurements can be used efficiently in assessing the impact of mining on a regional scale. This paper presents the results of underground packer testing undertaken at a mine site in New South Wales in Australia and numerical simulations conducted to assess the mining-induced strata permeability change. The underground packer test results indicated that the drivage of main headings (roadways) had induced a significant change in permeability into the solid coal barrier. Permeability increased by more than 50 times at a distance of 11.2-11.5 m from the roadway rib into the solid coal barrier. The tests conducted in the roof strata above the longwall goaf indicated more than 1,000-fold increase in permeability. The measured permeability values varied widely and strangely on a number of occasions; for example the test conducted from the main headings at the 8.2-8.5 m test section in the solid coal barrier showed a decline in permeability value as compared to that at the 11.2-11.5 m section contrary to the expectations. It is envisaged that a number of factors during the tests might have had affected the measured values of permeability: (a) swelling and smearing of the borehole, possibly lowering the permeability values; (b) packer bypass by larger fractures; (c) test section lying in small but intact (without fractures) rock segment, possibly resulting in lower permeability values; and (d) test section lying right at the extensive fractures, possibly measuring higher permeability values. Once the anomalous measurement data were discarded, the numerical model results could be seen to match the remaining field permeability measurement data

  4. Fractal Derivative Model for Air Permeability in Hierarchic Porous Media

    Directory of Open Access Journals (Sweden)

    Jie Fan

    2012-01-01

    Full Text Available Air permeability in hierarchic porous media does not obey Fick's equation or its modification because fractal objects have well-defined geometric properties, which are discrete and discontinuous. We propose a theoretical model dealing with, for the first time, a seemingly complex air permeability process using fractal derivative method. The fractal derivative model has been successfully applied to explain the novel air permeability phenomenon of cocoon. The theoretical analysis was in agreement with experimental results.

  5. Neural Approach for Calculating Permeability of Porous Medium

    Institute of Scientific and Technical Information of China (English)

    ZHANG Ji-Cheng; LIU Li; SONG Kao-Ping

    2006-01-01

    @@ Permeability is one of the most important properties of porous media. It is considerably difficult to calculate reservoir permeability precisely by using single well-logging response and simple formula because reservoir is of serious heterogeneity, and well-logging response curves are badly affected by many complicated factors underground. We propose a neural network method to calculate permeability of porous media. By improving the algorithm of the back-propagation neural network, convergence speed is enhanced and better results can be achieved. A four-layer back-propagation network is constructed to effectively calculate permeability from well log data.

  6. Characteristics of permeability in carbonate areas of Korea

    Science.gov (United States)

    Park, Y.; Lee, J.; Lim, H.; Keehm, Y.

    2010-12-01

    Permeability (hydraulic conductivity) in carbonate areas is affected by various factors such as fracture, pore and degree of weathering and diagenesis. Also, caves developed in carbonate area are main factors. This study was performed to understand factors controlling the permeability in carbonate areas in Korea. In order to conduct this study, the permeability and well logging data (n=30) were collected from many literatures and rock samples were collected around wells. Vertical profile of the carbonate areas can be classified into soil, weathered carbonate and fresh carbonate zone. They show a different range at each region. Most of the rock samples were hardly weathered. The permeability showed wide ranges (0.009 to 1.1 m/day). The average value of the permeability was 0.159 m/day. However, 80% (n=24) of total data had the permeability valves lower than 0.1 m/day. The permeability values were distinguished according to degree of development of fractures. The permeability showed low values (approximately 0.5 m/day) in highly fractured carbonate. These results mean that fractures are dominant factors controlling the permeability in carbonate areas of Korea than others. This work was supported by Energy Resource R&D program (2009T100200058) under the Ministry of Knowledge Economy, Republic of Korea.

  7. Gut permeability in neonates after a stage 1 Norwood procedure.

    Science.gov (United States)

    Malagon, Ignacio; Onkenhout, Willem; Klok, Margreet; van der Poel, Petrus F H; Bovill, James G; Hazekamp, Mark G

    2005-09-01

    Intestinal mucosal ischemia can occur during and after cardiac surgery. Severe decreases in mucosal perfusion may be a causative factor for postoperative mortality or complications such as necrotizing enterocolitis. Mesenteric perfusion is challenged preoperatively due to an imbalance between the systemic and pulmonary circulations and challenged intraoperatively due to hypothermic circulatory arrest. We have investigated gut permeability in seven patients undergoing stage 1 of the Norwood procedure, applying the dual sugar permeability test with L-rhamnose and lactulose. Seven patients with hypoplastic left heart syndrome: clinical presentation, gut permeability findings, and outcome. A 10-bed mixed pediatric intensive care unit in a university hospital. Seven patients admitted for postoperative care after cardiac surgery. Determination of gut permeability with the dual sugar permeability test using lactulose and rhamnose. Intestinal permeability was measured after induction of anesthesia and 12 and 24 hrs later. : All patients had abnormal lactulose/rhamnose ratios. One patient, who had a lactulose/rhamnose ratio 12 hrs after surgery of 2.3 (46-times normal), developed necrotizing enterocolitis postoperatively and died 3 days after surgery. Gut permeability as assessed by the dual sugar permeability test is abnormal in patients with hypoplastic left heart syndrome before and after surgery. Lactulose/rhamnose ratios 46 times the normal value reflect a highly permeable small intestine. This may be a sign of a low output state and may help to identify patients at risk of developing necrotizing enterocolitis.

  8. Influence of decenylsuccinic Acid on water permeability of plant cells.

    Science.gov (United States)

    Lee, O Y; Stadelmann, E J; Weiser, C J

    1972-11-01

    Decenylsuccinic acid altered permeability to water of epidermal cells of bulb scales of Allium cepa and of the leaf midrib of Rhoeo discolor. Water permeability, as determined by deplasmolysis time measurements, was related to the dose of undissociated decenylsuccinic acid (mm undissociated decenylsuccinic acid x minute). No relationship was found between permeability and total dose of decenylsuccinic acid, or dose of dissociated decenylsuccinic acid, suggesting that the undissociated molecule was the active factor in permeability changes and injury.At doses which did not damage cells (0.0008 to 0.6 [mm of the undissociated molecule x minute]) decenylsuccinic acid decreased water permeability. At higher doses (e.g., 4 to 8 [mm x minute]) injury to cells was common and decenylsuccinic acid increased permeability. Doses above the 10 to 20 (mm x minute) range were generally lethal. The plasmolysis form of uninjured cells was altered and protoplasmic swelling occasionally was observed. The dose-dependent reversal of water permeability changes (decreased to increased permeability) may reflect decenylsuccinic acid-induced changes in membrane structure. Reported effects of decenylsuccinic acid on temperature dependence of permeability and frost resistance were not verified.

  9. Dentin permeability: effects of endodontic procedures on root slabs.

    Science.gov (United States)

    Fogel, H M; Pashley, D H

    1990-09-01

    The permeability of human radicular dentin was measured as a hydraulic conductance before and after treatment with K files and before and after subsequent treatment of the endodontic smear layer with NaOCl, 50% citric acid, or 3% monopotassium-monohydrogen oxalate. Filing reduced dentin permeability 25 to 49%, respectively, depending upon whether outer or inner root dentin was filed. The permeability of these smear layers was unaffected by 5% NaOCl but increased many times after treatment with 50% citric acid for 2 min. Oxalate treatment lowered root dentin permeability to levels below that produced by creation of smear layers due to the production of a crystalline precipitate.

  10. Small-bowel permeability in collagenous colitis

    DEFF Research Database (Denmark)

    Wildt, Signe; Madsen, Jan L; Rumessen, Jüri J

    2006-01-01

    OBJECTIVE: Collagenous colitis (CC) is a chronic inflammatory bowel disease that affects the colon. However, some patients with CC present with accompanying pathologic small-bowel manifestations such as coeliac disease, defects in bile acid absorption and histopathologic changes in small-intestin......OBJECTIVE: Collagenous colitis (CC) is a chronic inflammatory bowel disease that affects the colon. However, some patients with CC present with accompanying pathologic small-bowel manifestations such as coeliac disease, defects in bile acid absorption and histopathologic changes in small......-intestinal biopsies, indicating that CC is a pan-intestinal disease. In small-intestinal disease, the intestinal barrier function may be impaired, and the permeability of the small intestine altered. The purpose of this research was to study small-bowel function in patients with CC as expressed by intestinal...

  11. Composite binders for concrete with reduced permeability

    Science.gov (United States)

    Fediuk, R.; Yushin, A.

    2016-02-01

    Composite binder consisting of cement (55%), acid fly ash (40%) and limestone (5%) has been designed. It is obtained by co-milling to a specific surface of 550 kg/m2, it has an activity of 77.3 MPa and can produce a more dense cement stone structure. Integrated study revealed that the concrete on the composite binder basis provides an effective diffusion coefficient D. So we can conclude that the concrete layer protects buildings from toxic effects of expanded polystyrene. Low water absorption of the material (2.5% by weight) is due to the structure of its cement stone pore space. Besides lime powder prevents the penetration of moisture, reduces water saturation of the coverage that has a positive effect on useful life period. It also explains rather low water vapor permeability of the material - 0.021 mg/(m- hour-Pa).

  12. Lattice Boltzmann modelling of intrinsic permeability

    CERN Document Server

    Li, Jun; Wu, Lei; Zhang, Yonghao

    2016-01-01

    Lattice Boltzmann method (LBM) has been applied to predict flow properties of porous media including intrinsic permeability, where it is implicitly assumed that the LBM is equivalent to the incompressible (or near incompressible) Navier-Stokes equation. However, in LBM simulations, high-order moments, which are completely neglected in the Navier-Stokes equation, are still available through particle distribution functions. To ensure that the LBM simulation is correctly working at the Navier-Stokes hydrodynamic level, the high-order moments have to be negligible. This requires that the Knudsen number (Kn) is small so that rarefaction effect can be ignored. In this technical note, we elaborate this issue in LBM modelling of porous media flows, which is particularly important for gas flows in ultra-tight media.

  13. Cadmium substituted high permeability lithium ferrite

    Indian Academy of Sciences (India)

    S S Bellad; S C Watawe; A M Shaikh; B K Chougule

    2000-04-01

    Polycrystalline Li0.5–/2 Cd Fe2.5–/2O4 ferrites where = 0, 0.1, 0.2, 0.3, 0.4, 0.5 and 0.6 were prepared by a double sintering ceramic technique and characterized by X-ray diffraction and scanning electron microscopy (SEM). The lattice parameter is found to increase monotonically with the cadmium content. It is explained in terms of the sizes of component ions. The grain size of the samples increases up to = 0.3 and then it decreases for higher values of . A similar trend is observed in the variation of Ms with Cd2+ content. The initial permeability () is however found to increase continuously with . The increase in is attributed to decrease of anisotropy constant K1 and higher grain size of the samples.

  14. Nitric oxide turnover in permeable river sediment

    DEFF Research Database (Denmark)

    Schreiber, Frank; Stief, Peter; Kuypers, Marcel M M;

    2014-01-01

    We measured nitric oxide (NO) microprofiles in relation to oxygen (O2) and all major dissolved N-species (ammonium, nitrate, nitrite, and nitrous oxide [N2O]) in a permeable, freshwater sediment (River Weser, Germany). NO reaches peak concentrations of 0.13 μmol L-1 in the oxic zone and is consumed...... in the oxic-anoxic transition zone. Apparently, NO is produced by ammonia oxidizers under oxic conditions and consumed by denitrification under microoxic conditions. Experimental percolation of sediment cores with aerated surface water resulted in an initial rate of NO production that was 12 times higher than...... the net NO production rate in steady state. This initial NO production rate is in the same range as the net ammonia oxidation rate, indicating that NO is transiently the main product of ammonia oxidizers. Stable isotope labeling experiments with the 15N-labeled chemical NO donor S...

  15. Parallel artificial membrane permeability assay for blood-brain permeability determination of illicit drugs and synthetic analogues.

    Science.gov (United States)

    Clemons, Kristina; Kretsch, Amanda; Verbeck, Guido

    2014-09-01

    With the number of designer drugs on the streets rampantly on the rise, it's becoming more and more important to be able to rapidly characterize them in a biologically relevant way. Using a parallel artificial membrane permeability assay (PAMPA) to assess the blood brain barrier permeability has shown to be a high throughput way to compare new drugs with currently controlled substances via their effective permeability values. This combined with direct infusion electrospray ionization-mass spectrometry creates a rapid technique for characterization of new designer drugs. PAMPA has successfully determined the effective permeabilities of cocaine, methamphetamine, heroin, MDMA, and several tryptamine derivatives.

  16. Back diffusion from thin low permeability zones.

    Science.gov (United States)

    Yang, Minjune; Annable, Michael D; Jawitz, James W

    2015-01-06

    Aquitards can serve as long-term contaminant sources to aquifers when contaminant mass diffuses from the aquitard following aquifer source mass depletion. This study describes analytical and experimental approaches to understand reactive and nonreactive solute transport in a thin aquitard bounded by an adjacent aquifer. A series of well-controlled laboratory experiments were conducted in a two-dimensional flow chamber to quantify solute diffusion from a high-permeability sand into and subsequently out of kaolinite clay layers of vertical thickness 15 mm, 20 mm, and 60 mm. One-dimensional analytical solutions were developed for diffusion in a finite aquitard with mass exchange with an adjacent aquifer using the method of images. The analytical solutions showed very good agreement with measured breakthrough curves and aquitard concentration distributions measured in situ by light reflection visualization. Solutes with low retardation accumulated more stored mass with greater penetration distance in the aquitard compared to high-retardation solutes. However, because the duration of aquitard mass release was much longer, high-retardation solutes have a greater long-term back diffusion risk. The error associated with applying a semi-infinite domain analytical solution to a finite diffusion domain increases as a function of the system relative diffusion length scale, suggesting that the solutions using image sources should be applied in cases with rapid solute diffusion and/or thin clay layers. The solutions presented here can be extended to multilayer aquifer/low-permeability systems to assess the significance of back diffusion from thin layers.

  17. Turbulent Hyporheic Exchange in Permeable Sediments

    Science.gov (United States)

    Roche, K. R.; Aubeneau, A. F.; Li, A.; Packman, A. I.

    2015-12-01

    Solute delivery from the water column into a streambed strongly influences metabolism in rivers. Current hydrological models simplify surface-subsurface (hyporheic) exchange by treating each domain separately, constraining turbulent flows to the water column. Studies have shown, however, that turbulence penetrates into permeable sediments. Evidence is lacking for how this highly coupled flow regime influences hyporheic exchange. We characterized the dynamics of turbulent exchange between surface and porewaters in a 2.5 m recirculating flume. The channel was packed with 3.8 cm PVC spheres to form a coarse gravel bed, with a total depth of 21 cm. We implanted microsensors onto an array of spheres to measure in situsalt concentrations within the streambed. Water was recirculated in the channel, and concentrated salt solution was continuously injected upstream of the sensor array. We observed solute exchange increased with free-stream Reynolds number and decreased with depth in the sediment bed. Mass of injected solute remaining in the bed decreased rapidly in all cases, with only 10-30% of mass recovered 50 cm downstream of the injection point at Re = 25,000. We observed high-frequency (1-10 Hz) concentration fluctuations at bed depths of at least 4.75 cm, and sporadic low-frequency fluctuations at depths of 12.5 cm. Spectral analysis revealed increased filtering of high frequencies with depth. We used particle-tracking simulations to fit depth-dependent turbulent diffusion profiles to experimental results. These results demonstrate that free-stream turbulence impacts hyporheic mixing deep into permeable streambeds, and mixing is strongly influenced by the coupled surface-subsurface flow field.

  18. Permeability of Dental Adhesives - A SEM Assessment.

    Science.gov (United States)

    Malacarne-Zanon, Juliana; de Andrade E Silva, Safira M; Wang, Linda; de Goes, Mario F; Martins, Adriano Luis; Narvaes-Romani, Eliene O; Anido-Anido, Andrea; Carrilho, Marcela R O

    2010-10-01

    To morphologically evaluate the permeability of different commercial dental adhesives using scanning electron microscopy. SEVEN ADHESIVE SYSTEMS WERE EVALUATED: one three-step system (Scotchbond Multi-Purpose - MP); one two-step self-etching primer system (Clearfil SE Bond - SE); three two-step etch-and-rinse systems (Single Bond 2 - SB; Excite - EX; One-Step - OS); and two single-step self-etching adhesives (Adper Prompt - AP; One-Up Bond F - OU). The mixture of primer and bond agents of the Clearfil SE Bond system (SE-PB) was also tested. The adhesives were poured into a brass mold (5.8 mm x 0.8 mm) and light-cured for 80 s at 650 mW/cm2. After a 24 h desiccation process, the specimens were immersed in a 50% ammoniac silver nitrate solution for tracer permeation. Afterwards, they were sectioned in ultra-fine slices, carbon-coated, and analyzed under backscattered electrons in a scanning electron microscopy. MP and SE showed slight and superficial tracer permeation. In EX, SB, and OS, permeation extended beyond the inner superficies of the specimens. SE-PB did not mix well, and most of the tracer was precipitated into the primer agent. In AP and OU, "water-trees" were observed all over the specimens. Different materials showed distinct permeability in aqueous solution. The extent of tracer permeation varied according to the composition of each material and it was more evident in the more hydrophilic and solvated ones.

  19. Permeability of alkaline magmas: a study from Campi Flegrei, Italy

    Science.gov (United States)

    Polacci, M.; Bouvet de Maissoneuve, C.; Giordano, D.; Piochi, M.; Degruyter, W.; Bachmann, O.; Mancini, L.

    2012-04-01

    Knowledge of permeability is of paramount importance for understanding the evolution of magma degassing during pre-, syn- and post-eruptive volcanic processes. Most permeability estimates existing to date refer to magmas of calc-alkaline compositions. We report here the preliminary results of permeability measurements performed on alkali-trachyte products erupted from the Campanian Ignimbrite (CI) and Monte Nuovo (MTN), two explosive eruptions from Campi Flegrei (CF), an active, hazardous caldera west of Naples, Southern Italy. Darcian (viscous) permeability spans a wide range between 10^-11 and 10^-14 m^2. We observe that the most permeable samples are the scoria clasts from the upper units of MTN; pumice samples from the Breccia Museo facies of CI are instead the least permeable. Non-Darcian (inertial) permeability follows the same trend as Darcian permeability. The first implication of this study is that porosity in alkaline as well as calc-alkaline magmas does not exert a first order control on permeability (e.g. the MTN samples are the most permeable but not the most porous). Second, sample geometry exhibits permeability anisotropy (higher permeability in the direction of vesicle elongation), suggesting stronger degassing in the vertical direction in the conduit. In addition, inertial effects are higher across the sample. As inertial effects are potentially generated by tortuosity (or tortuous vesicle paths), tortuosity is likely higher horizontally than vertically in the conduit. Finally, the measured CF permeability values overlap with those of rhyolitic pumice clasts from the Kos Plateau Tuff (Bouvet de Maisonneuve et al., 2009), together with CI one of the major Quaternary explosive eruptions of the Mediterranean region. This indicates that gas flow is strongly controlled by the geometry of the porous media, which is generated by the bubble dynamics during magma ascent. Therefore, permeability will depend on composition through the rheological properties

  20. Dynamics of Escherichia coli chromosome segregation during multifork replication.

    Science.gov (United States)

    Nielsen, Henrik J; Youngren, Brenda; Hansen, Flemming G; Austin, Stuart

    2007-12-01

    Slowly growing Escherichia coli cells have a simple cell cycle, with replication and progressive segregation of the chromosome completed before cell division. In rapidly growing cells, initiation of replication occurs before the previous replication rounds are complete. At cell division, the chromosomes contain multiple replication forks and must be segregated while this complex pattern of replication is still ongoing. Here, we show that replication and segregation continue in step, starting at the origin and progressing to the replication terminus. Thus, early-replicated markers on the multiple-branched chromosomes continue to separate soon after replication to form separate protonucleoids, even though they are not segregated into different daughter cells until later generations. The segregation pattern follows the pattern of chromosome replication and does not follow the cell division cycle. No extensive cohesion of sister DNA regions was seen at any growth rate. We conclude that segregation is driven by the progression of the replication forks.

  1. Optical tweezers reveal how proteins alter replication

    Science.gov (United States)

    Chaurasiya, Kathy

    Single molecule force spectroscopy is a powerful method that explores the DNA interaction properties of proteins involved in a wide range of fundamental biological processes such as DNA replication, transcription, and repair. We use optical tweezers to capture and stretch a single DNA molecule in the presence of proteins that bind DNA and alter its mechanical properties. We quantitatively characterize the DNA binding mechanisms of proteins in order to provide a detailed understanding of their function. In this work, we focus on proteins involved in replication of Escherichia coli (E. coli ), endogenous eukaryotic retrotransposons Ty3 and LINE-1, and human immunodeficiency virus (HIV). DNA polymerases replicate the entire genome of the cell, and bind both double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA) during DNA replication. The replicative DNA polymerase in the widely-studied model system E. coli is the DNA polymerase III subunit alpha (DNA pol III alpha). We use optical tweezers to determine that UmuD, a protein that regulates bacterial mutagenesis through its interactions with DNA polymerases, specifically disrupts alpha binding to ssDNA. This suggests that UmuD removes alpha from its ssDNA template to allow DNA repair proteins access to the damaged DNA, and to facilitate exchange of the replicative polymerase for an error-prone translesion synthesis (TLS) polymerase that inserts nucleotides opposite the lesions, so that bacterial DNA replication may proceed. This work demonstrates a biophysical mechanism by which E. coli cells tolerate DNA damage. Retroviruses and retrotransposons reproduce by copying their RNA genome into the nuclear DNA of their eukaryotic hosts. Retroelements encode proteins called nucleic acid chaperones, which rearrange nucleic acid secondary structure and are therefore required for successful replication. The chaperone activity of these proteins requires strong binding affinity for both single- and double-stranded nucleic

  2. Self-replication with magnetic dipolar colloids.

    Science.gov (United States)

    Dempster, Joshua M; Zhang, Rui; Olvera de la Cruz, Monica

    2015-10-01

    Colloidal self-replication represents an exciting research frontier in soft matter physics. Currently, all reported self-replication schemes involve coating colloidal particles with stimuli-responsive molecules to allow switchable interactions. In this paper, we introduce a scheme using ferromagnetic dipolar colloids and preprogrammed external magnetic fields to create an autonomous self-replication system. Interparticle dipole-dipole forces and periodically varying weak-strong magnetic fields cooperate to drive colloid monomers from the solute onto templates, bind them into replicas, and dissolve template complexes. We present three general design principles for autonomous linear replicators, derived from a focused study of a minimalist sphere-dimer magnetic system in which single binding sites allow formation of dimeric templates. We show via statistical models and computer simulations that our system exhibits nonlinear growth of templates and produces nearly exponential growth (low error rate) upon adding an optimized competing electrostatic potential. We devise experimental strategies for constructing the required magnetic colloids based on documented laboratory techniques. We also present qualitative ideas about building more complex self-replicating structures utilizing magnetic colloids.

  3. A Self-Replicating Ligase Ribozyme

    Science.gov (United States)

    Paul, Natasha; Joyce, Gerald F.

    2002-01-01

    A self-replicating molecule directs the covalent assembly of component molecules to form a product that is of identical composition to the parent. When the newly formed product also is able to direct the assembly of product molecules, the self-replicating system can be termed autocatalytic. A self-replicating system was developed based on a ribozyme that catalyzes the assembly of additional copies of Itself through an RNA-catalyzed RNA ligation reaction. The R3C ligase ribozyme was redesigned so that it would ligate two substrates to generate an exact copy of itself, which then would behave in a similar manner. This self-replicating system depends on the catalytic nature of the RNA for the generation of copies. A linear dependence was observed between the initial rate of formation of new copies and the starting concentration of ribozyme, consistent with exponential growth. The autocatalytic rate constant was 0.011 per min, whereas the initial rate of reaction in the absence of pre-existing ribozyme was only 3.3 x 10(exp -11) M per min. Exponential growth was limited, however, because newly formed ribozyme molecules had greater difficulty forming a productive complex with the two substrates. Further optimization of the system may lead to the sustained exponential growth of ribozymes that undergo self-replication.

  4. Spacetime replication of continuous variable quantum information

    Science.gov (United States)

    Hayden, Patrick; Nezami, Sepehr; Salton, Grant; Sanders, Barry C.

    2016-08-01

    The theory of relativity requires that no information travel faster than light, whereas the unitarity of quantum mechanics ensures that quantum information cannot be cloned. These conditions provide the basic constraints that appear in information replication tasks, which formalize aspects of the behavior of information in relativistic quantum mechanics. In this article, we provide continuous variable (CV) strategies for spacetime quantum information replication that are directly amenable to optical or mechanical implementation. We use a new class of homologically constructed CV quantum error correcting codes to provide efficient solutions for the general case of information replication. As compared to schemes encoding qubits, our CV solution requires half as many shares per encoded system. We also provide an optimized five-mode strategy for replicating quantum information in a particular configuration of four spacetime regions designed not to be reducible to previously performed experiments. For this optimized strategy, we provide detailed encoding and decoding procedures using standard optical apparatus and calculate the recovery fidelity when finite squeezing is used. As such we provide a scheme for experimentally realizing quantum information replication using quantum optics.

  5. COPI is required for enterovirus 71 replication.

    Directory of Open Access Journals (Sweden)

    Jianmin Wang

    Full Text Available Enterovirus 71 (EV71, a member of the Picornaviridae family, is found in Asian countries where it causes a wide range of human diseases. No effective therapy is available for the treatment of these infections. Picornaviruses undergo RNA replication in association with membranes of infected cells. COPI and COPII have been shown to be involved in the formation of picornavirus-induced vesicles. Replication of several picornaviruses, including poliovirus and Echovirus 11 (EV11, is dependent on COPI or COPII. Here, we report that COPI, but not COPII, is required for EV71 replication. Replication of EV71 was inhibited by brefeldin A and golgicide A, inhibitors of COPI activity. Furthermore, we found EV71 2C protein interacted with COPI subunits by co-immunoprecipitation and GST pull-down assay, indicating that COPI coatomer might be directed to the viral replication complex through viral 2C protein. Additionally, because the pathway is conserved among different species of enteroviruses, it may represent a novel target for antiviral therapies.

  6. Extremal dynamics in random replicator ecosystems

    Energy Technology Data Exchange (ETDEWEB)

    Kärenlampi, Petri P., E-mail: petri.karenlampi@uef.fi

    2015-10-02

    The seminal numerical experiment by Bak and Sneppen (BS) is repeated, along with computations with replicator models, including a greater amount of features. Both types of models do self-organize, and do obey power-law scaling for the size distribution of activity cycles. However species extinction within the replicator models interferes with the BS self-organized critical (SOC) activity. Speciation–extinction dynamics ruins any stationary state which might contain a steady size distribution of activity cycles. The BS-type activity appears as a dissimilar phenomenon in comparison to speciation–extinction dynamics in the replicator system. No criticality is found from the speciation–extinction dynamics. Neither are speciations and extinctions in real biological macroevolution known to contain any diverging distributions, or self-organization towards any critical state. Consequently, biological macroevolution probably is not a self-organized critical phenomenon. - Highlights: • Extremal Dynamics organizes random replicator ecosystems to two phases in fitness space. • Replicator systems show power-law scaling of activity. • Species extinction interferes with Bak–Sneppen type mutation activity. • Speciation–extinction dynamics does not show any critical phase transition. • Biological macroevolution probably is not a self-organized critical phenomenon.

  7. Chromatin Structure and Replication Origins: Determinants Of Chromosome Replication And Nuclear Organization

    OpenAIRE

    Smith, Owen K.; Aladjem, Mirit I.

    2014-01-01

    The DNA replication program is, in part, determined by the epigenetic landscape that governs local chromosome architecture and directs chromosome duplication. Replication must coordinate with other biochemical processes occurring concomitantly on chromatin, such as transcription and remodeling, to insure accurate duplication of both genetic and epigenetic features and to preserve genomic stability. The importance of genome architecture and chromatin looping in coordinating cellular processes ...

  8. Permeability of crust is key to crispness retention

    NARCIS (Netherlands)

    Hirte, A.; Hamer, R.J.; Meinders, M.B.J.; Primo-Martin, C.

    2010-01-01

    Bread loses crispness rapidly after baking because water originating from the wet crumb accumulates in the dry crust. This water accumulation might be increased by the dense and low permeable character of the bread crust. Our objective was to investigate the influence of permeability of the crust on

  9. Permeability dependence of streaming potential coefficient in porous media

    NARCIS (Netherlands)

    L.D. Thanh; R. Sprik

    2015-01-01

    In theory, the streaming potential coefficient depends not only on the zeta potential but also on the permeability of the rocks that partially determines the surface conductivity of the rocks. However, in practice, it is hard to show the permeability dependence of streaming potential coefficients be

  10. Permeability dependence of streaming potential coefficient in porous media

    NARCIS (Netherlands)

    Thanh, L.D.; Sprik, R.

    2015-01-01

    In theory, the streaming potential coefficient depends not only on the zeta potential but also on the permeability of the rocks that partially determines the surface conductivity of the rocks. However, in practice, it is hard to show the permeability dependence of streaming potential coefficients

  11. Duration of ultrasound-mediated enhanced plasma membrane permeability

    NARCIS (Netherlands)

    Lammertink, Bart; Deckers, Roel; Storm, Gert; Moonen, Chrit; Bos, Clemens

    2015-01-01

    Ultrasound (US) induced cavitation can be used to enhance the intracellular delivery of drugs by transiently increasing the cell membrane permeability. The duration of this increased permeability, termed temporal window, has not been fully elucidated. In this study, the temporal window was investiga

  12. Unsaturated and Saturated Permeabilities of Fiber Reinforcement: Critics and Suggestions

    Directory of Open Access Journals (Sweden)

    Chung Hae ePARK

    2015-04-01

    Full Text Available In general, permeability measurement results show a strong scattering according to the measurement method, the type of test fluid and the fluid injection condition, even though permeability is regarded as a unique property of porous medium. In particular, the discrepancy between the unsaturated and saturated permeabilities for the same fabric has been widely reported. In the literature, relative permeability has been adopted to model the unsaturated flow. This approach has some limits in the modeling of double-scale porosity medium. We address this issue of permeability measurement by rigorously examining the mass conservation condition. Finally, we identify that the pressure gradient is non-linear with positive curvature in the unsaturated flow and a misinterpretation of pressure gradient is the main reason for the difference between the saturated and unsaturated permeabilities of the same fiber reinforcement. We propose to use a fixed value of permeability and to modify the mass conservation equation if there are air voids which are entrapped inside the fiber tow. Finally, we also suggest some guidelines and future perspectives to obtain more consistent permeability measurement results.

  13. Selective permeability of PVA membranes. I - Radiation-crosslinked membranes

    Science.gov (United States)

    Katz, M. G.; Wydeven, T., Jr.

    1981-01-01

    The water and salt transport properties of ionizing radiation crosslinked poly(vinyl alcohol) (PVA) membranes were investigated. The studied membranes showed high permeabilities and low selectivities for both water and salt. The results were found to be in accord with a modified solution-diffusion model for transport across the membranes, in which pressure-dependent permeability coefficients are employed.

  14. Selective Permeability of PVA Membranes. I: Radiation-Crosslinked Membranes

    Science.gov (United States)

    Katz, Moshe G.; Wydeven, Theodore, Jr.

    1981-01-01

    The water and salt transport properties of ionizing radiation crosslinked poly(vinyl alcohol) (PVA) membranes were investigated. The studied membranes showed high permeabilities and low selectivities for both water and salt. The results were found to be in accord with a modified solution-diffusion model for transport across the membranes, in which pressure-dependent permeability coefficients are employed.

  15. Recovery of Porosity and Permeability for High Plasticity Clays

    DEFF Research Database (Denmark)

    Krogsbøll, Anette; Foged, Niels Nielsen

    Clays, which have been loaded to a high stress level, will under certain conditions keep low porosity and permeability due to the high degree of compression. In some situations it seems that porosity and permeability will recover to a very high extent when the clay is unloaded. This seems...... the clay will expand to an even higher porosity....

  16. Duration of ultrasound-mediated enhanced plasma membrane permeability

    NARCIS (Netherlands)

    Lammertink, Bart; Deckers, Roel; Storm, Gerrit; Moonen, Chrit; Bos, Clemens

    2015-01-01

    Ultrasound (US) induced cavitation can be used to enhance the intracellular delivery of drugs by transiently increasing the cell membrane permeability. The duration of this increased permeability, termed temporal window, has not been fully elucidated. In this study, the temporal window was

  17. Permeability of crust is key to crispness retention

    NARCIS (Netherlands)

    Hirte, A.; Hamer, R.J.; Meinders, M.B.J.; Primo-Martin, C.

    2010-01-01

    Bread loses crispness rapidly after baking because water originating from the wet crumb accumulates in the dry crust. This water accumulation might be increased by the dense and low permeable character of the bread crust. Our objective was to investigate the influence of permeability of the crust on

  18. Nitrogen Transformations in Three Types of Permeable Pavement

    Science.gov (United States)

    In 2009, USEPA constructed a 0.4-ha (1-ac) parking lot at the Edison Environmental Center in Edison, NJ, that incorporated three different permeable pavement types - permeable interlocking concrete pavers (PICP), pervious concrete (PC), and porous asphalt (PA). The driving lanes...

  19. Unsaturated and Saturated Permeabilities of Fiber Reinforcement: Critics and Suggestions

    Science.gov (United States)

    Park, Chung Hae; Krawczak, Patricia

    2015-04-01

    In general, permeability measurement results show a strong scattering according to the measurement method, the type of test fluid and the fluid injection condition, even though permeability is regarded as a unique property of porous medium. In particular, the discrepancy between the unsaturated and saturated permeabilities for the same fabric has been widely reported. In the literature, relative permeability has been adopted to model the unsaturated flow. This approach has some limits in the modeling of double-scale porosity medium. We address this issue of permeability measurement by rigorously examining the mass conservation condition. Finally, we identify that the pressure gradient is non-linear with positive curvature in the unsaturated flow and a misinterpretation of pressure gradient is the main reason for the difference between the saturated and unsaturated permeabilities of the same fiber reinforcement. We propose to use a fixed value of permeability and to modify the mass conservation equation if there are air voids which are entrapped inside the fiber tow. Finally, we also suggest some guidelines and future perspectives to obtain more consistent permeability measurement results.

  20. Formation and liquid permeability of dense colloidal cube packings

    NARCIS (Netherlands)

    Castillo, Sonja I R; Thies-Weesie, Dominique M E; Philipse, Albert P.

    2015-01-01

    The liquid permeability of dense random packings of cubic colloids with rounded corners is studied for solid hematite cubes and hollow microporous silica cubes. The permeabilities of these two types of packings are similar, confirming that the micropores in the silica shell of the hollow cubes do

  1. 21 CFR 876.5860 - High permeability hemodialysis system.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false High permeability hemodialysis system. 876.5860... hemodialysis system. (a) Identification. A high permeability hemodialysis system is a device intended for use... toxemic conditions by performing such therapies as hemodialysis, hemofiltration, hemoconcentration,...

  2. Content replication and placement in mobile networks

    CERN Document Server

    La, Chi-Anh; Casetti, Claudio; Chiasserini, Carla-Fabiana; Fiore, Marco

    2011-01-01

    Performance and reliability of content access in mobile networks is conditioned by the number and location of content replicas deployed at the network nodes. Location theory has been the traditional, centralized approach to study content replication: computing the number and placement of replicas in a static network can be cast as a facility location problem. The endeavor of this work is to design a practical solution to the above joint optimization problem that is suitable for mobile wireless environments. We thus seek a replication algorithm that is lightweight, distributed, and reactive to network dynamics. We devise a solution that lets nodes (i) share the burden of storing and providing content, so as to achieve load balancing, and (ii) autonomously decide whether to replicate or drop the information, so as to adapt the content availability to dynamic demands and time-varying network topologies. We evaluate our mechanism through simulation, by exploring a wide range of settings, including different node ...

  3. Evolution of Database Replication Technologies for WLCG

    CERN Document Server

    Baranowski, Zbigniew; Blaszczyk, Marcin; Dimitrov, Gancho; Canali, Luca

    2015-01-01

    In this article we summarize several years of experience on database replication technologies used at WLCG and we provide a short review of the available Oracle technologies and their key characteristics. One of the notable changes and improvement in this area in recent past has been the introduction of Oracle GoldenGate as a replacement of Oracle Streams. We report in this article on the preparation and later upgrades for remote replication done in collaboration with ATLAS and Tier 1 database administrators, including the experience from running Oracle GoldenGate in production. Moreover, we report on another key technology in this area: Oracle Active Data Guard which has been adopted in several of the mission critical use cases for database replication between online and offline databases for the LHC experiments.

  4. Replicating Cardiovascular Condition-Birth Month Associations

    Science.gov (United States)

    Li, Li; Boland, Mary Regina; Miotto, Riccardo; Tatonetti, Nicholas P.; Dudley, Joel T.

    2016-01-01

    Independent replication is vital for study findings drawn from Electronic Health Records (EHR). This replication study evaluates the relationship between seasonal effects at birth and lifetime cardiovascular condition risk. We performed a Season-wide Association Study on 1,169,599 patients from Mount Sinai Hospital (MSH) to compute phenome-wide associations between birth month and CVD. We then evaluated if seasonal patterns found at MSH matched those reported at Columbia University Medical Center. Coronary arteriosclerosis, essential hypertension, angina, and pre-infarction syndrome passed phenome-wide significance and their seasonal patterns matched those previously reported. Atrial fibrillation, cardiomyopathy, and chronic myocardial ischemia had consistent patterns but were not phenome-wide significant. We confirm that CVD risk peaks for those born in the late winter/early spring among the evaluated patient populations. The replication findings bolster evidence for a seasonal birth month effect in CVD. Further study is required to identify the environmental and developmental mechanisms. PMID:27624541

  5. Synchronization of DNA array replication kinetics

    Science.gov (United States)

    Manturov, Alexey O.; Grigoryev, Anton V.

    2016-04-01

    In the present work we discuss the features of the DNA replication kinetics at the case of multiplicity of simultaneously elongated DNA fragments. The interaction between replicated DNA fragments is carried out by free protons that appears at the every nucleotide attachment at the free end of elongated DNA fragment. So there is feedback between free protons concentration and DNA-polymerase activity that appears as elongation rate dependence. We develop the numerical model based on a cellular automaton, which can simulate the elongation stage (growth of DNA strands) for DNA elongation process with conditions pointed above and we study the possibility of the DNA polymerases movement synchronization. The results obtained numerically can be useful for DNA polymerase movement detection and visualization of the elongation process in the case of massive DNA replication, eg, under PCR condition or for DNA "sequencing by synthesis" sequencing devices evaluation.

  6. GFLV replication in electroporated grapevine protoplasts.

    Science.gov (United States)

    Valat; Toutain; Courtois; Gaire; Decout; Pinck; Mauro; Burrus

    2000-06-29

    Grapevine fanleaf virus (GFLV), responsible for the economically important court-noué disease, is exclusively transmitted to its natural host in the vineyards through Xiphinema nematodes. We have developed direct inoculation of GFLV into grapevine through protoplast electroporation. Protoplasts were isolated from mesophyll of in vitro-grown plants and from embryogenic cell suspensions. Permeation conditions were determined by monitoring calcein uptake. Low salt poration medium was selected. Electrical conditions leading to strong transient gene expression were also tested for GFLV inoculation (isolate F13). GFLV replication was detected with either virus particles (2 µg) or viral RNA (10 ng) in both protoplast populations, as shown by anti-P38 Western blotting. Direct inoculation and replication were also observed with Arabis mosaic virus (ArMV), a closely related nepovirus, as well as with another GFLV isolate. These results will be valuable in grapevine biotechnology, for GFLV replication studies, transgenic plant screening for GFLV resistance, and biorisk evaluation.

  7. Suppression of Adenovirus Replication by Cardiotonic Steroids.

    Science.gov (United States)

    Grosso, Filomena; Stoilov, Peter; Lingwood, Clifford; Brown, Martha; Cochrane, Alan

    2017-02-01

    The dependence of adenovirus on the host pre-RNA splicing machinery for expression of its complete genome potentially makes it vulnerable to modulators of RNA splicing, such as digoxin and digitoxin. Both drugs reduced the yields of four human adenoviruses (HAdV-A31, -B35, and -C5 and a species D conjunctivitis isolate) by at least 2 to 3 logs by affecting one or more steps needed for genome replication. Immediate early E1A protein levels are unaffected by the drugs, but synthesis of the delayed protein E4orf6 and the major late capsid protein hexon is compromised. Quantitative reverse transcription-PCR (qRT-PCR) analyses revealed that both drugs altered E1A RNA splicing (favoring the production of 13S over 12S RNA) early in infection and partially blocked the transition from 12S and 13S to 9S RNA at late stages of virus replication. Expression of multiple late viral protein mRNAs was lost in the presence of either drug, consistent with the observed block in viral DNA replication. The antiviral effect was dependent on the continued presence of the drug and was rapidly reversible. RIDK34, a derivative of convallotoxin, although having more potent antiviral activity, did not show an improved selectivity index. All three drugs reduced metabolic activity to some degree without evidence of cell death. By blocking adenovirus replication at one or more steps beyond the onset of E1A expression and prior to genome replication, digoxin and digitoxin show potential as antiviral agents for treatment of serious adenovirus infections. Furthermore, understanding the mechanism(s) by which digoxin and digitoxin inhibit adenovirus replication will guide the development of novel antiviral therapies.

  8. Chloride permeability of concrete under static and repeated compressive loading

    Energy Technology Data Exchange (ETDEWEB)

    Saito, Mitsuru; Ishimori, Hiroshi [Kanazawa Inst. of Technology, Ishikawa (Japan)

    1995-05-01

    The chloride permeability of normal weight concrete subjected to static and repeated compressive loading was evaluated by using the AASHTO T277 test method. The results of concrete under static loading showed that the application of loads up to 90% of the ultimate strength had little effect on the chloride permeability. It was found from the results of concrete under repeated loading that load repetitions at the maximum stress levels of 60% or more caused the chloride permeability to increase significantly. The test results also indicated that the chloride permeability of concrete subjected to static and repeated loading increased at an increasing rate with its residual strain. The relation between the chloride permeability obtained and the cracking behavior of concrete previously reported was discussed.

  9. Two-phase relative permeability models in reservoir engineering calculations

    Energy Technology Data Exchange (ETDEWEB)

    Siddiqui, S.; Hicks, P.J.; Ertekin, T.

    1999-01-15

    A comparison of ten two-phase relative permeability models is conducted using experimental, semianalytical and numerical approaches. Model predicted relative permeabilities are compared with data from 12 steady-state experiments on Berea and Brown sandstones using combinations of three white mineral oils and 2% CaCl1 brine. The model results are compared against the experimental data using three different criteria. The models are found to predict the relative permeability to oil, relative permeability to water and fractional flow of water with varying degrees of success. Relative permeability data from four of the experimental runs are used to predict the displacement performance under Buckley-Leverett conditions and the results are compared against those predicted by the models. Finally, waterflooding performances predicted by the models are analyzed at three different viscosity ratios using a two-dimensional, two-phase numerical reservoir simulator. (author)

  10. Permeability characterization of polymer matrix composites by RTM/VARTM

    Science.gov (United States)

    Naik, N. K.; Sirisha, M.; Inani, A.

    2014-02-01

    Cost effective manufacturing of high performance polymer matrix composite structures is an important consideration for the growth of its use. Resin transfer moulding (RTM) and vacuum assisted resin transfer moulding (VARTM) are the efficient processes for the cost effective manufacturing. These processes involve transfer of resin from the tank into the reinforcing preform loaded into a closed mould. Resin flow within the preform and reinforcement wetting can be characterized using the permeability properties. Different reinforcement and resin properties and process parameters affecting the permeability are discussed based on state of art literature review covering experimental studies. General theory for the determination of permeability is presented. Based on the literature review, permeability values for different reinforcement architecture, resin and processing conditions are presented. Further, possible sources of error during experimental determination of permeability and issues involved with reproducibility are discussed.

  11. Permeability of mono- and bi-dispersed porous media

    Directory of Open Access Journals (Sweden)

    Kim S.J.

    2013-04-01

    Full Text Available In this study, the permeability of mono- and bi-dispersed porous media is considered. The effects of the particle size distribution and the packing structure of particles on the permeability are investigated experimentally and analytically. Both experimental and analytic results suggest that the particlesize distribution is close to the log-normal distribution, and the permeability of the mono-dispersed porous media quasi-linearly decreases as the range of the particle size distribution increases. On the other hand, the effect of packing structure of particles on the permeability is shown to be negligible.The permeability of the bidispersed porous media quasi-linearly decreases as the range of cluster size increases, and nearly independent of the particle size distribution. The present model is valid over the range of parameters typically found in heat transfer applications.

  12. Stochastic back analysis of permeability coefficient using generalized Bayesian method

    Institute of Scientific and Technical Information of China (English)

    Zheng Guilan; Wang Yuan; Wang Fei; Yang Jian

    2008-01-01

    Owing to the fact that the conventional deterministic back analysis of the permeability coefficient cannot reflect the uncertainties of parameters, including the hydraulic head at the boundary, the permeability coefficient and measured hydraulic head, a stochastic back analysis taking consideration of uncertainties of parameters was performed using the generalized Bayesian method. Based on the stochastic finite element method (SFEM) for a seepage field, the variable metric algorithm and the generalized Bayesian method, formulas for stochastic back analysis of the permeability coefficient were derived. A case study of seepage analysis of a sluice foundation was performed to illustrate the proposed method. The results indicate that, with the generalized Bayesian method that considers the uncertainties of measured hydraulic head, the permeability coefficient and the hydraulic head at the boundary, both the mean and standard deviation of the permeability coefficient can be obtained and the standard deviation is less than that obtained by the conventional Bayesian method. Therefore, the present method is valid and applicable.

  13. The replication of expansive production knowledge

    DEFF Research Database (Denmark)

    Wæhrens, Brian Vejrum; Yang, Cheng; Madsen, Erik Skov

    2012-01-01

    . Design/methodology/approach – Two case studies are introduced. Empirical data were collected over a period of two years based on interviews and participating observations. Findings – The findings show that (1) knowledge transfer within the replication of a production line is a stepwise expansive process......Purpose – With the aim to support offshore production line replication, this paper specifically aims to explore the use of templates and principles to transfer expansive productive knowledge embedded in a production line and understand the contingencies that influence the mix of these approaches...... and principles to transfer productive knowledge in a specific context, which, in this paper, is a production line....

  14. Chromatin challenges during DNA replication and repair

    DEFF Research Database (Denmark)

    Groth, Anja; Rocha, Walter; Verreault, Alain

    2007-01-01

    Inheritance and maintenance of the DNA sequence and its organization into chromatin are central for eukaryotic life. To orchestrate DNA-replication and -repair processes in the context of chromatin is a challenge, both in terms of accessibility and maintenance of chromatin organization. To meet...... the challenge of maintenance, cells have evolved efficient nucleosome-assembly pathways and chromatin-maturation mechanisms that reproduce chromatin organization in the wake of DNA replication and repair. The aim of this Review is to describe how these pathways operate and to highlight how the epigenetic...

  15. Involvement of Autophagy in Coronavirus Replication

    Directory of Open Access Journals (Sweden)

    Paul Britton

    2012-11-01

    Full Text Available Coronaviruses are single stranded, positive sense RNA viruses, which induce the rearrangement of cellular membranes upon infection of a host cell. This provides the virus with a platform for the assembly of viral replication complexes, improving efficiency of RNA synthesis. The membranes observed in coronavirus infected cells include double membrane vesicles. By nature of their double membrane, these vesicles resemble cellular autophagosomes, generated during the cellular autophagy pathway. In addition, coronavirus infection has been demonstrated to induce autophagy. Here we review current knowledge of coronavirus induced membrane rearrangements and the involvement of autophagy or autophagy protein microtubule associated protein 1B light chain 3 (LC3 in coronavirus replication.

  16. Replication, recombination, and repair: going for the gold.

    Science.gov (United States)

    Klein, Hannah L; Kreuzer, Kenneth N

    2002-03-01

    DNA recombination is now appreciated to be integral to DNA replication and cell survival. Recombination allows replication to successfully maneuver through the roadblocks of damaged or collapsed replication forks. The signals and controls that permit cells to transition between replication and recombination modes are now being identified.

  17. Direct visualization of replication dynamics in early zebrafish embryos.

    Science.gov (United States)

    Kuriya, Kenji; Higashiyama, Eriko; Avşar-Ban, Eriko; Okochi, Nanami; Hattori, Kaede; Ogata, Shin; Takebayashi, Shin-Ichiro; Ogata, Masato; Tamaru, Yutaka; Okumura, Katsuzumi

    2016-05-01

    We analyzed DNA replication in early zebrafish embryos. The replicating DNA of whole embryos was labeled with the thymidine analog 5-ethynyl-2'-deoxyuridine (EdU), and spatial regulation of replication sites was visualized in single embryo-derived cells. The results unveiled uncharacterized replication dynamics during zebrafish early embryogenesis.

  18. Permeability, storage and hydraulic diffusivity controlled by earthquakes

    Science.gov (United States)

    Brodsky, E. E.; Fulton, P. M.; Xue, L.

    2016-12-01

    Earthquakes can increase permeability in fractured rocks. In the farfield, such permeability increases are attributed to seismic waves and can last for months after the initial earthquake. Laboratory studies suggest that unclogging of fractures by the transient flow driven by seismic waves is a viable mechanism. These dynamic permeability increases may contribute to permeability enhancement in the seismic clouds accompanying hydraulic fracking. Permeability enhancement by seismic waves could potentially be engineered and the experiments suggest the process will be most effective at a preferred frequency. We have recently observed similar processes inside active fault zones after major earthquakes. A borehole observatory in the fault that generated the M9.0 2011 Tohoku earthquake reveals a sequence of temperature pulses during the secondary aftershock sequence of an M7.3 aftershock. The pulses are attributed to fluid advection by a flow through a zone of transiently increased permeability. Directly after the M7.3 earthquake, the newly damaged fault zone is highly susceptible to further permeability enhancement, but ultimately heals within a month and becomes no longer as sensitive. The observation suggests that the newly damaged fault zone is more prone to fluid pulsing than would be expected based on the long-term permeability structure. Even longer term healing is seen inside the fault zone of the 2008 M7.9 Wenchuan earthquake. The competition between damage and healing (or clogging and unclogging) results in dynamically controlled permeability, storage and hydraulic diffusivity. Recent measurements of in situ fault zone architecture at the 1-10 meter scale suggest that active fault zones often have hydraulic diffusivities near 10-2 m2/s. This uniformity is true even within the damage zone of the San Andreas fault where permeability and storage increases balance each other to achieve this value of diffusivity over a 400 m wide region. We speculate that fault zones

  19. Spatial regulation and organization of DNA replication within the nucleus.

    Science.gov (United States)

    Natsume, Toyoaki; Tanaka, Tomoyuki U

    2010-01-01

    Duplication of chromosomal DNA is a temporally and spatially regulated process. The timing of DNA replication initiation at various origins is highly coordinated; some origins fire early and others late during S phase. Moreover, inside the nuclei, the bulk of DNA replication is physically organized in replication factories, consisting of DNA polymerases and other replication proteins. In this review article, we discuss how DNA replication is organized and regulated spatially within the nucleus and how this spatial organization is linked to temporal regulation. We focus on DNA replication in budding yeast and fission yeast and, where applicable, compare yeast DNA replication with that in bacteria and metazoans.

  20. Regulation of eukaryotic DNA replication and nuclear structure

    Institute of Scientific and Technical Information of China (English)

    WUJIARUI

    1999-01-01

    In eukaryote,nuclear structure is a key component for the functions of eukaryotic cells.More and more evidences show that the nuclear structure plays important role in regulating DNA replication.The nuclear structure provides a physical barrier for the replication licensing,participates in the decision where DNA replication initiates,and organizes replication proteins as replication factory for DNA replication.Through these works,new concepts on the regulation of DNA replication have emerged,which will be discussed in this minireview.

  1. Extreme Rainfall Impacts in Fractured Permeable Catchments

    Science.gov (United States)

    Ireson, A. M.; Butler, A. P.

    2009-12-01

    Serious groundwater flooding events have occurred on Chalk catchments in both the UK and north west Europe in the last decade, causing substantial amounts of disruption and economic damage. These fractured, permeable catchments are characterized by low surface runoff, high baseflow indices and strongly attenuated streamflow hydrographs. They have a general resilience to drought and pluvial/fluvial flooding. The small pore size of the Chalk matrix (~ 1 µm) exerts a high suction, such that dynamic storage is primarily due to the fractures, and amounts to ~ 1% of the total volume. As a result, under sustained rainfall the water table can rise up to exceptional levels leading to surface water emergence from springs and valleys. Floodwater may slowly drain with the topography, or, in localized depressions, it may simply pond until the groundwater levels decline. In winter 2000/1, a sequence of individually unexceptional rainfall events over several months led to large scale flooding in the Pang catchment, Berkshire, UK. By contrast, an extreme rainfall event on 20th July 2007 in the same catchment caused a very rapid response at the water table, but due to the antecedent conditions did not lead to flooding. The objective of this study is to quantify how the water table in a fractured permeable catchment responds to different types of rainfall, and the implications of this for groundwater flooding. We make use of measurements from the Pang catchment, including: rainfall (tipping bucket gauges); actual evaporation (eddy flux correlation); soil water content (profile probes and neutron probes); near surface matric potential (tensiometers and equitensiometers); deep (>10m) matric potential (deep jacking tensiometers); and water table elevation (piezometers). Conventional treatment of recharge in Chalk aquifers considers a fixed bypass component of rainfall, normally 15%, to account for the role of the fractures. However, interpretation of the field data suggest three modes

  2. Assembly of Slx4 signaling complexes behind DNA replication forks.

    Science.gov (United States)

    Balint, Attila; Kim, TaeHyung; Gallo, David; Cussiol, Jose Renato; Bastos de Oliveira, Francisco M; Yimit, Askar; Ou, Jiongwen; Nakato, Ryuichiro; Gurevich, Alexey; Shirahige, Katsuhiko; Smolka, Marcus B; Zhang, Zhaolei; Brown, Grant W

    2015-08-13

    Obstructions to replication fork progression, referred to collectively as DNA replication stress, challenge genome stability. In Saccharomyces cerevisiae, cells lacking RTT107 or SLX4 show genome instability and sensitivity to DNA replication stress and are defective in the completion of DNA replication during recovery from replication stress. We demonstrate that Slx4 is recruited to chromatin behind stressed replication forks, in a region that is spatially distinct from that occupied by the replication machinery. Slx4 complex formation is nucleated by Mec1 phosphorylation of histone H2A, which is recognized by the constitutive Slx4 binding partner Rtt107. Slx4 is essential for recruiting the Mec1 activator Dpb11 behind stressed replication forks, and Slx4 complexes are important for full activity of Mec1. We propose that Slx4 complexes promote robust checkpoint signaling by Mec1 by stably recruiting Dpb11 within a discrete domain behind the replication fork, during DNA replication stress.

  3. Spatial regulation and organization of DNA replication within the nucleus

    OpenAIRE

    2009-01-01

    Duplication of chromosomal DNA is a temporally and spatially regulated process. The timing of DNA replication initiation at various origins is highly coordinated; some origins fire early and others late during S phase. Moreover, inside the nuclei, the bulk of DNA replication is physically organized in replication factories, consisting of DNA polymerases and other replication proteins. In this review article, we discuss how DNA replication is organized and regulated spatially within the nucleu...

  4. Replication of biotinylated human immunodeficiency viruses.

    Science.gov (United States)

    Belshan, Michael; Matthews, John M; Madson, Christian J

    2011-01-01

    Previous work demonstrated recently the adaptation of the Escherichia coli biotin ligase BirA - biotin acceptor sequence (BAS) labeling system to produce human immunodeficiency virus type 1 viruses with biotinylated integrase (NLXIN(B)) and matrix (NLXMA(B)) proteins (Belshan et al., 2009). This report describes the construction of an HIV permissive cell line stably expressing BirA (SupT1.BirA). Consistent with the results in the previous report, NLXMA(B) replicated similar to wild-type levels and expressed biotinylated Gag and MA proteins in the SupT1.BirA cells, whereas the replication of NLXIN(B) was reduced severely. Three additional HIV type 2 (HIV-2) viruses were constructed with the BAS inserted into the vpx and vpr accessory genes. Two BAS insertions were made into the C-terminal half of the Vpx, including one internal insertion, and one at the N-terminus of Vpr. All three viruses were replication competent in the SupT1.BirA cells and their target proteins biotinylated efficiently and incorporated into virions. These results demonstrate the potential utility of the biotinylation system to label and capture HIV protein complexes in the context of replicating virus.

  5. Chemistry: Small molecular replicators go organic

    Science.gov (United States)

    Taylor, Annette F.

    2016-09-01

    The emergence of complex, dynamic molecular behaviour might have had a role in the origin of life. Such behaviour has now been seen in a reaction network involving small, organic, self-replicating molecules of biological relevance. See Letter p.656

  6. Surface Micro Topography Replication in Injection Moulding

    DEFF Research Database (Denmark)

    Arlø, Uffe Rolf; Hansen, Hans Nørgaard; Kjær, Erik Michael

    2005-01-01

    The surface micro topography of injection moulded plastic parts can be important for aesthetical and technical reasons. The quality of replication of mould surface topography onto the plastic surface depends among other factors on the process conditions. A study of this relationship has been...

  7. The replication of expansive production knowledge

    DEFF Research Database (Denmark)

    Wæhrens, Brian Vejrum; Yang, Cheng; Madsen, Erik Skov

    2012-01-01

    exploration, the small sample size is an obvious limitation for generalisation. Practical implications – A roadmap for knowledge transfer within the replication of a production line is suggested, which, together with four managerial suggestions, provides strong support and clear directions to managers...

  8. Replication and Inhibitors of Enteroviruses and Parechoviruses

    Directory of Open Access Journals (Sweden)

    Lonneke van der Linden

    2015-08-01

    Full Text Available The Enterovirus (EV and Parechovirus genera of the picornavirus family include many important human pathogens, including poliovirus, rhinovirus, EV-A71, EV-D68, and human parechoviruses (HPeV. They cause a wide variety of diseases, ranging from a simple common cold to life-threatening diseases such as encephalitis and myocarditis. At the moment, no antiviral therapy is available against these viruses and it is not feasible to develop vaccines against all EVs and HPeVs due to the great number of serotypes. Therefore, a lot of effort is being invested in the development of antiviral drugs. Both viral proteins and host proteins essential for virus replication can be used as targets for virus inhibitors. As such, a good understanding of the complex process of virus replication is pivotal in the design of antiviral strategies goes hand in hand with a good understanding of the complex process of virus replication. In this review, we will give an overview of the current state of knowledge of EV and HPeV replication and how this can be inhibited by small-molecule inhibitors.

  9. Representation dimension of m-replicated algebras

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Let A be a finite-dimensional hereditary algebra over an algebraically closed field and A(m) be the m-replicated algebra of A.We prove that the representation dimension of A(m) is at most 3,and that the dominant dimension of A(m) is at least m.

  10. Multiseason occupancy models for correlated replicate surveys

    Science.gov (United States)

    Hines, James; Nichols, James; Collazo, Jaime

    2014-01-01

    Occupancy surveys collecting data from adjacent (sometimes correlated) spatial replicates have become relatively popular for logistical reasons. Hines et al. (2010) presented one approach to modelling such data for single-season occupancy surveys. Here, we present a multiseason analogue of this model (with corresponding software) for inferences about occupancy dynamics. We include a new parameter to deal with the uncertainty associated with the first spatial replicate for both single-season and multiseason models. We use a case study, based on the brown-headed nuthatch, to assess the need for these models when analysing data from the North American Breeding Bird Survey (BBS), and we test various hypotheses about occupancy dynamics for this species in the south-eastern United States. The new model permits inference about local probabilities of extinction, colonization and occupancy for sampling conducted over multiple seasons. The model performs adequately, based on a small simulation study and on results of the case study analysis. The new model incorporating correlated replicates was strongly favoured by model selection for the BBS data for brown-headed nuthatch (Sitta pusilla). Latitude was found to be an important source of variation in local colonization and occupancy probabilities for brown-headed nuthatch, with both probabilities being higher near the centre of the species range, as opposed to more northern and southern areas. We recommend this new occupancy model for detection–nondetection studies that use potentially correlated replicates.

  11. Structure and replication of hepatitis delta virus

    African Journals Online (AJOL)

    STORAGESEVER

    2008-12-29

    Dec 29, 2008 ... Unidade de Biologia Molecular, Centro de Malária e outras Doenças Tropicais, Instituto de Higiene e Medicina Tropical, ... molecules of both delta antigens (Ryu et al., 1993). This ..... Glenn JS, Watson JA, Havel CM, White JO (1992). ... HDV RNA encoding the large delta antigen cannot replicate. J. Gen.

  12. Are renal ciliopathies (replication) stressed out?

    NARCIS (Netherlands)

    Slaats, Gisela G; Giles, R

    2015-01-01

    Juvenile renal failure is commonly caused by the ciliopathy nephronophthisis (NPHP). Since all NPHP genes regulate cilia function, it has been assumed that NPHP onset is due to cilia loss. However, recent data suggest that DNA damage caused by replication stress, possibly concomitant with or upstrea

  13. Suppression of Coronavirus Replication by Cyclophilin Inhibitors

    Directory of Open Access Journals (Sweden)

    Takashi Sasaki

    2013-05-01

    Full Text Available Coronaviruses infect a variety of mammalian and avian species and cause serious diseases in humans, cats, mice, and birds in the form of severe acute respiratory syndrome (SARS, feline infectious peritonitis (FIP, mouse hepatitis, and avian infectious bronchitis, respectively. No effective vaccine or treatment has been developed for SARS-coronavirus or FIP virus, both of which cause lethal diseases. It has been reported that a cyclophilin inhibitor, cyclosporin A (CsA, could inhibit the replication of coronaviruses. CsA is a well-known immunosuppressive drug that binds to cellular cyclophilins to inhibit calcineurin, a calcium-calmodulin-activated serine/threonine-specific phosphatase. The inhibition of calcineurin blocks the translocation of nuclear factor of activated T cells from the cytosol into the nucleus, thus preventing the transcription of genes encoding cytokines such as interleukin-2. Cyclophilins are peptidyl-prolyl isomerases with physiological functions that have been described for many years to include chaperone and foldase activities. Also, many viruses require cyclophilins for replication; these include human immunodeficiency virus, vesicular stomatitis virus, and hepatitis C virus. However, the molecular mechanisms leading to the suppression of viral replication differ for different viruses. This review describes the suppressive effects of CsA on coronavirus replication.

  14. Drainage hydraulics of permeable friction courses

    Science.gov (United States)

    Charbeneau, Randall J.; Barrett, Michael E.

    2008-04-01

    This paper describes solutions to the hydraulic equations that govern flow in permeable friction courses (PFC). PFC is a layer of porous asphalt approximately 50 mm thick that is placed as an overlay on top of an existing conventional concrete or asphalt road surface to help control splash and hydroplaning, reduce noise, and enhance quality of storm water runoff. The primary objective of this manuscript is to present an analytical system of equations that can be used in design and analysis of PFC systems. The primary assumptions used in this analysis are that the flow can be modeled as one-dimensional, steady state Darcy-type flow and that slopes are sufficiently small so that the Dupuit-Forchheimer assumptions apply. Solutions are derived for cases where storm water drainage is confined to the PFC bed and for conditions where the PFC drainage capacity is exceeded and ponded sheet flow occurs across the pavement surface. The mathematical solutions provide the drainage characteristics (depth and residence time) as a function of rainfall intensity, PFC hydraulic conductivity, pavement slope, and maximum drainage path length.

  15. Electrically Driven Ion Separations in Permeable Membranes

    Energy Technology Data Exchange (ETDEWEB)

    Bruening, Merlin [Michigan State Univ., East Lansing, MI (United States)

    2017-04-21

    Membranes are attractive for a wide range of separations due to their low energy costs and continuous operation. To achieve practical fluxes, most membranes consist of a thin, selective skin on a highly permeable substrate that provides mechanical strength. Thus, this project focused on creating new methods for forming highly selective ultrathin skins as well as modeling transport through these coatings to better understand their unprecedented selectivities. The research explored both gas and ion separations, and the latter included transport due to concentration, pressure and electrical potential gradients. This report describes a series of highlights of the research and then provides a complete list of publications supported by the grant. These publications have been cited more than 4000 times. Perhaps the most stunning finding is the recent discovery of monovalent/divalent cation and anion selectivities around 1000 when modifying cation- and anion-exchange membranes with polyelectrolyte multilayers (PEMs). This discovery builds on many years of exciting research. (Citation numbers refer to the journal articles in the bibliography.)

  16. Second law violations, continuum mechanics, and permeability

    Science.gov (United States)

    Ostoja-Starzewski, Martin

    2016-03-01

    The violations of the second law are relevant as the length and/or time scales become very small. The second law then needs to be replaced by the fluctuation theorem and mathematically, the irreversible entropy is a submartingale. First, we discuss the consequences of these results for the axioms of continuum mechanics, arguing in favor of a framework relying on stochastic functionals of energy and entropy. We next determine a Lyapunov function for diffusion-type problems governed by stochastic rather than deterministic functionals of internal energy and entropy, where the random field coefficients of diffusion are not required to satisfy the positive definiteness everywhere. Next, a formulation of micropolar fluid mechanics is developed, accounting for the lack of symmetry of stress tensor on molecular scales. This framework is then applied to employed to show that spontaneous random fluctuations of the microrotation field will arise in Couette—and Poiseuille-type flows in the absence of random (turbulence-like) fluctuations of the classical velocity field. Finally, while the permeability is classically modeled by the Darcy law or its modifications, besides considering the violations of the second law, one also needs to account for the spatial randomness of the channel network, implying a modification of the hierarchy of scale-dependent bounds on the macroscopic property of the network.

  17. ReplicationDomain: a visualization tool and comparative database for genome-wide replication timing data

    Directory of Open Access Journals (Sweden)

    Yokochi Tomoki

    2008-12-01

    Full Text Available Abstract Background Eukaryotic DNA replication is regulated at the level of large chromosomal domains (0.5–5 megabases in mammals within which replicons are activated relatively synchronously. These domains replicate in a specific temporal order during S-phase and our genome-wide analyses of replication timing have demonstrated that this temporal order of domain replication is a stable property of specific cell types. Results We have developed ReplicationDomain http://www.replicationdomain.org as a web-based database for analysis of genome-wide replication timing maps (replication profiles from various cell lines and species. This database also provides comparative information of transcriptional expression and is configured to display any genome-wide property (for instance, ChIP-Chip or ChIP-Seq data via an interactive web interface. Our published microarray data sets are publicly available. Users may graphically display these data sets for a selected genomic region and download the data displayed as text files, or alternatively, download complete genome-wide data sets. Furthermore, we have implemented a user registration system that allows registered users to upload their own data sets. Upon uploading, registered users may choose to: (1 view their data sets privately without sharing; (2 share with other registered users; or (3 make their published or "in press" data sets publicly available, which can fulfill journal and funding agencies' requirements for data sharing. Conclusion ReplicationDomain is a novel and powerful tool to facilitate the comparative visualization of replication timing in various cell types as well as other genome-wide chromatin features and is considerably faster and more convenient than existing browsers when viewing multi-megabase segments of chromosomes. Furthermore, the data upload function with the option of private viewing or sharing of data sets between registered users should be a valuable resource for the

  18. Update to Permeable Pavement Research at the Edison Environmental Center - proceedings

    Science.gov (United States)

    The EPA’s Urban Watershed Management Branch (UWMB) has been monitoring the permeable pavement demonstration site at the Edison Environmental Center, NJ since 2010. This site has three different types of permeable pavements including interlocking concrete permeable pavers, p...

  19. An apparent permeability model of shale gas under formation conditions

    Science.gov (United States)

    Chen, Peng; Jiang, Shan; Chen, Yan; Wang, Shanshan

    2017-08-01

    There are various types of pores in shale, mainly consisting of nanopores and micropores, causing flow regime variations and apparent permeability changes during the development of the reservoir. In this paper, a Knudsen number calculation model is proposed with the actual conditions of gas in a shale reservoir. Then, based on the distribution of pores in shale, an apparent permeability model is established using hydrodynamics, and a calculation method is put forward for the actual permeability of a reservoir. Finally, the Knudsen number model and the permeability correction coefficient model are used to analyze the flow regime and permeability correction coefficients in pores during the development of the shale gas reservoir. Results show that with a decreasing of pressure, the Knudsen number increases, the flow regime changes from continuous flow and slip flow to transition flow or free molecular flow. When the Knudsen number is Kn > 0.1, and with a further increasing of Kn, gas molecule slippage greatly intensifies and the permeability correction coefficient K app/Kd significantly increases. While the Knudsen number increases, the permeability correction coefficient significantly increases in the micropores and the small pores, but this does not appear in the macropores and the mesopores. These results can be used to guide flow regime analysis and production forecasting in shale gas reservoirs.

  20. Characterization and estimation of permeability correlation structure from performance data

    Energy Technology Data Exchange (ETDEWEB)

    Ershaghi, I.; Al-Qahtani, M. [Univ. of Southern California, Los Angeles, CA (United States)

    1997-08-01

    In this study, the influence of permeability structure and correlation length on the system effective permeability and recovery factors of 2-D cross-sectional reservoir models, under waterflood, is investigated. Reservoirs with identical statistical representation of permeability attributes are shown to exhibit different system effective permeability and production characteristics which can be expressed by a mean and variance. The mean and variance are shown to be significantly influenced by the correlation length. Detailed quantification of the influence of horizontal and vertical correlation lengths for different permeability distributions is presented. The effect of capillary pressure, P{sub c1} on the production characteristics and saturation profiles at different correlation lengths is also investigated. It is observed that neglecting P{sub c} causes considerable error at large horizontal and short vertical correlation lengths. The effect of using constant as opposed to variable relative permeability attributes is also investigated at different correlation lengths. Next we studied the influence of correlation anisotropy in 2-D reservoir models. For a reservoir under five-spot waterflood pattern, it is shown that the ratios of breakthrough times and recovery factors of the wells in each direction of correlation are greatly influenced by the degree of anisotropy. In fully developed fields, performance data can aid in the recognition of reservoir anisotropy. Finally, a procedure for estimating the spatial correlation length from performance data is presented. Both the production performance data and the system`s effective permeability are required in estimating the correlation length.

  1. Stress dependence of permeability of intact and fractured shale cores.

    Science.gov (United States)

    van Noort, Reinier; Yarushina, Viktoriya

    2016-04-01

    Whether a shale acts as a caprock, source rock, or reservoir, understanding fluid flow through shale is of major importance for understanding fluid flow in geological systems. Because of the low permeability of shale, flow is thought to be largely confined to fractures and similar features. In fracking operations, fractures are induced specifically to allow for hydrocarbon exploration. We have constructed an experimental setup to measure core permeabilities, using constant flow or a transient pulse. In this setup, we have measured the permeability of intact and fractured shale core samples, using either water or supercritical CO2 as the transporting fluid. Our measurements show decreasing permeability with increasing confining pressure, mainly due to time-dependent creep. Furthermore, our measurements show that for a simple splitting fracture, time-dependent creep will also eliminate any significant effect of this fracture on permeability. This effect of confinement on fracture permeability can have important implications regarding the effects of fracturing on shale permeability, and hence for operations depending on that.

  2. Prediction of Hydrocarbon Reservoirs Permeability Using Support Vector Machine

    Directory of Open Access Journals (Sweden)

    R. Gholami

    2012-01-01

    Full Text Available Permeability is a key parameter associated with the characterization of any hydrocarbon reservoir. In fact, it is not possible to have accurate solutions to many petroleum engineering problems without having accurate permeability value. The conventional methods for permeability determination are core analysis and well test techniques. These methods are very expensive and time consuming. Therefore, attempts have usually been carried out to use artificial neural network for identification of the relationship between the well log data and core permeability. In this way, recent works on artificial intelligence techniques have led to introduce a robust machine learning methodology called support vector machine. This paper aims to utilize the SVM for predicting the permeability of three gas wells in the Southern Pars field. Obtained results of SVM showed that the correlation coefficient between core and predicted permeability is 0.97 for testing dataset. Comparing the result of SVM with that of a general regression neural network (GRNN revealed that the SVM approach is faster and more accurate than the GRNN in prediction of hydrocarbon reservoirs permeability.

  3. Effects of CO2 laser energy on dentin permeability.

    Science.gov (United States)

    Pashley, E L; Horner, J A; Liu, M; Kim, S; Pashley, D H

    1992-06-01

    The effect of a CO2 laser on the structure and permeability of smear layer-covered human dentin was evaluated in vitro. Three different energy levels were used (11, 113, and 566 J/cm2). The lowest exposure to the laser energy increased dentin permeability, measured as a hydraulic conductance, due to partial measured as a hydraulic conductance, due to partial loss of the superficial smear layer and smear plugs. The intermediate energy level also increased dentin permeability by crater formation, making the dentin thinner. The lack of uniform glazing of the surface of the crater, leaving its surface porous and in communication with the underlying dentinal tubules also contributed to the increase in dentin permeability seen with the intermediate laser energy. The highest laser energy produced complete glazing of the crater surfaces and sealed the dentinal tubules beneath the crater. However, it also completely removed the smear layer in a halo zone about 100-microns wide around each crater which increased the permeability of the pericrater dentin at the same time it decreased the permeability of the dentin within the crater. The combined use of scanning electron microscopy and permeability measurements provides important complementary information that is essential in evaluating the effects of lasers on dentin.

  4. Wave transmission over permeable submerged breakwaters; Transmision del oleaje en rompeolas sumergidos permeables

    Energy Technology Data Exchange (ETDEWEB)

    Ruiz-y-Zurvia-Flores, Jaime Roberto; Fragoso-Sandoval, Lucio [Instituto Politecnico Nacional(Mexico)

    2008-10-15

    The permeable submerged breakwaters represent a coastal protection alternative, where some degree of wave energy transmission is acceptable. Such would be the case of tourist beach protection in Mexico. In previous researches, like those performed by D'Angremond et al. (1996), Seabrook and Hall (1998), and Briganti et al. (2003), the empirical formulas developed, give only some limited information over the spatial distribution of wave energy over the structure. Therefore, a decision was made to conduct a study on a reduced physical model of a permeable submerged breakwater based on the results presented by those researchers and with possible applications. Therefore this paper presents the development of a study of wave transmission over permeable submerged breakwaters performed in a reduced physical model of different sections of a submerged rockfill breakwater of the trapezoidal type. This was done in a narrow wave flume with a hydraulic irregular wave generator controlled by a computer that was used to generate and to reproduce different types of irregular waves to be used in the tests. It also has a wave meter with four sensors, and they are connected to a computer in order to process the wave data. The main objective of the study was to determine in an experimental way the influence of the several parameters of submerged breakwater over the wave transmission coefficient. Our experimental results were comparable to those obtained by D'Angremond et al. (1996) and Seabrook and Hall (1998). The results show that the sumerged breakwater parameters of most influence over the wave transmission coefficient were relative submergence and the relative width crest of the sumerged breakwater, and that the formula by Seabrook and Hall correlates best with our results. [Spanish] Los rompeolas sumergidos permeables representan actualmente una alternativa de proteccion de costas, donde un cierto grado de transmision de energia del oleaje es aceptable, como seria el

  5. Permeable Steel and Its Application in Plastic-injection Mould

    Institute of Scientific and Technical Information of China (English)

    ZHOU Zhaoyao; CAO Wenjiong; WU Zhengqiang; YU Minqiang; LI Yuanyuan

    2010-01-01

    The gas in plastics mould has great influence on performance, appearance and lifespan of the injection molded parts. Venting channel and its appendix system should be used for gas exhausting in general. However, the dependence on the venting system complicates the mould design. Furthermore in certain condition, it is difficult to integrate the venting system into the mould. Currently a kind of mold material which has gas permeability has been developed in abroad, but the applications of this mold material were restricted by its higher cost and smaller size. In this research, a porous material which was made by powder metallurgy was applied to plastic mould to replace the venting system. Permeability of the steel with different secondary processing was tested and compared with a special apparatus. The metallographic samples of the steel with different secondary processing were prepared and investigated. Finally an actual injection set was established to investigate the applications of permeable steel. The metallographies indicate that the micro-holes inside permeable steel were interconnected. Moulds made of permeable steel exhibit good permeability in the plastic-injection experiments and gas generated in the mould cavity was smoothly exhausted. The melted plastic did not penetrate into the mould or block in the micro-holes. After several times of plastic-injection experiments, the mould still retained good permeability. The strength of this permeable steel is between 200-250 MPa and suitable for industrial applications. The venting systems simplified by permeable steel in plastic-injection have simple structures, which can be applied into any place that requires gas exhausting.

  6. Capsid protein VP4 of human rhinovirus induces membrane permeability by the formation of a size-selective multimeric pore.

    Directory of Open Access Journals (Sweden)

    Anusha Panjwani

    2014-08-01

    Full Text Available Non-enveloped viruses must deliver their viral genome across a cell membrane without the advantage of membrane fusion. The mechanisms used to achieve this remain poorly understood. Human rhinovirus, a frequent cause of the common cold, is a non-enveloped virus of the picornavirus family, which includes other significant pathogens such as poliovirus and foot-and-mouth disease virus. During picornavirus cell entry, the small myristoylated capsid protein VP4 is released from the virus, interacts with the cell membrane and is implicated in the delivery of the viral RNA genome into the cytoplasm to initiate replication. In this study, we have produced recombinant C-terminal histidine-tagged human rhinovirus VP4 and shown it can induce membrane permeability in liposome model membranes. Dextran size-exclusion studies, chemical crosslinking and electron microscopy demonstrated that VP4 forms a multimeric membrane pore, with a channel size consistent with transfer of the single-stranded RNA genome. The membrane permeability induced by recombinant VP4 was influenced by pH and was comparable to permeability induced by infectious virions. These findings present a molecular mechanism for the involvement of VP4 in cell entry and provide a model system which will facilitate exploration of VP4 as a novel antiviral target for the picornavirus family.

  7. Fractal Analysis of Stress Sensitivity of Permeability in Porous Media

    Science.gov (United States)

    Tan, Xiao-Hua; Li, Xiao-Ping; Liu, Jian-Yi; Zhang, Lie-Hui; Cai, Jianchao

    2015-12-01

    A permeability model for porous media considering the stress sensitivity is derived based on mechanics of materials and the fractal characteristics of solid cluster size distribution. The permeability of porous media considering the stress sensitivity is related to solid cluster fractal dimension, solid cluster fractal tortuosity dimension, solid cluster minimum diameter and solid cluster maximum diameter, Young's modulus, Poisson's ratio, as well as power index. Every parameter has clear physical meaning without the use of empirical constants. The model predictions of permeability show good agreement with those obtained by the available experimental expression. The proposed model may be conducible to a better understanding of the mechanism for flow in elastic porous media.

  8. Timescales for permeability reduction and strength recovery in densifying magma

    Science.gov (United States)

    Heap, M. J.; Farquharson, J. I.; Wadsworth, F. B.; Kolzenburg, S.; Russell, J. K.

    2015-11-01

    Transitions between effusive and explosive behaviour are routine for many active volcanoes. The permeability of the system, thought to help regulate eruption style, is likely therefore in a state of constant change. Viscous densification of conduit magma during effusive periods, resulting in physical and textural property modifications, may reduce permeability to that preparatory for an explosive eruption. We present here a study designed to estimate timescales of permeability reduction and strength recovery during viscous magma densification by coupling measurements of permeability and strength (using samples from a suite of variably welded, yet compositionally identical, volcanic deposits) with a rheological model for viscous compaction and a micromechanical model, respectively. Bayesian Information Criterion analysis confirms that our porosity-permeability data are best described by two power laws that intersect at a porosity of 0.155 (the "changepoint" porosity). Above and below this changepoint, the permeability-porosity relationship has a power law exponent of 8.8 and 1.0, respectively. Quantitative pore size analysis and micromechanical modelling highlight that the high exponent above the changepoint is due to the closure of wide (∼200-300 μm) inter-granular flow channels during viscous densification and that, below the changepoint, the fluid pathway is restricted to narrow (∼50 μm) channels. The large number of such narrow channels allows porosity loss without considerable permeability reduction, explaining the switch to a lower exponent. Using these data, our modelling predicts a permeability reduction of four orders of magnitude (for volcanically relevant temperatures and depths) and a strength increase of a factor of six on the order of days to weeks. This discrepancy suggests that, while the viscous densification of conduit magma will inhibit outgassing efficiency over time, the regions of the conduit prone to fracturing, such as the margins, will

  9. The Effect of Bacteria Penetration on Chalk Permeability

    DEFF Research Database (Denmark)

    Halim, Amalia Yunita; Shapiro, Alexander; Nielsen, Sidsel Marie;

    , the spore forming Bacillus licheniformis 421 and the non-spore forming Pseudomonas putida K12, were used. The core plugs were Stevns Klint outcrop with initial permeability at 2-4 mD. The results revealed that bacteria were able to penetrate and to be transported through the chalk. Furthermore, a higher...... number of B. licheniformis was detected on the effluent compared with P. putida. However, in the experiment with B. licheniformis mainly spores were detected in the effluent. The core permeability decreased rapidly during injection of bacteria and a starvation period of 12 days did not allow...... the permeability to return to initial condition....

  10. Predicting the permeability of sedimentary rocks from microstructure

    Energy Technology Data Exchange (ETDEWEB)

    Schlueter, E.M.

    1995-01-01

    Permeability is linked to other properties of porous media such as capillary pressure and relative permeability. In order to understand the relationships, one has to understand how all those properties are conditioned by the connectivity and geometrical properties of the pore space. In this study, we look at a natural porous material which is defined as a two-phase material in which the interconnected pore space constitutes one phase and the solid matrix the other. Laboratory samples are tested using fluid flow experiments to determine the relationship of macroscopic properties such as permeability to rock microstructure. Kozeny-Carman and other equations are developed to further quantify these relationships.

  11. Studies on the induction of permeability in Ascaris lumbricoides eggs.

    Science.gov (United States)

    Barrett, J

    1976-08-01

    The initial process in the hatching mechanism of Ascaris eggs is the sudden onset of permeability in the previously impermeable ascaroside membrane. During this change the ascaroside membrane remains intact and no chemical changes can be detected. Using the molecular probe 1-anilino-8-naphthalene sulphonic acid no conformational changes were detected in the ascaroside membrane during the induction of permeability. It is suggested that either the permeability change is due to a very localized chemical or conformational change, not detectable by conventional analytical techniques, or the change is due to mechanical damage of the ascaroside membrane, brought about by the activity of the infective larva.

  12. The permeability of dentine from bovine incisors in vitro.

    Science.gov (United States)

    Tagami, J; Tao, L; Pashley, D H; Horner, J A

    1989-01-01

    The permeability of coronal dentine was investigated by measuring the hydraulic conductance of dentine discs. Reductions in dentine thickness from the enamel side of disc resulted in a greater increase in permeability than reductions from the pulpal side. Scanning electron microscopy revealed fewer dentinal tubules with smaller diameters in superficial dentine than in deep dentine. The permeability of coronal incisor bovine dentine is six to eight times less than that of unerupted coronal human third molar dentine but similar to that of human root dentine.

  13. Study on the micro-replication of shark skin

    Institute of Scientific and Technical Information of China (English)

    HAN Xin; ZHANG DeYuan

    2008-01-01

    Direct replication of creatural scarfskins to form biomimetic surfaces with relatively vivid morphology is a new attempt of the bio-replicated forming technology at animal body.Taking shark skins as the replication templates,and the micro-em-bossing and micro-molding as the material forming methods,the micro-replicating technology of the outward morphology on shark skins was demonstrated.The pre-liminary analysis on replication precision indicates that the bio-replicated forming technology can replicate the outward morphology of the shark scales with good precision,which validates the application of the bio-replicated forming technology in the direct morphology replication of the firm creatural scarfskins.

  14. The Role of the Transcriptional Response to DNA Replication Stress.

    Science.gov (United States)

    Herlihy, Anna E; de Bruin, Robertus A M

    2017-03-02

    During DNA replication many factors can result in DNA replication stress. The DNA replication stress checkpoint prevents the accumulation of replication stress-induced DNA damage and the potential ensuing genome instability. A critical role for post-translational modifications, such as phosphorylation, in the replication stress checkpoint response has been well established. However, recent work has revealed an important role for transcription in the cellular response to DNA replication stress. In this review, we will provide an overview of current knowledge of the cellular response to DNA replication stress with a specific focus on the DNA replication stress checkpoint transcriptional response and its role in the prevention of replication stress-induced DNA damage.

  15. A replication-time-controlling sequence element in Schizosaccharomyces pombe.

    Science.gov (United States)

    Tripathi, Vishnu P; Dubey, Dharani D

    2017-08-01

    Eukaryotic replication origins are highly variable in their activity and replication timing. The nature and role of cis-acting regulatory sequences that control chromosomal replication timing is not well defined. In the fission yeast, Schizosaccharomyces pombe, a 200-bp late-replication-enforcing element (LRE), has been shown to enforce late replication of ARS elements in plasmids. Here, we show that a short (133-bp) fragment of the LRE (shLRE) is required for causing late replication of adjoining origins in its native as well as in an ectopic early-replicating chromosomal location. Active from both sides of an early-replicating origin, the shLRE is a bona fide cis-acting regulatory element that imposes late replication timing in the chromosome.

  16. Single molecule analysis of Trypanosoma brucei DNA replication dynamics.

    Science.gov (United States)

    Calderano, Simone Guedes; Drosopoulos, William C; Quaresma, Marina Mônaco; Marques, Catarina A; Kosiyatrakul, Settapong; McCulloch, Richard; Schildkraut, Carl L; Elias, Maria Carolina

    2015-03-11

    Eukaryotic genome duplication relies on origins of replication, distributed over multiple chromosomes, to initiate DNA replication. A recent genome-wide analysis of Trypanosoma brucei, the etiological agent of sleeping sickness, localized its replication origins to the boundaries of multigenic transcription units. To better understand genomic replication in this organism, we examined replication by single molecule analysis of replicated DNA. We determined the average speed of replication forks of procyclic and bloodstream form cells and we found that T. brucei DNA replication rate is similar to rates seen in other eukaryotes. We also analyzed the replication dynamics of a central region of chromosome 1 in procyclic forms. We present evidence for replication terminating within the central part of the chromosome and thus emanating from both sides, suggesting a previously unmapped origin toward the 5' extremity of chromosome 1. Also, termination is not at a fixed location in chromosome 1, but is rather variable. Importantly, we found a replication origin located near an ORC1/CDC6 binding site that is detected after replicative stress induced by hydroxyurea treatment, suggesting it may be a dormant origin activated in response to replicative stress. Collectively, our findings support the existence of more replication origins in T. brucei than previously appreciated.

  17. High-Resolution Replication Profiles Define the Stochastic Nature of Genome Replication Initiation and Termination

    Directory of Open Access Journals (Sweden)

    Michelle Hawkins

    2013-11-01

    Full Text Available Eukaryotic genome replication is stochastic, and each cell uses a different cohort of replication origins. We demonstrate that interpreting high-resolution Saccharomyces cerevisiae genome replication data with a mathematical model allows quantification of the stochastic nature of genome replication, including the efficiency of each origin and the distribution of termination events. Single-cell measurements support the inferred values for stochastic origin activation time. A strain, in which three origins were inactivated, confirmed that the distribution of termination events is primarily dictated by the stochastic activation time of origins. Cell-to-cell variability in origin activity ensures that termination events are widely distributed across virtually the whole genome. We propose that the heterogeneity in origin usage contributes to genome stability by limiting potentially deleterious events from accumulating at particular loci.

  18. A method of determining the permeability coefficient of coal seam based on the permeability of loaded coal

    Institute of Scientific and Technical Information of China (English)

    Li Bo; Wei Jianping; Wang Kai; Li Peng; Wang Ke

    2014-01-01

    This study developed the equipment for thermo-fluid-solid coupling of methane-containing coal, and investigated the seepage character of loaded coal under different working conditions. Regarding the effective pressure as a variable, the variation characteristics of the gas permeability of loaded meth-ane-containing coal has been studied under the conditions of different confining pressures and pore pres-sures. The qualitative and quantitative relationship between effective stress and permeability of loaded methane-containing coal has been established, considering the adsorption of deformation, amount of pore gas compression and temperature variation. The results show that the permeability of coal samples decreases along with the increasing effective stress. Based on the Darcy law, the correlation equation between the effective stress and permeability coefficient of coal seam has been established by combining the permeability coefficient of loaded coal and effective stress. On the basis of experimental data, this equation is used for calculation, and the results are in accordance with the measured gas permeability coefficient of coal seam. In conclusion, this method can be accurate and convenient to determine the gas permeability coefficient of coal seam, and provide evidence for forecasting that of the deep coal seam.

  19. Novel Mutant AAV2 Rep Proteins Support AAV2 Replication without Blocking HSV-1 Helpervirus Replication

    Science.gov (United States)

    Seyffert, Michael; Glauser, Daniel L.; Schraner, Elisabeth M.; de Oliveira, Anna-Paula; Mansilla-Soto, Jorge; Vogt, Bernd; Büning, Hildegard; Linden, R. Michael; Ackermann, Mathias; Fraefel, Cornel

    2017-01-01

    As their names imply, parvoviruses of the genus Dependovirus rely for their efficient replication on the concurrent presence of a helpervirus, such as herpesvirus, adenovirus, or papilloma virus. Adeno-associated virus 2 (AAV2) is such an example, which in turn can efficiently inhibit the replication of each helpervirus by distinct mechanisms. In a previous study we have shown that expression of the AAV2 rep gene is not compatible with efficient replication of herpes simplex virus 1 (HSV-1). In particular, the combined DNA-binding and ATPase/helicase activities of the Rep68/78 proteins have been shown to exert opposite effects on the replication of AAV2 and HSV-1. While essential for AAV2 DNA replication these protein activities account for the Rep-mediated inhibition of HSV-1 replication. Here, we describe a novel Rep mutant (Rep-D371Y), which displayed an unexpected phenotype. Rep-D371Y did not block HSV-1 replication, but still supported efficient AAV2 replication, at least when a double-stranded AAV2 genome template was used. We also found that the capacity of Rep-D371Y to induce apoptosis and a Rep-specific DNA damage response was significantly reduced compared to wild-type Rep. These findings suggest that AAV2 Rep-helicase subdomains exert diverging activities, which contribute to distinct steps of the AAV2 life cycle. More important, the novel AAV2 mutant Rep-D371Y may allow deciphering yet unsolved activities of the AAV2 Rep proteins such as DNA second-strand synthesis, genomic integration or packaging, which all involve the Rep-helicase activity. PMID:28125695

  20. Composites with tuned effective magnetic permeability

    Science.gov (United States)

    Amirkhizi, Alireza V.; Nemat-Nasser, Sia

    2007-07-01

    Pendry et al. [J. B. Pendry, A. J. Holden, D. J. Robbins, and W. J. Stewart, IEEE Trans. Microwave Theory Tech. 47, 2075 (1999)] and Smith et al. [D. R. Smith, W. J. Padilla, D. C. Vier, S. C. Nemat-Nasser, and S. Schultz, Phys. Rev. Lett. 84, 4184 (2000)] have shown that the effective magnetic permeability, μ, of free space can be rendered negative over a certain frequency range by a periodic arrangement of very thin conductors with suitable magnetic resonance properties, the so-called split-ring resonators. Because of its rather bulky architecture, this structure does not lend itself to a proper integration into a reasonably thin real composite structural panel. To remedy this fundamental barrier, we invented a new magnetic resonator consisting of very thin folded plates that are suitably nested within one another to form folded-doubled resonators (FDRs) that can be integrated into an actual composite panel. Measurements, using a focused beam electromagnetic characterization system combined with time-domain numerical simulations of the reflection and transmission coefficients of such a composite slab have revealed that indeed the composite has a negative μ over a frequency range of about 9.1-9.35 GHz [S. Nemat-Nasser, S. C. Nemat-Nasser, T. A. Plaisted, A. Starr, and A. Vakil Amirkhizi, in Biomimetics: Biologically Inspired Technologies, edited by Y. Bar Cohen (CRC Press, Boca Raton, FL, 2006)]. Thus, it has become possible to construct a structural composite panel with negative index of refraction by simultaneously creating negative effective ɛ and μ [V. G. Veselago, Sov. Phys. Usp. 10, 509 (1968); R. A. Shelby, D. R. Smith, and S. Schultz, Science 292, 77 (2001); A. F. Starr, P. M. Rye, D. R. Smith, and S. Nemat-Nasser, Phys. Rev. B 70, 113102 (2004)].

  1. Membrane permeability properties of dental adhesive films.

    Science.gov (United States)

    Carrilho, Marcela R; Tay, Franklin R; Donnelly, Adam M; Agee, Kelli A; Carvalho, Ricardo M; Hosaka, Keiichi; Reis, Alessandra; Loguercio, Alessandro D; Pashley, David H

    2009-02-01

    This study evaluated the permeability properties of five experimental resin membranes that ranged from relatively hydrophobic to relatively hydrophilic to seal acid-etched dentin saturated with water or ethanol. The experimental resins (R1, R2, R3, R4, and R5) were evaluated as neat bonding agents or as solutions solvated with ethanol (70% resin/30% ethanol). The quality of dentin sealing by these experimental resins was expressed in terms of reflection coefficients calculated as the ratio of the effective osmotic pressure to the theoretical osmotic pressure of test solutions. The effective osmotic pressure produced across resin-bonded dentin was induced in hypertonic solutions (CaCl(2) or albumin) at zero hydrostatic pressure. The outward fluid flow induced by these solutions was brought to zero by applying an opposing negative hydrostatic pressure. The least hydrophilic resins blends, R1 and R2, exhibited significantly (p < 0.05) higher reflection coefficients than the most hydrophilic resins (R4 and R5) in both conditions of dentin saturation (water and ethanol). The reflection coefficients of neat resins were, in general, significantly higher when compared with their corresponding solvated versions in both conditions of dentin saturation. In dentin saturated with ethanol, bonding with neat or solvated resins, resulted in reflection coefficients that were significantly higher when compared with the results obtained in dentin saturated with water. Reflection coefficients of CaCl(2) (ca. 1 x 10(-4)) were significantly lower (p < 0.05) than for albumin (ca. 3 x 10(-2)). Application of hydrophobic resins may provide better sealing of acid-etched dentin if the substrate is saturated with ethanol, instead of water.

  2. Mcm10 regulates DNA replication elongation by stimulating the CMG replicative helicase

    Science.gov (United States)

    Lõoke, Marko; Maloney, Michael F.; Bell, Stephen P.

    2017-01-01

    Activation of the Mcm2–7 replicative DNA helicase is the committed step in eukaryotic DNA replication initiation. Although Mcm2–7 activation requires binding of the helicase-activating proteins Cdc45 and GINS (forming the CMG complex), an additional protein, Mcm10, drives initial origin DNA unwinding by an unknown mechanism. We show that Mcm10 binds a conserved motif located between the oligonucleotide/oligosaccharide fold (OB-fold) and A subdomain of Mcm2. Although buried in the interface between these domains in Mcm2–7 structures, mutations predicted to separate the domains and expose this motif restore growth to conditional-lethal MCM10 mutant cells. We found that, in addition to stimulating initial DNA unwinding, Mcm10 stabilizes Cdc45 and GINS association with Mcm2–7 and stimulates replication elongation in vivo and in vitro. Furthermore, we identified a lethal allele of MCM10 that stimulates initial DNA unwinding but is defective in replication elongation and CMG binding. Our findings expand the roles of Mcm10 during DNA replication and suggest a new model for Mcm10 function as an activator of the CMG complex throughout DNA replication. PMID:28270517

  3. Replicative Homeostasis: A fundamental mechanism mediating selective viral replication and escape mutation

    Directory of Open Access Journals (Sweden)

    Sallie Richard

    2005-02-01

    Full Text Available Abstract Hepatitis C (HCV, hepatitis B (HBV, the human immunodeficiency viruses (HIV, and other viruses that replicate via RNA intermediaries, cause an enormous burden of disease and premature death worldwide. These viruses circulate within infected hosts as vast populations of closely related, but genetically diverse, molecules known as "quasispecies". The mechanism(s by which this extreme genetic and antigenic diversity is stably maintained are unclear, but are fundamental to understanding viral persistence and pathobiology. The persistence of HCV, an RNA virus, is especially problematic and HCV stability, maintained despite rapid genomic mutation, is highly paradoxical. This paper presents the hypothesis, and evidence, that viruses capable of persistent infection autoregulate replication and the likely mechanism mediating autoregulation – Replicative Homeostasis – is described. Replicative homeostasis causes formation of stable, but highly reactive, equilibria that drive quasispecies expansion and generates escape mutation. Replicative homeostasis explains both viral kinetics and the enigma of RNA quasispecies stability and provides a rational, mechanistic basis for all observed viral behaviours and host responses. More importantly, this paradigm has specific therapeutic implication and defines, precisely, new approaches to antiviral therapy. Replicative homeostasis may also modulate cellular gene expression.

  4. Probing permeability and microstructure: Unravelling the role of a low-permeability dome on the explosivity of Merapi (Indonesia)

    Science.gov (United States)

    Kushnir, Alexandra R. L.; Martel, Caroline; Bourdier, Jean-Louis; Heap, Michael J.; Reuschlé, Thierry; Erdmann, Saskia; Komorowski, Jean-Christophe; Cholik, Noer

    2016-04-01

    Low permeability dome rocks may contribute to conduit overpressure development in volcanic systems, indirectly abetting explosive activity. The permeability of dome-forming rocks is primarily controlled by the volume, type (vesicles and/or microcracks), and connectivity of the void space present. Here we investigate the permeability-porosity relationship of dome-forming rocks and pumice clasts from Merapi's 1888 to 2013 eruptions and assess their possible role in eruptive processes, with particular emphasis on the 2010 paroxysmal eruption. Rocks are divided into three simple field classifications common to all eruptions: Type 1 samples have low bulk density and are pumiceous in texture; Type 2 samples, ubiquitous to the 2010 eruption, are dark grey to black in hand sample and vary greatly in vesicularity; and Type 3 samples are weakly vesicular, light grey in hand sample, and are the only samples that contain cristobalite. Type 2 and Type 3 rocks are present in all eruptions and their permeability and porosity data define similar power law relationships, whereas data for Type 1 samples are clearly discontinuous from these trends. A compilation of permeability and porosity data for andesites and basaltic andesites with published values highlights two microstructural transitions that exert control on permeability, confirmed by modified Bayesian Information Criterion (BIC) analysis. Permeability is microcrack- and diktytaxitic-controlled at connected porosities, φc, 31 vol.%. Type 3 basaltic andesites, the least permeable of the measured samples and therefore the most likely to have originated in the uppermost low-permeability dome, are identified as relicts of terminal domes (the last dome extruded prior to quiescence). Cristobalite commonly found in the voids of Type 3 blocks may not contribute significantly to the reduction of the permeability of these samples, mainly because it is associated with an extensive microporous, diktytaxitic texture. Indeed, the low

  5. Escalation of error catastrophe for enzymatic self-replicators

    Science.gov (United States)

    Obermayer, B.; Frey, E.

    2009-11-01

    It is a long-standing question in origin-of-life research whether the information content of replicating molecules can be maintained in the presence of replication errors. Extending standard quasispecies models of non-enzymatic replication, we analyze highly specific enzymatic self-replication mediated through an otherwise neutral recognition region, which leads to frequency-dependent replication rates. We find a significant reduction of the maximally tolerable error rate, because the replication rate of the fittest molecules decreases with the fraction of functional enzymes. Our analysis is extended to hypercyclic couplings as an example for catalytic networks.

  6. Airspace Analyzer for Assessing Airspace Directional Permeability Project

    Data.gov (United States)

    National Aeronautics and Space Administration — We build a software tool which enables the user (airline or Air Traffic Service Provider (ATSP)) the ability to analyze the flight-level-by-flight-level permeability...

  7. Topical tranexamic acid improves the permeability barrier in rosacea

    Directory of Open Access Journals (Sweden)

    Shaomin Zhong

    2015-06-01

    Conclusion: Topical tranexamic acid could improve the epidermal permeability barrier function and clinical signs of rosacea, likely resulting from inhibition of PAR-2 activation and consequent calcium influx. Thus, tranexamic acid could serve as an adjuvant therapy for rosacea.

  8. Applying COSISIM model to study the permeability of porous media

    Institute of Scientific and Technical Information of China (English)

    LIU Zhen; MU Chao-min

    2011-01-01

    Accuracy of simulated permeability can be improved using soft data during the process of simulation. Integrating soft data with hard data, a method based on COSISIM (sequential indicator cosimulation) was proposed to reconstruct permeability. The algorithm COSISIM extends the SISIM (sequential indicator simulation) algorithm to handle secondary data. At the difference of SISIM, data must already be an indicator-coded prior to using COSISIM. The soft data were integrated with hard data using the Markov-Bayes algorithm and must be coded into indicators before they are used. This method was tested on a regional simulation of permeability. The simulated results and the original distribution of permeability were compared. The experimental results demonstrate that this method is practical.

  9. AXISYMMETRIC FLOW THROUGH A PERMEABLE NEAR-SPHERE

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    An analytical approach is described for the axisymmetric flow through a permeable near-sphere with a modification to boundary conditions in order to account permeability. The Stokes equation was solved by a regular perturbation technique up to the second order correction in epsilon representing the deviation from the radius of nondeformed sphere. The drag and the flow rate were calculated and the results were evaluated from the point of geometry and the permeability of the surface. An attempt also was made to apply the theory to the filter feeding problem. The filter appendages of small ecologically important aquatic organisms were modeled as axisymmetric permeable bodies, therefore a rough model for this problem was considered here as an oblate spheroid or near-sphere.

  10. Effect Of Hot Water Injection On Sandstone Permeability

    DEFF Research Database (Denmark)

    Rosenbrand, Esther; Fabricius, Ida Lykke

    2012-01-01

    The seasonal imbalance between supply and demand of renewable energy requires temporary storage, which can be achieved by hot water injection in warm aquifers. This requires that the permeability and porosity of the aquifer are not reduced significantly by heating. We present an overview...... of published results regarding the effect of temperature on sandstone permeability. These tests are performed with mineral oil, nitrogen gas, distilled water and solutions of NaCl, KCl, CaCl2 as well as brines that contain a mixture of salts. Thirteen sandstone formations, ranging from quartz arenites...... not account for all the permeability reductions observed. Permeablity reduction occurs both when distilled water is the saturating fluid as well as in tests with NaCl, KCl or CaCl2 solutions, however, this is not the case in tests with mineral oil or nitrogen gas. The formation of a filter cake or influx...

  11. Permeability studies on 3D Ni foam/graphene composites

    Science.gov (United States)

    Yang, Zhuxian; Chen, Hongmei; Wang, Nannan; Xia, Yongde; Zhu, Yanqiu

    2017-09-01

    This study investigates the permeability of new 3D Ni foam/graphene composites (Ni foam covered with graphene) using compressed air, Ar and N2 as the probe gases. The results show that the introduction of graphene on the surface of Ni foam via in situ chemical vapour deposition is not detrimental to the permeability of the composites; on the contrary, in some cases it improves permeability. A modified Ergun-type correlation has been proposed, which represents very well the permeability of the Ni foam/graphene composites, especially at flow rates higher than 0.3 m s-1. Further studies show that graphene also helps to improve the thermal conductivity of the composite. These results suggest that the graphene involvement will make the Ni foam/graphene composite a good candidate for potential applications such as filters or heat exchangers suitable for working under harsh conditions such as at high temperatures, in corrosive environments, etc.

  12. Measurement of relative permeability of fuel cell diffusion media

    KAUST Repository

    Hussaini, I.S.

    2010-06-01

    Gas diffusion layer (GDL) in PEM fuel cells plays a pivotal role in water management. Modeling of liquid water transport through the GDL relies on knowledge of relative permeability functions in the in-plane and through-plane directions. In the present work, air and water relative permeabilities are experimentally determined as functions of saturation for typical GDL materials such as Toray-060, -090, -120 carbon paper and E-Tek carbon cloth materials in their plain, untreated forms. Saturation is measured using an ex situ gravimetric method. Absolute and relative permeability functions in the two directions of interest are presented and new correlations for in-plane relative permeability of water and air are established. © 2010 Elsevier B.V. All rights reserved.

  13. Interferon-gamma regulation of intestinal epithelial permeability.

    Science.gov (United States)

    Beaurepaire, Cécile; Smyth, David; McKay, Derek M

    2009-03-01

    The maintenance and regulation of the barrier function of the epithelial lining of the intestine are important homeostatic events, serving to allow selective absorption from the gut lumen while simultaneously limiting the access of bacteria into the mucosa. Interferon-gamma is a pleiotrophic cytokine produced predominantly by natural kill cells and CD4+ T cells that under normal circumstances, and particularly during infection or inflammation, will be a component of the intestinal milieu. Use of colon-derived epithelial cell lines and, to a less extent, murine in vivo analyses, have revealed that interferon-gamma (IFN-gamma) can increase epithelial permeability as gauged by markers of paracellular permeability and bacterial transcytosis, with at least a portion of the bacteria using the transcellular permeation pathway. In this review, we describe the main characteristics of epithelial permeability and then focus on the ability of IFN-gamma to increase epithelial permeability, and the mechanism(s) thereof.

  14. Water permeability of rat liver mitochondria: A biophysical study.

    Science.gov (United States)

    Calamita, Giuseppe; Gena, Patrizia; Meleleo, Daniela; Ferri, Domenico; Svelto, Maria

    2006-08-01

    The movement of water accompanying solutes between the cytoplasm and the mitochondrial spaces is central for mitochondrial volume homeostasis, an important function for mitochondrial activities and for preventing the deleterious effects of excess matrix swelling or contraction. While the discovery of aquaporin water channels in the inner mitochondrial membrane provided valuable insights into the basis of mitochondrial plasticity, questions regarding the identity of mitochondrial water permeability and its regulatory mechanism remain open. Here, we use a stopped flow light scattering approach to define the water permeability and Arrhenius activation energy of the rat liver whole intact mitochondrion and its membrane subcompartments. The water permeabilities of whole brain and testis mitochondria as well as liposome models of the lipid bilayer composing the liver inner mitochondrial membrane are also characterized. Besides finding remarkably high water permeabilities for both mitochondria and their membrane subcompartments, the existence of additional pathways of water movement other than aquaporins are suggested.

  15. Lightweight, Low Permeability, Cryogenic Thoraeus RubberTM Inflatables Project

    Data.gov (United States)

    National Aeronautics and Space Administration — NanoSonic has developed a candidate state-of-the-art inflatable as a novel bladder material for life critical, space habitats that maintains low air permeability...

  16. Permeability analysis for thermal binder removal from green ceramic bodies

    Science.gov (United States)

    Yun, Jeong Woo

    2007-12-01

    The permeability of unlaminated and laminated green tapes was determined as a function of binder content for binder removed by air oxidation. The tapes are comprised of barium titanate as the dielectric, and polyvinyl butyral and dioctyl phthalate as the main compoents of the binder mixture. The flow in porous media through the tapes was analyzed in terms of models for describing Knudsen, slip, and Poiseuille flow mechanisms. The characteristic pore size was determined to be 0.5-2 mum and thus Poiseuille flow was the dominant transport mechanism contributing to the flux. The permeability was then determined from Darcy's law for flow in porous media. The permeability was also determined from micro-structural attributes in terms of the specific surface, the pore fraction, and terms to account for tortuosity and constrictions. The permeability and adhesion strength of laminated green ceramic tapes were determined as a function of lamination conditions of time, temperature, and pressure.

  17. Determination of permeability distribution from well-test pressure data

    Energy Technology Data Exchange (ETDEWEB)

    Feitosa, G.S.; Chu, L.; Thompson, L.G.; Reynolds, A.C. (Univ. of Tulsa, OK (United States))

    1994-07-01

    The emergence of reservoir characterization has stimulated efforts to obtain improved information on reservoir heterogeneities. This work considers single-phase flow to a well in a reservoir where permeability varies with distance from the well. The authors consider methods for estimating the permeability distribution from well-test pressure data. The methods considered were obtained by modifying and extending elegant seminal works of Oliver and Yeh and Agarwal. This work considers the analysis of pressure data, both drawdown and buildup, obtained at a well producing reservoir in which the absolute permeability varies with position. A new inverse-solution algorithm is presented that can be applied to estimate the reservoir permeability distribution as a function of distance from the well.

  18. Porosity, permeability, and their relationship in granite, basalt, and tuff

    Energy Technology Data Exchange (ETDEWEB)

    1983-04-01

    This report discusses the porosity, storage, and permeability of fractured (mainly crystalline) rock types proposed as host rock for nuclear waste repositories. The emphasis is on the inter-relationships of these properties, but a number of reported measurements are included as well. The porosity of rock is shown to consist of fracture porosity and matrix porosity; techniques are described for determining the total interconnected porosity through both laboratory and field measurement. Permeability coefficient, as obtained by experiments ranging from laboratory to crustal scale, is discussed. Finally, the problem of determining the relationship between porosity and permeability is discussed. There is no simple, all encompassing relationship that describes the dependence of permeability upon porosity. However, two particular cases have been successfully analyzed: flow through a single rough fracture, and flow through isotropic porous rock. These two cases are discussed in this report.

  19. Buoyancy Effect on MHD Flow Past a Permeable Bed

    Directory of Open Access Journals (Sweden)

    S. Venkataramana

    1986-10-01

    Full Text Available In this paper, the effect of buoyancy force on the parallel flows bounded above by a rigid permeable plate which may be moving or stationary and below, by a permeable bed has been investigated. To discuss the solution, the flow region is divided into two zones. In Zone 1, the flow is laminar and is governed by the Navier-Stokes equations from the impermeable upper rigid plate to the permeable bed. In Zone 2, the flow is governed by the Darcy law in the permeable bed below the nominal surface. The expressions for velocity and temparature distributions, Slip velocity, slip temperature, mass flow rate and the rates of heat transfer coefficients are obtained. The effects of magnetic, porous, slip and buoyancy parameters and Biot number on the above physical quantities are investigated. The thickness of the boundary layer in Zone 2 has been evaluated.

  20. Gas Permeability of Porous Plasma-Sprayed Coatings

    Science.gov (United States)

    Wittmann-Ténèze, K.; Caron, N.; Alexandre, S.

    2008-12-01

    For different applications, such as solid oxide fuel cells, there is an interest in understanding the relationship between the microstructure and the gas permeability of plasma-sprayed coatings. Nevertheless, plasma spraying processes allow to elaborate coatings with singular microstructures, depending strongly on the initial material and plasma operating conditions. And so, the evolution of permeability is not directly linked to the porosity. In this work, coatings were manufactured using different initial feedstock and spray parameters to obtain various microporous structures. Measurements of their permeation with the pressure drop method and their open porosity just as the observation of the morphology and the structure by optical microscopy were achieved. The different data show that the evolution of the gas permeability with the open porosity follows the Kozeny-Carman equation. This result correlated with the microstructural observation highlights the relationship between the permeability and the physical properties of porous plasma-sprayed layers.

  1. Diagenetic effect on permeabilities of geothermal sandstone reservoirs

    DEFF Research Database (Denmark)

    Weibel, Rikke; Olivarius, Mette; Kristensen, Lars

    The Danish subsurface contains abundant sedimentary deposits, which can be utilized for geothermal heating. The Upper Triassic – Lower Jurassic continental-marine sandstones of the Gassum Formation has been utilised as a geothermal reservoir for the Thisted Geothermal Plant since 1984 extracting...... and permeability is caused by increased diagenetic changes of the sandstones due to increased burial depth and temperatures. Therefore, the highest water temperatures typically correspond with the lowest porosities and permeabilities. Especially the permeability is crucial for the performance of the geothermal......-line fractures. Continuous thin chlorite coatings results in less porosity- and permeability-reduction with burial than the general reduction with burial, unless carbonate cemented. Therefore, localities of sandstones characterized by these continuous chlorite coatings may represent fine geothermal reservoirs...

  2. Physically Embedded Minimal Self-Replicating Systems

    DEFF Research Database (Denmark)

    Fellermann, Harold

    Self-replication is a fundamental property of all living organisms, yet has only been accomplished to limited extend in manmade systems. This thesis is part of the ongoing research endeavor to bridge the two sides of this gap. In particular, we present simulation results of a minimal life......-like, artificial, molecular aggregate (i.e. protocell) that has been proposed by Steen Rasussen and coworkers and is currently pursued both experimentally and computationally in interdisciplinary international research projects. We develop a space-time continuous physically motivated simulation framework based...... computational models. This allows us to address key issues of the replicating subsystems – container, genome, and metabolism – both individually and in mutual coupling. We analyze each step in the life-cycle of the molecular aggregate, and a final integrated simulation of the entire life-cycle is prepared. Our...

  3. Choreography of bacteriophage T7 DNA replication.

    Science.gov (United States)

    Lee, Seung-Joo; Richardson, Charles C

    2011-10-01

    The replication system of phage T7 provides a model for DNA replication. Biochemical, structural, and single-molecule analyses together provide insight into replisome mechanics. A complex of polymerase, a processivity factor, and helicase mediates leading strand synthesis. Establishment of the complex requires an interaction of the C-terminal tail of the helicase with the polymerase. During synthesis the complex is stabilized by other interactions to provide for a processivity of 5 kilobase (kb). The C-terminal tail also interacts with a distinct region of the polymerase to captures dissociating polymerase to increase the processivity to >17kb. The lagging strand is synthesized discontinuously within a loop that forms and resolves during each cycle of Okazaki fragment synthesis. The synthesis of a primer as well as the termination of a fragment signal loop resolution.

  4. Surface micro topography replication in injection moulding

    DEFF Research Database (Denmark)

    Arlø, Uffe Rolf

    , the topography itself, and other factors were also investigated. The experimental work is based on a multi-purpose experimental injection mould with a collection of test surface inserts manufactured by EDM (electrical discharge machining). Experimental production took place with an injection moulding machine......Thermoplastic injection moulding is a widely used industrial process that involves surface generation by replication. The surface topography of injection moulded plastic parts can be important for aesthetical or technical reasons. With the emergence of microengineering and nanotechnology additional...... in a clean room environment. The mould and the injection moulding machine were fitted with transducers for subsequent process analysis. A total of 13 different plastic material grades were applied. Topographical characterisation was performed with an optical laser focus detection instrument. Replication...

  5. Entropy involved in fidelity of DNA replication

    CERN Document Server

    Arias-Gonzalez, J Ricardo

    2012-01-01

    Information has an entropic character which can be analyzed within the Statistical Theory in molecular systems. R. Landauer and C.H. Bennett showed that a logical copy can be carried out in the limit of no dissipation if the computation is performed sufficiently slowly. Structural and recent single-molecule assays have provided dynamic details of polymerase machinery with insight into information processing. We introduce a rigorous characterization of Shannon Information in biomolecular systems and apply it to DNA replication in the limit of no dissipation. Specifically, we devise an equilibrium pathway in DNA replication to determine the entropy generated in copying the information from a DNA template in the absence of friction. Both the initial state, the free nucleotides randomly distributed in certain concentrations, and the final state, a polymerized strand, are mesoscopic equilibrium states for the nucleotide distribution. We use empirical stacking free energies to calculate the probabilities of incorpo...

  6. The Solution to Science's Replication Crisis

    CERN Document Server

    Knuteson, Bruce

    2016-01-01

    The solution to science's replication crisis is a new ecosystem in which scientists sell what they learn from their research. In each pairwise transaction, the information seller makes (loses) money if he turns out to be correct (incorrect). Responsibility for the determination of correctness is delegated, with appropriate incentives, to the information purchaser. Each transaction is brokered by a central exchange, which holds money from the anonymous information buyer and anonymous information seller in escrow, and which enforces a set of incentives facilitating the transfer of useful, bluntly honest information from the seller to the buyer. This new ecosystem, capitalist science, directly addresses socialist science's replication crisis by explicitly rewarding accuracy and penalizing inaccuracy.

  7. Experimental Replication of an Aeroengine Combustion Instability

    Science.gov (United States)

    Cohen, J. M.; Hibshman, J. R.; Proscia, W.; Rosfjord, T. J.; Wake, B. E.; McVey, J. B.; Lovett, J.; Ondas, M.; DeLaat, J.; Breisacher, K.

    2000-01-01

    Combustion instabilities in gas turbine engines are most frequently encountered during the late phases of engine development, at which point they are difficult and expensive to fix. The ability to replicate an engine-traceable combustion instability in a laboratory-scale experiment offers the opportunity to economically diagnose the problem (to determine the root cause), and to investigate solutions to the problem, such as active control. The development and validation of active combustion instability control requires that the causal dynamic processes be reproduced in experimental test facilities which can be used as a test bed for control system evaluation. This paper discusses the process through which a laboratory-scale experiment was designed to replicate an instability observed in a developmental engine. The scaling process used physically-based analyses to preserve the relevant geometric, acoustic and thermo-fluid features. The process increases the probability that results achieved in the single-nozzle experiment will be scalable to the engine.

  8. Competition and cooperation in dynamic replication networks.

    Science.gov (United States)

    Dadon, Zehavit; Wagner, Nathaniel; Alasibi, Samaa; Samiappan, Manickasundaram; Mukherjee, Rakesh; Ashkenasy, Gonen

    2015-01-07

    The simultaneous replication of six coiled-coil peptide mutants by reversible thiol-thioester exchange reactions is described. Experimental analysis of the time dependent evolution of networks formed by the peptides under different conditions reveals a complex web of molecular interactions and consequent mutant replication, governed by competition for resources and by autocatalytic and/or cross-catalytic template-assisted reactions. A kinetic model, first of its kind, is then introduced, allowing simulation of varied network behaviour as a consequence of changing competition and cooperation scenarios. We suggest that by clarifying the kinetic description of these relatively complex dynamic networks, both at early stages of the reaction far from equilibrium and at later stages approaching equilibrium, one lays the foundation for studying dynamic networks out-of-equilibrium in the near future.

  9. Replicative DNA polymerase mutations in cancer.

    Science.gov (United States)

    Heitzer, Ellen; Tomlinson, Ian

    2014-02-01

    Three DNA polymerases - Pol α, Pol δ and Pol ɛ - are essential for DNA replication. After initiation of DNA synthesis by Pol α, Pol δ or Pol ɛ take over on the lagging and leading strand respectively. Pol δ and Pol ɛ perform the bulk of replication with very high fidelity, which is ensured by Watson-Crick base pairing and 3'exonuclease (proofreading) activity. Yeast models have shown that mutations in the exonuclease domain of Pol δ and Pol ɛ homologues can cause a mutator phenotype. Recently, we identified germline exonuclease domain mutations (EDMs) in human POLD1 and POLE that predispose to 'polymerase proofreading associated polyposis' (PPAP), a disease characterised by multiple colorectal adenomas and carcinoma, with high penetrance and dominant inheritance. Moreover, somatic EDMs in POLE have also been found in sporadic colorectal and endometrial cancers. Tumors with EDMs are microsatellite stable and show an 'ultramutator' phenotype, with a dramatic increase in base substitutions.

  10. DNA ligase I, the replicative DNA ligase.

    Science.gov (United States)

    Howes, Timothy R L; Tomkinson, Alan E

    2012-01-01

    Multiple DNA ligation events are required to join the Okazaki fragments generated during lagging strand DNA synthesis. In eukaryotes, this is primarily carried out by members of the DNA ligase I family. The C-terminal catalytic region of these enzymes is composed of three domains: a DNA binding domain, an adenylation domain and an OB-fold domain. In the absence of DNA, these domains adopt an extended structure but transition into a compact ring structure when they engage a DNA nick, with each of the domains contacting the DNA. The non-catalytic N-terminal region of eukaryotic DNA ligase I is responsible for the specific participation of these enzymes in DNA replication. This proline-rich unstructured region contains the nuclear localization signal and a PCNA interaction motif that is critical for localization to replication foci and efficient joining of Okazaki fragments. DNA ligase I initially engages the PCNA trimer via this interaction motif which is located at the extreme N-terminus of this flexible region. It is likely that this facilitates an additional interaction between the DNA binding domain and the PCNA ring. The similar size and shape of the rings formed by the PCNA trimer and the DNA ligase I catalytic region when it engages a DNA nick suggest that these proteins interact to form a double-ring structure during the joining of Okazaki fragments. DNA ligase I also interacts with replication factor C, the factor that loads the PCNA trimeric ring onto DNA. This interaction, which is regulated by phosphorylation of the non-catalytic N-terminus of DNA ligase I, also appears to be critical for DNA replication.

  11. Advanced Patient Data Replication and Recovery

    Science.gov (United States)

    2010-10-01

    able to “dial” the bandwidth back down to the 10Mbps range to reduce 8 the cost of the data link back to EMC. EMC2 Centera replication is the...automation robot (which fills pharmacy orders) and the drug dispensing kiosks located near the nurse stations in the hospital. These systems have...with appropriate workspaces, including telephone and internet service, for several weeks if needed. 11. Hotels must be available within 15

  12. Permeability testing of drilling core sample from pavement

    Institute of Scientific and Technical Information of China (English)

    Suda WANG; Zhengguang TANG; Xiaojun NING; Peiguan WU; Pingyi XING

    2008-01-01

    The permeability coefficient of pavement material is a very important parameter in designing the drainage of pavement structures and is also used to evalu-ate the quality of road construction. New equipment is used to measure the permeability coefficient of the pave-ment drilling core sample and relevant testing methods are introduced. Testing drilling core samples from a certain highway of Yunnan province has been proven to be feas-ible. The test results are also analyzed.

  13. Development of Low Permeability Oilfields in Shengli Oil Province

    Institute of Scientific and Technical Information of China (English)

    Wang Binhai; Fan Naifu

    1995-01-01

    @@ Shengli oil province,complicated in geology and rich in resources, is the second largest oil production basin of China. Except for some big/medium sized oil/gas field with high and medium permeability which have already been put into production. There are 11oil fields at great depth with low permeability of less than 50 ×10-3 μm2 have been discovered with 12. 2% of the total proved original oil in place.

  14. Factors Affecting Water Permeability of Aleurone Layer in Soybean Seeds

    OpenAIRE

    Noda, Hiroko; Fukuda, Mitsuru

    1999-01-01

    The effect of the immersion condition of soybean seeds on the water permeability in aleurone layer was investigated to clarify the water permeability at the initial stage of water sorption. The amounts of water absorbed in seeds coated with only aleurone layer (embryos uncovered with seed coat) and untreated seeds (embryos covered with seed coat and aleurone layer; intact seeds) were compared under several conditions of temperature, pH, ion species, and salt concentration. The relative weight...

  15. Regional variability in the permeability of human dentine.

    Science.gov (United States)

    Pashley, D H; Andringa, H J; Derkson, G D; Derkson, M E; Kalathoor, S R

    1987-01-01

    This was measured qualitatively by using dyes and quantitatively by hydraulic conductance in dentine discs and crown segments in vitro. Both types of preparation demonstrated large regional differences in permeability, with the highest values at the periphery and the lowest in the centre of the disc or crown. As dentine permeability may vary 3-10-fold across a few millimetres, investigators should use as large a surface area as possible to compensate for these regional differences.

  16. Swelling and Replicative DNA Synthesis of Detergent-treated Mouse Ascites Sarcoma Cells

    Directory of Open Access Journals (Sweden)

    Seki,Shuji

    1978-04-01

    Full Text Available Previous investigation showed that mouse ascites sarcoma cells permeabilized with appropriate concentrations of detergents (Triton X-100, Nonidet P-40 and Brij 58 had high replicative DNA synthesis in the presence of the four deoxyribonucleoside triphosphates, ATP, Mg2+ and proper ionic environment. The present study showed the optimum detergent concentration for DNA synthesis coincided closely with the minimum detergent concentration for inducing cell swelling. Phase contrast microscopy and electron microscopy of Triton-permeabilized cells showed the characteristic swollen cytoplasms and nucleus. Autoradiographic study showed that the DNA synthesis in permeable cells was confined to the nucleus. Cell viability and [3H] deoxythymidine uptake were impaired at much lower concentrations of Triton X-100 than the optimum concentration for in vitro DNA synthesis. In Triton-permeabilized cells, the minimum Triton concentration that produced cell swelling also seemed to produce high repliative DNA synthesis, which reflects the in vivo state of DNA synthesis.

  17. Ultrastructural Characterization of Zika Virus Replication Factories

    Directory of Open Access Journals (Sweden)

    Mirko Cortese

    2017-02-01

    Full Text Available A global concern has emerged with the pandemic spread of Zika virus (ZIKV infections that can cause severe neurological symptoms in adults and newborns. ZIKV is a positive-strand RNA virus replicating in virus-induced membranous replication factories (RFs. Here we used various imaging techniques to investigate the ultrastructural details of ZIKV RFs and their relationship with host cell organelles. Analyses of human hepatic cells and neural progenitor cells infected with ZIKV revealed endoplasmic reticulum (ER membrane invaginations containing pore-like openings toward the cytosol, reminiscent to RFs in Dengue virus-infected cells. Both the MR766 African strain and the H/PF/2013 Asian strain, the latter linked to neurological diseases, induce RFs of similar architecture. Importantly, ZIKV infection causes a drastic reorganization of microtubules and intermediate filaments forming cage-like structures surrounding the viral RF. Consistently, ZIKV replication is suppressed by cytoskeleton-targeting drugs. Thus, ZIKV RFs are tightly linked to rearrangements of the host cell cytoskeleton.

  18. Break-Induced Replication and Genome Stability

    Directory of Open Access Journals (Sweden)

    Anna Malkova

    2012-10-01

    Full Text Available Genetic instabilities, including mutations and chromosomal rearrangements, lead to cancer and other diseases in humans and play an important role in evolution. A frequent cause of genetic instabilities is double-strand DNA breaks (DSBs, which may arise from a wide range of exogeneous and endogeneous cellular factors. Although the repair of DSBs is required, some repair pathways are dangerous because they may destabilize the genome. One such pathway, break-induced replication (BIR, is the mechanism for repairing DSBs that possesses only one repairable end. This situation commonly arises as a result of eroded telomeres or collapsed replication forks. Although BIR plays a positive role in repairing DSBs, it can alternatively be a dangerous source of several types of genetic instabilities, including loss of heterozygosity, telomere maintenance in the absence of telomerase, and non-reciprocal translocations. Also, mutation rates in BIR are about 1000 times higher as compared to normal DNA replication. In addition, micro-homology-mediated BIR (MMBIR, which is a mechanism related to BIR, can generate copy-number variations (CNVs as well as various complex chromosomal rearrangements. Overall, activation of BIR may contribute to genomic destabilization resulting in substantial biological consequences including those affecting human health.

  19. The molecular biology of Bluetongue virus replication.

    Science.gov (United States)

    Patel, Avnish; Roy, Polly

    2014-03-01

    The members of Orbivirus genus within the Reoviridae family are arthropod-borne viruses which are responsible for high morbidity and mortality in ruminants. Bluetongue virus (BTV) which causes disease in livestock (sheep, goat, cattle) has been in the forefront of molecular studies for the last three decades and now represents the best understood orbivirus at a molecular and structural level. The complex nature of the virion structure has been well characterised at high resolution along with the definition of the virus encoded enzymes required for RNA replication; the ordered assembly of the capsid shell as well as the protein and genome sequestration required for it; and the role of host proteins in virus entry and virus release. More recent developments of Reverse Genetics and Cell-Free Assembly systems have allowed integration of the accumulated structural and molecular knowledge to be tested at meticulous level, yielding higher insight into basic molecular virology, from which the rational design of safe efficacious vaccines has been possible. This article is centred on the molecular dissection of BTV with a view to understanding the role of each protein in the virus replication cycle. These areas are important in themselves for BTV replication but they also indicate the pathways that related viruses, which includes viruses that are pathogenic to man and animals, might also use providing an informed starting point for intervention or prevention.

  20. Continuously Cumulating Meta-Analysis and Replicability.

    Science.gov (United States)

    Braver, Sanford L; Thoemmes, Felix J; Rosenthal, Robert

    2014-05-01

    The current crisis in scientific psychology about whether our findings are irreproducible was presaged years ago by Tversky and Kahneman (1971), who noted that even sophisticated researchers believe in the fallacious Law of Small Numbers-erroneous intuitions about how imprecisely sample data reflect population phenomena. Combined with the low power of most current work, this often leads to the use of misleading criteria about whether an effect has replicated. Rosenthal (1990) suggested more appropriate criteria, here labeled the continuously cumulating meta-analytic (CCMA) approach. For example, a CCMA analysis on a replication attempt that does not reach significance might nonetheless provide more, not less, evidence that the effect is real. Alternatively, measures of heterogeneity might show that two studies that differ in whether they are significant might have only trivially different effect sizes. We present a nontechnical introduction to the CCMA framework (referencing relevant software), and then explain how it can be used to address aspects of replicability or more generally to assess quantitative evidence from numerous studies. We then present some examples and simulation results using the CCMA approach that show how the combination of evidence can yield improved results over the consideration of single studies.

  1. Early steps of retrovirus replicative cycle

    Directory of Open Access Journals (Sweden)

    Saïb Ali

    2004-05-01

    Full Text Available Abstract During the last two decades, the profusion of HIV research due to the urge to identify new therapeutic targets has led to a wealth of information on the retroviral replication cycle. However, while the late stages of the retrovirus life cycle, consisting of virus replication and egress, have been partly unraveled, the early steps remain largely enigmatic. These early steps consist of a long and perilous journey from the cell surface to the nucleus where the proviral DNA integrates into the host genome. Retroviral particles must bind specifically to their target cells, cross the plasma membrane, reverse-transcribe their RNA genome, while uncoating the cores, find their way to the nuclear membrane and penetrate into the nucleus to finally dock and integrate into the cellular genome. Along this journey, retroviruses hijack the cellular machinery, while at the same time counteracting cellular defenses. Elucidating these mechanisms and identifying which cellular factors are exploited by the retroviruses and which hinder their life cycle, will certainly lead to the discovery of new ways to inhibit viral replication and to improve retroviral vectors for gene transfer. Finally, as proven by many examples in the past, progresses in retrovirology will undoubtedly also provide some priceless insights into cell biology.

  2. Regulation of AQP0 water permeability is enhanced by cooperativity.

    Science.gov (United States)

    Németh-Cahalan, Karin L; Clemens, Daniel M; Hall, James E

    2013-03-01

    Aquaporin 0 (AQP0), essential for lens clarity, is a tetrameric protein composed of four identical monomers, each of which has its own water pore. The water permeability of AQP0 expressed in Xenopus laevis oocytes can be approximately doubled by changes in calcium concentration or pH. Although each monomer pore functions as a water channel, under certain conditions the pores act cooperatively. In other words, the tetramer is the functional unit. In this paper, we show that changes in external pH and calcium can induce an increase in water permeability that exhibits either a positive cooperativity switch-like increase in water permeability or an increase in water permeability in which each monomer acts independently and additively. Because the concentrations of calcium and hydrogen ions increase toward the center of the lens, a concentration signal could trigger a regulatory change in AQP0 water permeability. It thus seems plausible that the cooperative modes of water permeability regulation by AQP0 tetramers mediated by decreased pH and elevated calcium are the physiologically important ones in the living lens.

  3. The Use Of Permeable Concrete For Ground Water Recharge

    Directory of Open Access Journals (Sweden)

    Akshay Tejankar

    2016-09-01

    Full Text Available In order to develop Smart Cities in India, we need to develop smart technologies and smart construction materials. Permeable concrete an innovative material is environment friendly and a smart material which can be used for construction of several structures. In India, the ground water table is decreasing at a faster rate due to reduction in ground water recharge. These days, the vegetation cover is replaced by infrastructure hence the water gets very less opportunity to infiltrate itself into the soil. If the permeable concrete which has a high porosity is used for the construction of pavements, walking tracks, parking lots, well lining, etc. then it can reduce the runoff from the site and help in the ground water recharge. Such type of smart materials will play an important role for Indian conditions where government is putting lot of efforts to implement ground water recharging techniques. During the research work, the runoff for a particular storm was calculated for a bitumen pavement on a sloping ground. Later after studying the various topographical features, the traffic intensity and the rainfall for that particular area, the concrete was designed and tested for the different proportion and thus the mix design for the permeable concrete was finalized based upon its permeability and strength characteristics. Later by using this permeable concrete the infiltration and runoff for the same storm was compared and studied. The research paper will thus give an account of the properties of permeable concrete where it can be used over an existing road.

  4. Hybrid green permeable pave with hexagonal modular pavement systems

    Science.gov (United States)

    Rashid, M. A.; Abustan, I.; Hamzah, M. O.

    2013-06-01

    Modular permeable pavements are alternatives to the traditional impervious asphalt and concrete pavements. Pervious pore spaces in the surface allow for water to infiltrate into the pavement during rainfall events. As of their ability to allow water to quickly infiltrate through the surface, modular permeable pavements allow for reductions in runoff quantity and peak runoff rates. Even in areas where the underlying soil is not ideal for modular permeable pavements, the installation of under drains has still been shown to reflect these reductions. Modular permeable pavements have been regarded as an effective tool in helping with stormwater control. It also affects the water quality of stormwater runoff. Places using modular permeable pavement has been shown to cause a significant decrease in several heavy metal concentrations as well as suspended solids. Removal rates are dependent upon the material used for the pavers and sub-base material, as well as the surface void space. Most heavy metals are captured in the top layers of the void space fill media. Permeable pavements are now considered an effective BMP for reducing stormwater runoff volume and peak flow. This study examines the extent to which such combined pavement systems are capable of handling load from the vehicles. Experimental investigation were undertaken to quantify the compressive characteristics of the modular. Results shows impressive results of achieving high safety factor for daily life vehicles.

  5. Internal filtration in dialyzers with different membrane permeabilities.

    Science.gov (United States)

    Sato, Yuichi; Kimura, Kenjiro; Chikaraishi, Tatsuya

    2010-07-01

    Over the last decade, hemodialysis with enhanced internal filtration (IF) has been investigated as an alternative to conventional dialysis. Several factors affect IF, including the geometry and permeability of hollow-fiber dialyzers. Although various studies have been performed, the association between IF and membrane permeability has not been fully examined because of the difficulty in measuring IF. Therefore, in this study, we set up an experimental circuit and attempted to directly measure IF as well as membrane permeability in five dialyzers. In the circuit, we placed two dialyzers of the same type in series, and a special sampling port between them, thereby making it possible to determine IF by measuring the extent to which blood was concentrated between the two dialyzers. We showed that a significant amount of IF occurred in this tandem-dialyzer circuit, ranging from 23.5 to 100 ml/min, which increased linearly with increasing membrane permeability. We also showed that membrane permeability was reduced in the first dialyzer to a greater extent than in the second one after four hours of circulation, suggesting that filtration caused substantial membrane fouling. In this study we practically demonstrated that membrane permeability is highly relevant to the phenomenon of IF.

  6. Degree of conversion and permeability of dental adhesives.

    Science.gov (United States)

    Cadenaro, Milena; Antoniolli, Francesca; Sauro, Salvatore; Tay, Franklin R; Di Lenarda, Roberto; Prati, Carlo; Biasotto, Matteo; Contardo, Luca; Breschi, Lorenzo

    2005-12-01

    The aim of this study was to analyse the extent of polymerization of different adhesive films in relation to their permeability. One adhesive of each class was investigated: OptiBond FL; One-Step; Clearfil Protect Bond; and Xeno III. Adhesive films were prepared and cured with XL-2500 (3M ESPE) for 20, 40 or 60 s. Polymerization kinetic curves of the adhesives tested were obtained with differential scanning calorimetry (DSC) and data were correlated with microhardness. The permeability of the adhesives under the same experimental conditions was evaluated on human extracted teeth connected to a permeability device and analysed statistically. The results showed that the extent of polymerization obtained from DSC exotherms was directly correlated with microhardness. An increased level of polymerization after prolonged light-curing was confirmed for all adhesives. Simplified adhesives exhibited a lower extent of polymerization and showed incomplete polymerization, even after 60 s. An inverse correlation was found between the degree of cure and the permeability. This study supports the hypothesis that the permeability of simplified adhesives is correlated with incomplete polymerization of resin monomers and the extent of light exposure. These adhesives may be rendered less permeable by using longer curing times than those recommended by the respective manufacturer.

  7. Replicative intermediates of maize streak virus found during leaf development.

    Science.gov (United States)

    Erdmann, Julia B; Shepherd, Dionne N; Martin, Darren P; Varsani, Arvind; Rybicki, Edward P; Jeske, Holger

    2010-04-01

    Geminiviruses of the genera Begomovirus and Curtovirus utilize three replication modes: complementary-strand replication (CSR), rolling-circle replication (RCR) and recombination-dependent replication (RDR). Using two-dimensional gel electrophoresis, we now show for the first time that maize streak virus (MSV), the type member of the most divergent geminivirus genus, Mastrevirus, does the same. Although mastreviruses have fewer regulatory genes than other geminiviruses and uniquely express their replication-associated protein (Rep) from a spliced transcript, the replicative intermediates of CSR, RCR and RDR could be detected unequivocally within infected maize tissues. All replicative intermediates accumulated early and, to varying degrees, were already present in the shoot apex and leaves at different maturation stages. Relative to other replicative intermediates, those associated with RCR increased in prevalence during leaf maturation. Interestingly, in addition to RCR-associated DNA forms seen in other geminiviruses, MSV also apparently uses dimeric open circular DNA as a template for RCR.

  8. On the scattering of DNA replication completion times

    Science.gov (United States)

    Meilikhov, E. Z.; Farzetdinova, R. M.

    2015-07-01

    Stochasticity of Eukaryotes' DNA replication should not lead to large fluctuations of replication times, which could result in mitotic catastrophes. Fundamental problem that cells face is how to be ensured that entire genome is replicated on time. We develop analytic approach of calculating DNA replication times, that being simplified and approximate, leads, nevertheless, to results practically coincident with those that were obtained by some sophisticated methods. In the framework of that model we consider replication times' scattering and discuss the influence of repair stopping on kinetics of DNA replication. Our main explicit formulae for DNA replication time t r ∝ ( N is the total number of DNA base pairs) is of general character and explains basic features of DNA replication kinetics.

  9. Effect of Antimony, Phosphorous and Salinity on Growth, Root Membrane Permeability and Root Antimony, Iron and Zinc Concentration of Corn in Hydroponic Media

    Directory of Open Access Journals (Sweden)

    H. Barangizi

    2010-08-01

    Full Text Available Antimony (Sb pollution has increased in recent years because of human activities and extensive usage of antimony compounds. To date, only a few researches have been conducted in this field in Iran. The purpose of this research is to determine fresh and dry weight, root permeability percentage and root concentration of Sb, Fe and Zn in the corn. This greenhouse research was performed in hydroponics. A factorial experiment (3 × 2 × 3 with three Sb concentrations (0, 6, 18 mgL-1, with and without P (0, 3 mgL-1, and three concentrations of NaCl (0, 60, 120 mM in three replications was conducted. After 40 days, plants were harvested and the roots and shoots were separated. Increasing Sb concentrations, significantly reduced shoot weight. In the presence of Sb, shoot wet and dry matter increased with phosphorous addition because of the positive effect of phosphorous. Increasing Sb concentration with the same level of phosphorous produced plants with less fresh matter. Roots with lower phosphorous level had higher permeability, and increasing phosphorous concentration had a significant effect on root permeability. The highest and lowest root permeability was related to blank Sb level and 6 mg L-1 level of Sb, respectively. Increasing Sb concentration in nutrient solution first reduced and then significantly increased the root permeability. Root permeability also increased significantly by increasing salinity level in nutrient solution. Root Fe concentration of blank phosphorous level was about 13 percent higher than 3 mg L-1 of phosphorous but there was no significant difference in root Fe concentration between species in nutrient solutions with different levels of Sb and NaCl concentrations. The addition of Sb decreased root Zn concentration.

  10. The Effect of Temperature and Rock Permeability on Oil-Water Relative Permeability Curves of Waxy Crude Oil

    Directory of Open Access Journals (Sweden)

    Liyuan Cao

    2016-04-01

    Full Text Available Wax deposition has always been a problem for the production of waxy crude oil. When the reservoir temperature is below the wax appearance temperature (WAT, wax would precipitate in the oil phase as wax crystals, which could increase the oil viscosity and decrease the permeability of the rock. In this study, a series of core flooding experiments under 5 different temperatures and using two groups of core samples with permeability liein300 md and 1000 md respectively were carried out to investigate the effect of temperature and rock permeability on waxy crude oil-water relative permeability curves under reservoir condition. The results revealed that temperature has a significant influence on relative permeability, especially when the temperature is below the WAT (70℃ in this study. The initial water decreased by 40% and the residual oil saturation increased to about 2.5 times when temperature decreased from 85℃ to 50℃ for experiments of both two groups in this study. Oil recovery decreased as the temperature dropped. There was not much difference between the oil recovery of cores with permeability of 1000 md and that with permeability of 300 md until the temperature dropped to 70℃, and the difference increased to 8% when temperature decreased to 50℃, which implies that reservoir with lower permeability is easier to be damaged by wax deposition only when the temperature drops to below WAT. According to this work, it is suggested that reservoir temperature should be better maintained higher than theWAT when extracting waxy crude oil of this reservoir, or at least above 60℃.

  11. Histophilus somni Stimulates Expression of Antiviral Proteins and Inhibits BRSV Replication in Bovine Respiratory Epithelial Cells.

    Directory of Open Access Journals (Sweden)

    C Lin

    Full Text Available Our previous studies showed that bovine respiratory syncytial virus (BRSV followed by Histophilus somni causes more severe bovine respiratory disease and a more permeable alveolar barrier in vitro than either agent alone. However, microarray analysis revealed the treatment of bovine alveolar type 2 (BAT2 epithelial cells with H. somni concentrated culture supernatant (CCS stimulated up-regulation of four antiviral protein genes as compared with BRSV infection or dual treatment. This suggested that inhibition of viral infection, rather than synergy, may occur if the bacterial infection occurred before the viral infection. Viperin (or radical S-adenosyl methionine domain containing 2--RSAD2 and ISG15 (IFN-stimulated gene 15--ubiquitin-like modifier were most up-regulated. CCS dose and time course for up-regulation of viperin protein levels were determined in treated bovine turbinate (BT upper respiratory cells and BAT2 lower respiratory cells by Western blotting. Treatment of BAT2 cells with H. somni culture supernatant before BRSV infection dramatically reduced viral replication as determined by qRT PCR, supporting the hypothesis that the bacterial infection may inhibit viral infection. Studies of the role of the two known H. somni cytotoxins showed that viperin protein expression was induced by endotoxin (lipooligosaccharide but not by IbpA, which mediates alveolar permeability and H. somni invasion. A naturally occurring IbpA negative asymptomatic carrier strain of H. somni (129Pt does not cause BAT2 cell retraction or permeability of alveolar cell monolayers, so lacks virulence in vitro. To investigate initial steps of pathogenesis, we showed that strain 129Pt attached to BT cells and induced a strong viperin response in vitro. Thus colonization of the bovine upper respiratory tract with an asymptomatic carrier strain lacking virulence may decrease viral infection and the subsequent enhancement of bacterial respiratory infection in vivo.

  12. A fast Laplace solver approach to pore scale permeability

    Science.gov (United States)

    Arns, Christoph; Adler, Pierre

    2017-04-01

    The permeability of a porous medium can be derived by solving the Stokes equations in the pore space with no slip at the walls. The resulting velocity averaged over the pore volume yields the permeability KS by application of the Darcy law. The Stokes equations can be solved by a number of different techniques such as finite differences, finite volume, Lattice Boltzmann, but whatever the technique it remains a heavy task since there are four unknowns at each node (the three velocity components and the pressure) which necessitate the solution of four equations (the projection of Newton's law on each axis and mass conservation). By comparison, the Laplace equation is scalar with a single unknown at each node. The objective of this work is to replace the Stokes equations by an elliptical equation with a space dependent permeability. More precisely, the local permeability k is supposed to be proportional to (r-alpha)**2 where r is the distance of the voxel to the closest wall, and alpha a constant; k is zero in the solid phase. The elliptical equation is div(k gradp)=0. A macroscopic pressure gradient is assumed to be exerted on the medium and again the resulting velocity averaged over space yields a permeability K_L. In order to validate this method, systematic calculations have been performed. First, elementary shapes (plane channel, circular pipe, rectangular channels) were studied for which flow occurs along parallel lines in which case KL is the arithmetic average of the k's. KL was calculated for various discretizations of the pore space and various values of alpha. For alpha=0.5, the agreement with the exact analytical value of KS is excellent for the plane and rectangular channels while it is only approximate for circular pipes. Second, the permeability KL of channels with sinusoidal walls was calculated and compared with analytical results and numerical ones provided by a Lattice Boltzmann algorithm. Generally speaking, the discrepancy does not exceed 25% when

  13. Replication of plasmids in gram-negative bacteria.

    OpenAIRE

    1989-01-01

    Replication of plasmid deoxyribonucleic acid (DNA) is dependent on three stages: initiation, elongation, and termination. The first stage, initiation, depends on plasmid-encoded properties such as the replication origin and, in most cases, the replication initiation protein (Rep protein). In recent years the understanding of initiation and regulation of plasmid replication in Escherichia coli has increased considerably, but it is only for the ColE1-type plasmids that significant biochemical d...

  14. PCNA Modifications for Regulation of Post-Replication Repair Pathways

    OpenAIRE

    2008-01-01

    Stalled DNA replication forks activate specific DNA repair mechanism called post-replication repair (PRR) pathways that simply bypass DNA damage. The bypassing of DNA damage by PRR prevents prolonged stalling of DNA replication that could result in double strand breaks (DSBs). Proliferating cell nuclear antigen (PCNA) functions to initiate and choose different bypassing pathways of PRR. In yeast, DNA replication forks stalled by DNA damage induces monoubiquitination of PCNA at K164, which is ...

  15. Mathematical Framework for A Novel Database Replication Algorithm

    Directory of Open Access Journals (Sweden)

    Divakar Singh Yadav

    2013-10-01

    Full Text Available In this paper, the detailed overview of the database replication is presented. Thereafter, PDDRA (Pre-fetching based dynamic data replication algorithm algorithm as recently published is detailed. In this algorithm, further, modifications are suggested to minimize the delay in data replication. Finally a mathematical framework is presented to evaluate mean waiting time before a data can be replicated on the requested site.

  16. Checkpoint responses to replication stalling: inducing tolerance and preventing mutagenesis

    Energy Technology Data Exchange (ETDEWEB)

    Kai, Mihoko; Wang, Teresa S.-F

    2003-11-27

    Replication mutants often exhibit a mutator phenotype characterized by point mutations, single base frameshifts, and the deletion or duplication of sequences flanked by homologous repeats. Mutation in genes encoding checkpoint proteins can significantly affect the mutator phenotype. Here, we use fission yeast (Schizosaccharomyces pombe) as a model system to discuss the checkpoint responses to replication perturbations induced by replication mutants. Checkpoint activation induced by a DNA polymerase mutant, aside from delay of mitotic entry, up-regulates the translesion polymerase DinB (Pol{kappa}). Checkpoint Rad9-Rad1-Hus1 (9-1-1) complex, which is loaded onto chromatin by the Rad17-Rfc2-5 checkpoint complex in response to replication perturbation, recruits DinB onto chromatin to generate the point mutations and single nucleotide frameshifts in the replication mutator. This chain of events reveals a novel checkpoint-induced tolerance mechanism that allows cells to cope with replication perturbation, presumably to make possible restarting stalled replication forks. Fission yeast Cds1 kinase plays an essential role in maintaining DNA replication fork stability in the face of DNA damage and replication fork stalling. Cds1 kinase is known to regulate three proteins that are implicated in maintaining replication fork stability: Mus81-Eme1, a hetero-dimeric structure-specific endonuclease complex; Rqh1, a RecQ-family helicase involved in suppressing inappropriate recombination during replication; and Rad60, a protein required for recombinational repair during replication. These Cds1-regulated proteins are thought to cooperatively prevent mutagenesis and maintain replication fork stability in cells under replication stress. These checkpoint-regulated processes allow cells to survive replication perturbation by preventing stalled replication forks from degenerating into deleterious DNA structures resulting in genomic instability and cancer development.

  17. Systematic determination of replication activity type highlights interconnections between replication, chromatin structure and nuclear localization.

    Directory of Open Access Journals (Sweden)

    Shlomit Farkash-Amar

    Full Text Available DNA replication is a highly regulated process, with each genomic locus replicating at a distinct time of replication (ToR. Advances in ToR measurement technology enabled several genome-wide profiling studies that revealed tight associations between ToR and general genomic features and a remarkable ToR conservation in mammals. Genome wide studies further showed that at the hundreds kb-to-megabase scale the genome can be divided into constant ToR regions (CTRs in which the replication process propagates at a faster pace due to the activation of multiple origins and temporal transition regions (TTRs in which the replication process propagates at a slower pace. We developed a computational tool that assigns a ToR to every measured locus and determines its replication activity type (CTR versus TTR. Our algorithm, ARTO (Analysis of Replication Timing and Organization, uses signal processing methods to fit a constant piece-wise linear curve to the measured raw data. We tested our algorithm and provide performance and usability results. A Matlab implementation of ARTO is available at http://bioinfo.cs.technion.ac.il/people/zohar/ARTO/. Applying our algorithm to ToR data measured in multiple mouse and human samples allowed precise genome-wide ToR determination and replication activity type characterization. Analysis of the results highlighted the plasticity of the replication program. For example, we observed significant ToR differences in 10-25% of the genome when comparing different tissue types. Our analyses also provide evidence for activity type differences in up to 30% of the probes. Integration of the ToR data with multiple aspects of chromosome organization characteristics suggests that ToR plays a role in shaping the regional chromatin structure. Namely, repressive chromatin marks, are associated with late ToR both in TTRs and CTRs. Finally, characterization of the differences between TTRs and CTRs, with matching ToR, revealed that TTRs are

  18. Chromatin Dynamics During DNA Replication and Uncharacterized Replication Factors determined by Nascent Chromatin Capture (NCC) Proteomics

    Science.gov (United States)

    Alabert, Constance; Bukowski-Wills, Jimi-Carlo; Lee, Sung-Bau; Kustatscher, Georg; Nakamura, Kyosuke; de Lima Alves, Flavia; Menard, Patrice; Mejlvang, Jakob; Rappsilber, Juri; Groth, Anja

    2014-01-01

    SUMMARY To maintain genome function and stability, DNA sequence and its organization into chromatin must be duplicated during cell division. Understanding how entire chromosomes are copied remains a major challenge. Here, we use Nascent Chromatin Capture (NCC) to profile chromatin proteome dynamics during replication in human cells. NCC relies on biotin-dUTP labelling of replicating DNA, affinity-purification and quantitative proteomics. Comparing nascent chromatin with mature post-replicative chromatin, we provide association dynamics for 3995 proteins. The replication machinery and 485 chromatin factors like CAF-1, DNMT1, SUV39h1 are enriched in nascent chromatin, whereas 170 factors including histone H1, DNMT3, MBD1-3 and PRC1 show delayed association. This correlates with H4K5K12diAc removal and H3K9me1 accumulation, while H3K27me3 and H3K9me3 remain unchanged. Finally, we combine NCC enrichment with experimentally derived chromatin probabilities to predict a function in nascent chromatin for 93 uncharacterized proteins and identify FAM111A as a replication factor required for PCNA loading. Together, this provides an extensive resource to understand genome and epigenome maintenance. PMID:24561620

  19. Decontamination of groundwater by permeable reactive barriers; Descontaminacion de aguas subterraneas mediante barreras reactivas permeables

    Energy Technology Data Exchange (ETDEWEB)

    Navarro Flores, A.; Chimenos, J. M.

    2002-07-01

    Passive in-situ remediation techniques have seen increased application at contaminated aquifers in recent years as a means of contaminant control and as means of passively treating contaminants in groundwater, because of their low economic cost and minor ground occupation. Permeable reactive barriers (PRBs) are based on the creation of a subsurface barrier, where groundwater contaminants are intercepted in the saturated zone, establishing a passive system of control and contamination treatment, in particular in the heavy metals removal. This paper discusses, related to PRBs experimentation, the results obtained from laboratory experiences by means of Mg oxides and sandy soils as barrier materials, showing a high removal of Cd, Cu, Ni, Fe, Pb and Zn. (Author) 21 refs.

  20. Building up and breaking down: mechanisms controlling recombination during replication.

    Science.gov (United States)

    Branzei, Dana; Szakal, Barnabas

    2017-08-01

    The complete and faithful duplication of the genome is an essential prerequisite for proliferating cells to maintain genome integrity. This objective is greatly challenged by DNA damage encountered during replication, which causes fork stalling and in certain cases, fork breakage. DNA damage tolerance (DDT) pathways mitigate the effects on fork stability induced by replication fork stalling by mediating damage-bypass and replication fork restart. These DDT mechanisms, largely relying on homologous recombination (HR) and specialized polymerases, can however contribute to genome rearrangements and mutagenesis. There is a profound connection between replication and recombination: recombination proteins protect replication forks from nuclease-mediated degradation of the nascent DNA strands and facilitate replication completion in cells challenged by DNA damage. Moreover, in case of fork collapse and formation of double strand breaks (DSBs), the recombination factors present or recruited to the fork facilitate HR-mediated DSB repair, which is primarily error-free. Disruption of HR is inexorably linked to genome instability, but the premature activation of HR during replication often leads to genome rearrangements. Faithful replication necessitates the downregulation of HR and disruption of active RAD51 filaments at replication forks, but upon persistent fork stalling, building up of HR is critical for the reorganization of the replication fork and for filling-in of the gaps associated with discontinuous replication induced by DNA lesions. Here we summarize and reflect on our understanding of the mechanisms that either suppress recombination or locally enhance it during replication, and the principles that underlie this regulation.

  1. Uncoupling of Sister Replisomes during Eukaryotic DNA Replication

    NARCIS (Netherlands)

    Yardimci, Hasan; Loveland, Anna B.; Habuchi, Satoshi; van Oijen, Antoine M.; Walter, Johannes C.

    2010-01-01

    The duplication of eukaryotic genomes involves the replication of DNA from multiple origins of replication. In S phase, two sister replisomes assemble at each active origin, and they replicate DNA in opposite directions. Little is known about the functional relationship between sister replisomes.

  2. Visualizing Single-molecule DNA Replication with Fluorescence Microscopy

    NARCIS (Netherlands)

    Tanner, Nathan A.; Loparo, Joseph J.; Oijen, Antoine M. van

    2009-01-01

    We describe a simple fluorescence microscopy-based real-time method for observing DNA replication at the single-molecule level. A circular, forked DNA template is attached to a functionalized glass coverslip and replicated extensively after introduction of replication proteins and nucleotides. The

  3. Uncoupling of Sister Replisomes during Eukaryotic DNA Replication

    NARCIS (Netherlands)

    Yardimci, Hasan; Loveland, Anna B.; Habuchi, Satoshi; van Oijen, Antoine M.; Walter, Johannes C.

    2010-01-01

    The duplication of eukaryotic genomes involves the replication of DNA from multiple origins of replication. In S phase, two sister replisomes assemble at each active origin, and they replicate DNA in opposite directions. Little is known about the functional relationship between sister replisomes. So

  4. Geminin: a major DNA replication safeguard in higher eukaryotes

    DEFF Research Database (Denmark)

    Melixetian, Marina; Helin, Kristian

    2004-01-01

    Eukaryotes have evolved multiple mechanisms to restrict DNA replication to once per cell cycle. These mechanisms prevent relicensing of origins of replication after initiation of DNA replication in S phase until the end of mitosis. Most of our knowledge of mechanisms controlling prereplication...

  5. Anaphase onset before complete DNA replication with intact checkpoint responses

    DEFF Research Database (Denmark)

    Torres-Rosell, Jordi; De Piccoli, Giacomo; Cordon-Preciado, Violeta

    2007-01-01

    Cellular checkpoints prevent mitosis in the presence of stalled replication forks. Whether checkpoints also ensure the completion of DNA replication before mitosis is unknown. Here, we show that in yeast smc5-smc6 mutants, which are related to cohesin and condensin, replication is delayed, most...

  6. Visualizing Single-molecule DNA Replication with Fluorescence Microscopy

    NARCIS (Netherlands)

    Tanner, Nathan A.; Loparo, Joseph J.; Oijen, Antoine M. van

    2009-01-01

    We describe a simple fluorescence microscopy-based real-time method for observing DNA replication at the single-molecule level. A circular, forked DNA template is attached to a functionalized glass coverslip and replicated extensively after introduction of replication proteins and nucleotides. The g

  7. Geminin: a major DNA replication safeguard in higher eukaryotes

    DEFF Research Database (Denmark)

    Melixetian, Marina; Helin, Kristian

    2004-01-01

    Eukaryotes have evolved multiple mechanisms to restrict DNA replication to once per cell cycle. These mechanisms prevent relicensing of origins of replication after initiation of DNA replication in S phase until the end of mitosis. Most of our knowledge of mechanisms controlling prereplication...

  8. Replication NAND gate with light as input and output.

    Science.gov (United States)

    Samiappan, Manickasundaram; Dadon, Zehavit; Ashkenasy, Gonen

    2011-01-14

    Logic operations can highlight information transfer within complex molecular networks. We describe here the design of a peptide-based replication system that can be detected by following its fluorescence quenching. This process is used to negate the signal of light-activated replication, and thus to prepare the first replication NAND gate.

  9. Evaluation of permeable and non-permeable tritium in normal condition in a fusion reactor

    Energy Technology Data Exchange (ETDEWEB)

    Marta, V; Manuel, P J [Instituto de Fusion Nuclear (DENIM)/ETSII, Universidad Politecnica Madrid (UPM) (Spain); Sedano Luis, A [Ministerio de Educacion y Ciencia, Ciemat (Spain)], E-mail: marta@denim.upm.es

    2008-05-15

    The tritium cycle, technologies of process and control of the tritium in the plant will constitute a fraction of the environmental impact of the first generation of DT fusion reactors. The efforts of conceptual development of the tritium cycle are centered in the Internal Regenerator Cycle. The tritium could be recovered from a flow of He gas, or directly from solid breeder. The limits of transfers to the atmosphere are assumed {approx} 1 gr-T/a ({approx}20 Ci/a) (without species distinction). In the case of ITER, for example, we have global demands of control of 5 orders of magnitude have been demonstrated at experimental level. The transfer limits determine the key parameters in tritium Cycle (HT, HTO, as dominant, and T2, T2O as marginal). Presently, the transfer from the cycle to the environment is assumed through the exchange system of the power plant (primary to secondary). That transport is due to the permeation through HT, T2, or leakage to the coolant in the primary system. It is key the chemical optimization in the primary system, that needs to be reanalyzed in terms of radiological impact both for permeable, HT, T2, and non-permeable HTO, T2O. It is necessary considered the pathway of tritium from the reactor to the atmosphere, these processes are modelled adequately. Results of the assessments were early and chronic doses which have been evaluated for the Most Exposed Individual at particular distance bands from the release point. The impact evaluations will be performed with the computational tools (NORMTRI), besides national regulatory models, internationally accepted computer these code for dosimetric evaluations of tritiated effluents in operational conditions.

  10. Assembling semiconductor nanocomposites using DNA replication technologies.

    Energy Technology Data Exchange (ETDEWEB)

    Heimer, Brandon W.; Crown, Kevin K.; Bachand, George David

    2005-11-01

    Deoxyribonucleic acid (DNA) molecules represent Nature's genetic database, encoding the information necessary for all cellular processes. From a materials engineering perspective, DNA represents a nanoscale scaffold with highly refined structure, stability across a wide range of environmental conditions, and the ability to interact with a range of biomolecules. The ability to mass-manufacture functionalized DNA strands with Angstrom-level resolution through DNA replication technology, however, has not been explored. The long-term goal of the work presented in this report is focused on exploiting DNA and in vitro DNA replication processes to mass-manufacture nanocomposite materials. The specific objectives of this project were to: (1) develop methods for replicating DNA strands that incorporate nucleotides with ''chemical handles'', and (2) demonstrate attachment of nanocrystal quantum dots (nQDs) to functionalized DNA strands. Polymerase chain reaction (PCR) and primer extension methodologies were used to successfully synthesize amine-, thiol-, and biotin-functionalized DNA molecules. Significant variability in the efficiency of modified nucleotide incorporation was observed, and attributed to the intrinsic properties of the modified nucleotides. Noncovalent attachment of streptavidin-coated nQDs to biotin-modified DNA synthesized using the primer extension method was observed by epifluorescence microscopy. Data regarding covalent attachment of nQDs to amine- and thiol-functionalized DNA was generally inconclusive; alternative characterization tools are necessary to fully evaluate these attachment methods. Full realization of this technology may facilitate new approaches to manufacturing materials at the nanoscale. In addition, composite nQD-DNA materials may serve as novel recognition elements in sensor devices, or be used as diagnostic tools for forensic analyses. This report summarizes the results obtained over the course of this 1-year

  11. The IFITMs Inhibit Zika Virus Replication

    Directory of Open Access Journals (Sweden)

    George Savidis

    2016-06-01

    Full Text Available Zika virus has emerged as a severe health threat with a rapidly expanding range. The IFITM family of restriction factors inhibits the replication of a broad range of viruses, including the closely related flaviruses West Nile virus and dengue virus. Here, we show that IFITM1 and IFITM3 inhibit Zika virus infection early in the viral life cycle. Moreover, IFITM3 can prevent Zika-virus-induced cell death. These results suggest that strategies to boost the actions and/or levels of the IFITMs might be useful for inhibiting a broad range of emerging viruses.

  12. Multiscale modeling of virus replication and spread.

    Science.gov (United States)

    Kumberger, Peter; Frey, Felix; Schwarz, Ulrich S; Graw, Frederik

    2016-07-01

    Replication and spread of human viruses is based on the simultaneous exploitation of many different host functions, bridging multiple scales in space and time. Mathematical modeling is essential to obtain a systems-level understanding of how human viruses manage to proceed through their life cycles. Here, we review corresponding advances for viral systems of large medical relevance, such as human immunodeficiency virus-1 (HIV-1) and hepatitis C virus (HCV). We will outline how the combination of mathematical models and experimental data has advanced our quantitative knowledge about various processes of these pathogens, and how novel quantitative approaches promise to fill remaining gaps.

  13. Accounting for PDMS shrinkage when replicating structures

    DEFF Research Database (Denmark)

    Madsen, Morten Hannibal; Feidenhans'l, Nikolaj Agentoft; Hansen, Poul-Erik

    2014-01-01

    are seldom applied to counteract the shrinkage of PDMS. Also, to perform metrological measurements using replica techniques one has to take the shrinkage into account. Thus we report a study of the shrinkage of PDMS with several different mixing ratios and curing temperatures. The shrinkage factor, with its...... associated uncertainty, for PDMS in the range 40 to 120 °C is provided. By applying this correction factor, it is possible to replicate structures with a standard uncertainty of less than 0.2% in lateral dimensions using typical curing temperatures and PDMS mixing ratios in the range 1:6 to 1:20 (agent:base)....

  14. Replication of DNA during barley endosperm development

    DEFF Research Database (Denmark)

    Giese, H.

    1992-01-01

    The incorporation of [6-H-3]-thymidine into DNA of developing barley end sperm was examined by autoradiography of cross sections of seeds and DNA analysis. The majority of nuclear divisions took place in the very young endosperm, but as late as 25 days after anthesis there was evidence for DNA...... replication. The DNA content of the endosperm increases during development and in response to nitrogen application in parallel to the storage protein synthesis profile. The hordein genes were hypersensitive to DNase I treatment throughout development....

  15. The Nature of Stability in Replicating Systems

    Directory of Open Access Journals (Sweden)

    Addy Pross

    2011-02-01

    Full Text Available We review the concept of dynamic kinetic stability, a type of stability associated specifically with replicating entities, and show how it differs from the well-known and established (static kinetic and thermodynamic stabilities associated with regular chemical systems. In the process we demonstrate how the concept can help bridge the conceptual chasm that continues to separate the physical and biological sciences by relating the nature of stability in the animate and inanimate worlds, and by providing additional insights into the physicochemical nature of abiogenesis.

  16. Simulation Studies in Data Replication Strategies

    Institute of Scientific and Technical Information of China (English)

    HarveyB.Newman; IosifC.Legrand

    2001-01-01

    The aim of this work is to present the simulation studies in evaluating different data replication strategies between Regional Centers.The simulation Framework developed within the "Models of Networked Analysis at Rgional Centers”(MONARC) project,as a design and optimization tool for large scale distributed systems,has been used for these modeling studies.Remote client-serer access to database servers as well as ftp-like data transfers have been ralistically simulated and the performance and limitations are presented as a function of the characteristics of the protocol used and the network parameters.

  17. Replication intermediate analysis confirms that chromosomal replication origin initiates from an unusual intergenic region in Caulobacter crescentus.

    Science.gov (United States)

    Brassinga, A K; Marczynski, G T

    2001-11-01

    The alpha-proteobacterium Caulobacter crescentus possesses a developmental cell cycle that restricts chromosome replication to a stalked cell type. The proposed C.crescentus chromosome replication origin (Cori) lies between hemE and RP001, an unusual intergenic region not previously associated with bacterial replication origins, although a similar genomic arrangement is also present at the putative replication origin in the related bacterium Rickettsia prowazekii. The cloned Cori supports autonomous plasmid replication selectively in the stalked cell type implying that replication of the entire chromosome also initiates between hemE and RP001. To confirm this location, we applied the 2-D (N/N) agarose gel electrophoresis technique to resolve and identify chromosome replication intermediates throughout a 30 kb region spanning Cori. Replication initiation in Cori was uniquely characterized by an 'origin bubble and Y-arc' pattern and this observation was supported by simple replication fork 'Y-arc' patterns that characterized the regions flanking Cori. These replication forks originated bi-directionally from within Cori as determined by the fork direction assay. Therefore, chromosomal replication initiates from the unusual hemE/RP001 intergenic region that we propose represents a new class of replication origins.

  18. Method of producing an item with enhanced wetting properties by fast replication and replication tool used in the method

    DEFF Research Database (Denmark)

    2016-01-01

    The invention relates to a replication tool (1) for producing an item (4) with enhanced wetting properties by fast replication, such as injection moulding or extrusion coating. The replication tool (1) comprises a tool surface (2a, 2b) defining a general shape of the item (4). The tool surface (2a...

  19. Theoretical studies of permeability inversion from seismoelectric logs

    Science.gov (United States)

    Hu, H.; Guan, W.; Zhao, W.

    2012-04-01

    Permeability is one of the most important parameters for evaluating the level of difficulty in oil and gas exploitation. A quick, continuous and accurate in-situ estimate of reservoir permeability is highly significant. Stoneley wave logs have been used to determine formation permeability (Tang and Cheng, 1996). However, the inversion errors of this method are too big in low-permeability formations, especially in high-porosity and low-permeability formations resulting from the high clay content in pores. In this study, we propose to invert permeability by using the full waveforms of seismoelectric logs with low frequencies. This method is based on the relationship of permeability with the ratio of the electric excitation intensity to the pressure field's (REP) with respect to the Stoneley wave in seismoelectric logs. By solving the governing equations for electrokinetic coupled wavefields in homogeneous fluid-saturated porous media (Pride, 1994), we calculate the full waveforms of the borehole seismoelectric wavefields excited by a point pressure source and investigate frequency-dependent excitation intensities of the mode waves and excitation intensities of the real branch points in seismoelectric logs. It is found that the REP's phase, which reflects the phase discrepancy between the Stoneley-wave-induced electric field and the acoustic pressure, is sensitive to formation permeability. To check the relation between permeability and REP's phase qualitatively, an approximate expression of the tangent of the REP's argument is derived theoretically as tan(θEP) ≈-ωc/ω = -φη/ (2πfα ∞ρfκ0), where θEPdenotes the arguments of the REP and their principal value is the REP's phase,ω is the angular frequency,ωc is a critical angular frequency that separates the low-frequency viscous flow from the high-frequency inertial flow, φ is the porosity, α∞ is the tortuosity, κ0 is the Darcy permeability, ρf and η are the density and the viscosity of the pore

  20. Evolution of Mudstone Porosity, Permeability, and Microstructure in the Presence of Microorganisms During Vertical Compression

    Science.gov (United States)

    Mills, T.; Reece, J. S.

    2016-12-01

    Here we investigate the influence of microbial activity on the mechanical and transport properties of mudstones during early diagenesis. Despite the proven presence of microbial communities in marine sediments to depths of >500 meters below sea floor (mbsf), little is known about the interactions between microorganisms and sediments, especially during the early stages of burial and compression. To characterize and quantify the impact of microbial activity on mudstone properties, we compare natural mudstone samples treated with iron reducing bacteria Shewanella Oneidensis MR-1 and those without bacteria. Two bulk mudstones are experimentally prepared using sediments from Integrated Ocean Drilling Program Sites U1319 and U1324 in the Gulf of Mexico. The sediments originated from 4-13 mbsf in the Brazos-Trinity Basin and from three depth intervals (3-14 mbsf, 23-32 mbsf, and 493-502 mbsf) in the Ursa Basin. The sediments are dried and ground to clay- and silt-sized particles and homogenized into two natural mudstone powders. These powders are then used to make reproducible mudstone samples through a process called resedimentation, which replicates natural deposition and burial. Changes in microstructure, porosity, compressibility, and permeability are measured while the biotic (with bacteria) and abiotic (without bacteria) mudstones are being uniaxially compressed over several weeks to a maximum stress of 100 kPa. We anticipate that biofilm growth in pore spaces will decrease porosity, compressibility, and permeability, and the resultant microstructural changes created by microorganisms will be evident in high-resolution scanning electron microscope (SEM) images. Recognition of the micro-scale processes that take place during the early stages of mudstone diagenesis, especially those mediated by microbial activity, and their long-term effects on mudstone properties can lead to better identification and more effective production of unconventional hydrocarbon reservoirs.

  1. How reaction and permeability develop in dehydrating systems

    Science.gov (United States)

    Leclère, H. J.; Faulkner, D. R.; Wheeler, J.; Bedford, J. D.

    2016-12-01

    The triggering of earthquakes at intermediate-depth along subduction zones is often explained by dehydration reactions, releasing free-water and allowing pore-fluid pressure build-up. During dehydration reactions, pore-fluid pressure is increased when permeability is low enough to prevent fluid escape. Permeability is not constant during dehydration reactions but is rather changed by porosity changes (i.e. solid volume reduction or pore compaction). The evolution of permeability during dehydration reactions will thus dictate the pore-fluid pressure evolution that will affect rock strength and earthquake triggering. However, our understanding on the coupling between permeability, pore-fluid pressure, microstructures, deformation and reaction rate is incomplete. In some cases, the development of reactions is distributed uniformly and permeability increases steadily throughout the reaction progress. In other cases, reactions will not proceed uniformly and nature along with previous experiments indicate that "reaction fronts" develop. On the large scale, reaction rate and fluid pressure evolution depend on the movement of these fronts. Experimental results are presented on permeability and reaction front evolution during gypsum dehydration - an analogue for silicate dehydration. Triaxial experiments were conducted using polycrystalline gypsum cores with very low initial porosity. Pore-fluid pressure is controlled at one end of the sample and monitored at the other in order to measure permeability. Gypsum cores were dehydrated at a constant temperature of 115°C. Two parameter spaces were explored: the pore-fluid pressure (20, 40 or 60 MPa) that influences reaction rate, and effective confining pressure (60 or 110 MPa) that influences pore-compaction. The evolution of permeability, porosity, reaction rate and pore-fluid pressure are measured throughout the reaction. SEM observations of post-mortem samples collected at three key stages during the reaction shows how the

  2. Experimental investigation of turbulent flow over a permeable rough wall

    Science.gov (United States)

    Kim, T.; Blois, G.; Best, J.; Christensen, K. T.

    2015-12-01

    Permeable walls are encountered in a variety of geophysical flows, including alluvial river beds, canopies and urban environments. Permeable walls possess very different boundary conditions as compared to classic impermeable walls (i.e. the slip condition and penetration of flow into the bed). Permeability allows flow interactions across the wall interface, resulting in notable mass, momentum and energy exchange. Such exchange takes place in the so-called transition layer and often occurs through turbulent flow mechanisms. It is increasingly recognized that turbulence plays a key role in a number of important natural functions, including biogeochemical as well as geomorphological processes. However, the flow physics of the transition layer are still poorly understood due to a lack of quantitative investigation of these permeable systems within which physical and optical access are severely compromised. This is particularly true for state-of-the-art flow measurement techniques such as particle image velocimetry (PIV) that require unaberrated optical access to the measurement locations. To overcome optical limitations, a refractive index matching (RIM) technique was employed herein to gain full optical access to the transition layer. Sodium Iodide aqueous solution (63% by weight and RI ~ 1.496 at 20°C) served as a working fluid, and an acrylic resin (RI ~ 1.499) was chosen for fabricating wall models. Measurements were performed using high-resolution planar PIV in different configurations to characterize the turbulent boundary layer and the transition layer. The wall models comprised uniform spheres packed in a cubic arrangement, and two cases were modeled - impermeable and permeable walls that were both rough. To eliminate the effect of roughness, and thus isolate the effect of permeability, the surface roughness of the two wall models was kept identical. This allowed us to obtain a more meaningful comparison and highlight the impact of wall permeability in natural

  3. Permeability Modification Using a Reactive Alkaline-Soluble Biopolymer

    Energy Technology Data Exchange (ETDEWEB)

    Snadra L. Fox; X. Xie; K. D. Schaller; E. P. Robertson; G. A. Bala

    2003-10-01

    Polymer injection has been used in reservoirs to alleviate contrasting permeability zones. Current technology relies on the use of cross-linking agents to initiate gelation. The use of biological polymers are advantageous in that they can block high permeability areas, are environmentally friendly, and have potential to form reversible gels without the use of hazardous cross-linkers. Recent efforts at the Idaho National Engineering and Environmental Laboratory (INEEL) have produced a reactive alkaline-soluble biopolymer from Agrobacterium sp. ATCC no. 31749 that gels upon decreasing the pH of the polymeric solution. The focus of this study was to determine the impact an alkaline-soluble biopolymer can have on sandstone permeability. Permeability modification was investigated by injecting solubilized biopolymer into Berea sandstone cores and defining the contribution of pH, salt, temperature, and Schuricht crude oil on biopolymer gelation. The biopolymer was soluble in KOH at a pH greater than 11.4 and gelled when the pH dropped below 10.8. The Berea sandstone core buffered the biopolymer solution, decreasing the pH sufficiently to form a gel, which subsequently decreased the permeability. The effluent pH of the control cores injected with 0.01 {und M} KOH (pH 12.0) and 0.10{und M} KOH (pH 13.0) decreased to 10.6 and 12.7, respectively. The permeability of the sandstone core injected with biopolymer was decreased to greater than 95% of the original permeability at 25 C in the presence of 2% NaCl, and Schuricht crude oil; however, the permeability increased when the temperature of the core was increased to 60 C. Residual resistance factors as high as 792 were seen in Berea cores treated with biopolymer. The buffering capacity of sandstone has been demonstrated to reduce the pH of a biopolymer solution sufficiently to cause the polymer to form a stable in-situ gel. This finding could potentially lead to alternate technology for permeability modification, thus

  4. Materials Chemistry and Performance of Silicone-Based Replicating Compounds.

    Energy Technology Data Exchange (ETDEWEB)

    Brumbach, Michael T.; Mirabal, Alex James; Kalan, Michael; Trujillo, Ana B; Hale, Kevin

    2014-11-01

    Replicating compounds are used to cast reproductions of surface features on a variety of materials. Replicas allow for quantitative measurements and recordkeeping on parts that may otherwise be difficult to measure or maintain. In this study, the chemistry and replicating capability of several replicating compounds was investigated. Additionally, the residue remaining on material surfaces upon removal of replicas was quantified. Cleaning practices were tested for several different replicating compounds. For all replicating compounds investigated, a thin silicone residue was left by the replica. For some compounds, additional inorganic species could be identified in the residue. Simple solvent cleaning could remove some residue.

  5. DNA replication origin activation in space and time.

    Science.gov (United States)

    Fragkos, Michalis; Ganier, Olivier; Coulombe, Philippe; Méchali, Marcel

    2015-06-01

    DNA replication begins with the assembly of pre-replication complexes (pre-RCs) at thousands of DNA replication origins during the G1 phase of the cell cycle. At the G1-S-phase transition, pre-RCs are converted into pre-initiation complexes, in which the replicative helicase is activated, leading to DNA unwinding and initiation of DNA synthesis. However, only a subset of origins are activated during any S phase. Recent insights into the mechanisms underlying this choice reveal how flexibility in origin usage and temporal activation are linked to chromosome structure and organization, cell growth and differentiation, and replication stress.

  6. Bovine Colostrum Supplementation During Running Training Increases Intestinal Permeability

    Directory of Open Access Journals (Sweden)

    Grant D. Brinkworth

    2009-12-01

    Full Text Available Endurance exercise training can increase intestinal permeability which may contribute to the development of gastrointestinal symptoms in some athletes. Bovine colostrum (BC supplementation reduces intestinal permeability induced by non-steroidal anti-inflammatory drugs. This study aimed to determine whether BC could also reduce intestinal permeability induced by endurance exercise. Thirty healthy adult males (25.0 ± 4.7 yr; mean ± SD completed eight weeks of running three times per week for 45 minutes at their lactate threshold while consuming 60 g/day of BC, whey protein (WP or control (CON. Intestinal permeability was assessed at baseline and after eight weeks by measuring the ratio of urinary lactulose (L and rhamnose (R excretion. After eight weeks the L/R ratio increased significantly more in volunteers consuming BC (251 ± 140% compared with WP (21 ± 35%, P < 0.05 and CON (−7 ± 13%, P < 0.02. The increase in intestinal permeability with BC may have been due to BC inducing greater leakiness of tight junctions between enterocytes or by increasing macromolecular transport as it does in neonatal gut. Further research should investigate the potential for BC to increase intestinal macromolecular transport in adults.

  7. Transparent anodes for polymer photovoltaics: Oxygen permeability of PEDOT

    DEFF Research Database (Denmark)

    Andersen, M.; Carlé, Jon Eggert; Cruys-Bagger, N.

    2007-01-01

    The oxygen permeability of the transparent organic anode poly(3,4,-ethylene dioxythiophene) with paratoluenesulphonate as the anion (PEDOT:pTS) was determined to be 2.5 +/- 0.7 x 10(-15) cm(3) (STP) CM cm(-2) S-1 Pa-1, and is thus comparable in magnitude to the oxygen permeability of polyethylene......The oxygen permeability of the transparent organic anode poly(3,4,-ethylene dioxythiophene) with paratoluenesulphonate as the anion (PEDOT:pTS) was determined to be 2.5 +/- 0.7 x 10(-15) cm(3) (STP) CM cm(-2) S-1 Pa-1, and is thus comparable in magnitude to the oxygen permeability...... of polyethyleneterephthalate (PET). The oxygen diffusion through bilayers of polyethylene (PE) and PEDOT:pTS and bilayers of PET and PEDOT:pTS was established. The bilayer structures were applied as the carrier substrate and the transparent anode in polymer-based photovoltaic devices employing a mixture of poly(1-methoxy-4......-(2-ethylhexyloxy)-p-phenylenevinylene) (MEH-PPV) and [6,6]-phenyt-C-61-butanoicacidmethylester (PCBM) as the active layer and aluminium as the cathode. The oxygen permeability of the layers and the aluminium cathode was correlated with the lifetime of the solar cell devices. It was found that the performance...

  8. The evaluation of rock permeability with streaming current measurements

    Science.gov (United States)

    Wang, Jun; Hu, Hengshan; Guan, Wei

    2016-09-01

    Rock permeability is an important parameter for the formation evaluation. In this paper, a new method with streaming current is proposed to determine the sample permeability based on the electrokinetic effects, and is proved by the experimental measurements. Corresponding to this method, we have designed an experimental setup and a test system, then performed the streaming current (potential) and electro-osmosis pressure experiments with 23 sandstone samples at 0.05 mol l-1 NaCl solution. The streaming current (potential) coefficient and electro-osmosis pressure coefficient are obtained, respectively, with the experimental data at low frequencies with AC lock-in technique. The electrokinetic permeabilities are further calculated with these coefficients. The results are consistent well with the gas permeability measured with Darcy's law, which verifies the current method for estimating rock permeability. Our measurements are also analysed and compared with previous measurements. The results indicate that our method can reflect the essence of electrokinetic effects better and simplify the electrokinetic measurements as well. In addition, we discuss the influences of experimental artefacts (core holder and confining pressure installation) on the electrokinetic data. The results show that the trough phenomenon, appeared in frequency curves of streaming current (potential) coefficients, is induced by the resonance of the core-holder/vibrator system. This is important for the design of electrokinetic setup and the analysis of low-frequency response of the electrokinetic coupling coefficients.

  9. Dispersion controlled by permeable surfaces: surface properties and scaling

    Energy Technology Data Exchange (ETDEWEB)

    Ling, Bowen; Tartakovsky, Alexandre M.; Battiato, Ilenia

    2016-07-19

    Permeable and porous surfaces are common in natural and engineered systems. Flow and transport above such surfaces are significantly affected by the surface properties, e.g. matrix porosity and permeability. However, the relationship between such properties and macroscopic solute transport is largely unknown. In this work, we focus on mass transport in a two-dimensional channel with permeable porous walls under fully developed laminar flow conditions. By means of perturbation theory and asymptotic analysis, we derive the set of upscaled equations describing mass transport in the coupled channel–porous-matrix system and an analytical expression relating the dispersion coefficient with the properties of the surface, namely porosity and permeability. Our analysis shows that their impact on the dispersion coefficient strongly depends on the magnitude of the Péclet number, i.e. on the interplay between diffusive and advective mass transport. Additionally, we demonstrate different scaling behaviours of the dispersion coefficient for thin or thick porous matrices. Our analysis shows the possibility of controlling the dispersion coefficient, i.e. transverse mixing, by either active (i.e. changing the operating conditions) or passive mechanisms (i.e. controlling matrix effective properties) for a given Péclet number. By elucidating the impact of matrix porosity and permeability on solute transport, our upscaled model lays the foundation for the improved understanding, control and design of microporous coatings with targeted macroscopic transport features.

  10. Testing protein permeability of dialysis membranes using SDS-PAGE.

    Science.gov (United States)

    Mann, H; Melzer, H; Al-Bashir, A; Xu, X Q; Stiller, S

    2002-05-01

    Permeability of dialysis membranes for high molecular weight compounds should be similar to that of the glomerular membrane in order to remove uremic toxins like the human kidney does. In order to evaluate permeability of high-flux dialysis membranes SDS-PAGE is applied for examination of filtrate of dialysers during routine dialysis with different membranes. SDS-PAGE analysis is performed with silver staining method according to the modification of Melzer (5) and consecutive laser densitometry. The protein pattern of filtrate from dialysis membranes is similar to that of the glomerular membrane containing IgG, transferrin, albumin, alpha-1-microglobulin, retinol binding protein and beta-2-microglobulin. Comparing different membranes there are considerable differences depending on cut-off, charge and adsorption capacity of the particular membrane. In all membranes tested permeability of proteins decreases during one treatment session. Protein permeability of high-flux dialysis membranes is similar to the gloemerular membrane but modified according to pore-size, surface charge, adsorption and time on dialysis. In contrast to the glomerular membrane in each of the investigated membranes protein permeability decreases during function.

  11. Hydrogen permeability of Nb membrane annealed under ultra high vacuum

    Energy Technology Data Exchange (ETDEWEB)

    Uchida, Helmut T.; Pundt, Astrid; Kirchheim, Reiner [Institut fuer Materialphysik, Goettingen (Germany); Yamazaki, Yoshihiro [California Institute of Technology, California (United States); Kamegawa, Atsunori; Takamura, Hitoshi; Koike, Junichi; Okada, Masuo [Department of Materials Science, School of Engineering, Tohoku University, Sendai (Japan)

    2007-07-01

    In this research, hydrogen permeability of Pd-free Nb membrane using hydrogen annealing process by ultra high vacuum equipment was investigated. Pure Nb (99.85 percent) was used as membrane. The hydrogen permeation experiment was carried out in the temperature range of 773-1173 K, and the H{sub 2} pressure range of 1-3.5 atm in the inlet side. Hydrogen flux and hydrogen pressures in the inlet side and outlet side of chamber were measured using mass flow meter and capacitance manometer, respectively. Hydrogen permeability was determined by Fick's first low. Effects of annealing conditions and heat treatment under hydrogen atmosphere on hydrogen permeability were investigated. It is supposed that the surface oxidation of Nb is reduced by the hydrogen annealing. Moreover, it is found that the value of hydrogen permeability becomes almost equivalent to the theoretical value when the sample preparation was optimized by an extension of the evacuating time. The best hydrogen permeability is obtained in metal membranes using the annealing under ultra-high vacuum and pure hydrogen atmosphere.

  12. An integrated approach to permeability modeling using micro-models

    Energy Technology Data Exchange (ETDEWEB)

    Hosseini, A.H.; Leuangthong, O.; Deutsch, C.V. [Society of Petroleum Engineers, Canadian Section, Calgary, AB (Canada)]|[Alberta Univ., Edmonton, AB (Canada)

    2008-10-15

    An important factor in predicting the performance of steam assisted gravity drainage (SAGD) well pairs is the spatial distribution of permeability. Complications that make the inference of a reliable porosity-permeability relationship impossible include the presence of short-scale variability in sand/shale sequences; preferential sampling of core data; and uncertainty in upscaling parameters. Micro-modelling is a simple and effective method for overcoming these complications. This paper proposed a micro-modeling approach to account for sampling bias, small laminated features with high permeability contrast, and uncertainty in upscaling parameters. The paper described the steps and challenges of micro-modeling and discussed the construction of binary mixture geo-blocks; flow simulation and upscaling; extended power law formalism (EPLF); and the application of micro-modeling and EPLF. An extended power-law formalism to account for changes in clean sand permeability as a function of macroscopic shale content was also proposed and tested against flow simulation results. There was close agreement between the model and simulation results. The proposed methodology was also applied to build the porosity-permeability relationship for laminated and brecciated facies of McMurray oil sands. Experimental data was in good agreement with the experimental data. 8 refs., 17 figs.

  13. Stochastic back analysis of permeability coefficient using generalized Bayesian method

    Directory of Open Access Journals (Sweden)

    Gui-lan ZHENG

    2008-09-01

    Full Text Available Owing to the fact that the conventional deterministic back analysis of the permeability coefficient cannot reflect the uncertainties of parameters, including the hydraulic head at the boundary, the permeability coefficient and measured hydraulic head, a stochastic back analysis taking consideration of uncertainties of parameters was performed using the generalized Bayesian method. Based on the stochastic finite element method (SFEM for a seepage field, the variable metric algorithm and the generalized Bayesian method, formulas for stochastic back analysis of the permeability coefficient were derived. A case study of seepage analysis of a sluice foundation was performed to illustrate the proposed method. The results indicate that, with the generalized Bayesian method that considers the uncertainties of measured hydraulic head, the permeability coefficient and the hydraulic head at the boundary, both the mean and standard deviation of the permeability coefficient can be obtained and the standard deviation is less than that obtained by the conventional Bayesian method. Therefore, the present method is valid and applicable.

  14. Stress-Induced Permeability Alterations in an Argillaceous Limestone

    Science.gov (United States)

    Selvadurai, A. P. S.; Głowacki, A.

    2017-05-01

    The paper presents the results of experiments that were conducted to determine the influence of a triaxial stress state on the evolution of the permeability of an argillaceous limestone. The limestone rock is found in the Ordovician rock formations above the Precambrian basement located in southern Ontario, Canada, which is being considered as a potential host rock for the construction of a deep ground repository for storing low- and intermediate-level nuclear waste. The paper presents the results of an extensive series of hydraulic pulse tests and steady-state tests that were conducted to determine the permeability alterations in zones that can experience levels of damage that can be present in vicinity of an excavated underground opening. A "state-space" relationship is developed to describe permeability evolution with the triaxial stress in the pre-failure regime. The permeability evolution in extensively damaged post-failure states of the rock is also investigated. It is shown that permeability alterations were four orders of magnitude higher as a result of significant damage to the material, which is an important consideration in establishing the efficiency of the host rock formation as a barrier for the long-term containment of radionuclide migration.

  15. Optimal Allocation of Replicates for Measurement Evaluation Studies

    Institute of Scientific and Technical Information of China (English)

    Stanislav O.Zakharkin; Kyoungmi Kim; Alfred A.Bartolucci; Grier P.Page; David B.Allison

    2006-01-01

    Optimal experimental design is important for the efficient use of modern highthroughput technologies such as microarrays and proteomics. Multiple factors including the reliability of measurement system, which itself must be estimated from prior experimental work, could influence design decisions. In this study, we describe how the optimal number of replicate measures (technical replicates) for each biological sample (biological replicate) can be determined. Different allocations of biological and technical replicates were evaluated by minimizing the variance of the ratio of technical variance (measurement error) to the total variance (sum of sampling error and measurement error). We demonstrate that if the number of biological replicates and the number of technical replicates per biological sample are variable, while the total number of available measures is fixed, then the optimal allocation of replicates for measurement evaluation experiments requires two technical replicates for each biological replicate. Therefore, it is recommended to use two technical replicates for each biological replicate if the goal is to evaluate the reproducibility of measurements.

  16. The Genomic Replication of the Crenarchaeal Virus SIRV2

    DEFF Research Database (Denmark)

    Martinez Alvarez, Laura

    of the crenarchaeal virus SIRV2, a model among archaeal viruses. SIRV2 was found to employ multiple replication mechanisms, with DNA synthesis starting by a strand-displacement mode that later derived in a rolling-circle replication from a circular intermediate. Interestingly, evidence for a secondary, bidirectional...... reinitiation events may partially explain the branched topology of the viral replication intermediates. We also analyzed the intracellular location of viral replication, showing the formation of viral peripheral replication centers in SIRV2-infected cells, where viral DNA synthesis and replication......-related proteins are concentrated. Our data indicates that the host DNA polymerase Dpo1 is also the viral replicative polymerase. Moreover, additional data suggests that other processes, such as translation, are also reorganized after infection. Based on our results, a model for the organization of viral...

  17. Regulation of replication fork progression through histone supply and demand

    DEFF Research Database (Denmark)

    Groth, Anja; Corpet, Armelle; Cook, Adam J L

    2007-01-01

    DNA replication in eukaryotes requires nucleosome disruption ahead of the replication fork and reassembly behind. An unresolved issue concerns how histone dynamics are coordinated with fork progression to maintain chromosomal stability. Here, we characterize a complex in which the human histone...... chaperone Asf1 and MCM2-7, the putative replicative helicase, are connected through a histone H3-H4 bridge. Depletion of Asf1 by RNA interference impedes DNA unwinding at replication sites, and similar defects arise from overproduction of new histone H3-H4 that compromises Asf1 function. These data link Asf......1 chaperone function, histone supply, and replicative unwinding of DNA in chromatin. We propose that Asf1, as a histone acceptor and donor, handles parental and new histones at the replication fork via an Asf1-(H3-H4)-MCM2-7 intermediate and thus provides a means to fine-tune replication fork...

  18. Replication, falsification, and the crisis of confidence in social psychology

    Directory of Open Access Journals (Sweden)

    Brian D. Earp

    2015-05-01

    Full Text Available The (latest crisis in confidence in social psychology has generated much heated discussion about the importance of replication, including how such replication should be carried out as well as interpreted by scholars in the field. What does it mean if a replication attempt fails—does it mean that the original results, or the theory that predicted them, have been falsified? And how should failed replications affect our belief in the validity of the original research? In this paper, we consider the replication debate from a historical and philosophical perspective, and provide a conceptual analysis of both replication and falsification as they pertain to this important discussion. Along the way, we introduce a Bayesian framework for assessing failed replications in terms of how they should affect our confidence in purported findings.

  19. Replication, falsification, and the crisis of confidence in social psychology.

    Science.gov (United States)

    Earp, Brian D; Trafimow, David

    2015-01-01

    The (latest) crisis in confidence in social psychology has generated much heated discussion about the importance of replication, including how it should be carried out as well as interpreted by scholars in the field. For example, what does it mean if a replication attempt "fails"-does it mean that the original results, or the theory that predicted them, have been falsified? And how should "failed" replications affect our belief in the validity of the original research? In this paper, we consider the replication debate from a historical and philosophical perspective, and provide a conceptual analysis of both replication and falsification as they pertain to this important discussion. Along the way, we highlight the importance of auxiliary assumptions (for both testing theories and attempting replications), and introduce a Bayesian framework for assessing "failed" replications in terms of how they should affect our confidence in original findings.

  20. The Alleged Crisis and the Illusion of Exact Replication.

    Science.gov (United States)

    Stroebe, Wolfgang; Strack, Fritz

    2014-01-01

    There has been increasing criticism of the way psychologists conduct and analyze studies. These critiques as well as failures to replicate several high-profile studies have been used as justification to proclaim a "replication crisis" in psychology. Psychologists are encouraged to conduct more "exact" replications of published studies to assess the reproducibility of psychological research. This article argues that the alleged "crisis of replicability" is primarily due to an epistemological misunderstanding that emphasizes the phenomenon instead of its underlying mechanisms. As a consequence, a replicated phenomenon may not serve as a rigorous test of a theoretical hypothesis because identical operationalizations of variables in studies conducted at different times and with different subject populations might test different theoretical constructs. Therefore, we propose that for meaningful replications, attempts at reinstating the original circumstances are not sufficient. Instead, replicators must ascertain that conditions are realized that reflect the theoretical variable(s) manipulated (and/or measured) in the original study.

  1. Replication, falsification, and the crisis of confidence in social psychology

    Science.gov (United States)

    Earp, Brian D.; Trafimow, David

    2015-01-01

    The (latest) crisis in confidence in social psychology has generated much heated discussion about the importance of replication, including how it should be carried out as well as interpreted by scholars in the field. For example, what does it mean if a replication attempt “fails”—does it mean that the original results, or the theory that predicted them, have been falsified? And how should “failed” replications affect our belief in the validity of the original research? In this paper, we consider the replication debate from a historical and philosophical perspective, and provide a conceptual analysis of both replication and falsification as they pertain to this important discussion. Along the way, we highlight the importance of auxiliary assumptions (for both testing theories and attempting replications), and introduce a Bayesian framework for assessing “failed” replications in terms of how they should affect our confidence in original findings. PMID:26042061

  2. Prevention of DNA re-replication in eukaryotic cells

    Institute of Scientific and Technical Information of China (English)

    Lan N. Truong; Xiaohua Wu

    2011-01-01

    DNA replication is a highly regulated process involving a number of licensing and replication factors that function in a carefully orchestrated manner to faithfully replicate DNA during every cell cycle. Loss of proper licensing control leads to deregulated DNA replication including DNA re-replication, which can cause genome instability and tumorigenesis. Eukaryotic organisms have established several conserved mechanisms to prevent DNA re-replication and to counteract its potentially harmful effects. These mechanisms include tightly controlled regulation of licensing factors and activation of cell cycle and DNA damage checkpoints.Deregulated licensing control and its associated compromised checkpoints have both been observed in tumor cells, indicating that proper functioning of these pathways is essential for maintaining genome stability. In this review, we discuss the regulatory mechanisms of licensing control, the deleterious consequences when both licensing and checkpoints are compromised, and present possible mechanisms to prevent re-replication in order to maintain genome stability.

  3. Eukaryotic Mismatch Repair in Relation to DNA Replication.

    Science.gov (United States)

    Kunkel, Thomas A; Erie, Dorothy A

    2015-01-01

    Three processes act in series to accurately replicate the eukaryotic nuclear genome. The major replicative DNA polymerases strongly prevent mismatch formation, occasional mismatches that do form are proofread during replication, and rare mismatches that escape proofreading are corrected by mismatch repair (MMR). This review focuses on MMR in light of increasing knowledge about nuclear DNA replication enzymology and the rate and specificity with which mismatches are generated during leading- and lagging-strand replication. We consider differences in MMR efficiency in relation to mismatch recognition, signaling to direct MMR to the nascent strand, mismatch removal, and the timing of MMR. These studies are refining our understanding of relationships between generating and repairing replication errors to achieve accurate replication of both DNA strands of the nuclear genome.

  4. Control of DNA replication by anomalous reaction-diffusion kinetics

    Science.gov (United States)

    Bechhoefer, John; Gauthier, Michel

    2010-03-01

    DNA replication requires two distinct processes: the initiation of pre-licensed replication origins and the propagation of replication forks away from the fired origins. Experiments indicate that these origins are triggered over the whole genome at a rate I(t) (the number of initiations per unreplicated length per time) that increases throughout most of the synthesis (S) phase, before rapidly decreasing to zero at the end of the replication process. We propose a simple model for the control of DNA replication in which the rate of initiation of replication origins is controlled by protein-DNA interactions. Analyzing recent data from Xenopus frog embryos, we find that the initiation rate is reaction limited until nearly the end of replication, when it becomes diffusion limited. Initiation of origins is suppressed when the diffusion-limited search time dominates. To fit the experimental data, we find that the interaction between DNA and the rate-limiting protein must be subdiffusive.

  5. Decreased replication origin activity in temporal transition regions.

    Science.gov (United States)

    Guan, Zeqiang; Hughes, Christina M; Kosiyatrakul, Settapong; Norio, Paolo; Sen, Ranjan; Fiering, Steven; Allis, C David; Bouhassira, Eric E; Schildkraut, Carl L

    2009-11-30

    In the mammalian genome, early- and late-replicating domains are often separated by temporal transition regions (TTRs) with novel properties and unknown functions. We identified a TTR in the mouse immunoglobulin heavy chain (Igh) locus, which contains replication origins that are silent in embryonic stem cells but activated during B cell development. To investigate which factors contribute to origin activation during B cell development, we systematically modified the genetic and epigenetic status of the endogenous Igh TTR and used a single-molecule approach to analyze DNA replication. Introduction of a transcription unit into the Igh TTR, activation of gene transcription, and enhancement of local histone modifications characteristic of active chromatin did not lead to origin activation. Moreover, very few replication initiation events were observed when two ectopic replication origin sequences were inserted into the TTR. These findings indicate that the Igh TTR represents a repressive compartment that inhibits replication initiation, thus maintaining the boundaries between early and late replication domains.

  6. Le Chatelier's principle in replicator dynamics

    Science.gov (United States)

    Allahverdyan, Armen E.; Galstyan, Aram

    2011-10-01

    The Le Chatelier principle states that physical equilibria are not only stable, but they also resist external perturbations via short-time negative-feedback mechanisms: a perturbation induces processes tending to diminish its results. The principle has deep roots, e.g., in thermodynamics it is closely related to the second law and the positivity of the entropy production. Here we study the applicability of the Le Chatelier principle to evolutionary game theory, i.e., to perturbations of a Nash equilibrium within the replicator dynamics. We show that the principle can be reformulated as a majorization relation. This defines a stability notion that generalizes the concept of evolutionary stability. We determine criteria for a Nash equilibrium to satisfy the Le Chatelier principle and relate them to mutualistic interactions (game-theoretical anticoordination) showing in which sense mutualistic replicators can be more stable than (say) competing ones. There are globally stable Nash equilibria, where the Le Chatelier principle is violated even locally: in contrast to the thermodynamic equilibrium a Nash equilibrium can amplify small perturbations, though both types of equilibria satisfy the detailed balance condition.

  7. DNA instability in replicating Huntington's disease lymphoblasts

    Directory of Open Access Journals (Sweden)

    Frati Luigi

    2009-02-01

    Full Text Available Abstract Background The expanded CAG repeat in the Huntington's disease (HD gene may display tissue-specific variability (e.g. triplet mosaicism in repeat length, the longest mutations involving mitotic (germ and glial cells and postmitotic (neurons cells. What contributes to the triplet mutability underlying the development of HD nevertheless remains unknown. We investigated whether, besides the increased DNA instability documented in postmitotic neurons, possible environmental and genetic mechanisms, related to cell replication, may concur to determine CAG repeat mutability. To test this hypothesis we used, as a model, cultured HD patients' lymphoblasts with various CAG repeat lengths. Results Although most lymphoblastoid cell lines (88% showed little or no repeat instability even after six or more months culture, in lymphoblasts with large expansion repeats beyond 60 CAG repeats the mutation size and triplet mosaicism always increased during replication, implying that the repeat mutability for highly expanded mutations may quantitatively depend on the triplet expansion size. None of the investigated genetic factors, potentially acting in cis to the mutation, significantly influence the repeat changes. Finally, in our experiments certain drugs controlled triplet expansion in two prone-to-expand HD cell lines carrying large CAG mutations. Conclusion Our data support quantitative evidence that the inherited CAG length of expanded alleles has a major influence on somatic repeat variation. The longest triplet expansions show wide somatic variations and may offer a mechanistic model to study triplet drug-controlled instability and genetic factors influencing it.

  8. Why threefold-replication of families?

    Science.gov (United States)

    Fitzpatrick, Gerald L.

    1998-04-01

    In spite of the many successes of the standard model of particle physics, the observed proliferation of matter-fields, in the form of ``replicated'' generations or families, is a major unsolved problem. In this paper, I explore some of the algebraic, geometric and physical consequences of a new organizing principle for fundamental fermions (quarks and leptons)(Gerald L. Fitzpatrick, phThe Family Problem--New Internal Algebraic and Geometric Regularities), Nova Scientific Press, Issaquah, Washington, 1997. Read more about this book (ISBN 0--9655695--0--0) and its subject matter at: http://www.tp.umu.se/TIPTOP and/or amazon.com>http://www.amazon.com.. The essence of the new organizing principle is the idea that the standard-model concept of scalar fermion numbers f can be generalized. In particular, a ``generalized fermion number,'' which consists of a 2× 2 matrix F that ``acts'' on an internal 2-space, instead of spacetime, is taken to describe certain internal properties of fundamental fermions. This generalization automatically introduces internal degrees of freedom that ``explain,'' among other things, family replication and the number (three) of families observed in nature.

  9. Replicative DNA polymerase mutations in cancer☆

    Science.gov (United States)

    Heitzer, Ellen; Tomlinson, Ian

    2014-01-01

    Three DNA polymerases — Pol α, Pol δ and Pol ɛ — are essential for DNA replication. After initiation of DNA synthesis by Pol α, Pol δ or Pol ɛ take over on the lagging and leading strand respectively. Pol δ and Pol ɛ perform the bulk of replication with very high fidelity, which is ensured by Watson–Crick base pairing and 3′exonuclease (proofreading) activity. Yeast models have shown that mutations in the exonuclease domain of Pol δ and Pol ɛ homologues can cause a mutator phenotype. Recently, we identified germline exonuclease domain mutations (EDMs) in human POLD1 and POLE that predispose to ‘polymerase proofreading associated polyposis’ (PPAP), a disease characterised by multiple colorectal adenomas and carcinoma, with high penetrance and dominant inheritance. Moreover, somatic EDMs in POLE have also been found in sporadic colorectal and endometrial cancers. Tumors with EDMs are microsatellite stable and show an ‘ultramutator’ phenotype, with a dramatic increase in base substitutions. PMID:24583393

  10. Identification and characterization of interferon-induced proteins that inhibit alphavirus replication.

    Science.gov (United States)

    Zhang, Yugen; Burke, Crystal W; Ryman, Kate D; Klimstra, William B

    2007-10-01

    Alpha/beta interferon (IFN-alpha/beta) produces antiviral effects through upregulation of many interferon-stimulated genes (ISGs) whose protein products are effectors of the antiviral state. Previous data from our laboratory have shown that IFN-alpha/beta can limit Sindbis virus (SB) replication through protein kinase R (PKR)-dependent and PKR-independent mechanisms and that one PKR-independent mechanism inhibits translation of the infecting virus genome (K. D. Ryman et al., J. Virol. 79:1487-1499, 2005). Further, using Affymetrix microarray technology, we identified 44 genes as candidates for PKR/RNase L-independent IFN-induced antiviral activities. In the current studies, we have begun analyzing these gene products for antialphavirus activity using three techniques: (i) overexpression of the protein from SB vectors and assessment of virulence attenuation in mice; (ii) overexpression of the proteins in a stable tetracycline-inducible murine fibroblast culture system and assessment of effects upon SB replication; and (iii) small interfering RNA-mediated knockdown of gene mRNA in fibroblast cultures followed by SB replication assessment as above. Tested proteins included those we hypothesized had potential to affect virus genome translation and included murine ISG20, ISG15, the zinc finger antiviral protein (ZAP), viperin, p56, p54, and p49. Interestingly, the pattern of antiviral activity for some gene products was different between in vitro and in vivo assays. Viperin and ZAP attenuated virulence most profoundly in mice. However, ISG20 and ZAP potently inhibited SB replication in vitro, whereas and viperin, p56, and ISG15 exhibited modest replication inhibition in vitro. In contrast, p54 and p49 had little to no effect in any assay.

  11. Benthic exchange and biogeochemical cycling in permeable sediments.

    Science.gov (United States)

    Huettel, Markus; Berg, Peter; Kostka, Joel E

    2014-01-01

    The sandy sediments that blanket the inner shelf are situated in a zone where nutrient input from land and strong mixing produce maximum primary production and tight coupling between water column and sedimentary processes. The high permeability of the shelf sands renders them susceptible to pressure gradients generated by hydrodynamic and biological forces that modulate spatial and temporal patterns of water circulation through these sediments. The resulting dynamic three-dimensional patterns of particle and solute distribution generate a broad spectrum of biogeochemical reaction zones that facilitate effective decomposition of the pelagic and benthic primary production products. The intricate coupling between the water column and sediment makes it challenging to quantify the production and decomposition processes and the resultant fluxes in permeable shelf sands. Recent technical developments have led to insights into the high biogeochemical and biological activity of these permeable sediments and their role in the global cycles of matter.

  12. Transport zonation limits coupled nitrification-denitrification in permeable sediments

    DEFF Research Database (Denmark)

    Kessler, Adam John; Glud, R.N.; Cardenas, M.B.

    2013-01-01

    Measurement of biogeochemical processes in permeable sediments (including the hyporheic zone) is difficult because of complex multidimensional advective transport. This is especially the case for nitrogen cycling, which involves several coupled redox-sensitive reactions. To provide detailed insig......- and N-15-N-2 gas. The measured two-dimensional profiles correlate with computational model simulations, showing a deep pool of N-2 gas forming, and being advected to the surface below ripple peaks. Further isotope pairing calculations on these data indicate that coupled nitrification......-denitrification is severely limited in permeable sediments because the flow and transport field limits interaction between oxic and anoxic pore water. The approach allowed for new detailed insight into subsurface denitrification zones in complex permeable sediments....

  13. Effect of anionic macromolecules on intestinal permeability of furosemide.

    Science.gov (United States)

    Valizadeh, Hadi; Fahimfar, Hadi; Ghanbarzadeh, Saeed; Islambulchilar, Ziba; Zakeri-Milani, Parvin

    2015-02-01

    Furosemide is an anionic molecule and has very low absorption in gastro intestinal tract. The aim of this study was to investigate the effect of anionic macromolecules on the intestinal permeability of Furosemide. The intestinal permeability of Furosemide was determined using single-pass intestinal perfusion technique in rats. Briefly a jejunal segment of ∼10 cm was isolated and cannulated in both ends for inlet and outlet solution. The perfusate was collected every 10 min and samples were analyzed using the RP-HPLC method. Test samples containing furosemide and two anionic macromolecules, sodium carboxy methyl cellulose and sodium alginate, at different concentrations were used. The obtained data showed that existence of Sodium carboxy methyl cellulose significantly increased the Peff values in all three investigated concentrations (p macromolecules at specific concentrations could alter the permeability of anionic drugs across the biological membranes. Donnan phenomenon and chelating property of macromolecules could be attributed to the observed effect.

  14. Permeability Description by Characteristic Length, Tortuosity, Constriction and Porosity

    CERN Document Server

    Berg, Carl Fredrik

    2015-01-01

    In this article we investigate the permeability of a porous medium as given in Darcy's law. The permeability is described by an effective hydraulic pore radius in the porous medium, the fluctuation in local hydraulic pore radii, the length of streamlines, and the fractional volume conducting flow. The effective hydraulic pore radius is related to a characteristic hydraulic length, the fluctuation in local hydraulic radii is related to a constriction factor, the length of streamlines is characterized by a tortuosity, and the fractional volume conducting flow from inlet to outlet is described by an effective porosity. The characteristic length, the constriction factor, the tortuosity and the effective porosity are thus intrinsic descriptors of the pore structure relative to direction. We show that the combined effect of our pore structure description fully describes the permeability of a porous medium. The theory is applied to idealized porous media, where it reproduces Darcy's law for fluid flow derived from t...

  15. Endodontic sealers: Intratubular penetration and permeability to Enterococcus faecalis

    Directory of Open Access Journals (Sweden)

    Bortolini Maria Cecilia

    2010-01-01

    Full Text Available Aim : Evaluate in vitro the intratubular penetration and permeability of endodontic sealers in teeth contaminated with Enterococcus faecalis. Materials and Methods : Human canines were filled with AHPlus ® , Endo CPM-sealer ® or EndoRez ® sealers. To evaluate permeability, the coronary portion of each tooth was contaminated with E. faecalis, then the apical portion was immersed in brain heart infusion (BHI broth, and medium turbidity was observed for thirty days. Scanning electron microscope (SEM was used to evaluate the intratubular penetration of each sealer at the cervical, middle, and apical thirds of the tooth. Results : Only one tooth from the Endo CPM-sealer ® group presented broth contamination. EndoRez ® showed increased intratubular penetration compared to AHPlus ® and Endo CPM-sealer ® . Conclusions : Endo CPM-sealer ® showed greater permeability to E. faecalis and EndoRez ® showed increased intratubular penetration.

  16. A REVISED SOLUTION OF EQUIVALENT PERMEABILITY TENSOR FOR DISCONTINUOUS FRACTURES

    Institute of Scientific and Technical Information of China (English)

    HE Ji; CHEN Sheng-hong; SHAHROUR Isam

    2012-01-01

    The equivalent permeability tensor is essential to the application of the equivalent porous media model in the numerical seepage simulation for fractured rock masses.In this paper,a revised solution of the equivalent permeability tensor is proposed to represent the influence of the fracture connectivity in discontinuous fractures.A correction coefficient is involved to reflect the complex seepage flow type through the rock bridge.This correction coefficient is back analyzed from single-hole packer tests,based on the Artificial Neural Network (ANN) back analysis and the Finite Element Method (FEM) seepage simulation.The limitation of this back analysis algorithm is that the number of single-hole packer tests should be equal or greater than the number of fracture sets,and three is the maximum number of the fracture sets.The proposed solution and the back analysis algorithm are applied in the permeability measurement and the seepage simulation for the Xiaowan arch dam foundation.

  17. System level permeability modeling of porous hydrogen storage materials.

    Energy Technology Data Exchange (ETDEWEB)

    Kanouff, Michael P.; Dedrick, Daniel E.; Voskuilen, Tyler (Purdue University, West Lafayette, IN)

    2010-01-01

    A permeability model for hydrogen transport in a porous material is successfully applied to both laboratory-scale and vehicle-scale sodium alanate hydrogen storage systems. The use of a Knudsen number dependent relationship for permeability of the material in conjunction with a constant area fraction channeling model is shown to accurately predict hydrogen flow through the reactors. Generally applicable model parameters were obtained by numerically fitting experimental measurements from reactors of different sizes and aspect ratios. The degree of channeling was experimentally determined from the measurements and found to be 2.08% of total cross-sectional area. Use of this constant area channeling model and the Knudsen dependent Young & Todd permeability model allows for accurate prediction of the hydrogen uptake performance of full-scale sodium alanate and similar metal hydride systems.

  18. Oxygen Permeability of Polypropylene Containing Polyisobutene with Magnesium Acetate

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    The oxygen permeabilities of polypropylene films are reduced by adding a minor percentage of a polyisobutene ionomer. The polyisobutene ionomers were prepared by in situ salt exchange of magnesium acetate with maleated polyisobutenes of commercially available low relative molecular mass. The more polar magnesium salts aided phase separation during crystallization from the molten polypropylene mixture. Scanning electron microscope photographs revealed that the polyisobutene ionomer is largely concentrated in the amorphous regions between the polypropylene spherulites, where the ionomer tends to concentrate during crystallization. The influence of the polyisobutene ionomer on the oxygen permeability of polypropylene was found to be slightly dependent upon the relative molecular mass of the polyisobutene precursor. Under optimum conditions, the oxygen permeability of polypropylene is reduced by 20% with only 1% additive.

  19. Analysis of Stokes flow through periodic permeable tubules

    Directory of Open Access Journals (Sweden)

    A.M. Siddiqui

    2017-03-01

    Full Text Available This article reports the detailed analysis of the Stokes flow through permeable tubes. The objective of this investigation was to search for exact solutions to the Stokes flow and thereby observe the effects on radial flow component, provided the permeability on the tubular surface is an elementary trigonometric function. Mathematical expressions for the pressure distribution, velocity components, volume flux, average wall shear stress and leakage flux are presented explicitly. Graphical analysis of the fluid flow is presented for a set of parametric values. Important conclusions are drawn for Stokes flow through tubes with low as well as high permeability. The classical Poiseuille flow is presented as a limiting case of this immense study of Stokes flow.

  20. The mitochondrial permeability transition pore: a mystery solved?

    Science.gov (United States)

    Bernardi, Paolo

    2013-01-01

    The permeability transition (PT) denotes an increase of the mitochondrial inner membrane permeability to solutes with molecular masses up to about 1500 Da. It is presumed to be mediated by opening of a channel, the permeability transition pore (PTP), whose molecular nature remains a mystery. Here I briefly review the history of the PTP, discuss existing models, and present our new results indicating that reconstituted dimers of the FOF1 ATP synthase form a channel with properties identical to those of the mitochondrial megachannel (MMC), the electrophysiological equivalent of the PTP. Open questions remain, but there is now promise that the PTP can be studied by genetic methods to solve the large number of outstanding problems. PMID:23675351

  1. Flow and permeability structure of the Beowawe, Nevada hydrothermal system

    Energy Technology Data Exchange (ETDEWEB)

    Faulder, D.D. [Lockheed Idaho Technologies Co., Idaho Falls, ID (United States); Johnson, S.D.; Benoit, W.R. [Oxbow Power Services, Inc., Reno, NV (United States)

    1997-05-01

    A review of past geologic, geochemical, hydrological, pressure transient, and reservoir engineering studies of Beowawe suggests a different picture of the reservoir than previously presented. The Beowawe hydrothermal contains buoyant thermal fluid dynamically balanced with overlying cold water, as shown by repeated temperature surveys and well test results. Thermal fluid upwells from the west of the currently developed reservoir at the intersection of the Malpais Fault and an older structural feature associated with mid-Miocene rifting. A tongue of thermal fluid rises to the east up the high permeability Malpais Fault, discharges at the Geysers area, and is in intimate contact with overlying cooler water. The permeability structure is closely related to the structural setting, with the permeability of the shallow hydrothermal system ranging from 500 to 1,000 D-ft, while the deeper system ranges from 200 to 400 D-ft.

  2. Correlation between permeability and groundwater flow patterns in carbonate rocks

    Science.gov (United States)

    Park, Y.; Lee, J.; Park, Y.; Keehm, Y.

    2011-12-01

    Groundwater flow in carbonate rocks is controlled by many factors such as degree of fracture and pore development, weathering and diagenesis. Among these factors, fracture is main factor and can form main flow path. Also, flow patterns in carbonate area are decided by these factors. This study was performed to understand factors controlling permeability and flow patterns in carbonate area and to evaluate correlation between permeability and flow patterns. Data used in this study were collected from many literatures and these data were analyzed and evaluated using graphic and statistical analysis. In many carbonate areas, branching conduit patterns were dominant. Of these areas, permeability was relatively high in areas where moving distance of flow was short and hydraulic gradient was steep. This work was supported by the Energy Resources R&D program of the Korea Institute of Energy Technology Evaluation and Planning (KETEP) grant funded by the Korea government Ministry of Knowledge Economy (No. 2009201030001A).

  3. Saturated versus non-saturated two-scales permeability

    Science.gov (United States)

    Lopez, Elena; Ammar, Amine; Abisset-Chavanne, Emmanuelle; Binetruy, Christophe; Chinesta, Francisco

    2016-10-01

    A crucial step in many composites manufacturing processes is the impregnation of fibrous medium with the resin. The fundamental property needed to quantify the flow is the permeability of the fibrous medium. Process models require the permeability as input data to predict flow patterns and pressure fields. Efficient numerical techniques are needed to solve homogenization problems with geometrical data coming from high-resolution images, involving two-scales and linear fluids. Within this frame-work, this work addresses the question of how to compute the macroscopic permeability from a microscopic description consisting of a viscous fluid flow model defined in a two-scale porous medium, considering the saturated and unsaturated cases.

  4. Review of permeability evolution model for fractured porous media

    Institute of Scientific and Technical Information of China (English)

    Jianjun Ma

    2015-01-01

    The ability to capture permeability of fractured porous media plays a significant role in several engi-neering applications, including reservoir, mining, petroleum and geotechnical engineering. In order to solve fluid flow and coupled flow-deformation problems encountered in these engineering applications, both empirical and theoretical models had been proposed in the past few decades. Some of them are simple but still work in certain circumstances;others are complex but also need some modifications to be applicable. Thus, the understanding of state-of-the-art permeability evolution model would help researchers and engineers solve engineering problems through an appropriate approach. This paper summarizes permeability evolution models proposed by earlier and recent researchers with emphasis on their characteristics and limitations.

  5. Investigating the Relationship between Knitted Fabric Porosity and Light Permeability

    Directory of Open Access Journals (Sweden)

    Manoj Kumar Imrith

    2016-01-01

    Full Text Available The present paper attempts to investigate the relationship between fabric porosity and light permeability of the knitted structures, namely, rib 1 × 1, rib 2 × 1, single jersey, and plain structure. The rationale is that pores (in a fabric would allow light to pass through but at the same time provide a quantitative assessment of the UV light permeability of the knitted fabrics, an indication of the protective capacity of the fabrics against UV radiation. The porosity and corresponding light permeability of the knitted structures were measured after varying the following knitting parameters: stitch length, stitch density, and tension on the machine. Furthermore, this work has enabled the development of an apparatus that can measure the amount of light transmitted through the knitted fabrics. The results generated by the equipment were validated through the use of regression equations.

  6. Effect of periodontal root planing on dentin permeability.

    Science.gov (United States)

    Fogel, H M; Pashley, D H

    1993-10-01

    The purpose of this study was to quantitate the effects of root planing on the permeability of human root dentin in vitro. Unerupted 3rd molars were used. The crowns were removed and longitudinal slices made of the root. The hydraulic conductance of the root dentin was measured before and after root planing, acid etching and potassium oxalate application using a fluid filtration method. The results showed that root planing creates a smear layer that reduces the permeability of the underlying dentin. However, this smear layer is acid labile. Thus, root planing may ultimately cause increased dentin permeability and the associated sequelae of sensitive dentin, bacterial invasion of tubules, reduced periodontal reattachment and pulpal irritation.

  7. Replication of CMV in the gut of HIV-infected individuals and epithelial barrier dysfunction

    Science.gov (United States)

    Somsouk, Ma; Hunt, Peter W.

    2017-01-01

    Although invasive cytomegalovirus (CMV) disease is uncommon in the era of antiretroviral therapy (ART), asymptomatic CMV coinfection is nearly ubiquitous in HIV infected individuals. While microbial translocation and gut epithelial barrier dysfunction may promote persistent immune activation in treated HIV infection, potentially contributing to morbidity and mortality, it has been unclear whether CMV replication in individuals with no symptoms of CMV disease might play a role in this process. We hypothesized that persistent CMV replication in the intestinal epithelium of HIV/CMV-coinfected individuals impairs gut epithelial barrier function. Using a combination of state-of-the-art in situ hybridization technology (RNAscope) and immunohistochemistry, we detected CMV DNA and proteins and evidence of intestinal damage in rectosigmoid samples from CMV-positive individuals with both untreated and ART-suppressed HIV infection. Two different model systems, primary human intestinal cells differentiated in vitro to form polarized monolayers and a humanized mouse model of human gut, together demonstrated that intestinal epithelial cells are fully permissive to CMV replication. Independent of HIV, CMV disrupted tight junctions of polarized intestinal cells, significantly reducing transepithelial electrical resistance, a measure of monolayer integrity, and enhancing transepithelial permeability. The effect of CMV infection on the intestinal epithelium is mediated, at least in part, by the CMV-induced proinflammatory cytokine IL-6. Furthermore, letermovir, a novel anti-CMV drug, dampened the effects of CMV on the epithelium. Together, our data strongly suggest that CMV can disrupt epithelial junctions, leading to bacterial translocation and chronic inflammation in the gut and that CMV could serve as a target for therapeutic intervention to prevent or treat gut epithelial barrier dysfunction during HIV infection. PMID:28241080

  8. Late-replicating X-chromosome: replication patterns in mammalian females

    Directory of Open Access Journals (Sweden)

    Tunin Karen

    2002-01-01

    Full Text Available The GTG-banding and 5-BrdU incorporation patterns of the late-replicating X-chromosome were studied in female dogs and cattle, and compared to human female patterns. The replication patterns of the short arm of the X-chromosomes did not show any difference between human, dog and cattle females. As to the long arm, some bands showed differences among the three studied species regarding the replication kinetics pattern. These differences were observed in a restricted region of the X-chromosome, delimited by Xq11 -> q25 in humans, by Xq1 -> q8 in dogs, and by Xq12 -> q32 in cattle. In an attempt to find out if these differences in the replication kinetics could be a reflection of differences in the localization of genes in that region of the X-chromosome, we used the probe for the human androgen receptor gene (AR localized at Xq12, which is in the region where we observed differences among the three studied species. We did not, however, observe hybridization signals. Our study goes on, using other human probes for genes located in the region Xq11 -> Xq25.

  9. Replication regions of two pairs of incompatible lactococcal theta-replicating plasmids.

    Science.gov (United States)

    Gravesen, A; von Wright, A; Josephsen, J; Vogensen, F K

    1997-01-01

    Incompatibility tests were performed employing 12 replicons belonging to a family of homologous lactococcal theta-replicating plasmids. Two pairs of incompatible plasmids were found, namely, pFV1001 and pFV1201, and pJW565 and pFW094. The replicons of plasmids pFV1001, pFV1201, pJW565, pJW566, and pFW094 were sequenced. Alignments were made of the replicational origins (repA) and putative replication proteins (RepB) of these and 11 related plasmid sequences. Comparison of the alignments with the incompatibility data indicated that the incompatibility determinant could be contained within the 22-bp tandem repeats DRII and/or the inverted repeat IR1 in repA. In support, the incompatibility determinant of pJW563 was localized to a 743-bp fragment encompassing repA. A stretch of 13 amino acids of RepB was proposed to be responsible for the plasmid-specific initiation of replication. This stretch is part of a domain containing features that are highly conserved within the proposed DNA binding regions of the initiation proteins from several well-characterized plasmids from Gram-negative bacteria, including pSC101, R6K, and mini-F.

  10. Committee neural network model for rock permeability prediction

    Science.gov (United States)

    Bagheripour, Parisa

    2014-05-01

    Quantitative formulation between conventional well log data and rock permeability, undoubtedly the most critical parameter of hydrocarbon reservoir, could be a potent tool for solving problems associated with almost all tasks involved in petroleum engineering. The present study proposes a novel approach in charge of the quest for high-accuracy method of permeability prediction. At the first stage, overlapping of conventional well log data (inputs) was eliminated by means of principal component analysis (PCA). Subsequently, rock permeability was predicted from extracted PCs using multi-layer perceptron (MLP), radial basis function (RBF), and generalized regression neural network (GRNN). Eventually, a committee neural network (CNN) was constructed by virtue of genetic algorithm (GA) to enhance the precision of ultimate permeability prediction. The values of rock permeability, derived from the MPL, RBF, and GRNN models, were used as inputs of CNN. The proposed CNN combines results of different ANNs to reap beneficial advantages of all models and consequently producing more accurate estimations. The GA, embedded in the structure of the CNN assigns a weight factor to each ANN which shows relative involvement of each ANN in overall prediction of rock permeability from PCs of conventional well logs. The proposed methodology was applied in Kangan and Dalan Formations, which are the major carbonate reservoir rocks of South Pars Gas Field-Iran. A group of 350 data points was used to establish the CNN model, and a group of 245 data points was employed to assess the reliability of constructed CNN model. Results showed that the CNN method performed better than individual intelligent systems performing alone.

  11. Assembly of alphavirus replication complexes from RNA and protein components in a novel trans-replication system in mammalian cells.

    Science.gov (United States)

    Spuul, Pirjo; Balistreri, Giuseppe; Hellström, Kirsi; Golubtsov, Andrey V; Jokitalo, Eija; Ahola, Tero

    2011-05-01

    For positive-strand RNA viruses, the viral genomic RNA also acts as an mRNA directing the translation of the replicase proteins of the virus. Replication takes place in association with cytoplasmic membranes, which are heavily modified to create specific replication compartments. Here we have expressed by plasmid DNA transfection the large replicase polyprotein of Semliki Forest virus (SFV) in mammalian cells from a nonreplicating mRNA and provided a separate RNA containing the replication signals. The replicase proteins were able to efficiently and specifically replicate the template in trans, leading to accumulation of RNA and marker gene products expressed from the template RNA. The replicase proteins and double-stranded RNA replication intermediates localized to structures similar to those seen in SFV-infected cells. Using correlative light electron microscopy (CLEM) with fluorescent marker proteins to relocate those transfected cells, in which active replication was ongoing, abundant membrane modifications, representing the replication complex spherules, were observed both at the plasma membrane and in intracellular endolysosomes. Thus, replication complexes are faithfully assembled and localized in the trans-replication system. We demonstrated, using CLEM, that the replication proteins alone or a polymerase-negative polyprotein mutant together with the template did not give rise to spherule formation. Thus, the trans-replication system is suitable for cell biological dissection and examination in a mammalian cell environment, and similar systems may be possible for other positive-strand RNA viruses.

  12. Crystal Structure of an Ammonia-Permeable Aquaporin

    DEFF Research Database (Denmark)

    Kirscht, Andreas; Kaptan, Shreyas S; Bienert, Gerd Patrick;

    2016-01-01

    the structure determined at 1.18 Å resolution from twinned crystals of Arabidopsis thaliana aquaporin AtTIP2;1 and confirm water and ammonia permeability of the purified protein reconstituted in proteoliposomes as further substantiated by molecular dynamics simulations. The structure of AtTIP2;1 reveals...... an extended selectivity filter with the conserved arginine of the filter adopting a unique unpredicted position. The relatively wide pore and the polar nature of the selectivity filter clarify the ammonia permeability. By mutational studies, we show that the identified determinants in the extended selectivity...

  13. Striatal blood-brain barrier permeability in Parkinson's disease.

    Science.gov (United States)

    Gray, Madison T; Woulfe, John M

    2015-05-01

    In vivo studies have shown that blood-brain barrier (BBB) dysfunction is involved in the course of Parkinson's disease (PD). However, these have lacked either anatomic definition or the ability to recognize minute changes in BBB integrity. Here, using histologic markers of serum protein, iron, and erythrocyte extravasation, we have shown significantly increased permeability of the BBB in the postcommissural putamen of PD patients. The dense innervation of the striatum by PD-affected regions allows for exploitation of this permeability for therapeutic goals. These results are also discussed in the context of the retrograde trans-synaptic hypothesis of PD spread.

  14. Whole-body microvascular permeability of small molecules in man

    DEFF Research Database (Denmark)

    Henriksen, J H

    1985-01-01

    In order to estimate whole-body permeability-surface area (PS) product, the initial slope of the plasma disappearance curve was determined after simultaneous i.v. injection of 24Na+ (mol.wt 24) and 51Cr-EDTA (mol.wt 342). Twelve subjects were studied. Plasma volume (PV) was measured by the indica......In order to estimate whole-body permeability-surface area (PS) product, the initial slope of the plasma disappearance curve was determined after simultaneous i.v. injection of 24Na+ (mol.wt 24) and 51Cr-EDTA (mol.wt 342). Twelve subjects were studied. Plasma volume (PV) was measured...

  15. Influence of Core Permeability on Accropode Armour Layer Stability

    DEFF Research Database (Denmark)

    Burcharth, H. F.; Christensen, M.; Jensen, T.

    1998-01-01

    Hedar and van der Meer studied the influence of core permeability on the stability of two layer rock armour. In both cases a significant influence was found. However, it is to be expected that for single layer armour there will be an even larger influence on the core permeability. This is because...... the dissipation of wave energy in single layer armour will e smaller than in double layer armour, thus giving room for larger flow velocities in and over armour layer On this background a laboratory stud of single layer Accropode stability was undertaken at Aalborg University in 1995. The test results as well...

  16. Upscaling verticle permeability within a fluvio-aeolian reservoir

    Energy Technology Data Exchange (ETDEWEB)

    Thomas, S.D.; Corbett, P.W.M.; Jensen, J.L. [Heriot-Watt Univ., Edinburgh (United Kingdom)

    1997-08-01

    Vertical permeability (k{sub v}) is a crucial factor in many reservoir engineering issues. To date there has been little work undertaken to understand the wide variation of k{sub v} values measured at different scales in the reservoir. This paper presents the results of a study in which we have modelled the results of a downhole well tester using a statistical model and high resolution permeability data. The work has demonstrates and quantifies a wide variation in k{sub v} at smaller, near wellbore scales and has implications for k{sub v} modelling at larger scales.

  17. Permeability in a state of partial solidification of aqueous solution

    Science.gov (United States)

    Okada, Masashi; Kang, Chaedong; Okiyama, Haruhiko

    A mushy region was formed by solidifying NaCl aqueous solution in a circular tube or a rectangular tube. The measurements of permeability were performed by changing volume fraction of liquid region in the mushy region. The dendritic ice in the solidification process was observed with a CCD microscope. The following results were obtained. The permeability increases with the volume fraction of liquid phase, and decreases with increasing the super-cooling degree of the solution or increasing the initial concentration of the solution, and is constant after the mushy region was formed. The arm space of dendrite becomes narrower as the super-cooling degree of the solution increases.

  18. Rhamnose and rhamnitol in dual sugar permeability tests.

    Science.gov (United States)

    Malagon, Ignacio; Onkenhout, Willem; Klok, Margreet; van der Poel, Petrus F H; Bovill, James G; Hazekamp, Mark G

    2006-08-01

    Rhamnose is one of the sugars regularly used to conduct the dual sugar permeability test. For more than 30 years, it has been assumed that rhamnose is an inert sugar not metabolized by the human body and only fermented by some colonic bacteria into rhamnulose. While conducting an investigation on gut permeability in children undergoing cardiac surgery, increased concentrations of rhamnitol were found in the urine samples. The present report suggests that rhamnose is not an inert sugar and it is partially metabolized into rhamnitol by the human body.

  19. Dynamic up-scaling of relative permeability in chalk

    Energy Technology Data Exchange (ETDEWEB)

    Frykman, P.; Lindgaard, H.F.

    1997-12-31

    This paper describes how fine-scale geo-statistic reservoir models can be utilised for the up-scaling of two-phase flow properties, including both relative permeability and capillary pressure function. The procedure is applied to a North Sea chalk carbonate reservoir example, which is a high-porosity/low-permeability reservoir type. The study focuses on waterflooding as the main recovery scheme and for the given flow regime in the reservoir. The main purpose of the paper is to demonstrate the use of dynamic multi-step up-scaling methods in the preparation of detailed geological information for full field reservoir simulation studies. (au) EFP-96. 39 refs.

  20. Direct Visualization of DNA Replication Dynamics in Zebrafish Cells.

    Science.gov (United States)

    Kuriya, Kenji; Higashiyama, Eriko; Avşar-Ban, Eriko; Tamaru, Yutaka; Ogata, Shin; Takebayashi, Shin-ichiro; Ogata, Masato; Okumura, Katsuzumi

    2015-12-01

    Spatiotemporal regulation of DNA replication in the S-phase nucleus has been extensively studied in mammalian cells because it is tightly coupled with the regulation of other nuclear processes such as transcription. However, little is known about the replication dynamics in nonmammalian cells. Here, we analyzed the DNA replication processes of zebrafish (Danio rerio) cells through the direct visualization of replicating DNA in the nucleus and on DNA fiber molecules isolated from the nucleus. We found that zebrafish chromosomal DNA at the nuclear interior was replicated first, followed by replication of DNA at the nuclear periphery, which is reminiscent of the spatiotemporal regulation of mammalian DNA replication. However, the relative duration of interior DNA replication in zebrafish cells was longer compared to mammalian cells, possibly reflecting zebrafish-specific genomic organization. The rate of replication fork progression and ori-to-ori distance measured by the DNA combing technique were ∼ 1.4 kb/min and 100 kb, respectively, which are comparable to those in mammalian cells. To our knowledge, this is a first report that measures replication dynamics in zebrafish cells.

  1. Effect of different concentrations of permeable and non-permeable cryoprotectants on the hatching rate of goldfish (Carassius auratus) embryos

    Institute of Scientific and Technical Information of China (English)

    Fardin Shaluei; Mohamad Reza Imanpoor; Ali Shabani; Mohamad Hossein Nasr-Esfahani

    2013-01-01

    Objective: To assess the toxicity of various cryoprotective agents(CPAs) to goldfish embryos. Methods: Heart-beat embryos were immersed in: five permeable CPAs, dimethyl sulfoxide (DMSO), methanol (MeOH), 1,2- propylene glycol (PG), glycerol (Gly), ethylene glycol (EG), and two non-permeable CPAs: polyvinylpyrrolidone (PVP) and sucrose in concentrations of 5%, 10%, 15% or 20% for 5, 15, or 30 min. The viability of the embryos after the treatments was estimated from hatching rates. Results: The results showed that the toxicity to goldfish embryos of the five permeable CPAs were in the following sequence: PG 0.05). In this experiment none of the concentrations tested for sucrose reduced the hatching rate, but embryos exposed to PVP did not tolerate concentration 20%, at 30 min exposure. Conclusion: These finding will be advantageous for designing optimized Cryo-media for cryopreservation of goldfish embryos.

  2. Influence of permeability on hydrothermal circulation in the sediment-buried oceanic crust

    Institute of Scientific and Technical Information of China (English)

    WANG Xingtao; ZHAI Shikui; MENG Fanshun; LI Huaiming; YU Zenghui; SUN Ge; XUE Gang

    2006-01-01

    Hydrothermal convection in the upper oceanic crust has been inferred to be a common and important process. Under the simplified conditions of planar boundaries, permeability provides a strong constraint on the pattern of circulation, the dimensions of convective cells and flow field of hydrothermal circulation. By applying an advanced numerical modeling method, to our knowledge, it is the first time to investigate convection as it is influenced by different strata permeability structures,formational anisotropy, fracture zone and cooling intrusion. The simplified geological model is composed of 3 layers, sedimentary layer, high permeable basement layer and low permeable basement layer from top to bottom. When permeability in high permeable layer is 10 times larger than that in sedimentary layer, convection occurs in high permeable layer. The pattern of hydrothermal circulation and flow velocity of hydrothermal fluid are strongly influenced by strata permeability structures,changes of permeability in high permeable basement layer, fracture zone and cooling intrusion.However, formational anisotropy relatively exerts weak influence on hydrothermal circulation, with the ratio up to 1.5 of vertical permeability to lateral permeability in high permeable layer. Fracture zone existing in basement is the most important factor affecting the circulation field. The effects of a local intrusion are limited to convection intensity above the intrusion and have little impact on the fluid flow on a regional scale. As the result of numerical modelling, key factors affecting the hydrothermal circulation are good permeable zone and long-term heat source, not including fluid source.

  3. Replication Regulates Volume Weighting in Quantum Cosmology

    CERN Document Server

    Hartle, James

    2009-01-01

    Probabilities for observations in cosmology are conditioned both on the universe's quantum state and on local data specifying the observational situation. We show the quantum state defines a measure for prediction through such conditional probabilities that is well behaved for spatially large or infinite universes when the probabilities that our data is replicated are taken into account. In histories where our data are rare volume weighting connects top-down probabilities conditioned on both the data and the quantum state to the bottom-up probabilities conditioned on the quantum state alone. We apply these principles to a calculation of the number of inflationary e-folds in a homogeneous, isotropic minisuperspace model with a single scalar field moving in a quadratic potential. We find that volume weighting is justified and the top-down probabilities favor a large number of e-folds.

  4. Star Trek replicators and diatom nanotechnology.

    Science.gov (United States)

    Drum, Ryan W; Gordon, Richard

    2003-08-01

    Diatoms are single celled algae, the 10(5)-10(6) species of which create a wide variety of three-dimensional amorphous silica shells. If we could get them to produce useful structures, perhaps by compustat selection experiments (i.e. forced evolution of development or evodevo), their exponential growth in suspension cultures could compete with the lithography techniques of present day nanotechnology, which have limited 3D capabilities. Alternatively, their fine detail could be used for templates for MEMS (micro electro mechanical systems), or their silica deposition systems isolated for guiding silica deposition. A recent paper has demonstrated that silica can be replaced atom for atom without change of shape--a step towards the Star Trek replicator.

  5. Replicator dynamics for optional public good games

    DEFF Research Database (Denmark)

    Hauert, C.; De Monte, Silvia; Hofbauer, J.;

    2002-01-01

    The public goods game represents a straightforward generalization of the prisoner's dilemma to an arbitrary number of players. Since the dominant strategy is to defect, both classical and evolutionary game theory predict the asocial outcome that no player contributes to the public goods....... In contrast to the compulsory public goods game, optional participation provides a natural way to avoid deadlocks in the state of mutual defection. The three resulting strategies-collaboration or defection in the public goods game, as well as not joining at all-are studied by means of a replicator dynamics...... participation makes cooperation feasible. But for each strategy, the average payoff value remains equal to the earnings of those not participating in the public goods game....

  6. Dynamic combinatorial self-replicating systems.

    Science.gov (United States)

    Moulin, Emilie; Giuseppone, Nicolas

    2012-01-01

    Thanks to their intrinsic network topologies, dynamic combinatorial libraries (DCLs) represent new tools for investigating fundamental aspects related to self-organization and adaptation processes. Very recently the first examples integrating self-replication features within DCLs have pushed even further the idea of implementing dynamic combinatorial chemistry (DCC) towards minimal systems capable of self-construction and/or evolution. Indeed, feedback loop processes - in particular in the form of autocatalytic reactions - are keystones to build dynamic supersystems which could possibly approach the roots of "Darwinian" evolvability at mesoscale. This topic of current interest also shows significant potentialities beyond its fundamental character, because truly smart and autonomous materials for the future will have to respond to changes of their environment by selecting and by exponentially amplifying their fittest constituents.

  7. Entanglement Swapping Model of DNA Replication

    CERN Document Server

    Pusuluk, Onur

    2011-01-01

    Molecular biology explains function of molecules by their geometric and electronic structures which are mainly determined by utilization of quantum effects in chemistry. However, further quantum effects are not thought to play any significant role in the essential processes of life. On the contrary, consideration of quantum circuits/protocols and organic molecules as software and hardware of living systems that are co-optimized during evolution, may be useful to pass over the difficulties raised by biochemical complexity and to understand the physics of life. In this sense, we model DNA replication with a reliable qubit representation of the nucleotides: 1) molecular recognition of a nucleotide is assumed to trigger an intrabase entanglement corresponding to a superposition of different tautomer forms and 2) pairing of complementary nucleotides is described by swapping intrabase entanglements with interbase entanglements. We examine possible realizations of quantum circuits/protocols to be used to obtain intr...

  8. Suggestibility and negative priming: two replication studies.

    Science.gov (United States)

    David, Daniel; Brown, Richard J

    2002-07-01

    Research suggests that inhibiting the effect of irrelevant stimuli on subsequent thought and action (cognitive inhibition) may be an important component of suggestibility. Two small correlation studies were conducted to address the relationship between different aspects of suggestibility and individual differences in cognitive inhibition, operationalized as the degree of negative priming generated by to-be-ignored stimuli in a semantic categorization task. The first study found significant positive correlations between negative priming, hypnotic suggestibility, and creative imagination; a significant negative correlation was obtained between negative priming and interrogative suggestibility, demonstrating the discriminant validity of the study results. The second study replicated the correlation between negative priming and hypnotic suggestibility, using a different suggestibility measurement procedure that assessed subjective experience and hypnotic involuntariness as well as objective responses to suggestions. These studies support the notion that the ability to engage in cognitive inhibition may be an important component of hypnotic responsivity and maybe of other forms of suggestibility.

  9. Self-replicating alphavirus RNA vaccines.

    Science.gov (United States)

    Ljungberg, Karl; Liljeström, Peter

    2015-02-01

    Recombinant nucleic acids are considered as promising next-generation vaccines. These vaccines express the native antigen upon delivery into tissue, thus mimicking live attenuated vaccines without having the risk of reversion to pathogenicity. They also stimulate the innate immune system, thus potentiating responses. Nucleic acid vaccines are easy to produce at reasonable cost and are stable. During the past years, focus has been on the use of plasmid DNA for vaccination. Now mRNA and replicon vaccines have come into focus as promising technology platforms for vaccine development. This review discusses self-replicating RNA vaccines developed from alphavirus expression vectors. These replicon vaccines can be delivered as RNA, DNA or as recombinant virus particles. All three platforms have been pre-clinically evaluated as vaccines against a number of infectious diseases and cancer. Results have been very encouraging and propelled the first human clinical trials, the results of which have been promising.

  10. Security in a Replicated Metadata Catalogue

    CERN Document Server

    Koblitz, B

    2007-01-01

    The gLite-AMGA metadata has been developed by NA4 to provide simple relational metadata access for the EGEE user community. As advanced features, which will be the focus of this presentation, AMGA provides very fine-grained security also in connection with the built-in support for replication and federation of metadata. AMGA is extensively used by the biomedical community to store medical images metadata, digital libraries, in HEP for logging and bookkeeping data and in the climate community. The biomedical community intends to deploy a distributed metadata system for medical images consisting of various sites, which range from hospitals to computing centres. Only safe sharing of the highly sensitive metadata as provided in AMGA makes such a scenario possible. Other scenarios are digital libraries, which federate copyright protected (meta-) data into a common catalogue. The biomedical and digital libraries have been deployed using a centralized structure already for some time. They now intend to decentralize ...

  11. Intracellular protease activation in apoptosis and cell-mediated cytotoxicity characterized by cell-permeable fluorogenic protease substrates

    Institute of Scientific and Technical Information of China (English)

    Beverly Z Packard; Akira Komoriya

    2008-01-01

    Over the past decade the importance of signaling from reporter molecules inside live cells and tissues has been clearly established. Biochemical events related to inflammation, tumor metastasis and proliferation, and viral infectivity and replication are examples of processes being further defined as more molecular tools for live cell measurements become available. Moreover, in addition to quantitating parameters related to physiologic processes, real-time imaging of molecular interactions that compose basic cellular activities are providing insights into understanding disease mechanisms as well as extending clinical efficacy of therapeutic regimens. In this review the use of highly cell-permeable fluorogenic substrates that report protease activities inside live cells is described; applications to defining the molecular events of two cellular processes, i.e., apoptosis and cell-mediated cytotoxicity, are then illustrated.

  12. Heterogeneity, permeability patterns, and permeability upscaling: Physical characterization of a block of Massillon sandstone exhibiting nested scales of heterogeneity

    Energy Technology Data Exchange (ETDEWEB)

    TIDWELL,VINCENT C.; WILSON,JOHN L.

    2000-04-20

    Over 75,000 permeability measurements were collected from a meter-scale block of Massillon sandstone, characterized by conspicuous cross bedding that forms two distinct nested-scales of heterogeneity. With the aid of a gas minipermeameter, spatially exhaustive fields of permeability data were acquired at each of five different sample supports (i.e. sample volumes) from each block face. These data provide a unique opportunity to physically investigate the relationship between the multi-scale cross-stratified attributes of the sandstone and the corresponding statistical characteristics of the permeability. These data also provide quantitative physical information concerning the permeability upscaling of a complex heterogeneous medium. Here, a portion of the data taken from a single block face cut normal to stratification is analyzed. Results indicate a strong relationship between the calculated summary statistics and the cross-stratified structural features visible evident in the sandstone sample. Specifically, the permeability fields and semivariograms are characterized by two nested scales of heterogeneity, including a large-scale structure defined by the cross-stratified sets (delineated by distinct bounding surfaces) and a small-scale structure defined by the low-angle cross-stratification within each set. The permeability data also provide clear evidence of upscaling. That is, each calculated summary statistic exhibits distinct and consistent trends with increasing sample support. Among these trends are an increasing mean, decreasing variance, and an increasing semivariogram range. Results also clearly indicate that the different scales of heterogeneity upscale differently, with the small-scale structure being preferentially filtered from the data while the large-scale structure is preserved. Finally, the statistical and upscaling characteristics of individual cross-stratified sets were found to be very similar owing to their shared depositional environment

  13. Dengue virus binding and replication by platelets.

    Science.gov (United States)

    Simon, Ayo Y; Sutherland, Michael R; Pryzdial, Edward L G

    2015-07-16

    Dengue virus (DENV) infection causes ∼200 million cases of severe flulike illness annually, escalating to life-threatening hemorrhagic fever or shock syndrome in ∼500,000. Although thrombocytopenia is typical of both mild and severe diseases, the mechanism triggering platelet reduction is incompletely understood. As a probable initiating event, direct purified DENV-platelet binding was followed in the current study by quantitative reverse transcription-polymerase chain reaction and confirmed antigenically. Approximately 800 viruses specifically bound per platelet at 37°C. Fewer sites were observed at 25°C, the blood bank storage temperature (∼350 sites), or 4°C, known to attenuate virus cell entry (∼200 sites). Dendritic cell-specific intercellular adhesion molecule-3-grabbing nonintegrin (DC-SIGN) and heparan sulfate proteoglycan were implicated as coreceptors because only the combination of anti-DC-SIGN and low-molecular-weight heparin prevented binding. Interestingly, at 37°C and 25°C, platelets replicated the positive sense single-stranded RNA genome of DENV by up to ∼4-fold over 7 days. Further time course experiments demonstrated production of viral NS1 protein, which is known to be highly antigenic in patient serum. The infectivity of DENV intrinsically decayed in vitro, which was moderated by platelet-mediated generation of viable progeny. This was shown using a transcription inhibitor and confirmed by freeze-denatured platelets being incapable of replicating the DENV genome. For the first time, these data demonstrate that platelets directly bind DENV saturably and produce infectious virus. Thus, expression of antigen encoded by DENV is a novel consideration in the pathogen-induced thrombocytopenia mechanism. These results furthermore draw attention to the possibility that platelets may produce permissive RNA viruses in addition to DENV.

  14. Predicting chemically-induced skin reactions. Part II: QSAR models of skin permeability and the relationships between skin permeability and skin sensitization

    Energy Technology Data Exchange (ETDEWEB)

    Alves, Vinicius M. [Laboratory of Molecular Modeling and Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, GO 74605-220 (Brazil); Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599 (United States); Muratov, Eugene [Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599 (United States); Laboratory of Theoretical Chemistry, A.V. Bogatsky Physical–Chemical Institute NAS of Ukraine, Odessa 65080 (Ukraine); Fourches, Denis [Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599 (United States); Strickland, Judy; Kleinstreuer, Nicole [ILS/Contractor supporting the NTP Interagency Center for the Evaluation of Alternative Toxicological Methods (NICEATM), P.O. Box 13501, Research Triangle Park, NC 27709 (United States); Andrade, Carolina H. [Laboratory of Molecular Modeling and Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, GO 74605-220 (Brazil); Tropsha, Alexander, E-mail: alex_tropsha@unc.edu [Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599 (United States)

    2015-04-15

    Skin permeability is widely considered to be mechanistically implicated in chemically-induced skin sensitization. Although many chemicals have been identified as skin sensitizers, there have been very few reports analyzing the relationships between molecular structure and skin permeability of sensitizers and non-sensitizers. The goals of this study were to: (i) compile, curate, and integrate the largest publicly available dataset of chemicals studied for their skin permeability; (ii) develop and rigorously validate QSAR models to predict skin permeability; and (iii) explore the complex relationships between skin sensitization and skin permeability. Based on the largest publicly available dataset compiled in this study, we found no overall correlation between skin permeability and skin sensitization. In addition, cross-species correlation coefficient between human and rodent permeability data was found to be as low as R{sup 2} = 0.44. Human skin permeability models based on the random forest method have been developed and validated using OECD-compliant QSAR modeling workflow. Their external accuracy was high (Q{sup 2}{sub ext} = 0.73 for 63% of external compounds inside the applicability domain). The extended analysis using both experimentally-measured and QSAR-imputed data still confirmed the absence of any overall concordance between skin permeability and skin sensitization. This observation suggests that chemical modifications that affect skin permeability should not be presumed a priori to modulate the sensitization potential of chemicals. The models reported herein as well as those developed in the companion paper on skin sensitization suggest that it may be possible to rationally design compounds with the desired high skin permeability but low sensitization potential. - Highlights: • It was compiled the largest publicly-available skin permeability dataset. • Predictive QSAR models were developed for skin permeability. • No concordance between skin

  15. An optimal replication strategy for data grid systems

    Institute of Scientific and Technical Information of China (English)

    JIANG Jianjin; YANG Guangwen

    2007-01-01

    Data access latency is an important metric of system performance in data grid.By means of efficient replication strategy,the amount of data transferred in a wide area network will decrease,and the average access latency of data will decrease ultimately.The motivation of our research is to solve the optimized replica distribution problem in a data grid;that is,the system should utilize many replicas for every data with storage constraints to minimize the average access latency of data.This paper proposes a model of replication strategy in federated data grid and gives the optimized solution.The analysis results and simulation results show that the optimized replication strategy proposed in this paper is superior to LRU caching strategy,uniform replication strategy,proportional replication strategy and square root replication strategy in terms of wide area network bandwidth requirement and in the average access latency of data.

  16. Causation and the origin of life. Metabolism or replication first?

    Science.gov (United States)

    Pross, Addy

    2004-06-01

    The conceptual gulf that separates the 'metabolism first' and 'replication first' mechanisms for the emergence of life continues to cloud the origin of life debate. In the present paper we analyze this aspect of the origin of life problem and offer arguments in favor of the 'replication first' school. Utilizing Wicken's two-tier approach to causation we argue that a causal connection between replication and metabolism can only be demonstrated if replication would have preceded metabolism. In conjunction with existing empirical evidence and theoretical reasoning, our analysis concludes that there is no substantive evidence for a 'metabolism first' mechanism for life's emergence, while a coherent case can be made for the 'replication first' group of mechanisms. The analysis reaffirms our conviction that life is an extreme expression of kinetic control, and that the emergence of metabolic pathways can be understood by considering life as a manifestation of 'replicative chemistry'.

  17. Replication of Avocado Sunblotch Viroid in the Yeast Saccharomyces cerevisiae▿

    Science.gov (United States)

    Delan-Forino, Clémentine; Maurel, Marie-Christine; Torchet, Claire

    2011-01-01

    Viroids are the smallest known pathogenic agents. They are noncoding, single-stranded, closed-circular, “naked” RNAs, which replicate through RNA-RNA transcription. Viroids of the Avsunviroidae family possess a hammerhead ribozyme in their sequence, allowing self-cleavage during their replication. To date, viroids have only been detected in plant cells. Here, we investigate the replication of Avocado sunblotch viroid (ASBVd) of the Avsunviroidae family in a nonconventional host, the yeast Saccharomyces cerevisiae. We demonstrate that ASBVd RNA strands of both polarities are able to self-cleave and to replicate in a unicellular eukaryote cell. We show that the viroid monomeric RNA is destabilized by the nuclear 3′ and the cytoplasmic 5′ RNA degradation pathways. For the first time, our results provide evidence that viroids can replicate in other organisms than plants and that yeast contains all of the essential cellular elements for the replication of ASBVd. PMID:21270165

  18. Evidence for sequential and increasing activation of replication origins along replication timing gradients in the human genome.

    Science.gov (United States)

    Guilbaud, Guillaume; Rappailles, Aurélien; Baker, Antoine; Chen, Chun-Long; Arneodo, Alain; Goldar, Arach; d'Aubenton-Carafa, Yves; Thermes, Claude; Audit, Benjamin; Hyrien, Olivier

    2011-12-01

    Genome-wide replication timing studies have suggested that mammalian chromosomes consist of megabase-scale domains of coordinated origin firing separated by large originless transition regions. Here, we report a quantitative genome-wide analysis of DNA replication kinetics in several human cell types that contradicts this view. DNA combing in HeLa cells sorted into four temporal compartments of S phase shows that replication origins are spaced at 40 kb intervals and fire as small clusters whose synchrony increases during S phase and that replication fork velocity (mean 0.7 kb/min, maximum 2.0 kb/min) remains constant and narrowly distributed through S phase. However, multi-scale analysis of a genome-wide replication timing profile shows a broad distribution of replication timing gradients with practically no regions larger than 100 kb replicating at less than 2 kb/min. Therefore, HeLa cells lack large regions of unidirectional fork progression. Temporal transition regions are replicated by sequential activation of origins at a rate that increases during S phase and replication timing gradients are set by the delay and the spacing between successive origin firings rather than by the velocity of single forks. Activation of internal origins in a specific temporal transition region is directly demonstrated by DNA combing of the IGH locus in HeLa cells. Analysis of published origin maps in HeLa cells and published replication timing and DNA combing data in several other cell types corroborate these findings, with the interesting exception of embryonic stem cells where regions of unidirectional fork progression seem more abundant. These results can be explained if origins fire independently of each other but under the control of long-range chromatin structure, or if replication forks progressing from early origins stimulate initiation in nearby unreplicated DNA. These findings shed a new light on the replication timing program of mammalian genomes and provide a general

  19. Experimental study on gas permeability by adsorption under 3D-stress

    Institute of Scientific and Technical Information of China (English)

    LONG Qing-ming; WEN Guang-cai; ZOU Yin-hui; ZHAO Xu-sheng

    2009-01-01

    Using self-developed gas-seepage experimental installation, under the same effective stress conditions, coal permeability experiments on different adsorption charac-teristics of gases, different temperatures and different gas adsorption contents were per-formed, and the influence law of adsorption on coal permeability was studied. At the same time, experimental analogy showed clearly that gas drawing plucks the permeability varia-tion law. The results show that adsorption has a major impact on coal permeability. The greater the adsorption, the more the gas adsorption capacity and the coal permeability becomes smaller. Permeability becomes smaller along with confining of pressure and temperature, and this is in accord with local practice results.

  20. Mechanisms of formation damage in matrix-permeability geothermal wells

    Energy Technology Data Exchange (ETDEWEB)

    Bergosh, J.L.; Wiggins, R.B.; Enniss, D.O.

    1982-04-01

    Tests were conducted to determine mechanisms of formation damage that can occur in matrix permeability geothermal wells. Two types of cores were used in the testing, actual cores from the East Mesa Well 78-30RD and cores from a fairly uniform generic sandstone formation. Three different types of tests were run. The East Mesa cores were used in the testing of the sensitivity of core to filtrate chemistry. The tests began with the cores exposed to simulated East Mesa brine and then different filtrates were introduced and the effects of the fluid contrast on core permeability were measured. The East Mesa cores were also used in the second series of tests which tested formation sandstone cores were used in the third test series which investigated the effects of different sizes of entrained particles in the fluid. Tests were run with both single-particle sizes and distributions of particle mixes. In addition to the testing, core preparation techniques for simulating fracture permeability were evaluated. Three different fracture formation mechanisms were identified and compared. Measurement techniques for measuring fracture size and permeability were also developed.